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Opened 4 years ago
Last modified 4 years ago
#4877 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.10.0-1034-oem-x86_64-with-glibc2.14
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/ucsf-commands.cxc
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3EI4.pdbqt
Chain information for 3EI4.pdbqt #1
---
Chain | Description
A C E | No description available
B D F | No description available
Opened 3EI4.pdbqt containing 1 structures (70284 atoms, 71031 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 3EI4.pdbqt #1
---
warnings | Not adding hydrogens to /A GLU 368 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A ARG 369 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLN 759 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 779 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A THR 780 CB because it is missing heavy-atom bond
partners
49 messages similar to the above omitted
notes | No usable SEQRES records for 3EI4.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 3EI4.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 3EI4.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 3EI4.pdbqt (#1) chain D; guessing termini instead
No usable SEQRES records for 3EI4.pdbqt (#1) chain E; guessing termini instead
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A MET 1, /B TRP 54, /C MET
1, /D TRP 54, /E MET 1, /F TRP 54
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A HIS 1140, /B GLU 421, /C
HIS 1140, /D GLU 421, /E HIS 1140, /F GLU 421
Chain-final residues that are not actual C termini:
2812 hydrogen bonds
114 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3EI4--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3EI4--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 3EI4--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
40 contacts
atom1 atom2 overlap distance
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 HE 0.326 2.554
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 458 O 0.049 3.311
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 NE -0.005 3.510
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 HN -0.006 2.886
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HB2 -0.009 2.889
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 O -0.028 3.388
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 HN -0.045 2.065
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 O -0.050 3.410
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 O -0.056 3.416
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 HG2 -0.071 2.831
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 CG1 -0.071 3.531
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C VAL 637 2HG1 -0.089 2.509
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 C -0.092 3.672
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 HB2 -0.115 2.995
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 CB -0.121 3.701
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HD2 -0.131 2.891
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C SER 590 HA -0.193 2.613
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 HB2 -0.227 3.107
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C TYR 678 HD2 -0.237 2.997
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 CG -0.240 3.700
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C TYR 678 CD2 -0.246 3.706
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ILE 591 O -0.258 3.618
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ARG 639 HE -0.271 3.031
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 O -0.284 3.184
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 O -0.286 3.226
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CD2 -0.291 3.751
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CD2 -0.291 3.751
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 HB2 -0.296 3.176
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 HD2 -0.312 3.072
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C MET 679 O -0.331 3.691
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C ARG 639 2HH2 -0.331 3.211
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C SER 590 CA -0.344 3.464
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 2HG1 -0.350 3.110
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 638 C -0.357 3.937
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C ALA 501 CB -0.367 3.947
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 N -0.374 3.019
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C VAL 637 CG1 -0.386 3.696
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3EI4.pdbqt #1/C LEU 410 N -0.387 3.892
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C PHE 459 CB -0.394 3.974
3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 C 3EI4.pdbqt #1/C LEU 592 HB1 -0.394 3.274
40 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3EI4.pdbqt
2.1 3EI4--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3EI4.pdbqt #1/C ILE 591 N 3EI4--WRM-16.result.pdbqt #2.1/? UNL 1 O 3EI4.pdbqt #1/C ILE 591 HN 3.019 2.065
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.8 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "3EI4 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3EI4--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2PA2.pdbqt
Chain information for 2PA2.pdbqt #1
---
Chain | Description
A B | No description available
Opened 2PA2.pdbqt containing 1 structures (3578 atoms, 3614 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2PA2.pdbqt #1
---
notes | No usable SEQRES records for 2PA2.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 2PA2.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A LYS 40, /B LYS 40
Chain-initial residues that are not actual N termini: /A GLY 124, /B GLY 124
Chain-final residues that are actual C termini: /A PHE 176, /B PHE 176
Chain-final residues that are not actual C termini: /A PHE 94, /B PHE 94
173 hydrogen bonds
Adding 'H' to /A GLY 124
Adding 'H' to /B GLY 124
/A PHE 94 is not terminus, removing H atom from 'C'
/B PHE 94 is not terminus, removing H atom from 'C'
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2PA2--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2PA2--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.4 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2PA2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
42 contacts
atom1 atom2 overlap distance
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH1 0.226 2.384
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 0.203 1.817
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 0.129 2.481
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 HB2 0.110 2.650
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE1 0.107 2.773
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 0.007 2.753
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 0.001 2.759
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 -0.038 2.648
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 -0.039 2.649
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH2 -0.042 2.922
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH2 -0.049 2.109
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B HIS 92 O -0.078 3.438
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 CE1 -0.094 3.674
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 1HH2 -0.105 2.985
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 CG1 -0.107 3.687
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A PRO 47 HA -0.111 2.531
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HD1 -0.114 2.874
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HD1 -0.119 2.879
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B ARG 128 O -0.121 3.481
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/B HIS 130 HE1 -0.121 2.581
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 NH1 -0.139 2.784
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 NH1 -0.150 3.385
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.172 3.557
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HB2 -0.175 2.785
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CD1 -0.211 3.671
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A LYS 169 O -0.229 3.319
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A ARG 139 NH2 -0.235 3.740
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A VAL 43 O -0.237 3.137
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.243 3.478
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 HD2 -0.251 3.011
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CB -0.266 3.576
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A TRP 171 HB2 -0.278 2.698
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A PRO 47 CB -0.283 3.863
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B ARG 128 CB -0.291 3.751
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 1HG1 -0.297 3.177
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2PA2.pdbqt #1/B HIS 92 HN -0.300 3.180
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CD1 -0.306 3.766
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 CB -0.325 3.785
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 NE2 -0.331 3.566
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A TRP 171 HN -0.354 3.234
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/A VAL 43 HB -0.364 2.974
2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2PA2.pdbqt #1/B HIS 130 HE2 -0.383 3.143
42 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2PA2.pdbqt
2.1 2PA2--WRM-16.result.pdbqt
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2PA2.pdbqt #1/A ARG 139 NH1 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 3.380 2.525
2PA2.pdbqt #1/A ARG 139 NH1 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH1 2.784 1.817
2PA2.pdbqt #1/A ARG 139 NH2 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A ARG 139 1HH2 3.087 2.109
2PA2.pdbqt #1/A TRP 171 N 2PA2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2PA2.pdbqt #1/A TRP 171 HN 3.576 2.621
4 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2PA2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2PA2--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KV2.pdbqt
Chain information for 2KV2.pdbqt #1
---
Chain | Description
A | No description available
Opened 2KV2.pdbqt containing 1 structures (1351 atoms, 1361 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2KV2.pdbqt #1
---
notes | No usable SEQRES records for 2KV2.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLN 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASP 85
Chain-final residues that are not actual C termini:
61 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KV2--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KV2--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.4 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2KV2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
52 contacts
atom1 atom2 overlap distance
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 0.640 2.240
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 0.469 2.291
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB 0.306 3.274
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 0.278 2.482
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 HB 0.207 2.673
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 CE 0.105 3.055
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HD2 0.105 2.655
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 CB 0.100 3.360
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HB2 0.075 2.685
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 CB 0.039 3.541
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CD2 -0.031 3.491
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HE3 -0.057 2.817
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HD1 -0.060 2.820
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CE3 -0.080 3.540
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CD1 -0.084 3.544
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HZ3 -0.099 2.979
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CD1 -0.106 3.686
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A THR 80 HB -0.115 2.875
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 -0.131 3.011
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE2 -0.136 2.596
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HA -0.165 2.775
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HA -0.207 2.817
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 CD -0.208 3.668
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A THR 80 OG1 -0.214 3.594
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CB -0.214 3.674
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 -0.227 2.837
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CE3 -0.237 3.547
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 -0.262 3.142
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 C -0.263 3.723
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 CE3 -0.272 3.852
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 CZ3 -0.273 3.853
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 HZ3 -0.277 3.157
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KV2.pdbqt #1/A TRP 79 HE3 -0.280 3.160
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB -0.297 3.607
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CD2 -0.310 3.890
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 CB -0.317 3.897
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 O -0.323 3.563
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE2 -0.324 2.744
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 75 HB3 -0.325 2.785
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 O -0.329 3.569
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 75 CB -0.330 3.490
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HB2 -0.331 2.941
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 O -0.336 3.576
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A TRP 79 CG -0.355 3.515
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 HE3 -0.360 2.970
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 NZ -0.373 3.878
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TRP 79 CG -0.376 3.956
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A VAL 72 3HG2 -0.383 2.803
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KV2.pdbqt #1/A LYS 8 HE3 -0.388 2.848
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A TYR 76 HD2 -0.388 3.148
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 75 HB3 -0.391 3.151
2KV2--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KV2.pdbqt #1/A LYS 8 HE2 -0.399 3.009
52 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2KV2.pdbqt
2.1 2KV2--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2KV2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KV2--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3CO6.pdbqt
Chain information for 3CO6.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Opened 3CO6.pdbqt containing 1 structures (2476 atoms, 2572 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 3CO6.pdbqt #1
---
warnings | Not adding hydrogens to /C LYS 192 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /C LYS 198 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C ASN 204 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C GLU 242 CB because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 3CO6.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 3CO6.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 3CO6.pdbqt (#1) chain C; guessing termini instead
Chain-initial residues that are actual N termini: /A DT -4, /B DC 13, /C SER
154
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A DG 12, /B DA 28, /C GLY 244
Chain-final residues that are not actual C termini:
127 hydrogen bonds
4 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3CO6--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3CO6--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.1 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 3CO6--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
57 contacts
atom1 atom2 overlap distance
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3CO6.pdbqt #1/A DT 4 H4' 0.285 2.595
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 234 HA 0.279 2.481
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C GLN 227 OE1 0.215 3.025
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 O3' 0.090 3.290
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 2HH1 0.039 2.721
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 NH1 0.011 3.374
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 C5' 0.002 3.578
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 24 H3 0.000 2.880
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 O4' -0.016 3.396
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 H4' -0.026 2.906
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 1H5' -0.041 2.921
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C2 -0.066 3.226
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 234 CA -0.080 3.540
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H22 -0.090 2.850
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H3 -0.095 2.155
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C LYS 233 O -0.116 3.356
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3CO6.pdbqt #1/A DT 4 C4' -0.123 3.703
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H3 -0.125 2.885
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 OG -0.180 3.440
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H22 -0.187 2.947
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 H4' -0.190 2.800
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 23 H2 -0.212 2.632
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 2H5' -0.212 3.092
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 OG -0.222 3.482
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 N3 -0.223 2.908
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 23 C2 -0.223 3.343
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 C4' -0.229 3.809
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 C4' -0.230 3.810
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H2 -0.237 2.697
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 P -0.239 3.990
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 O4' -0.260 3.180
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 H4' -0.264 2.724
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 H4' -0.269 2.879
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C LYS 233 O -0.273 3.513
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 24 N3 -0.286 3.791
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 O4' -0.296 3.216
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H2 -0.297 2.717
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 C4' -0.299 3.759
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C GLN 227 CD -0.302 3.762
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 H4' -0.308 2.918
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 N3 -0.316 3.701
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 H4' -0.322 3.202
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DG 3 N2 -0.323 3.708
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 H4' -0.326 3.086
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 NH1 -0.332 3.717
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C4 -0.337 3.457
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/A DT 2 O2 -0.341 3.281
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C ARG 225 2HH1 -0.352 3.112
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 O4' -0.360 3.620
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 N3 -0.360 3.005
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 C5' -0.366 3.946
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/A DT 4 C4' -0.374 3.684
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 N -0.392 3.777
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 C1' -0.394 3.514
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/C SER 235 N -0.394 3.779
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DC 26 OP1 -0.397 3.777
3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 3CO6.pdbqt #1/B DA 25 C4' -0.400 3.980
57 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3CO6.pdbqt
2.1 3CO6--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3CO6.pdbqt #1/B DA 24 N3 3CO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 3CO6.pdbqt #1/B DA 24 H3 2.908 2.155
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -9.1 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "3CO6 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3CO6--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1D7G.pdbqt
Chain information for 1D7G.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
Opened 1D7G.pdbqt containing 1 structures (2929 atoms, 3008 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1D7G.pdbqt #1
---
warnings | Not adding hydrogens to /A G 5 C2' because it is missing heavy-atom
bond partners
Not adding hydrogens to /A C 6 C2' because it is missing heavy-atom bond
partners
Not adding hydrogens to /A C 7 C2' because it is missing heavy-atom bond
partners
Not adding hydrogens to /A C 8 C2' because it is missing heavy-atom bond
partners
Not adding hydrogens to /A A 10 C2' because it is missing heavy-atom bond
partners
19 messages similar to the above omitted
notes | No usable SEQRES records for 1D7G.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1D7G.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 1D7G.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 1D7G.pdbqt (#1) chain D; guessing termini instead
Chain-initial residues that are actual N termini: /A G 5, /B G 5, /C GLU 1, /D
SER 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A C 18, /B C 18, /C THR 59,
/D LEU 59
Chain-final residues that are not actual C termini:
153 hydrogen bonds
4 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1D7G--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1D7G--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.9 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1D7G--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
39 contacts
atom1 atom2 overlap distance
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HE 0.329 2.431
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 1H2' 0.256 2.624
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 HG1 0.119 2.641
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 2HH1 0.015 2.005
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 NE -0.009 3.394
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D LYS 5 CG -0.009 3.589
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HB2 -0.018 2.778
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 H7 -0.024 2.044
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 H7 -0.025 2.045
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D LYS 5 HG1 -0.045 2.925
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H7 -0.079 2.959
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 CZ -0.085 3.245
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 C2' -0.096 3.676
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1D7G.pdbqt #1/D SER 1 O -0.112 3.472
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 2HH1 -0.121 2.731
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HB2 -0.137 2.897
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 N7 -0.144 3.649
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B C 18 H41 -0.162 3.042
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 NH1 -0.162 3.397
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 17 H7 -0.174 2.784
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 15 C8 -0.195 3.315
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 HG1 -0.207 2.817
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 NH1 -0.209 2.894
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H7 -0.210 2.820
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 C8 -0.227 3.387
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 C8 -0.227 3.807
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 CG -0.232 3.692
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 N7 -0.234 3.469
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 O2P -0.237 3.197
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 CB -0.252 3.712
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D LYS 5 N -0.277 3.662
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 O2P -0.310 3.570
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 16 H8 -0.331 3.211
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 NH1 -0.333 2.978
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/B G 15 C8 -0.337 3.647
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 C 1D7G.pdbqt #1/D ARG 4 HE -0.343 2.953
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 N7 -0.347 2.992
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 N7 -0.366 3.011
1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 O6 -0.397 3.297
39 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1D7G.pdbqt
2.1 1D7G--WRM-16.result.pdbqt
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1D7G.pdbqt #1/B G 16 N7 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 16 H7 2.992 2.045
1D7G.pdbqt #1/B G 17 N7 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/B G 17 H7 3.011 2.044
1D7G.pdbqt #1/D ARG 4 NH1 1D7G--WRM-16.result.pdbqt #2.1/? UNL 1 O 1D7G.pdbqt #1/D ARG 4 2HH1 2.978 2.005
3 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1D7G WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1D7G--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1GXC.pdbqt
Chain information for 1GXC.pdbqt #1
---
Chain | Description
A D G J | No description available
B E H K | No description available
Opened 1GXC.pdbqt containing 1 structures (8116 atoms, 8224 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1GXC.pdbqt #1
---
warnings | Not adding hydrogens to /A ASP 111 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /D ASP 111 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /G ASP 111 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /H ARG 7 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /J ASP 111 CB because it is missing heavy-atom bond
partners
1 messages similar to the above omitted
notes | No usable SEQRES records for 1GXC.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1GXC.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 1GXC.pdbqt (#1) chain D; guessing termini instead
No usable SEQRES records for 1GXC.pdbqt (#1) chain E; guessing termini instead
No usable SEQRES records for 1GXC.pdbqt (#1) chain G; guessing termini instead
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A PRO 92, /B HIS 0, /D PRO
92, /E HIS 0, /G PRO 92, /H HIS 0, /J PRO 92, /K HIS 0
Chain-initial residues that are not actual N termini: /B TYR 4, /E TYR 4, /H
TYR 4, /K TYR 4
Chain-final residues that are actual C termini: /A ASP 207, /B ARG 7, /D ASP
207, /E ARG 7, /G ASP 207, /H ARG 7, /J ASP 207, /K ARG 7
Chain-final residues that are not actual C termini: /B ASP 2, /E ASP 2, /H ASP
2, /K ASP 2
388 hydrogen bonds
Adding 'H' to /B TYR 4
Adding 'H' to /E TYR 4
Adding 'H' to /H TYR 4
Adding 'H' to /K TYR 4
/B ASP 2 is not terminus, removing H atom from 'C'
/E ASP 2 is not terminus, removing H atom from 'C'
/H ASP 2 is not terminus, removing H atom from 'C'
/K ASP 2 is not terminus, removing H atom from 'C'
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1GXC--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1GXC--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.0 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1GXC--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
30 contacts
atom1 atom2 overlap distance
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 184 HB2 0.193 2.567
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HA 0.144 2.736
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 0.103 2.657
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 HN 0.074 2.806
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 HB2 0.014 2.866
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HA -0.111 2.721
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 CB -0.140 3.720
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CA -0.141 3.721
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 186 O -0.141 3.381
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 -0.151 2.761
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G ARG 132 HD1 -0.159 2.619
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 O -0.179 3.539
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 184 CB -0.181 3.641
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 N -0.199 3.584
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 HB2 -0.204 2.964
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G LEU 129 HA -0.211 2.631
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 O -0.218 3.458
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G ARG 132 CD -0.232 3.392
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 186 HB1 -0.235 2.995
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/G LEU 129 O -0.252 3.152
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/D ASN 185 HN -0.264 3.024
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.264 3.724
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1GXC.pdbqt #1/D ASN 185 N -0.278 3.783
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 3HD1 -0.301 3.061
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 HB1 -0.310 3.070
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 N -0.338 3.843
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.354 3.664
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G ARG 132 HD1 -0.355 3.235
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 O 1GXC.pdbqt #1/D ASN 186 HB2 -0.377 2.837
1GXC--WRM-16.result.pdbqt #2.1/? UNL 1 C 1GXC.pdbqt #1/G LEU 129 CD1 -0.396 3.856
30 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1GXC.pdbqt
2.1 1GXC--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1GXC WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1GXC--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1KO6.pdbqt
Chain information for 1KO6.pdbqt #1
---
Chain | Description
A | No description available
B D | No description available
C | No description available
Opened 1KO6.pdbqt containing 1 structures (4955 atoms, 5004 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1KO6.pdbqt #1
---
warnings | Not adding hydrogens to /A MET 712 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A LYS 814 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /C THR 737 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /D ASP 870 CB because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 1KO6.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1KO6.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 1KO6.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 1KO6.pdbqt (#1) chain D; guessing termini instead
Chain-initial residues that are actual N termini: /A MET 712, /B LYS 865, /C
HIS 713, /D LYS 865
Chain-initial residues that are not actual N termini: /C GLU 742
Chain-final residues that are actual C termini: /A PHE 863, /B ASP 870, /C PHE
863, /D ASP 870
Chain-final residues that are not actual C termini: /C ASN 738
223 hydrogen bonds
Adding 'H' to /C GLU 742
/C ASN 738 is not terminus, removing H atom from 'C'
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1KO6--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1KO6--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.3 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1KO6--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
36 contacts
atom1 atom2 overlap distance
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 0.149 2.461
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 0.075 2.535
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 0.038 2.722
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 0.022 2.738
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 3HD2 -0.109 2.869
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A VAL 783 2HG1 -0.121 2.731
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 NH2 -0.144 3.649
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CD2 -0.149 3.459
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 CE1 -0.153 3.613
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HD1 -0.165 2.925
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 C -0.168 3.628
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C GLU 848 OE2 -0.172 3.412
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HD1 -0.179 2.939
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 CZ -0.190 3.770
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 CZ -0.200 3.780
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A ARG 778 CZ -0.201 3.361
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A LEU 786 3HD2 -0.234 2.694
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 ND1 -0.236 3.621
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CD2 -0.243 3.553
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 HE1 -0.244 3.004
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 C -0.255 3.715
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ARG 778 NE -0.258 3.763
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 N -0.265 3.650
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 O 1KO6.pdbqt #1/A ARG 778 CZ -0.299 3.419
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 ND1 -0.302 3.687
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 HB2 -0.308 3.068
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 HB2 -0.317 3.077
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C ARG 850 HD1 -0.328 3.088
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/C ARG 850 CD -0.334 3.794
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A HIS 776 CE1 -0.338 3.798
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A ASP 787 CB -0.340 3.800
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CB -0.345 3.805
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 O -0.353 3.593
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A VAL 783 CG1 -0.358 3.668
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 CB -0.362 3.822
1KO6--WRM-16.result.pdbqt #2.1/? UNL 1 C 1KO6.pdbqt #1/A LEU 786 HB2 -0.365 3.125
36 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1KO6.pdbqt
2.1 1KO6--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.3 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1KO6 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1KO6--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2I2Y.pdbqt
Chain information for 2I2Y.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 2I2Y.pdbqt containing 1 structures (2441 atoms, 2472 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2I2Y.pdbqt #1
---
notes | No usable SEQRES records for 2I2Y.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 2I2Y.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A MET 1, /B C 151
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ARG 150, /B C 154
Chain-final residues that are not actual C termini:
171 hydrogen bonds
10 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2I2Y--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2I2Y--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2I2Y--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
42 contacts
atom1 atom2 overlap distance
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 O 0.082 3.158
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 0.042 2.568
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD1 0.038 2.722
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 0.018 2.592
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 0.002 2.608
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 -0.056 2.936
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HA -0.087 2.847
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 HG2 -0.102 2.862
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD1 -0.104 2.864
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 N -0.108 3.613
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.117 2.877
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 O 2I2Y.pdbqt #1/A ASP 73 O -0.129 3.029
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HA -0.132 3.012
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.137 3.717
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CA -0.151 3.731
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HB3 -0.156 2.916
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 3HD2 -0.160 2.920
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 OD1 -0.177 3.417
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 HB3 -0.188 2.798
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.194 3.504
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 C -0.215 3.795
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 CZ -0.217 3.797
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 NH1 -0.264 3.769
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.268 3.578
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.274 3.034
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD1 -0.276 3.736
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CB -0.297 3.877
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A VAL 127 CG1 -0.301 3.761
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.306 3.616
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A VAL 127 CG1 -0.313 3.773
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 HB3 -0.320 2.930
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2I2Y.pdbqt #1/A ARG 150 NH2 -0.323 3.828
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 HG2 -0.332 3.092
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 68 O -0.337 3.577
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ASP 73 CB -0.338 3.648
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 CB -0.338 3.918
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ARG 128 CG -0.343 3.803
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 O 2I2Y.pdbqt #1/A SER 69 OG -0.346 2.866
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 124 CA -0.358 3.818
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A SER 69 OG -0.359 3.469
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A LEU 144 CD2 -0.367 3.677
2I2Y--WRM-16.result.pdbqt #2.1/? UNL 1 C 2I2Y.pdbqt #1/A ALA 123 HB2 -0.389 3.269
42 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2I2Y.pdbqt
2.1 2I2Y--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2I2Y WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2I2Y--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2CPE.pdbqt
Chain information for 2CPE.pdbqt #1
---
Chain | Description
A | No description available
Opened 2CPE.pdbqt containing 1 structures (1663 atoms, 1680 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2CPE.pdbqt #1
---
notes | No usable SEQRES records for 2CPE.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLY 346
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A GLY 458
Chain-final residues that are not actual C termini:
43 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CPE--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CPE--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.4 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2CPE--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
45 contacts
atom1 atom2 overlap distance
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 HB2 0.239 2.521
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A ILE 400 H 0.104 2.776
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB 0.090 2.670
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A VAL 372 O 0.010 2.930
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.008 2.768
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 ND1 -0.011 3.516
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 O -0.023 3.263
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CD1 -0.043 3.503
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 2HG2 -0.051 2.511
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 CE1 -0.060 3.640
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 CB -0.065 3.525
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.072 2.832
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.104 2.714
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 H -0.106 2.126
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 2HD2 -0.122 3.002
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.144 2.754
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 3HD1 -0.145 2.755
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A VAL 372 O -0.165 3.525
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.165 3.625
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A GLY 407 O -0.173 3.413
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.190 2.800
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 402 3HD1 -0.198 2.658
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A ILE 400 N -0.226 3.731
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.233 2.993
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.257 3.717
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 2HD1 -0.296 3.176
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.306 3.766
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CPE.pdbqt #1/A HIS 399 HA -0.312 3.192
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.326 3.086
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A THR 373 2HG2 -0.326 3.206
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 HA -0.326 2.746
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 H -0.328 2.938
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A THR 373 HA -0.343 3.223
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.348 3.808
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CG1 -0.351 3.811
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 HB -0.367 2.977
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 374 HB2 -0.373 3.133
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A THR 373 CG2 -0.376 3.536
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A ASP 370 O -0.382 3.282
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 1HD1 -0.384 3.144
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 N -0.385 3.030
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CB -0.390 3.850
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A GLY 407 O -0.392 3.632
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A ILE 400 CD1 -0.398 3.708
2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CPE.pdbqt #1/A LEU 402 CD1 -0.400 3.710
45 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2CPE.pdbqt
2.1 2CPE--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2CPE.pdbqt #1/A LEU 374 N 2CPE--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CPE.pdbqt #1/A LEU 374 H 3.030 2.126
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2CPE WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CPE--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XQZ.pdbqt
Chain information for 1XQZ.pdbqt #1
---
Chain | Description
A | No description available
Opened 1XQZ.pdbqt containing 1 structures (4460 atoms, 4520 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1XQZ.pdbqt #1
---
notes | No usable SEQRES records for 1XQZ.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLU 32
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A SER 308
Chain-final residues that are not actual C termini:
219 hydrogen bonds
5 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XQZ--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XQZ--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.1 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1XQZ--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
84 contacts
atom1 atom2 overlap distance
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.680 2.080
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.609 2.151
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 2HG1 0.394 2.366
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 0.391 3.069
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN 0.374 2.386
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HB1 0.366 2.514
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 0.197 3.263
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CE1 0.188 3.392
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 0.163 2.597
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 2HG1 0.161 2.599
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N 0.156 3.229
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 HZ3 0.141 2.619
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ARG 122 HG1 0.131 2.289
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 0.128 2.752
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG1 0.076 3.384
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 44 3HD1 0.076 2.684
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A GLU 121 O 0.067 3.293
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN 0.067 2.693
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 0.066 2.694
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A LEU 174 1HD1 0.058 2.402
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CB 0.050 3.530
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CZ 0.039 3.541
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD2 0.018 2.742
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HN -0.011 2.771
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ALA 65 CB -0.021 3.601
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HA -0.021 2.781
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG1 -0.024 3.484
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD1 -0.026 3.486
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.033 2.913
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.053 2.513
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N -0.056 3.441
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CA -0.060 3.520
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 -0.062 2.822
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CD1 -0.070 3.650
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CD2 -0.091 3.551
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.091 2.701
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG1 -0.109 3.569
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 NZ -0.112 3.497
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A PHE 49 CE1 -0.120 3.280
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CA -0.125 3.585
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.127 2.887
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 174 1HD1 -0.155 3.035
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 -0.155 2.765
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 HA -0.161 2.921
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG1 -0.171 3.631
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CD1 -0.174 3.634
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.176 3.636
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ARG 122 CG -0.191 3.311
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CD1 -0.193 3.773
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ALA 65 HB3 -0.203 3.083
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 3HG1 -0.203 2.813
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A LEU 174 CD1 -0.209 3.369
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 3HD1 -0.219 2.829
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LYS 67 HD1 -0.229 2.989
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 3HD1 -0.241 2.851
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CB -0.253 3.713
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 HB -0.285 2.895
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.295 3.605
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 2HG2 -0.296 2.906
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1XQZ.pdbqt #1/A VAL 126 O -0.301 3.661
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CB -0.302 3.612
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 CG -0.304 3.884
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CG2 -0.306 3.886
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A VAL 52 1HG1 -0.309 2.769
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ASP 186 N -0.313 3.698
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD1 -0.313 3.073
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ARG 122 HD2 -0.324 3.084
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 52 1HG1 -0.325 2.935
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 44 CD1 -0.326 3.786
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 185 2HG2 -0.327 2.787
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 174 1HD2 -0.328 3.208
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 1HG2 -0.336 3.096
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CD1 -0.337 3.647
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A PHE 49 CE2 -0.340 3.920
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 CG2 -0.342 3.652
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 2HD1 -0.346 3.106
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 52 1HG2 -0.351 2.961
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CG -0.363 3.823
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 185 1HG2 -0.366 3.126
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XQZ.pdbqt #1/A ILE 185 CG2 -0.373 3.533
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 CB -0.387 3.967
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A LEU 120 HB2 -0.393 3.273
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A ILE 104 CB -0.393 3.853
1XQZ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XQZ.pdbqt #1/A VAL 126 CG2 -0.396 3.856
84 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1XQZ.pdbqt
2.1 1XQZ--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -9.1 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1XQZ WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XQZ--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1Z00.pdbqt
Chain information for 1Z00.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 1Z00.pdbqt containing 1 structures (2620 atoms, 2640 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1Z00.pdbqt #1
---
notes | No usable SEQRES records for 1Z00.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1Z00.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A MET 219, /B MET 822
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A HIS 302, /B LYS 905
Chain-final residues that are not actual C termini:
131 hydrogen bonds
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1Z00--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1Z00--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1Z00--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
52 contacts
atom1 atom2 overlap distance
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB2 0.383 2.377
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 222 3HD2 0.372 2.388
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB 0.368 3.092
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 HA 0.193 2.687
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 O 0.163 3.197
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 0.104 2.656
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 HB3 0.064 2.696
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 CB 0.063 3.397
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 222 CD2 0.020 3.440
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB 0.011 3.449
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CD1 -0.010 3.470
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CA -0.022 3.602
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.036 3.496
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.039 2.649
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HZ3 -0.040 2.800
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HZ3 -0.042 2.802
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 -0.083 2.843
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 HB2 -0.087 2.507
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB2 -0.092 2.852
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HB2 -0.100 2.860
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 HB3 -0.122 2.882
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 3HD1 -0.124 2.884
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.127 3.367
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 HB3 -0.147 2.907
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CB -0.189 3.349
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 O -0.208 3.568
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB -0.211 3.671
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.218 2.828
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CD -0.225 3.685
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.228 3.688
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB1 -0.260 3.020
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 NZ -0.264 3.649
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CB -0.269 3.729
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/B GLN 885 OE1 -0.287 3.227
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 CD1 -0.288 3.868
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 HB3 -0.291 3.051
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1Z00.pdbqt #1/A LEU 222 CD2 -0.295 3.875
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CB -0.302 3.762
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A MET 219 O -0.310 3.400
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HB3 -0.324 3.084
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 HA -0.326 3.086
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CG -0.329 3.489
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 NZ -0.336 3.721
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LEU 227 N -0.340 3.845
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ALA 220 CA -0.348 3.658
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 HB3 -0.357 2.817
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B GLN 885 CB -0.359 3.819
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/B PRO 845 CB -0.362 3.822
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A LYS 226 CB -0.369 3.829
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.371 3.461
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 C 1Z00.pdbqt #1/A ASP 230 OD2 -0.380 3.470
1Z00--WRM-16.result.pdbqt #2.1/? UNL 1 O 1Z00.pdbqt #1/A ASP 230 CB -0.386 3.506
52 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1Z00.pdbqt
2.1 1Z00--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.8 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1Z00 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1Z00--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2N1I.pdbqt
Chain information for 2N1I.pdbqt #1
---
Chain | Description
A | No description available
Opened 2N1I.pdbqt containing 1 structures (2650 atoms, 2682 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2N1I.pdbqt #1
---
notes | No usable SEQRES records for 2N1I.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLY 51
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A GLU 226
Chain-final residues that are not actual C termini:
70 hydrogen bonds
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2N1I--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2N1I--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2N1I--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
54 contacts
atom1 atom2 overlap distance
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 H 0.318 2.562
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 0.108 2.652
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 HB3 0.091 2.789
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 0.063 2.547
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 O 0.016 3.344
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 0.000 2.760
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 -0.025 2.635
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 N -0.031 3.536
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 HA -0.034 2.794
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 3HG1 -0.037 2.797
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A ARG 102 NH2 -0.075 3.580
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.088 3.548
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 H -0.095 2.975
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 NH1 -0.100 3.605
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 O -0.123 3.483
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 2HH1 -0.129 3.009
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB2 -0.146 2.756
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 83 OD1 -0.153 3.513
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 CB -0.155 3.735
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.170 2.780
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 HE2 -0.171 3.051
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB3 -0.175 2.935
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 CG -0.213 3.673
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.216 3.526
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A ARG 102 CZ -0.232 3.812
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HA -0.236 3.116
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.246 3.006
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 105 H -0.256 3.016
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 102 NH1 -0.256 3.641
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 159 N -0.266 3.771
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 O -0.268 3.208
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 O -0.271 3.631
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CA -0.275 3.855
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HA -0.288 3.048
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A CYS 157 O -0.304 3.544
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.306 3.616
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 HB2 -0.307 3.187
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A MET 104 SD -0.309 3.511
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 H -0.310 2.370
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.311 3.891
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A MET 104 HA -0.317 3.197
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CG1 -0.327 3.787
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2N1I.pdbqt #1/A LYS 103 CE -0.328 3.908
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 CG -0.330 3.790
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A VAL 158 CA -0.338 3.798
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.339 3.099
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ARG 109 NH1 -0.340 3.845
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HG2 -0.369 2.979
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A GLU 108 CB -0.369 3.679
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A VAL 158 CG1 -0.385 3.545
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 C -0.387 3.547
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A MET 104 HA -0.391 3.001
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 C 2N1I.pdbqt #1/A ASP 83 OD2 -0.395 3.635
2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ARG 109 O -0.398 3.298
54 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2N1I.pdbqt
2.1 2N1I--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2N1I.pdbqt #1/A ASP 159 N 2N1I--WRM-16.result.pdbqt #2.1/? UNL 1 O 2N1I.pdbqt #1/A ASP 159 H 3.116 2.370
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2N1I WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2N1I--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1P4U.pdbqt
Chain information for 1P4U.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 1P4U.pdbqt containing 1 structures (2389 atoms, 2419 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1P4U.pdbqt #1
---
notes | No usable SEQRES records for 1P4U.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1P4U.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A LEU 579, /B ASP -1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LEU 723, /B ALA 6
Chain-final residues that are not actual C termini:
95 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1P4U--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1P4U--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.2 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1P4U--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
55 contacts
atom1 atom2 overlap distance
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A THR 677 2HG2 0.351 2.409
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PRO 593 HA 0.208 2.212
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ALA 614 HA 0.167 2.253
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 O 0.103 3.257
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 HB 0.100 2.320
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 3HG2 0.090 2.790
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 0.056 2.704
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HA 0.043 2.567
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A THR 677 CG2 0.014 3.446
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.042 2.652
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 2HG1 -0.044 2.804
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 3HG2 -0.081 2.501
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 CG2 -0.090 3.670
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 N -0.098 3.603
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A SER 594 OG -0.119 3.499
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.120 2.730
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.124 3.004
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.157 2.917
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PRO 593 CA -0.173 3.293
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.186 2.796
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ALA 614 CA -0.187 3.307
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.198 2.808
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.204 3.439
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 CG2 -0.210 3.370
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A VAL 628 3HG2 -0.214 2.674
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 CB -0.242 3.362
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A PHE 613 O -0.248 3.148
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A ALA 596 O -0.255 3.615
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD2 -0.257 3.717
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HD1 -0.261 3.021
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 HG -0.270 3.030
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD2 -0.273 3.033
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.277 3.782
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A LYS 592 O -0.287 3.187
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CB -0.297 3.877
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CE1 -0.299 3.879
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD1 -0.303 3.763
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A VAL 628 3HG2 -0.306 2.916
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 -0.312 2.922
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A SER 594 HN -0.324 3.204
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1P4U.pdbqt #1/A LEU 588 1HD2 -0.333 3.213
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 CA -0.342 3.652
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PHE 613 HN -0.343 3.223
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A SER 594 HN -0.343 2.403
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.350 3.735
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 HB1 -0.352 2.962
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A ILE 591 CG2 -0.367 3.527
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HA -0.370 2.980
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 CA -0.376 3.956
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 1HD1 -0.379 3.139
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 ND1 -0.389 3.624
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A HIS 612 C -0.391 3.971
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CG -0.391 3.851
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A LEU 588 CD2 -0.395 3.705
1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 C 1P4U.pdbqt #1/A PRO 593 HB2 -0.395 3.005
55 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1P4U.pdbqt
2.1 1P4U--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1P4U.pdbqt #1/A SER 594 N 1P4U--WRM-16.result.pdbqt #2.1/? UNL 1 O 1P4U.pdbqt #1/A SER 594 HN 3.335 2.403
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1P4U WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1P4U--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KCX.pdbqt
Chain information for 2KCX.pdbqt #1
---
Chain | Description
A | No description available
Opened 2KCX.pdbqt containing 1 structures (1066 atoms, 1073 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2KCX.pdbqt #1
---
notes | No usable SEQRES records for 2KCX.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A SER 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LYS 74
Chain-final residues that are not actual C termini:
56 hydrogen bonds
10 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KCX--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KCX--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.4 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2KCX--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
41 contacts
atom1 atom2 overlap distance
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 0.106 2.504
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.085 2.675
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.014 2.596
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 0.013 2.747
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 HD3 0.006 2.874
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 HE2 -0.031 2.091
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.034 3.344
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A ALA 55 HB2 -0.081 2.961
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 -0.125 2.885
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 HA -0.126 2.886
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A ALA 55 CB -0.136 3.716
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 CB -0.155 3.615
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 NE2 -0.167 3.402
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CA -0.168 3.628
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 CD -0.169 3.749
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.185 3.645
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 HG3 -0.195 2.955
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 CG -0.207 3.787
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 CB -0.220 3.800
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 HA -0.222 2.982
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 -0.225 3.105
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 55 CB -0.229 3.689
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 HA -0.239 2.999
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 HE2 -0.246 3.126
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.247 3.557
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KCX.pdbqt #1/A PRO 28 HG3 -0.250 3.130
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.250 3.560
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 45 HB1 -0.258 3.018
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ARG 59 CG -0.260 3.720
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A HIS 61 NE2 -0.261 3.766
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A GLU 52 OE1 -0.267 3.507
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A THR 46 O -0.276 3.516
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.276 3.736
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CE2 -0.281 3.591
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CB -0.323 3.783
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A TYR 47 CD2 -0.340 3.800
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 N -0.347 3.732
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 CB -0.361 3.941
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 56 HB2 -0.382 3.142
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 NE2 -0.387 3.072
2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KCX.pdbqt #1/A ALA 55 HB3 -0.388 3.148
41 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2KCX.pdbqt
2.1 2KCX--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2KCX.pdbqt #1/A HIS 61 NE2 2KCX--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KCX.pdbqt #1/A HIS 61 HE2 3.072 2.091
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.4 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2KCX WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KCX--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1VR2.pdbqt
Chain information for 1VR2.pdbqt #1
---
Chain | Description
A | No description available
Opened 1VR2.pdbqt containing 1 structures (4310 atoms, 4361 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1VR2.pdbqt #1
---
warnings | Not adding hydrogens to /A LYS 838 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A ARG 842 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A PHE 845 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A TYR 938 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 939 CB because it is missing heavy-atom bond
partners
6 messages similar to the above omitted
notes | No usable SEQRES records for 1VR2.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A LEU 820
Chain-initial residues that are not actual N termini: /A ASP 998, /A ASP 1064
Chain-final residues that are actual C termini: /A ALA 1168
Chain-final residues that are not actual C termini: /A LYS 939, /A PHE 1047
222 hydrogen bonds
Adding 'H' to /A ASP 998
Adding 'H' to /A ASP 1064
/A LYS 939 is not terminus, removing H atom from 'C'
/A PHE 1047 is not terminus, removing H atom from 'C'
2 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1VR2--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1VR2--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1VR2--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
47 contacts
atom1 atom2 overlap distance
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLY 846 HA1 0.221 2.659
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A LYS 868 HB1 0.195 2.685
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 HN 0.178 2.582
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 0.116 2.764
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 HN 0.070 2.690
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLN 847 HN 0.070 2.810
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 0.032 3.548
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 3HG2 0.032 2.428
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 HB3 -0.025 2.785
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A LYS 868 CB -0.077 3.657
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 CB -0.081 3.541
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLY 846 CA -0.093 3.673
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.095 2.855
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 CB -0.107 3.567
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1VR2.pdbqt #1/A GLN 847 N -0.119 3.624
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HE1 -0.150 2.910
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 CD1 -0.161 3.621
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 HA -0.164 2.924
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 N -0.209 3.594
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A GLN 847 N -0.223 3.608
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HG2 -0.224 2.984
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 N -0.239 3.624
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A LEU 840 O -0.244 3.184
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 2HG1 -0.254 2.714
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A CYS 919 O -0.260 3.500
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.269 3.729
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.280 3.740
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 -0.284 2.894
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CE -0.291 3.751
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 2HG1 -0.295 2.905
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CG -0.303 3.763
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.308 3.068
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 2HD1 -0.310 3.070
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 O 1VR2.pdbqt #1/A VAL 848 CG2 -0.320 3.480
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.324 2.934
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A PHE 918 CE1 -0.326 3.786
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 HE1 -0.332 3.092
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.343 3.803
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 CG2 -0.351 3.811
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 3HG2 -0.354 2.964
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 1HG2 -0.357 3.117
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 1HG2 -0.371 3.131
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A ALA 866 HB1 -0.375 3.135
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A VAL 848 2HG2 -0.383 3.143
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.387 2.997
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LYS 868 CD -0.393 3.853
1VR2--WRM-16.result.pdbqt #2.1/? UNL 1 C 1VR2.pdbqt #1/A LEU 840 HB2 -0.399 3.159
47 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1VR2.pdbqt
2.1 1VR2--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.7 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1VR2 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1VR2--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5AX3.pdbqt
Chain information for 5AX3.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 5AX3.pdbqt containing 1 structures (5669 atoms, 5733 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 5AX3.pdbqt #1
---
notes | No usable SEQRES records for 5AX3.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 5AX3.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A GLY 1, /B LEU 349
Chain-initial residues that are not actual N termini: /A TYR 27, /A PHE 174,
/A THR 181, /A GLY 194, /A LEU 248
Chain-final residues that are actual C termini: /A TYR 348, /B GLU 360
Chain-final residues that are not actual C termini: /A GLU 24, /A ALA 165, /A
VAL 179, /A LEU 191, /A ASP 241
195 hydrogen bonds
Adding 'H' to /A TYR 27
Adding 'H' to /A PHE 174
Adding 'H' to /A THR 181
Adding 'H' to /A GLY 194
Adding 'H' to /A LEU 248
/A GLU 24 is not terminus, removing H atom from 'C'
/A ALA 165 is not terminus, removing H atom from 'C'
/A VAL 179 is not terminus, removing H atom from 'C'
/A LEU 191 is not terminus, removing H atom from 'C'
/A ASP 241 is not terminus, removing H atom from 'C'
-9 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5AX3--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5AX3--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.2 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 5AX3--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
52 contacts
atom1 atom2 overlap distance
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 HG1 0.154 2.606
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 0.099 2.661
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 HD1 0.056 2.404
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 CG2 0.037 3.543
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 3HG2 0.002 2.878
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 HD1 -0.003 2.423
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HG2 -0.004 2.764
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A GLY 13 HA1 -0.068 2.488
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.084 2.844
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.109 2.719
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 13 HA1 -0.127 3.007
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 CD -0.127 3.247
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 15 HE -0.129 2.889
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 82 O -0.141 3.501
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HD2 -0.141 2.901
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ILE 81 2HG2 -0.151 3.031
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 HG1 -0.154 2.914
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.158 2.768
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.158 2.768
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 CB -0.174 3.294
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 CG -0.181 3.641
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.184 2.794
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ASP 79 OD2 -0.194 3.434
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HB2 -0.210 2.970
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CB -0.218 3.528
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.235 2.845
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 13 HA1 -0.241 3.121
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.249 2.859
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLN 345 CG -0.250 3.710
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 82 O -0.279 3.519
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A GLY 13 CA -0.284 3.404
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 HN -0.284 3.044
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG2 -0.287 3.047
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ILE 81 CG2 -0.288 3.448
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HB1 -0.297 2.717
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 14 CD -0.304 3.464
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.311 3.771
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A ARG 15 HE -0.322 2.932
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CB -0.324 3.634
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HN -0.330 2.350
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.346 3.806
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 HN -0.347 3.107
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.353 3.663
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A GLY 347 N -0.365 3.750
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HG2 -0.368 3.128
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A PRO 346 HB2 -0.371 2.831
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.379 2.989
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HG1 -0.386 2.996
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.388 3.698
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 CG -0.391 3.851
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 346 HD2 -0.396 3.006
5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 C 5AX3.pdbqt #1/A PRO 84 HA -0.399 3.159
52 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5AX3.pdbqt
2.1 5AX3--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5AX3.pdbqt #1/A ARG 15 N 5AX3--WRM-16.result.pdbqt #2.1/? UNL 1 O 5AX3.pdbqt #1/A ARG 15 HN 3.304 2.350
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "5AX3 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5AX3--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2KMU.pdbqt
Chain information for 2KMU.pdbqt #1
---
Chain | Description
A | No description available
Opened 2KMU.pdbqt containing 1 structures (957 atoms, 963 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2KMU.pdbqt #1
---
notes | No usable SEQRES records for 2KMU.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLY 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A GLN 56
Chain-final residues that are not actual C termini:
40 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KMU--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2KMU--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2KMU--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
55 contacts
atom1 atom2 overlap distance
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB2 0.691 2.069
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB 0.326 3.134
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 1HH2 0.311 2.449
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NH2 0.233 3.152
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB2 0.185 2.575
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 HE2 0.153 2.727
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 1HH2 0.129 2.631
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HE3 0.035 2.575
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 0.021 2.589
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 OH -0.037 3.147
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A TRP 16 HA -0.042 2.502
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD3 -0.069 2.829
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 HH -0.072 2.682
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 CE2 -0.105 3.685
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD3 -0.109 2.869
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ARG 12 NH1 -0.111 2.796
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB -0.121 3.581
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NE -0.127 3.512
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 HB1 -0.128 2.738
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 NH1 -0.135 3.370
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 HE -0.136 2.896
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A THR 40 2HG2 -0.154 2.914
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.168 3.628
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 NH2 -0.173 3.558
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.176 2.786
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.188 3.648
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HE3 -0.191 2.801
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 NH1 -0.202 3.587
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CE3 -0.202 3.512
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 CB -0.205 3.785
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 24 CZ -0.217 3.677
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 C -0.231 3.691
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 15 O -0.232 3.592
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 HB1 -0.241 3.121
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CZ3 -0.251 3.561
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 HB1 -0.264 3.144
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.289 3.749
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.305 3.065
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A THR 40 OG1 -0.306 3.566
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.310 3.770
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A TRP 16 CA -0.310 3.470
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 HD2 -0.313 3.073
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PHE 20 N -0.315 3.700
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CG -0.334 3.794
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2KMU.pdbqt #1/A PRO 37 HG3 -0.336 3.216
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ALA 15 O -0.344 3.284
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 O 2KMU.pdbqt #1/A ARG 12 2HH1 -0.344 2.404
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 19 C -0.359 3.819
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PHE 20 N -0.363 3.748
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A PRO 37 CD -0.364 3.674
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 CZ3 -0.366 3.676
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ALA 36 CB -0.371 3.681
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TYR 44 OH -0.376 3.756
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A ARG 12 1HH1 -0.384 3.144
2KMU--WRM-16.result.pdbqt #2.1/? UNL 1 C 2KMU.pdbqt #1/A TRP 16 HZ3 -0.391 3.001
55 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2KMU.pdbqt
2.1 2KMU--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.8 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2KMU WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2KMU--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2D68.pdbqt
Chain information for 2D68.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 2D68.pdbqt containing 1 structures (2419 atoms, 2436 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2D68.pdbqt #1
---
warnings | Not adding hydrogens to /A LYS 69 CD because it is missing heavy-
atom bond partners
Not adding hydrogens to /B LYS 69 CG because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 2D68.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 2D68.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A VAL 58, /B ASN 59
Chain-initial residues that are not actual N termini: /A LEU 104
Chain-final residues that are actual C termini: /A TRP 135, /B TRP 135
Chain-final residues that are not actual C termini: /A THR 100
143 hydrogen bonds
Adding 'H' to /A LEU 104
/A THR 100 is not terminus, removing H atom from 'C'
-3 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D68--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D68--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.5 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2D68--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
45 contacts
atom1 atom2 overlap distance
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD2 0.473 2.407
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD1 0.376 2.384
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HB1 0.240 2.640
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HA 0.211 2.669
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD 0.179 3.281
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B PHE 65 HD1 0.147 2.733
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD 0.095 3.485
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD1 0.057 2.703
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HD1 0.023 2.437
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HA 0.004 2.456
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CB -0.002 3.582
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 HD1 -0.029 2.449
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CD1 -0.031 3.151
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 85 HZ -0.041 2.461
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.069 2.829
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CZ -0.108 3.568
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A GLY 124 O -0.108 3.468
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 O -0.119 3.479
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CA -0.139 3.719
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.157 2.917
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 O -0.164 3.404
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CA -0.169 3.329
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 85 CZ -0.174 3.294
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B PHE 65 CD1 -0.195 3.775
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A PHE 84 HE2 -0.224 2.684
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CE2 -0.261 3.721
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CD1 -0.269 3.429
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A PHE 84 CZ -0.272 3.582
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CD -0.275 3.735
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.282 2.892
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.283 3.043
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.310 3.070
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 CE1 -0.322 3.902
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/A GLY 124 O -0.324 3.414
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HD2 -0.344 3.104
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B SER 61 HB1 -0.355 2.815
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/A GLY 124 O -0.356 3.296
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CB -0.368 3.828
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D68.pdbqt #1/A PHE 84 CD1 -0.372 3.952
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CB -0.384 3.844
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 HB1 -0.385 2.995
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 CA -0.390 3.970
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B SER 61 HB1 -0.391 3.151
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D68.pdbqt #1/B LYS 64 CB -0.395 3.705
2D68--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D68.pdbqt #1/B PHE 65 CB -0.395 3.555
45 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2D68.pdbqt
2.1 2D68--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.5 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2D68 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D68--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1OW1.pdbqt
Chain information for 1OW1.pdbqt #1
---
Chain | Description
A | No description available
Opened 1OW1.pdbqt containing 1 structures (2619 atoms, 2644 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1OW1.pdbqt #1
---
notes | No usable SEQRES records for 1OW1.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A PRO 3495
Chain-initial residues that are not actual N termini: /A PRO 3545
Chain-final residues that are actual C termini: /A VAL 3664
Chain-final residues that are not actual C termini: /A SER 3541
124 hydrogen bonds
/A SER 3541 is not terminus, removing H atom from 'C'
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OW1--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OW1--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.1 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1OW1--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
54 contacts
atom1 atom2 overlap distance
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 0.457 2.423
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A HIS 3656 HE1 0.285 2.595
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 0.241 2.639
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 HD2 0.208 2.552
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A HIS 3656 CE1 0.058 3.522
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 ND2 0.047 3.188
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB 0.042 3.538
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 1HD2 0.027 2.583
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 1HE2 0.008 2.602
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 1HE2 0.006 2.054
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 OE2 -0.046 3.286
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 CG2 -0.051 3.511
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HG2 -0.056 2.936
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 CD -0.060 3.520
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 -0.069 2.679
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 HG1 -0.070 2.490
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 2HD1 -0.102 2.982
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 ND2 -0.113 2.798
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 HG1 -0.117 2.537
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 CG2 -0.123 3.703
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OW1.pdbqt #1/A THR 3601 OG1 -0.128 3.508
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 1HD2 -0.143 2.203
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 OE1 -0.160 3.400
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.161 3.471
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 CD -0.162 3.622
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.171 2.781
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 -0.189 2.799
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 CG -0.210 3.330
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 1HG2 -0.214 2.974
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A SER 3651 HA -0.252 3.132
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.262 2.872
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN -0.264 2.284
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.265 3.575
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CB -0.274 3.584
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 CG -0.287 3.407
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 OE1 -0.287 3.527
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A PRO 3655 CB -0.295 3.415
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN -0.297 2.357
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 CG -0.300 3.880
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB1 -0.312 2.922
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLU 3636 CD -0.313 3.773
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 CG -0.322 3.782
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A LYS 3596 HB1 -0.332 3.092
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 N -0.332 2.977
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 NE2 -0.343 3.578
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ILE 3600 3HG2 -0.343 3.103
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 CA -0.344 3.464
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 HN -0.347 3.227
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 NE2 -0.358 3.043
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A LYS 3596 CD -0.367 3.487
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A GLN 3604 NE2 -0.367 3.752
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 1HD2 -0.377 2.987
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A PRO 3631 HB2 -0.377 2.987
1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OW1.pdbqt #1/A ASN 3652 HN -0.390 3.000
54 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1OW1.pdbqt
2.1 1OW1--WRM-16.result.pdbqt
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1OW1.pdbqt #1/A GLN 3604 NE2 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A GLN 3604 1HE2 3.043 2.054
1OW1.pdbqt #1/A ASN 3652 N 1OW1--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OW1.pdbqt #1/A ASN 3652 HN 3.284 2.357
2 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.1 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1OW1 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OW1--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1RJB.pdbqt
Chain information for 1RJB.pdbqt #1
---
Chain | Description
A | No description available
Opened 1RJB.pdbqt containing 1 structures (4781 atoms, 4839 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1RJB.pdbqt #1
---
notes | No usable SEQRES records for 1RJB.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A TYR 572
Chain-initial residues that are not actual N termini: /A ARG 655, /A LEU 783
Chain-final residues that are actual C termini: /A LEU 947
Chain-final residues that are not actual C termini: /A GLU 648, /A PHE 710
249 hydrogen bonds
Adding 'H' to /A ARG 655
Adding 'H' to /A LEU 783
/A GLU 648 is not terminus, removing H atom from 'C'
/A PHE 710 is not terminus, removing H atom from 'C'
3 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RJB--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RJB--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.6 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1RJB--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
51 contacts
atom1 atom2 overlap distance
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 2HE2 0.378 2.502
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 2HG2 0.292 2.468
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 0.238 3.267
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A PHE 621 HE2 0.094 2.666
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A TYR 865 HH 0.037 2.723
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O 0.021 3.069
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 1HG1 -0.003 2.763
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CG -0.016 3.596
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ALA 848 HB3 -0.091 2.851
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.091 2.701
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.093 3.403
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 CG2 -0.117 3.577
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG1 -0.148 2.908
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 HD2 -0.162 2.582
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HN -0.174 2.784
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG1 -0.178 2.938
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 1HD2 -0.179 2.939
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A TYR 842 CE1 -0.179 3.339
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 1HD2 -0.188 2.948
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A PHE 621 CE2 -0.192 3.652
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 2HG2 -0.200 2.960
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ALA 848 HA -0.214 2.674
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 CD -0.219 3.339
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 HG2 -0.221 3.101
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 CG -0.223 3.683
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ASP 811 HB2 -0.228 2.648
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A GLN 575 HG2 -0.230 2.650
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 CG -0.243 3.703
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A LEU 850 CD2 -0.254 3.714
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 HG1 -0.259 3.139
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.259 3.839
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A TYR 865 OH -0.259 3.519
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.268 3.358
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.269 3.359
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ALA 848 CB -0.277 3.737
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.297 3.387
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 O -0.301 3.391
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HG2 -0.313 3.073
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 -0.318 3.553
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.331 3.091
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.332 3.692
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 NE2 -0.352 3.857
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.357 3.667
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 OE1 -0.366 3.726
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A TYR 842 HE1 -0.375 2.835
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ARG 810 CZ -0.376 3.496
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ASP 811 OD1 -0.387 3.747
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A GLN 575 CD -0.389 3.969
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ARG 849 HB1 -0.395 3.005
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RJB.pdbqt #1/A ILE 836 CG1 -0.395 3.855
1RJB--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RJB.pdbqt #1/A ASP 811 CB -0.397 3.517
51 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1RJB.pdbqt
2.1 1RJB--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.6 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1RJB WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RJB--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1IFR.pdbqt
Chain information for 1IFR.pdbqt #1
---
Chain | Description
A | No description available
Opened 1IFR.pdbqt containing 1 structures (1747 atoms, 1765 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1IFR.pdbqt #1
---
notes | No usable SEQRES records for 1IFR.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLY 432
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A VAL 544
Chain-final residues that are not actual C termini:
96 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1IFR--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1IFR--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1IFR--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
43 contacts
atom1 atom2 overlap distance
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 HE1 0.513 2.367
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 CE1 0.243 3.337
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 HA 0.157 2.723
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HD2 0.117 2.643
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 HE1 0.011 2.869
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.034 3.494
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A TRP 514 HD1 -0.075 2.495
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ALA 516 HB1 -0.130 3.010
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ALA 516 CB -0.132 3.712
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.132 3.442
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.156 3.616
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 CA -0.164 3.744
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CD -0.170 3.630
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A VAL 513 O -0.173 3.533
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.177 2.937
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A LYS 515 HN -0.199 2.809
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A PRO 484 HG1 -0.203 2.963
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.212 2.972
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A VAL 513 O -0.218 3.458
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 NE1 -0.230 3.735
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.238 3.698
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LYS 515 HB2 -0.256 2.676
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LEU 512 HB1 -0.279 2.699
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.284 3.044
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 OH -0.290 3.670
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TRP 514 HD1 -0.300 2.910
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A PRO 484 HG1 -0.303 2.723
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.312 3.772
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 NE2 -0.315 3.700
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A PRO 484 HA -0.316 2.776
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 CE1 -0.321 3.781
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A ALA 516 HN -0.348 2.368
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CB -0.362 3.822
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HD2 -0.363 3.123
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB1 -0.365 3.125
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 ND1 -0.367 3.752
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A TYR 481 CZ -0.368 3.948
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 HB2 -0.368 3.128
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 CD -0.382 3.842
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A HIS 506 HE1 -0.384 2.994
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A HIS 506 HE1 -0.385 2.805
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A TRP 514 CD1 -0.396 3.516
1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 C 1IFR.pdbqt #1/A ARG 482 O -0.398 3.488
43 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1IFR.pdbqt
2.1 1IFR--WRM-16.result.pdbqt
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1IFR.pdbqt #1/A LYS 515 N 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A LYS 515 HN 3.558 2.542
1IFR.pdbqt #1/A ALA 516 N 1IFR--WRM-16.result.pdbqt #2.1/? UNL 1 O 1IFR.pdbqt #1/A ALA 516 HN 3.125 2.368
2 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1IFR WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1IFR--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1DNQ.pdbqt
Chain information for 1DNQ.pdbqt #1
---
Chain | Description
A | No description available
Opened 1DNQ.pdbqt containing 1 structures (4770 atoms, 4812 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1DNQ.pdbqt #1
---
notes | No usable SEQRES records for 1DNQ.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A LEU 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A VAL 312
Chain-final residues that are not actual C termini:
155 hydrogen bonds
26 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1DNQ--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1DNQ--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.9 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1DNQ--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
44 contacts
atom1 atom2 overlap distance
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 HN 0.298 2.582
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CD1 0.113 3.467
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 0.112 2.648
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 1HD2 0.109 1.911
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HG2 0.095 2.665
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 HB2 0.074 2.686
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 N 0.071 3.434
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.020 2.780
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 HB1 -0.041 2.921
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HA -0.076 2.836
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.088 2.698
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.089 2.849
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 HD1 -0.098 2.978
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HA -0.117 2.877
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A TYR 45 HE1 -0.135 2.555
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CE2 -0.142 3.452
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 CB -0.172 3.632
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 CG -0.199 3.659
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.208 2.968
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 1HD2 -0.212 2.822
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 CB -0.218 3.798
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 104 C -0.227 3.687
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 CA -0.229 3.689
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CA -0.237 3.697
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 N -0.252 3.637
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.253 3.713
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A ALA 68 HB3 -0.257 3.137
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.260 3.720
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A ALA 68 CB -0.260 3.840
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 ND2 -0.271 2.916
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 OD1 -0.279 3.519
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1DNQ.pdbqt #1/A TYR 45 CA -0.290 3.870
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A LYS 105 HA -0.291 3.051
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CD2 -0.304 3.614
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HD1 -0.326 2.936
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CZ -0.334 3.644
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.353 3.663
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 HB1 -0.356 2.966
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ASN 70 OD1 -0.365 3.455
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 101 CE2 -0.368 3.678
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.383 3.843
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A TYR 45 CD1 -0.385 3.845
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 68 C -0.385 3.845
1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 C 1DNQ.pdbqt #1/A ALA 103 O -0.388 3.628
44 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1DNQ.pdbqt
2.1 1DNQ--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1DNQ.pdbqt #1/A ASN 70 ND2 1DNQ--WRM-16.result.pdbqt #2.1/? UNL 1 O 1DNQ.pdbqt #1/A ASN 70 1HD2 2.916 1.911
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1DNQ WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1DNQ--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3U84.pdbqt
Chain information for 3U84.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 3U84.pdbqt containing 1 structures (15424 atoms, 15596 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 3U84.pdbqt #1
---
warnings | Not adding hydrogens to /B ARG 206 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /B ARG 207 CB because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 3U84.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 3U84.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A SER 1, /B GLY 2
Chain-initial residues that are not actual N termini: /A SER 402, /A THR 534,
/A GLY 548, /A SER 596, /B LEU 75, /B ARG 206, /B SER 402, /B ALA 523, /B GLY
548
Chain-final residues that are actual C termini: /A LYS 608, /B ALA 581
Chain-final residues that are not actual C termini: /A GLY 386, /A GLY 528, /A
ALA 539, /A ALA 581, /B ASP 70, /B HIS 199, /B ALA 385, /B SER 459, /B GLY 528
784 hydrogen bonds
Adding 'H' to /A SER 402
Adding 'H' to /A THR 534
Adding 'H' to /A GLY 548
Adding 'H' to /A SER 596
Adding 'H' to /B LEU 75
4 messages similar to the above omitted
/A GLY 386 is not terminus, removing H atom from 'C'
/A GLY 528 is not terminus, removing H atom from 'C'
/A ALA 539 is not terminus, removing H atom from 'C'
/A ALA 581 is not terminus, removing H atom from 'C'
/B ASP 70 is not terminus, removing H atom from 'C'
4 messages similar to the above omitted
-13 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3U84--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3U84--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.5 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 3U84--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
37 contacts
atom1 atom2 overlap distance
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 HB2 0.433 2.027
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TRP 341 HZ2 0.260 2.620
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B VAL 371 1HG1 0.250 2.630
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLY 326 HA1 0.185 2.695
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B CYS 329 HG 0.091 2.789
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 CB 0.060 3.100
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLU 363 OE2 -0.030 3.390
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CD2 -0.086 3.546
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B VAL 371 CG1 -0.103 3.683
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TRP 341 HE1 -0.116 2.136
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TRP 341 CZ2 -0.126 3.706
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 HB1 -0.165 2.585
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLY 326 CA -0.175 3.755
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 HB2 -0.189 3.069
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 O -0.208 3.148
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CE1 -0.214 3.674
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B VAL 371 1HG2 -0.215 2.675
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CE2 -0.234 3.694
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B CYS 329 SG -0.241 3.903
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 CB -0.245 3.365
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 HA -0.261 3.141
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 C -0.269 3.429
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CE2 -0.282 3.742
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.292 3.752
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.312 3.772
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TYR 323 CD2 -0.317 3.437
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B MET 322 C -0.325 3.445
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.327 3.587
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.330 3.440
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 C -0.334 3.914
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 319 CG -0.349 3.809
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 OH -0.353 3.613
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B TYR 323 CZ -0.360 3.670
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TYR 323 N -0.378 3.023
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 HB2 -0.382 2.992
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B GLU 363 OE2 -0.387 3.477
3U84--WRM-16.result.pdbqt #2.1/? UNL 1 C 3U84.pdbqt #1/B MET 322 O -0.399 3.759
37 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3U84.pdbqt
2.1 3U84--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3U84.pdbqt #1/B TRP 341 NE1 3U84--WRM-16.result.pdbqt #2.1/? UNL 1 O 3U84.pdbqt #1/B TRP 341 HE1 3.103 2.136
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "3U84 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3U84--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2YSM.pdbqt
Chain information for 2YSM.pdbqt #1
---
Chain | Description
A | No description available
Opened 2YSM.pdbqt containing 1 structures (1584 atoms, 1601 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2YSM.pdbqt #1
---
notes | No usable SEQRES records for 2YSM.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLY 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A GLY 111
Chain-final residues that are not actual C termini:
29 hydrogen bonds
15 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2YSM--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2YSM--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.5 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2YSM--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
58 contacts
atom1 atom2 overlap distance
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 HG2 0.549 2.331
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 HB2 0.263 2.617
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 CG 0.262 3.318
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 2HG1 0.200 2.560
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 H 0.194 2.566
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 CA 0.171 3.409
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 HA 0.167 2.713
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 2HG1 0.075 2.685
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 3HD2 0.068 2.692
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 52 HB3 0.066 2.814
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 CB 0.017 3.563
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 55 HZ1 0.014 2.866
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 C -0.022 3.602
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG1 -0.039 2.919
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG2 -0.053 3.633
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.053 2.933
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A ASN 94 N -0.094 3.599
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.109 2.719
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A MET 69 O -0.119 3.479
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.129 2.739
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 3HD2 -0.130 2.890
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.136 3.716
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 CB -0.142 3.722
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 HB -0.142 2.752
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A GLY 95 N -0.146 3.651
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 CG1 -0.151 3.611
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 O -0.156 3.516
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 N -0.158 3.543
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 92 O -0.216 3.456
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.219 2.829
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.219 3.529
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A THR 93 C -0.221 3.801
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 CD2 -0.255 3.715
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 CD2 -0.258 3.718
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 76 OD1 -0.259 3.499
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 C -0.264 3.844
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.266 3.146
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ILE 39 CG1 -0.271 3.731
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.280 2.890
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 52 CB -0.282 3.862
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 2HG2 -0.286 2.896
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LEU 70 HA -0.289 3.049
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 73 OD1 -0.292 3.532
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 N -0.297 3.802
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.297 3.877
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CG1 -0.299 3.609
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A PRO 92 HB2 -0.302 3.182
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 3HG1 -0.309 3.069
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A TRP 96 CB -0.331 3.791
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 H -0.335 3.215
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.338 3.648
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 45 HZ3 -0.358 3.118
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A PRO 92 HG2 -0.359 2.969
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A THR 93 O -0.359 3.599
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2YSM.pdbqt #1/A TRP 96 N -0.383 3.888
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A LYS 55 NZ -0.384 3.889
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A VAL 71 CB -0.385 3.695
2YSM--WRM-16.result.pdbqt #2.1/? UNL 1 C 2YSM.pdbqt #1/A ASP 76 OD1 -0.395 3.635
58 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2YSM.pdbqt
2.1 2YSM--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2YSM WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2YSM--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2LNK.pdbqt
Chain information for 2LNK.pdbqt #1
---
Chain | Description
A B | No description available
C | No description available
Opened 2LNK.pdbqt containing 1 structures (3899 atoms, 3931 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2LNK.pdbqt #1
---
notes | No usable SEQRES records for 2LNK.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 2LNK.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 2LNK.pdbqt (#1) chain C; guessing termini instead
Chain-initial residues that are actual N termini: /A MET 1, /B MET 1, /C GLN
1897
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LYS 101, /B LYS 101, /C ALA
1935
Chain-final residues that are not actual C termini:
191 hydrogen bonds
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LNK--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LNK--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.0 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2LNK--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
34 contacts
atom1 atom2 overlap distance
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 0.362 2.518
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 0.342 3.238
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 1HD2 0.261 2.349
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/C THR 1906 2HG2 0.132 2.628
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 0.076 2.534
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A GLU 88 HB2 0.041 2.379
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 0.005 3.230
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.072 2.952
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.095 3.637
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A MET 84 O -0.109 3.049
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 ND2 -0.119 2.804
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 1HD2 -0.126 2.146
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/C THR 1906 CG2 -0.131 3.591
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CD1 -0.159 3.619
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A ASN 87 1HD2 -0.162 2.222
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.219 2.829
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CD1 -0.222 3.682
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CZ -0.228 3.688
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/A GLU 88 CB -0.228 3.348
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 -0.254 3.564
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CE2 -0.261 3.841
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 HB3 -0.283 3.043
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.288 3.830
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 -0.291 3.796
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.298 3.608
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 CD2 -0.300 3.880
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.300 3.760
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE1 -0.318 3.778
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 72 HD2 -0.356 2.966
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LNK.pdbqt #1/B PHE 27 CD2 -0.368 3.488
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CG -0.376 3.836
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/B PHE 27 CE2 -0.386 3.846
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A MET 84 SD -0.386 3.928
2LNK--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LNK.pdbqt #1/A ASN 87 ND2 -0.390 3.895
34 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2LNK.pdbqt
2.1 2LNK--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2LNK WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LNK--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XUM.pdbqt
Chain information for 1XUM.pdbqt #1
---
Chain | Description
A | No description available
Opened 1XUM.pdbqt containing 1 structures (2876 atoms, 2908 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1XUM.pdbqt #1
---
notes | No usable SEQRES records for 1XUM.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A THR 54
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A THR 236
Chain-final residues that are not actual C termini:
96 hydrogen bonds
59 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XUM--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1XUM--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1XUM--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
50 contacts
atom1 atom2 overlap distance
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 HD2 0.493 2.387
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 HG1 0.216 2.664
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 CD 0.190 3.390
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CE2 0.101 3.359
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 134 HG 0.100 2.660
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 HZ2 0.069 2.691
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 CD 0.018 3.102
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 CE 0.016 3.104
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.001 2.761
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 HD2 -0.002 2.422
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASP 160 OD2 -0.014 2.914
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 CB -0.062 3.372
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 HG1 -0.100 2.980
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 OG1 -0.102 3.482
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 110 2HD2 -0.109 2.869
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A GLU 157 OE1 -0.125 3.485
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.126 2.886
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 HD2 -0.128 2.888
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 NZ -0.138 3.523
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 HE2 -0.140 2.900
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CD2 -0.142 3.602
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 HB2 -0.156 2.766
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A GLU 157 CD -0.190 3.770
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 HB2 -0.198 2.618
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 CD2 -0.208 3.368
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A LYS 209 HE1 -0.225 2.645
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 HD2 -0.234 2.994
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 CD -0.246 3.706
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.257 3.762
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 134 OG -0.264 3.524
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CD2 -0.267 3.727
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 110 ND2 -0.276 3.661
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 1HG2 -0.283 3.163
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.289 2.899
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASP 160 CG -0.294 3.414
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ASN 186 ND2 -0.305 3.540
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.309 3.694
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A TYR 185 CE2 -0.315 3.475
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A THR 159 OG1 -0.321 2.841
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.331 3.716
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.334 3.719
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 185 CG -0.343 3.653
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 CG2 -0.352 3.932
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 NH1 -0.358 3.743
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A THR 159 HG1 -0.360 2.380
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A TYR 206 CE2 -0.371 3.831
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A SER 234 HG -0.378 3.258
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A LYS 183 CE -0.381 3.841
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A THR 159 OG1 -0.387 3.767
1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 C 1XUM.pdbqt #1/A ARG 109 2HH1 -0.390 3.150
50 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1XUM.pdbqt
2.1 1XUM--WRM-16.result.pdbqt
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1XUM.pdbqt #1/A ASN 186 ND2 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASN 186 1HD2 3.170 2.565
1XUM.pdbqt #1/A ASN 208 ND2 1XUM--WRM-16.result.pdbqt #2.1/? UNL 1 O 1XUM.pdbqt #1/A ASN 208 2HD2 3.318 2.547
2 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.8 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1XUM WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1XUM--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/6LTH.pdbqt
Chain information for 6LTH.pdbqt #1
---
Chain | Description
I | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
Opened 6LTH.pdbqt containing 1 structures (30136 atoms, 30416 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 6LTH.pdbqt #1
---
warnings | Not adding hydrogens to /M LYS 199 CD because it is missing heavy-
atom bond partners
Not adding hydrogens to /M LYS 211 CG because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 6LTH.pdbqt (#1) chain I; guessing termini
instead
No usable SEQRES records for 6LTH.pdbqt (#1) chain L; guessing termini instead
No usable SEQRES records for 6LTH.pdbqt (#1) chain M; guessing termini instead
No usable SEQRES records for 6LTH.pdbqt (#1) chain N; guessing termini instead
No usable SEQRES records for 6LTH.pdbqt (#1) chain O; guessing termini instead
3 messages similar to the above omitted
Chain-initial residues that are actual N termini: /I SER 350, /L ILE 1639, /M
SER 7, /N HIS 423, /O HIS 423, /P LYS 125, /Q SER 172, /R GLY 13
Chain-initial residues that are not actual N termini: /I LEU 396, /L GLU 1802,
/L ILE 1954, /L GLU 2047, /L PRO 2225, /M ASP 78, /M ASP 172, /M GLN 257, /M
PRO 332, /N THR 602, /N ASN 671, /N LEU 858, /O THR 598, /O LEU 656, /O ALA
867, /P GLN 291, /P THR 399
Chain-final residues that are actual C termini: /I LEU 476, /L SER 2285, /M
THR 357, /N GLN 952, /O GLN 952, /P GLU 505, /Q LEU 276, /R LYS 82
Chain-final residues that are not actual C termini: /I LEU 388, /L ASP 1746,
/L LYS 1862, /L LYS 2025, /L GLN 2210, /M SER 67, /M ASP 101, /M PRO 249, /M
TYR 326, /N ASP 515, /N ARG 641, /N MET 703, /O GLN 545, /O ASP 651, /O ARG
717, /P LYS 177, /P GLU 369
1386 hydrogen bonds
Adding 'H' to /I LEU 396
Adding 'H' to /L GLU 1802
Adding 'H' to /L ILE 1954
Adding 'H' to /L GLU 2047
Adding 'H' to /M ASP 78
10 messages similar to the above omitted
/I LEU 388 is not terminus, removing H atom from 'C'
/L ASP 1746 is not terminus, removing H atom from 'C'
/L LYS 1862 is not terminus, removing H atom from 'C'
/L LYS 2025 is not terminus, removing H atom from 'C'
/L GLN 2210 is not terminus, removing H atom from 'C'
12 messages similar to the above omitted
-24 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LTH--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LTH--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.3 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 6LTH--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
48 contacts
atom1 atom2 overlap distance
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HG1 0.557 2.203
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CG 0.147 3.313
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 HG2 0.113 2.647
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L PHE 1999 HE1 0.078 2.342
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HG1 0.071 2.689
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 OH 0.045 3.215
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 HA 0.021 2.399
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HA 0.009 2.871
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 CE1 0.003 3.577
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CA 0.002 3.578
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HG2 -0.053 2.813
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.064 2.824
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 CZ -0.085 3.665
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L PRO 2075 HB1 -0.087 2.967
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 CG -0.091 3.551
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L TYR 2076 OH -0.096 3.476
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.114 2.874
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L ASP 2072 HB1 -0.134 3.014
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.135 2.895
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CB -0.137 3.717
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 HG2 -0.165 2.775
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HG2 -0.175 2.785
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 CD -0.176 3.336
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.189 2.949
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 HB2 -0.190 2.950
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LTH.pdbqt #1/L PRO 2075 CB -0.197 3.777
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 HB2 -0.207 3.087
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2128 OE1 -0.214 3.304
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.215 2.825
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PRO 2075 CG -0.225 3.685
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 CA -0.232 3.352
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PHE 1999 HE1 -0.235 2.845
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2070 CD -0.238 3.358
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLN 464 CG -0.240 3.700
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 N -0.245 3.750
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L ASP 2072 CB -0.251 3.831
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L PHE 1999 CE1 -0.258 3.378
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I LYS 461 CG -0.263 3.723
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 CZ -0.264 3.724
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L TYR 2076 HH -0.283 3.043
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2128 2HE2 -0.292 2.902
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L PHE 1999 HE1 -0.313 3.193
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 CG -0.322 3.782
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L GLN 2070 NE2 -0.333 3.568
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 HG2 -0.349 2.959
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/I GLU 465 HG2 -0.380 3.140
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 OE1 -0.393 3.333
6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LTH.pdbqt #1/L LYS 2003 CG -0.397 3.857
48 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 6LTH.pdbqt
2.1 6LTH--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6LTH.pdbqt #1/L GLN 2128 NE2 6LTH--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LTH.pdbqt #1/L GLN 2128 2HE2 3.227 2.606
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.3 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "6LTH WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LTH--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3H9R.pdbqt
Chain information for 3H9R.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 3H9R.pdbqt containing 1 structures (6620 atoms, 6691 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 3H9R.pdbqt #1
---
warnings | Not adding hydrogens to /A ARG 218 CD because it is missing heavy-
atom bond partners
Not adding hydrogens to /A SER 276 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ASP 499 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /B ARG 14 CB because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 3H9R.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 3H9R.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A THR 172, /B GLY 2
Chain-initial residues that are not actual N termini: /A SER 276, /A ARG 375
Chain-final residues that are actual C termini: /A ASP 499, /B GLU 108
Chain-final residues that are not actual C termini: /A SER 272, /A HIS 361
360 hydrogen bonds
Adding 'H' to /A SER 276
Adding 'H' to /A ARG 375
/A SER 272 is not terminus, removing H atom from 'C'
/A HIS 361 is not terminus, removing H atom from 'C'
7 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3H9R--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3H9R--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -10.1 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 3H9R--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
56 contacts
atom1 atom2 overlap distance
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A GLY 215 HA2 0.237 2.643
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A LYS 340 HE1 0.199 2.681
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A SER 290 HG 0.131 2.629
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 0.091 2.669
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 OH 0.084 3.296
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 0.026 2.734
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.001 2.611
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.040 3.500
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HE1 -0.051 2.811
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HE1 -0.053 2.663
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A GLY 215 CA -0.076 3.656
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 2HD1 -0.077 2.687
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.104 3.344
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HH -0.112 2.992
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 214 1HG2 -0.136 2.896
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.146 3.506
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HH -0.154 2.914
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 -0.157 2.767
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.158 2.768
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A ASP 293 OD2 -0.168 3.528
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CZ -0.169 3.749
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 214 CG2 -0.171 3.631
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 CD1 -0.171 3.631
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A SER 290 OG -0.174 3.434
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CE -0.180 3.640
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 3HD2 -0.205 2.815
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A LYS 340 CE -0.206 3.786
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HE2 -0.256 3.016
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CE2 -0.259 3.839
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CG -0.261 3.721
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A LEU 343 2HD1 -0.276 2.736
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 CD2 -0.279 3.589
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A ALA 353 HB1 -0.284 2.704
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 -0.287 3.047
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 HG1 -0.287 2.897
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB1 -0.289 3.049
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB2 -0.297 3.177
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB1 -0.298 3.058
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 343 CD2 -0.307 3.617
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A TYR 292 CD2 -0.308 3.888
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 3HG2 -0.317 2.927
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 HB2 -0.319 3.079
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 CE1 -0.325 3.785
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3H9R.pdbqt #1/A TYR 292 HD2 -0.326 3.206
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.326 3.786
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 2HG1 -0.350 3.110
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 CG1 -0.350 3.810
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 CE2 -0.367 3.677
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 CE -0.368 3.678
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 219 HE2 -0.371 2.981
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LYS 340 O -0.374 3.464
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A ALA 233 CB -0.376 3.956
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A LEU 263 1HD2 -0.382 3.262
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 O 3H9R.pdbqt #1/A LEU 263 CD2 -0.384 3.544
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A TYR 285 HD1 -0.388 3.148
3H9R--WRM-16.result.pdbqt #2.1/? UNL 1 C 3H9R.pdbqt #1/A VAL 222 CG1 -0.390 3.970
56 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3H9R.pdbqt
2.1 3H9R--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -10.1 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "3H9R WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3H9R--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1A5E.pdbqt
Chain information for 1A5E.pdbqt #1
---
Chain | Description
A | No description available
Opened 1A5E.pdbqt containing 1 structures (2306 atoms, 2328 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1A5E.pdbqt #1
---
notes | No usable SEQRES records for 1A5E.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASP 156
Chain-final residues that are not actual C termini:
64 hydrogen bonds
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1A5E--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1A5E--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.6 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1A5E--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
45 contacts
atom1 atom2 overlap distance
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 0.185 2.695
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 1HH1 0.171 1.889
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 HA3 0.148 2.732
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HD3 0.134 2.626
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A LEU 117 2HD1 0.063 2.817
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 CA 0.033 3.547
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 NH1 0.030 3.475
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD2 -0.013 3.593
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A LEU 117 CD1 -0.018 3.598
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.022 2.782
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CG -0.036 3.616
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A PRO 151 HD3 -0.038 2.918
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.064 2.824
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.074 3.384
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.085 2.845
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 NH1 -0.090 2.775
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A LEU 117 3HD1 -0.118 2.538
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 87 NH2 -0.119 3.624
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.131 2.891
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A PRO 151 CD -0.159 3.739
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.161 2.771
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.174 3.634
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ASP 108 OD2 -0.193 3.133
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A GLY 111 N -0.213 3.598
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.218 3.678
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.221 3.681
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A GLY 111 N -0.227 3.732
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 CD -0.234 3.694
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CZ3 -0.255 3.565
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD1 -0.273 3.853
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A LEU 117 CD1 -0.275 3.395
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CE2 -0.277 3.857
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CZ3 -0.277 3.587
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CH2 -0.289 3.599
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HD3 -0.299 3.059
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 HB3 -0.303 2.913
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A GLY 111 C -0.323 3.783
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 -0.339 2.949
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1A5E.pdbqt #1/A TRP 110 C -0.352 3.932
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 HB2 -0.359 3.119
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 46 NH2 -0.361 3.746
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 87 2HH2 -0.361 3.241
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CD1 -0.370 3.830
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A TRP 110 CB -0.386 3.846
1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 C 1A5E.pdbqt #1/A ARG 112 1HH1 -0.399 3.009
45 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1A5E.pdbqt
2.1 1A5E--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1A5E.pdbqt #1/A ARG 112 NH1 1A5E--WRM-16.result.pdbqt #2.1/? UNL 1 O 1A5E.pdbqt #1/A ARG 112 1HH1 2.775 1.889
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.6 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1A5E WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1A5E--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1ES7.pdbqt
Chain information for 1ES7.pdbqt #1
---
Chain | Description
A C | No description available
B | No description available
D | No description available
Opened 1ES7.pdbqt containing 1 structures (5745 atoms, 5815 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1ES7.pdbqt #1
---
notes | No usable SEQRES records for 1ES7.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1ES7.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 1ES7.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 1ES7.pdbqt (#1) chain D; guessing termini instead
Chain-initial residues that are actual N termini: /A LYS 11, /B THR 232, /C
LYS 511, /D THR 732
Chain-initial residues that are not actual N termini: /B GLU 270, /D GLU 770
Chain-final residues that are actual C termini: /A ARG 114, /B PRO 317, /C ARG
614, /D ILE 820
Chain-final residues that are not actual C termini: /B ASP 266, /D ASP 766
270 hydrogen bonds
Adding 'H' to /B GLU 270
Adding 'H' to /D GLU 770
/B ASP 266 is not terminus, removing H atom from 'C'
/D ASP 766 is not terminus, removing H atom from 'C'
28 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1ES7--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1ES7--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.5 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1ES7--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
46 contacts
atom1 atom2 overlap distance
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HN 0.266 2.614
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 HN 0.165 1.855
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B PRO 245 HB2 0.115 2.645
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 ND1 0.101 3.404
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HD1 0.099 2.781
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 HN 0.038 2.022
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HB2 -0.021 2.781
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.077 2.687
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 N -0.107 3.612
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 1HD2 -0.114 2.134
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B PRO 245 CB -0.134 3.594
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 HN -0.134 2.744
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ASN 56 1HD2 -0.156 2.766
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 N -0.177 2.822
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HN -0.181 2.791
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 CB -0.198 3.658
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 HN -0.206 2.966
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A GLY 110 HA1 -0.216 2.636
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD1 -0.230 3.470
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 OD2 -0.233 3.473
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.234 2.994
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 CB -0.239 3.699
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HB2 -0.244 3.004
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.248 3.128
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 246 HB2 -0.253 3.013
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 O -0.274 3.364
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A GLY 110 CA -0.280 3.400
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 O -0.305 3.205
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 CB -0.311 3.771
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD1 -0.316 3.556
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A LYS 15 CA -0.326 3.446
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 O -0.327 3.567
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 2HD2 -0.328 2.388
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A LYS 15 HA -0.330 2.750
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 OD2 -0.331 3.571
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 CB -0.338 3.648
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 N -0.338 3.573
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 N -0.339 3.024
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 O -0.361 3.301
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ASN 56 ND2 -0.363 3.598
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A ARG 16 N -0.363 3.748
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 ND2 -0.369 3.014
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/B ASP 247 CG -0.374 3.834
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A HIS 54 HB2 -0.375 2.985
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 ND2 -0.381 3.066
1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 C 1ES7.pdbqt #1/A CYS 111 HN -0.394 3.274
46 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1ES7.pdbqt
2.1 1ES7--WRM-16.result.pdbqt
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1ES7.pdbqt #1/A ARG 16 N 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ARG 16 HN 2.822 1.855
1ES7.pdbqt #1/A ASN 56 ND2 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 1HD2 3.014 2.134
1ES7.pdbqt #1/A ASN 56 ND2 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A ASN 56 2HD2 3.066 2.388
1ES7.pdbqt #1/A CYS 111 N 1ES7--WRM-16.result.pdbqt #2.1/? UNL 1 O 1ES7.pdbqt #1/A CYS 111 HN 3.024 2.022
4 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.5 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1ES7 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1ES7--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3TGX.pdbqt
Chain information for 3TGX.pdbqt #1
---
Chain | Description
A M O | No description available
B | No description available
C G I K | No description available
D | No description available
E | No description available
F | No description available
H | No description available
J | No description available
L | No description available
N | No description available
P | No description available
Opened 3TGX.pdbqt containing 1 structures (41174 atoms, 41719 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 3TGX.pdbqt #1
---
warning | Not adding hydrogens to /J ARG 126 CB because it is missing heavy-
atom bond partners
notes | No usable SEQRES records for 3TGX.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 3TGX.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 3TGX.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 3TGX.pdbqt (#1) chain D; guessing termini instead
No usable SEQRES records for 3TGX.pdbqt (#1) chain E; guessing termini instead
11 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A CYS 1, /B GLY 2, /C CYS
1, /D GLY 2, /E CYS 1, /F GLY 2, /G CYS 1, /H ASP 4, /I CYS 1, /J GLY 2, /K
CYS 1, /L ASP 4, /M CYS 1, /N ASP 4, /O CYS 1, /P ASP 4
Chain-initial residues that are not actual N termini: /B HIS 89, /D LEU 91, /F
THR 92, /H GLN 87, /J LEU 91, /L LEU 91, /N THR 92, /P THR 92
Chain-final residues that are actual C termini: /A SER 208, /B LEU 123, /C GLU
209, /D LEU 123, /E GLN 207, /F LEU 123, /G GLU 209, /H LEU 123, /I GLU 209,
/J ARG 126, /K GLU 209, /L HIS 122, /M SER 208, /N HIS 120, /O SER 208, /P LEU
123
Chain-final residues that are not actual C termini: /B THR 81, /D ARG 85, /F
ASN 82, /H ASN 82, /J THR 81, /L THR 81, /N THR 81, /P THR 81
1792 hydrogen bonds
Adding 'H' to /B HIS 89
Adding 'H' to /D LEU 91
Adding 'H' to /F THR 92
Adding 'H' to /H GLN 87
Adding 'H' to /J LEU 91
3 messages similar to the above omitted
/B THR 81 is not terminus, removing H atom from 'C'
/D ARG 85 is not terminus, removing H atom from 'C'
/F ASN 82 is not terminus, removing H atom from 'C'
/H ASN 82 is not terminus, removing H atom from 'C'
/J THR 81 is not terminus, removing H atom from 'C'
3 messages similar to the above omitted
80 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3TGX--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3TGX--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.5 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 3TGX--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
84 contacts
atom1 atom2 overlap distance
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 0.702 2.058
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 2HD2 0.553 2.327
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 HB2 0.512 2.368
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 0.484 2.901
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASP 81 OD1 0.349 3.011
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 HH 0.297 2.463
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/E ALA 127 HB1 0.227 2.533
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 1HE2 0.207 2.403
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 0.181 2.579
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CB 0.180 3.400
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 OH 0.166 3.094
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 ND2 0.163 3.342
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CB 0.149 3.431
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 CD1 0.133 3.447
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 NE 0.132 3.373
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB1 0.131 2.749
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 HD1 0.115 2.765
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CB 0.110 3.470
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 0.094 2.786
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 CG1 0.089 3.491
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HN 0.077 2.683
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/E ALA 127 CB 0.016 3.444
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 NE1 0.005 3.500
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 2HG1 0.001 2.879
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.001 2.611
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 CB -0.006 3.586
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASP 81 OD1 -0.008 3.248
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 1HG1 -0.043 2.923
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HN -0.056 2.816
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TRP 21 HE1 -0.056 2.936
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M ASN 22 ND2 -0.057 3.292
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 1HE2 -0.067 2.127
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CG -0.098 3.678
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 NE2 -0.104 3.339
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.107 3.612
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 HD2 -0.112 2.872
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB1 -0.119 2.879
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB1 -0.134 3.014
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 HB1 -0.143 3.023
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.158 2.768
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CG -0.159 3.619
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 -0.159 3.039
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/F ASN 62 HB2 -0.163 2.623
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 -0.178 2.938
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 -0.185 3.690
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CG -0.188 3.648
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 N -0.192 3.577
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.208 2.818
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.228 3.108
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB2 -0.235 3.115
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.240 3.000
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CE1 -0.248 3.708
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 HH -0.249 3.009
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CG -0.260 3.840
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 CB -0.262 3.842
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CD -0.265 3.845
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 CZ -0.271 3.851
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ILE 66 N -0.274 3.779
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB1 -0.281 3.161
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/F ARG 65 HE -0.296 3.176
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 HB2 -0.296 3.176
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.298 3.533
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/A ASP 81 OD1 -0.308 3.248
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3TGX.pdbqt #1/E ALA 127 HB2 -0.313 3.193
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.319 2.929
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M TYR 86 OH -0.336 3.596
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 CD -0.339 3.799
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HB2 -0.343 2.953
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 CB -0.346 3.806
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 HG1 -0.347 3.107
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 CD2 -0.354 3.814
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 HB2 -0.356 2.816
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ARG 65 HB2 -0.357 3.117
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 ND2 -0.361 3.746
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 2HD2 -0.361 3.121
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 CG -0.362 3.522
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/F ASN 62 ND2 -0.368 3.603
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A ASN 22 1HD2 -0.370 3.250
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 CB -0.370 3.680
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M GLN 82 1HE2 -0.388 3.268
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 NE2 -0.389 3.774
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/A GLN 82 HB2 -0.390 3.150
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 C 3TGX.pdbqt #1/M HIS 24 ND1 -0.394 3.779
3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/A ASN 22 ND2 -0.395 3.080
84 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3TGX.pdbqt
2.1 3TGX--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
3TGX.pdbqt #1/M GLN 82 NE2 3TGX--WRM-16.result.pdbqt #2.1/? UNL 1 O 3TGX.pdbqt #1/M GLN 82 1HE2 3.121 2.127
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.5 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "3TGX WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3TGX--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/4JUP.pdbqt
Chain information for 4JUP.pdbqt #1
---
Chain | Description
A B | No description available
Opened 4JUP.pdbqt containing 1 structures (2664 atoms, 2690 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 4JUP.pdbqt #1
---
notes | No usable SEQRES records for 4JUP.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 4JUP.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A LEU 22, /B LEU 22
Chain-initial residues that are not actual N termini: /A ASN 71, /B ASN 71
Chain-final residues that are actual C termini: /A GLY 108, /B GLY 108
Chain-final residues that are not actual C termini: /A ALA 63, /B ALA 63
116 hydrogen bonds
Adding 'H' to /A ASN 71
Adding 'H' to /B ASN 71
/A ALA 63 is not terminus, removing H atom from 'C'
/B ALA 63 is not terminus, removing H atom from 'C'
-2 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/4JUP--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/4JUP--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.9 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 4JUP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
77 contacts
atom1 atom2 overlap distance
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 HA 0.493 1.967
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 HA 0.445 2.315
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 HB1 0.307 2.573
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG 0.303 2.457
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 O 0.286 3.074
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 HB1 0.217 2.663
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 HD2 0.197 2.683
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CA 0.183 2.977
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG2 0.161 2.599
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B HIS 31 CE1 0.142 3.018
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG 0.130 2.630
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH2 0.110 2.770
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CB 0.083 3.497
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 HA 0.074 2.686
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 CA 0.055 3.405
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 CG 0.047 3.413
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 2HH2 0.027 1.993
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 HG1 -0.010 2.770
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 HB1 -0.017 2.777
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG -0.018 2.778
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.024 2.634
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH2 -0.029 3.534
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CB -0.049 3.629
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.079 3.339
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 HG1 -0.087 2.697
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A THR 82 HG1 -0.105 2.985
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CD -0.111 3.691
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 HA -0.119 2.999
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.153 3.243
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 NH2 -0.159 2.804
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.165 3.255
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A THR 82 1HG2 -0.181 3.061
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A THR 82 OG1 -0.189 3.449
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 HA -0.191 2.951
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 CE1 -0.199 3.779
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 HD2 -0.203 2.963
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 CD -0.205 3.665
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 1HG1 -0.205 2.965
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH2 -0.206 2.816
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH1 -0.210 3.445
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG2 -0.213 2.973
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASN 71 2HD2 -0.213 3.093
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ILE 79 CA -0.215 3.675
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HB1 -0.220 3.100
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A ILE 79 CG1 -0.228 3.808
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.243 3.503
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CG -0.244 3.824
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.246 2.856
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 4JUP.pdbqt #1/A ILE 79 1HG1 -0.248 3.128
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD2 -0.258 3.498
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 OD1 -0.262 3.622
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 CB -0.272 3.732
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 HB2 -0.297 2.717
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CB -0.302 3.422
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B HIS 31 ND1 -0.304 2.989
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASN 71 ND2 -0.305 3.810
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 C -0.306 3.886
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/B ASN 71 CG -0.306 3.426
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CB -0.308 3.768
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 C -0.314 3.774
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 OG -0.315 3.575
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 CG -0.316 3.776
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 C -0.326 3.786
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HG -0.329 3.089
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B HIS 31 ND1 -0.343 3.848
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 OD1 -0.346 3.706
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 30 HG1 -0.355 3.115
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 NH2 -0.360 3.595
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ARG 35 CA -0.362 3.942
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 CG -0.365 3.675
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 HB1 -0.370 3.130
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B ASN 71 HA -0.375 2.985
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 CZ -0.378 3.498
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 30 NH1 -0.384 3.769
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ASP 78 C -0.385 3.845
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/B SER 34 CB -0.388 3.698
4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 C 4JUP.pdbqt #1/A ARG 75 2HH1 -0.396 3.276
77 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 4JUP.pdbqt
2.1 4JUP--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
4JUP.pdbqt #1/A ARG 75 NH2 4JUP--WRM-16.result.pdbqt #2.1/? UNL 1 O 4JUP.pdbqt #1/A ARG 75 2HH2 2.804 1.993
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "4JUP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/4JUP--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1FLI.pdbqt
Chain information for 1FLI.pdbqt #1
---
Chain | Description
A | No description available
Opened 1FLI.pdbqt containing 1 structures (1589 atoms, 1612 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1FLI.pdbqt #1
---
notes | No usable SEQRES records for 1FLI.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A PRO 276
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A PRO 373
Chain-final residues that are not actual C termini:
38 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1FLI--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1FLI--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.4 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1FLI--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
45 contacts
atom1 atom2 overlap distance
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 HE1 0.444 2.316
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 1HD2 0.247 2.513
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 1HD2 0.080 2.680
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 CE1 0.065 3.395
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 0.055 2.555
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 0.017 3.563
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 0.004 2.606
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 HA -0.026 2.786
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 CD1 -0.029 3.609
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 HZ3 -0.038 2.918
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.055 3.515
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 CA -0.065 3.525
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 CG -0.089 3.669
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 CD2 -0.091 3.551
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 O -0.144 3.384
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 2HD1 -0.165 2.925
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.166 3.476
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB3 -0.197 2.957
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 CD2 -0.206 3.666
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CH2 -0.224 3.684
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 -0.228 3.688
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 HH2 -0.228 2.838
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PRO 371 N -0.247 3.632
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE2 -0.250 3.710
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A TRP 302 HH2 -0.251 2.671
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 369 C -0.269 3.729
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A SER 292 CB -0.272 3.392
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 3HD2 -0.277 2.887
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CD2 -0.286 3.596
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CD1 -0.287 3.747
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 3HD2 -0.291 2.901
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CB -0.294 3.604
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE3 -0.311 3.771
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ2 -0.324 3.784
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CE3 -0.330 3.790
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 2HD1 -0.331 3.091
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A PHE 309 HE1 -0.348 3.108
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 CD1 -0.365 3.825
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CD2 -0.368 3.828
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A LEU 288 HB2 -0.373 3.133
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A TRP 302 CZ3 -0.388 3.698
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A TRP 302 CH2 -0.390 3.550
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 O 1FLI.pdbqt #1/A LEU 288 C -0.393 3.553
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1FLI.pdbqt #1/A TRP 302 NE1 -0.396 3.901
1FLI--WRM-16.result.pdbqt #2.1/? UNL 1 C 1FLI.pdbqt #1/A GLN 370 C -0.400 3.860
45 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1FLI.pdbqt
2.1 1FLI--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.4 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1FLI WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1FLI--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5LTY.pdbqt
Chain information for 5LTY.pdbqt #1
---
Chain | Description
A B | No description available
E F | No description available
K | No description available
M | No description available
Opened 5LTY.pdbqt containing 1 structures (4847 atoms, 5029 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 5LTY.pdbqt #1
---
warnings | Not adding hydrogens to /A DT 1 P because it is missing heavy-atom
bond partners
Not adding hydrogens to /B DT 1 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /F DG 19 P because it is missing heavy-atom bond
partners
Not adding hydrogens to /E DG 19 P because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 5LTY.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 5LTY.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 5LTY.pdbqt (#1) chain E; guessing termini instead
No usable SEQRES records for 5LTY.pdbqt (#1) chain F; guessing termini instead
No usable SEQRES records for 5LTY.pdbqt (#1) chain K; guessing termini instead
1 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A DT 1, /B DT 1, /E DG 19,
/F DG 19, /K THR 185, /M LYS 186
Chain-initial residues that are not actual N termini: /A DG 12, /B DG 12, /E
DG 26, /F DG 26
Chain-final residues that are actual C termini: /A DC 18, /B DC 18, /E DA 36,
/F DA 36, /K GLN 255, /M GLN 255
Chain-final residues that are not actual C termini: /A DA 10, /B DA 10, /E DT
24, /F DT 24
250 hydrogen bonds
4 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5LTY--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5LTY--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.4 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 5LTY--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
53 contacts
atom1 atom2 overlap distance
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 HZ2 0.418 2.462
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 0.241 2.639
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 HB1 0.235 2.645
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 NZ 0.227 3.278
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 0.212 1.808
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 HB2 0.183 2.577
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 HB1 0.168 2.592
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 9 H71 0.135 2.625
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H71 0.114 2.766
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 0.090 2.670
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 28 H61 0.080 2.530
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 CB 0.033 3.427
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H71 0.003 2.877
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 29 H61 -0.009 2.889
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 C7 -0.033 3.613
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 H73 -0.045 2.505
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 -0.046 2.806
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.051 2.931
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 CB -0.069 3.529
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 CB -0.072 3.652
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 OP2 -0.079 3.459
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 9 C7 -0.099 3.559
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 -0.100 2.710
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 H73 -0.122 3.002
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 HB2 -0.125 2.735
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.130 2.740
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H72 -0.133 2.743
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M LYS 240 HB2 -0.145 3.025
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.147 3.727
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 O4 -0.148 3.508
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 29 N6 -0.149 3.654
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.153 3.613
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 N6 -0.168 2.813
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.179 3.489
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DA 28 N6 -0.183 3.418
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.193 3.503
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/B DT 9 C7 -0.198 3.778
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.209 3.669
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 C -0.248 3.828
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 240 CG -0.262 3.722
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/E DT 27 C7 -0.285 3.595
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 H71 -0.289 2.899
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M LYS 240 HD2 -0.299 3.179
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H72 -0.302 2.912
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 H71 -0.305 3.185
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 7 C7 -0.311 3.891
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 O -0.320 3.560
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 C5 -0.325 3.445
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/B DT 8 C7 -0.349 3.929
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M LYS 243 HZ3 -0.354 3.234
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5LTY.pdbqt #1/M ASN 236 O -0.369 3.729
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DT 27 C7 -0.383 3.543
5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 C 5LTY.pdbqt #1/M ASN 236 HB1 -0.396 3.006
53 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5LTY.pdbqt
2.1 5LTY--WRM-16.result.pdbqt
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5LTY.pdbqt #1/E DA 28 N6 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 3.435 2.808
5LTY.pdbqt #1/E DA 28 N6 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H61 2.813 1.808
5LTY.pdbqt #1/E DA 28 N7 5LTY--WRM-16.result.pdbqt #2.1/? UNL 1 O 5LTY.pdbqt #1/E DA 28 H7 3.287 2.424
3 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "5LTY WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5LTY--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1JDH.pdbqt
Chain information for 1JDH.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 1JDH.pdbqt containing 1 structures (8191 atoms, 8243 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1JDH.pdbqt #1
---
warnings | Not adding hydrogens to /A ILE 140 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A ARG 151 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 158 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 163 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLN 177 CB because it is missing heavy-atom bond
partners
28 messages similar to the above omitted
notes | No usable SEQRES records for 1JDH.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1JDH.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A ALA 135, /B LEU 12
Chain-initial residues that are not actual N termini: /A ARG 151, /A PHE 560
Chain-final residues that are actual C termini: /A SER 663, /B VAL 49
Chain-final residues that are not actual C termini: /A ILE 140, /A GLN 548
502 hydrogen bonds
Adding 'H' to /A ARG 151
Adding 'H' to /A PHE 560
/A ILE 140 is not terminus, removing H atom from 'C'
/A GLN 548 is not terminus, removing H atom from 'C'
5 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1JDH--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1JDH--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1JDH--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
49 contacts
atom1 atom2 overlap distance
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 2HG1 0.358 2.522
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE 0.338 2.542
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HE 0.255 1.805
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 HA 0.243 2.517
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 HA 0.123 2.757
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HB2 0.103 2.357
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 3HG2 0.097 2.783
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HB2 0.055 2.555
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 CG1 0.046 3.534
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 CA 0.013 3.567
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 NE 0.003 3.502
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 CB -0.018 3.598
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 HA -0.027 2.487
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 CB -0.038 3.198
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 2HH2 -0.088 2.968
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.090 2.850
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.106 3.611
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLN 165 1HE2 -0.115 2.995
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 NE -0.118 2.803
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 HA -0.118 2.538
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 1HD2 -0.126 2.736
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A VAL 168 CG2 -0.146 3.726
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HB2 -0.155 3.035
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 CA -0.159 3.619
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLU 163 HA -0.171 2.781
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 CB -0.177 3.487
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 CB -0.204 3.664
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 HB2 -0.206 3.086
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 1HD2 -0.213 2.823
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 OG1 -0.218 2.738
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASP 162 O -0.235 3.475
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 CB -0.251 3.561
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 NH2 -0.267 3.772
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 CA -0.284 3.404
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A GLN 165 OE1 -0.287 3.647
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE -0.295 3.175
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 161 O -0.303 3.543
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.310 3.545
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 CZ -0.336 3.496
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.340 2.950
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 HE -0.356 2.966
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1JDH.pdbqt #1/A GLU 163 O -0.363 3.723
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A LEU 160 O -0.365 3.725
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 HB1 -0.368 3.128
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ASN 204 ND2 -0.369 3.604
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A THR 201 2HG2 -0.380 3.260
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A THR 201 CA -0.385 3.545
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 C 1JDH.pdbqt #1/A ARG 200 CB -0.389 3.969
1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 -0.395 2.415
49 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1JDH.pdbqt
2.1 1JDH--WRM-16.result.pdbqt
4 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1JDH.pdbqt #1/A ASN 161 ND2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ASN 161 1HD2 3.118 2.516
1JDH.pdbqt #1/A ARG 200 NE 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 HE 2.803 1.805
1JDH.pdbqt #1/A ARG 200 NH2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 3.325 2.546
1JDH.pdbqt #1/A ARG 200 NH2 1JDH--WRM-16.result.pdbqt #2.1/? UNL 1 O 1JDH.pdbqt #1/A ARG 200 2HH2 3.343 2.415
4 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.7 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1JDH WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1JDH--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/6LZP.pdbqt
Chain information for 6LZP.pdbqt #1
---
Chain | Description
A | No description available
Opened 6LZP.pdbqt containing 1 structures (1381 atoms, 1395 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 6LZP.pdbqt #1
---
notes | No usable SEQRES records for 6LZP.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A HIS 171
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A SER 258
Chain-final residues that are not actual C termini:
35 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LZP--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/6LZP--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.5 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 6LZP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
42 contacts
atom1 atom2 overlap distance
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 HE3 0.364 2.516
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 0.319 2.441
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 HE1 0.260 2.620
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 CE3 0.181 3.399
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 HA 0.168 2.712
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 0.150 2.460
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 CA 0.145 3.435
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 CE1 0.125 3.455
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 N 0.050 3.455
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HE1 0.040 2.840
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 H 0.034 1.986
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 H -0.009 2.619
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HE1 -0.027 2.637
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CG -0.029 3.489
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A THR 214 C -0.067 3.647
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 HG1 -0.077 2.687
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HB2 -0.091 2.701
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 -0.093 2.703
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HB2 -0.114 2.874
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.120 2.880
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 CZ3 -0.132 3.712
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 HG1 -0.139 2.159
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 HG2 -0.146 2.906
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.174 3.484
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 O -0.176 3.116
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.179 2.789
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 HE1 -0.191 2.951
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CE -0.193 3.773
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 CE1 -0.195 3.505
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 HE2 -0.234 2.844
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 204 CB -0.256 3.836
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.256 3.566
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 N -0.271 3.506
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A TRP 206 HE3 -0.271 3.031
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CB -0.294 3.754
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A MET 213 CG -0.298 3.758
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PRO 215 CB -0.314 3.894
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 N -0.320 2.965
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A TRP 206 HZ3 -0.324 3.204
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 6LZP.pdbqt #1/A PHE 204 CZ -0.337 3.917
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A THR 205 OG1 -0.354 3.464
6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 C 6LZP.pdbqt #1/A PHE 218 CE2 -0.361 3.821
42 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 6LZP.pdbqt
2.1 6LZP--WRM-16.result.pdbqt
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
6LZP.pdbqt #1/A THR 205 N 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 H 2.965 1.986
6LZP.pdbqt #1/A THR 205 OG1 6LZP--WRM-16.result.pdbqt #2.1/? UNL 1 O 6LZP.pdbqt #1/A THR 205 HG1 3.071 2.159
2 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.5 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "6LZP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/6LZP--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2CS1.pdbqt
Chain information for 2CS1.pdbqt #1
---
Chain | Description
A | No description available
Opened 2CS1.pdbqt containing 1 structures (1441 atoms, 1451 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2CS1.pdbqt #1
---
notes | No usable SEQRES records for 2CS1.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLY 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A GLY 92
Chain-final residues that are not actual C termini:
43 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CS1--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2CS1--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.0 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2CS1--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
50 contacts
atom1 atom2 overlap distance
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 14 HB2 0.371 2.389
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 HG 0.226 1.834
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 HB1 0.195 2.685
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HD2 0.150 2.610
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 HG2 0.131 2.629
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HG2 0.080 2.680
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HD2 0.072 2.688
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 14 CB 0.013 3.447
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.019 3.599
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.028 2.908
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 HG2 -0.041 2.801
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 3HD1 -0.049 2.929
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.068 2.948
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 OG -0.074 3.454
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CE2 -0.090 3.550
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CG -0.104 3.564
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CD -0.117 3.577
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HG -0.124 2.734
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 HZ1 -0.129 3.009
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 OG -0.138 2.698
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 CB -0.158 3.738
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 CG -0.166 3.626
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 CD -0.172 3.632
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 HD3 -0.195 3.075
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 HN -0.208 2.968
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A ALA 61 O -0.211 3.571
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.220 3.530
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 OE1 -0.227 3.467
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HG2 -0.229 3.109
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CD2 -0.237 3.697
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A ALA 61 HB3 -0.242 2.662
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 HA2 -0.267 3.147
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 CG -0.272 3.732
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLU 58 OE1 -0.276 3.516
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 HA -0.296 3.176
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 HD2 -0.304 3.064
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 2HD1 -0.327 2.937
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CD -0.330 3.790
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HB3 -0.331 3.091
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 CB -0.332 3.912
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD1 -0.334 3.644
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TYR 68 CZ -0.337 3.797
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2CS1.pdbqt #1/A LYS 54 NZ -0.359 3.864
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A SER 13 OG -0.373 3.483
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LYS 10 HD2 -0.378 3.138
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A GLY 1 N -0.379 3.764
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A PRO 11 CG -0.380 3.840
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A TRP 46 HZ2 -0.386 3.146
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A ALA 61 CB -0.386 3.506
2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 C 2CS1.pdbqt #1/A LEU 65 CD2 -0.388 3.968
50 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2CS1.pdbqt
2.1 2CS1--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2CS1.pdbqt #1/A SER 13 OG 2CS1--WRM-16.result.pdbqt #2.1/? UNL 1 O 2CS1.pdbqt #1/A SER 13 HG 2.698 1.834
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.0 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2CS1 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2CS1--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2GU8.pdbqt
Chain information for 2GU8.pdbqt #1
---
Chain | Description
A | No description available
C | No description available
Opened 2GU8.pdbqt containing 1 structures (5803 atoms, 5874 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2GU8.pdbqt #1
---
warnings | Not adding hydrogens to /A VAL 15 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A LYS 16 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A GLU 17 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 21 CB because it is missing heavy-atom bond
partners
notes | No usable SEQRES records for 2GU8.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 2GU8.pdbqt (#1) chain C; guessing termini instead
Chain-initial residues that are actual N termini: /A SER 14, /C THR 505
Chain-initial residues that are not actual N termini: /A LEU 198, /A ILE 339
Chain-final residues that are actual C termini: /A PHE 350, /C ASP 524
Chain-final residues that are not actual C termini: /A TRP 196, /A VAL 337
290 hydrogen bonds
Adding 'H' to /A LEU 198
Adding 'H' to /A ILE 339
/A TRP 196 is not terminus, removing H atom from 'C'
/A VAL 337 is not terminus, removing H atom from 'C'
-2 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2GU8--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2GU8--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.1 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2GU8--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
57 contacts
atom1 atom2 overlap distance
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HG2 0.382 2.498
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 O 0.347 3.013
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HN 0.332 2.428
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 HD1 0.278 2.602
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 HA 0.244 2.516
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A VAL 310 3HG2 0.217 2.663
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 CG2 0.191 3.269
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 HB2 0.173 2.707
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HE 0.160 1.900
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HE 0.104 2.506
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 1HG2 0.094 2.666
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 CD 0.077 3.503
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A ASP 301 HB2 0.074 2.806
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HN 0.042 2.718
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 HG1 0.035 1.985
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 CG 0.002 3.578
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 O -0.001 3.241
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 N -0.038 3.423
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 HA -0.045 2.655
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CB -0.051 3.631
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 1HH2 -0.078 2.098
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A PRO 141 HA -0.089 2.549
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A VAL 310 CG2 -0.106 3.686
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2GU8.pdbqt #1/A ASP 301 CB -0.132 3.712
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 CA -0.133 3.593
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 3HG2 -0.136 2.896
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 1HH2 -0.140 2.750
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 NE -0.171 2.856
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A VAL 310 3HG2 -0.210 2.970
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A GLU 311 O -0.241 3.601
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 313 CG -0.249 3.829
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CD1 -0.251 3.831
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 CD -0.252 3.372
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 C -0.252 3.832
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 O -0.253 3.493
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 NE -0.260 3.495
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 N -0.268 3.653
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 HB -0.289 3.169
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HG2 -0.290 3.170
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CG -0.293 3.873
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A PRO 141 CA -0.296 3.456
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A VAL 310 CG1 -0.301 3.461
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ARG 144 HE -0.306 3.186
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 300 CG2 -0.311 3.771
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 300 CA -0.313 3.433
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ASP 301 HB2 -0.319 3.079
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 N -0.333 3.838
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 CA -0.337 3.917
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PHE 145 CA -0.342 3.922
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A ILE 305 1HD1 -0.361 3.121
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 C -0.363 3.483
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 HB2 -0.372 2.982
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 NH2 -0.373 3.018
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 OG1 -0.378 2.898
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A THR 299 OG1 -0.384 3.494
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HG2 -0.393 2.813
2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 C 2GU8.pdbqt #1/A PRO 141 HA -0.395 3.275
57 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2GU8.pdbqt
2.1 2GU8--WRM-16.result.pdbqt
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2GU8.pdbqt #1/A ARG 144 NE 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 HE 2.856 1.900
2GU8.pdbqt #1/A ARG 144 NH2 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A ARG 144 1HH2 3.018 2.098
2GU8.pdbqt #1/A THR 299 OG1 2GU8--WRM-16.result.pdbqt #2.1/? UNL 1 O 2GU8.pdbqt #1/A THR 299 HG1 2.898 1.985
3 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.1 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2GU8 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2GU8--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5VTB.pdbqt
Chain information for 5VTB.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 5VTB.pdbqt containing 1 structures (5433 atoms, 5510 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 5VTB.pdbqt #1
---
warnings | Not adding hydrogens to /A LYS 25 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A LYS 26 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A VAL 35 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ASP 52 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 59 CB because it is missing heavy-atom bond
partners
32 messages similar to the above omitted
notes | No usable SEQRES records for 5VTB.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 5VTB.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A LYS 25, /B ARG 3
Chain-initial residues that are not actual N termini: /A LYS 59, /A GLY 113,
/A PRO 363
Chain-final residues that are actual C termini: /A ASP 411, /B GLU 16
Chain-final residues that are not actual C termini: /A THR 54, /A ASN 88, /A
GLU 352
287 hydrogen bonds
Adding 'H' to /A LYS 59
Adding 'H' to /A GLY 113
/A THR 54 is not terminus, removing H atom from 'C'
/A ASN 88 is not terminus, removing H atom from 'C'
/A GLU 352 is not terminus, removing H atom from 'C'
-2 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VTB--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VTB--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.4 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 5VTB--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
47 contacts
atom1 atom2 overlap distance
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 2HE2 0.542 2.338
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 HB2 0.411 2.469
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 NE2 0.359 3.146
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A TRP 382 O 0.261 3.099
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 HN 0.260 2.500
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CB 0.243 3.337
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 HB2 0.217 2.543
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 HG1 0.111 2.769
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 HA 0.106 2.654
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 HB2 0.056 2.554
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 HG -0.008 2.028
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CA -0.067 3.647
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 280 HA -0.085 2.505
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 CG -0.089 3.669
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A TRP 325 HB1 -0.103 2.523
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 2HE2 -0.108 2.988
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 N -0.114 3.499
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 2HE2 -0.124 2.734
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 OG -0.150 3.410
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 234 HG -0.157 2.767
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 HB2 -0.165 3.045
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 327 CB -0.167 3.747
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 382 HB2 -0.167 2.927
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 CA -0.177 3.637
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 184 HA -0.183 2.943
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 CB -0.192 3.652
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A PRO 327 CB -0.197 3.507
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A LEU 183 O -0.205 3.565
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 N -0.232 3.737
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 OG -0.239 2.759
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CD -0.256 3.836
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 325 O -0.266 3.506
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 1HE2 -0.291 3.051
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A TRP 185 HN -0.309 3.069
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A GLN 324 OE1 -0.311 3.251
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A VAL 233 O -0.314 3.674
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 CD -0.319 3.899
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A SER 234 OG -0.319 3.429
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 OG -0.328 2.888
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 NE2 -0.330 3.715
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 HA -0.334 3.214
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 CB -0.341 3.461
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 324 NE2 -0.343 3.728
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 CB -0.350 3.510
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A LEU 279 O -0.370 3.270
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VTB.pdbqt #1/A GLN 48 1HE2 -0.379 3.139
5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 CL 5VTB.pdbqt #1/A PRO 384 CG -0.388 3.968
47 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5VTB.pdbqt
2.1 5VTB--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
5VTB.pdbqt #1/A SER 234 OG 5VTB--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VTB.pdbqt #1/A SER 234 HG 2.759 2.028
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.4 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "5VTB WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VTB--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2D3J.pdbqt
Chain information for 2D3J.pdbqt #1
---
Chain | Description
A | No description available
Opened 2D3J.pdbqt containing 1 structures (2441 atoms, 2470 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2D3J.pdbqt #1
---
notes | No usable SEQRES records for 2D3J.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A GLY 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A GLU 157
Chain-final residues that are not actual C termini:
134 hydrogen bonds
2 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D3J--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2D3J--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.9 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2D3J--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
45 contacts
atom1 atom2 overlap distance
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D3J.pdbqt #1/A LEU 85 2HD1 0.384 2.496
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 55 HB3 0.246 2.514
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ 0.218 2.542
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2D3J.pdbqt #1/A LEU 85 CD1 0.198 3.382
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 3HG1 0.151 2.609
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 N 0.137 3.368
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CZ 0.129 3.451
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HD1 0.115 2.645
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HG2 0.068 2.692
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 HB3 0.051 2.829
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.008 2.888
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 55 CB -0.044 3.504
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.047 2.657
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 HD3 -0.064 2.824
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 CA -0.071 3.651
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD2 -0.087 3.667
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.097 2.977
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ALA 49 CB -0.100 3.680
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CE2 -0.125 3.705
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.137 3.717
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.142 2.752
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CZ -0.164 3.624
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 CD1 -0.196 3.656
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CB -0.221 3.681
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 CG1 -0.221 3.681
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A VAL 123 3HG1 -0.232 2.992
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CG -0.235 3.695
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PRO 54 HB2 -0.236 2.996
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD2 -0.247 3.557
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A LYS 48 C -0.250 3.830
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 3HG2 -0.280 3.040
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ILE 148 CG2 -0.287 3.747
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HD2 -0.289 3.169
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CD1 -0.292 3.752
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CE1 -0.296 3.876
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D3J.pdbqt #1/A ARG 47 NH1 -0.304 2.949
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HZ -0.325 3.085
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 O 2D3J.pdbqt #1/A ARG 47 1HH1 -0.329 2.349
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.348 3.658
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CG -0.349 3.659
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 CB -0.352 3.812
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HE2 -0.357 3.237
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 CD -0.365 3.825
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A ARG 47 O -0.370 3.730
2D3J--WRM-16.result.pdbqt #2.1/? UNL 1 C 2D3J.pdbqt #1/A PHE 150 HB3 -0.374 3.134
45 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2D3J.pdbqt
2.1 2D3J--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.9 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2D3J WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2D3J--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2E50.pdbqt
Chain information for 2E50.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
P | No description available
Q | No description available
Opened 2E50.pdbqt containing 1 structures (11470 atoms, 11602 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2E50.pdbqt #1
---
warning | Not adding hydrogens to /B MET 145 CB because it is missing heavy-
atom bond partners
notes | No usable SEQRES records for 2E50.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 2E50.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 2E50.pdbqt (#1) chain P; guessing termini instead
No usable SEQRES records for 2E50.pdbqt (#1) chain Q; guessing termini instead
Chain-initial residues that are actual N termini: /A MET 1, /B SER 24, /P MET
1, /Q SER 24
Chain-initial residues that are not actual N termini: /A ASP 21, /A SER 152,
/A PHE 189, /A ALA 201, /B SER 152, /B PHE 189, /B GLY 200, /P ALA 20, /P SER
152, /P PHE 189, /P GLY 200, /Q SER 152, /Q PHE 189, /Q ALA 201
Chain-final residues that are actual C termini: /A VAL 222, /B PRO 223, /P VAL
222, /Q PRO 223
Chain-final residues that are not actual C termini: /A SER 15, /A HIS 144, /A
MET 166, /A THR 194, /B MET 145, /B MET 166, /B THR 194, /P ASN 16, /P HIS
144, /P THR 167, /P THR 194, /Q HIS 144, /Q TRP 160, /Q THR 194
568 hydrogen bonds
Adding 'H' to /A ASP 21
Adding 'H' to /A SER 152
Adding 'H' to /A PHE 189
Adding 'H' to /A ALA 201
Adding 'H' to /B SER 152
9 messages similar to the above omitted
/A SER 15 is not terminus, removing H atom from 'C'
/A HIS 144 is not terminus, removing H atom from 'C'
/A MET 166 is not terminus, removing H atom from 'C'
/A THR 194 is not terminus, removing H atom from 'C'
/B MET 145 is not terminus, removing H atom from 'C'
9 messages similar to the above omitted
-41 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2E50--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2E50--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.8 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2E50--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
49 contacts
atom1 atom2 overlap distance
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HB2 0.217 2.543
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 HG1 0.160 2.720
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HN 0.145 2.735
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A GLN 65 HB2 0.121 2.339
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HB1 0.092 2.668
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 HD1 0.078 2.682
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 O 0.052 3.308
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 CD1 -0.046 3.506
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 CG -0.080 3.660
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASP 117 HN -0.136 2.896
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.144 3.024
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A GLN 65 CB -0.152 3.312
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 N -0.156 3.541
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 CB -0.162 3.622
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HB2 -0.168 2.928
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE1 -0.182 3.642
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 CB -0.188 3.768
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 N -0.196 3.701
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.198 2.808
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 HE1 -0.224 2.984
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 HB1 -0.225 2.835
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 HB1 -0.236 3.116
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.245 3.705
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 CB -0.258 3.718
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.261 3.721
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 NE -0.263 3.648
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 CZ -0.277 3.737
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE2 -0.278 3.738
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 NH1 -0.279 3.664
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 O 2E50.pdbqt #1/A ASN 61 O -0.292 3.232
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 HD2 -0.294 3.054
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 HN -0.296 3.056
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 O -0.298 3.538
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 HD2 -0.303 3.063
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 OD1 -0.315 3.405
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 N -0.318 3.703
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 114 CB -0.319 3.899
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ARG 64 CD -0.323 3.783
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2E50.pdbqt #1/A PRO 214 CB -0.323 3.903
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 ND2 -0.330 3.835
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 OD1 -0.332 3.422
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CE2 -0.337 3.797
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.340 3.650
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A ASN 61 CA -0.362 3.942
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 NE1 -0.364 3.749
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.365 3.825
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A PHE 68 CZ -0.379 3.839
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A GLU 116 CB -0.383 3.843
2E50--WRM-16.result.pdbqt #2.1/? UNL 1 C 2E50.pdbqt #1/A TRP 213 NE1 -0.385 3.770
49 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2E50.pdbqt
2.1 2E50--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.8 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2E50 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2E50--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/5VBN.pdbqt
Chain information for 5VBN.pdbqt #1
---
Chain | Description
A E | No description available
B F | No description available
Opened 5VBN.pdbqt containing 1 structures (17529 atoms, 17769 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 5VBN.pdbqt #1
---
notes | No usable SEQRES records for 5VBN.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 5VBN.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 5VBN.pdbqt (#1) chain E; guessing termini instead
No usable SEQRES records for 5VBN.pdbqt (#1) chain F; guessing termini instead
Chain-initial residues that are actual N termini: /A HIS 84, /B SER 2150, /E
HIS 84, /F SER 2150
Chain-initial residues that are not actual N termini: /A PHE 163, /B PRO 2183,
/E PHE 163, /F PRO 2183
Chain-final residues that are actual C termini: /A PHE 527, /B PRO 2282, /E
PHE 527, /F PRO 2282
Chain-final residues that are not actual C termini: /A GLU 145, /B SER 2174,
/E GLU 145, /F SER 2174
854 hydrogen bonds
Adding 'H' to /A PHE 163
Adding 'H' to /E PHE 163
/A GLU 145 is not terminus, removing H atom from 'C'
/B SER 2174 is not terminus, removing H atom from 'C'
/E GLU 145 is not terminus, removing H atom from 'C'
/F SER 2174 is not terminus, removing H atom from 'C'
35 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VBN--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/5VBN--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.3 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 5VBN--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
63 contacts
atom1 atom2 overlap distance
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 1HD2 0.442 2.438
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 HB2 0.235 2.525
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 CD2 0.213 3.367
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLN 189 O 0.052 3.308
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 0.023 2.737
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 0.015 2.595
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.011 2.621
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 HG -0.027 2.787
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 3HG2 -0.054 2.814
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.055 2.815
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.081 2.841
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HA -0.095 2.855
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.121 3.581
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.126 2.886
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CZ -0.136 3.596
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 HB1 -0.136 2.896
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB2 -0.139 3.019
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 HB1 -0.152 2.912
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.156 3.616
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 CE -0.163 3.623
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HD1 -0.168 3.048
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 CB -0.173 3.633
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 OG -0.175 3.555
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HA -0.177 2.937
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLN 189 C -0.183 3.763
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CA -0.202 3.662
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.204 3.664
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CG -0.206 3.666
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HB1 -0.216 2.826
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 CB -0.222 3.682
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 OG -0.228 3.488
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 190 HA -0.229 3.109
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LEU 456 3HD1 -0.231 3.111
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CE2 -0.231 3.691
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 HE2 -0.236 2.996
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VBN.pdbqt #1/A GLU 220 OE2 -0.242 3.182
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B SER 2231 HG -0.247 3.007
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 3HD1 -0.254 3.014
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 HB -0.257 3.137
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PHE 130 CE2 -0.260 3.720
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.262 3.722
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.265 3.725
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.268 3.578
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 O 5VBN.pdbqt #1/B LEU 2216 O -0.275 3.175
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LYS 126 HE2 -0.301 3.181
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB1 -0.303 3.063
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CA -0.313 3.773
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CB -0.313 3.773
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A ALA 221 CB -0.323 3.783
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A MET 186 HE2 -0.328 3.088
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A THR 188 CG2 -0.330 3.790
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A GLU 220 OE2 -0.346 3.586
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 O -0.348 3.588
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CB -0.353 3.663
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 -0.363 3.123
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HE1 -0.366 2.976
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 HG2 -0.374 3.134
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A LYS 126 CE -0.382 3.962
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CG -0.383 3.843
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 HB1 -0.385 2.995
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A PRO 455 CG -0.387 3.847
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/A TYR 457 CD1 -0.395 3.975
5VBN--WRM-16.result.pdbqt #2.1/? UNL 1 C 5VBN.pdbqt #1/B LEU 2216 HB2 -0.398 3.158
63 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 5VBN.pdbqt
2.1 5VBN--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.3 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "5VBN WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/5VBN--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3ALN.pdbqt
Chain information for 3ALN.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
Opened 3ALN.pdbqt containing 1 structures (11428 atoms, 11539 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 3ALN.pdbqt #1
---
warnings | Not adding hydrogens to /A SER 83 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /A LYS 86 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LYS 88 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /A LEU 105 C because it is missing heavy-atom bond
partners
Not adding hydrogens to /A ASP 138 CB because it is missing heavy-atom bond
partners
30 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A PRO 308 N
notes | No usable SEQRES records for 3ALN.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 3ALN.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 3ALN.pdbqt (#1) chain C; guessing termini instead
Chain-initial residues that are actual N termini: /A SER 83, /B SER 84, /C GLU
100
Chain-initial residues that are not actual N termini: /A TYR 284, /A THR 318,
/B TYR 284, /B ASP 324, /C ASN 117, /C ILE 127, /C CYS 158, /C CYS 174, /C LYS
231, /C SER 288, /C PRO 325
Chain-final residues that are actual C termini: /A PRO 389, /B ALA 390, /C ALA
390
Chain-final residues that are not actual C termini: /A GLN 253, /A TRP 310, /B
LEU 254, /B PRO 308, /C GLU 107, /C VAL 120, /C THR 136, /C TYR 165, /C LYS
224, /C PHE 248, /C PHE 305
465 hydrogen bonds
Adding 'H' to /A TYR 284
Adding 'H' to /A THR 318
Adding 'H' to /B TYR 284
Adding 'H' to /B ASP 324
Adding 'H' to /C ASN 117
5 messages similar to the above omitted
/A GLN 253 is not terminus, removing H atom from 'C'
/A TRP 310 is not terminus, removing H atom from 'C'
/B LEU 254 is not terminus, removing H atom from 'C'
/B PRO 308 is not terminus, removing H atom from 'C'
/C GLU 107 is not terminus, removing H atom from 'C'
6 messages similar to the above omitted
-6 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3ALN--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/3ALN--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 3ALN--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
50 contacts
atom1 atom2 overlap distance
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A TYR 113 HN 0.426 2.454
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.385 2.375
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 HE1 0.145 2.615
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 HA 0.134 2.626
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.097 2.513
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A TYR 113 N 0.090 3.415
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 3HG2 0.087 2.523
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 187 HE1 0.085 2.795
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A LYS 131 HZ1 0.045 2.835
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 0.033 2.727
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 0.027 2.733
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A MET 181 O -0.005 3.245
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.019 3.479
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 3HD1 -0.024 2.904
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 CE -0.041 3.501
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A MET 178 SD -0.068 3.730
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 CD1 -0.070 3.650
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A VAL 116 3HG2 -0.075 2.495
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 233 HG -0.104 2.864
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 -0.125 2.885
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A ALA 112 N -0.153 3.658
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 187 CE -0.159 3.739
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LYS 131 NZ -0.161 3.546
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CG2 -0.166 3.626
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A LYS 131 NZ -0.194 3.699
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 HA1 -0.208 2.968
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 CA -0.221 3.681
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A ALA 129 CB -0.224 3.384
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 1HG2 -0.224 2.984
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CG2 -0.237 3.697
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A ALA 129 HB2 -0.237 2.697
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.248 3.558
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 111 CA -0.257 3.717
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A THR 183 HA -0.278 3.038
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A SER 233 OG -0.287 2.807
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 CG2 -0.305 3.615
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 233 OG -0.305 3.565
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A GLY 114 N -0.308 3.813
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 112 HN -0.324 3.084
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 O 3ALN.pdbqt #1/A VAL 116 CG2 -0.327 3.447
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 129 CB -0.329 3.909
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 3HD1 -0.337 3.097
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 CL 3ALN.pdbqt #1/A ALA 112 HN -0.339 3.219
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 2HD1 -0.352 3.112
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A LEU 236 2HD1 -0.353 3.233
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A SER 182 O -0.357 3.597
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A GLY 114 O -0.359 3.599
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ILE 108 CD1 -0.382 3.842
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A VAL 116 3HG2 -0.398 3.008
3ALN--WRM-16.result.pdbqt #2.1/? UNL 1 C 3ALN.pdbqt #1/A ALA 129 HB3 -0.400 3.280
50 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
> WRM-16.hbonds.txt
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 3ALN.pdbqt #1/A PRO 308 N
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 3ALN.pdbqt
2.1 3ALN--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.7 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "3ALN WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/3ALN--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1BJ8.pdbqt
Chain information for 1BJ8.pdbqt #1
---
Chain | Description
A | No description available
Opened 1BJ8.pdbqt containing 1 structures (1763 atoms, 1786 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1BJ8.pdbqt #1
---
notes | No usable SEQRES records for 1BJ8.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ARG 109
Chain-final residues that are not actual C termini:
53 hydrogen bonds
1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1BJ8--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1BJ8--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -6.1 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1BJ8--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
46 contacts
atom1 atom2 overlap distance
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HN 0.407 2.473
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 0.307 2.573
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CD1 0.188 3.392
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HD2 0.101 2.659
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HD2 0.099 2.661
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TRP 94 HD1 0.093 2.367
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 N 0.055 3.450
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 0.042 2.568
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HA 0.032 2.848
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1BJ8.pdbqt #1/A TYR 93 HE1 0.021 2.859
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A ARG 84 1HH1 -0.035 2.915
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HD1 -0.079 2.959
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1BJ8.pdbqt #1/A TYR 93 CE1 -0.079 3.659
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 -0.085 2.965
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A GLY 92 O -0.136 3.496
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CG -0.149 3.609
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 CD -0.166 3.626
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HD1 -0.172 2.782
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.174 3.264
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 1HH1 -0.175 2.235
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CE1 -0.177 3.487
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 -0.200 2.810
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 HE1 -0.226 2.836
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.231 3.471
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CB -0.254 3.714
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A GLY 92 O -0.270 3.510
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CE1 -0.273 3.733
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TYR 93 CA -0.283 3.863
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TRP 94 CD1 -0.288 3.448
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 HZ2 -0.299 3.059
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 HG2 -0.302 3.062
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 5 CD -0.307 3.767
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 91 O -0.315 3.555
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 HB2 -0.317 2.777
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 NH1 -0.328 3.013
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 HB1 -0.331 2.941
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 CD -0.332 3.792
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 HD1 -0.338 2.798
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A LYS 3 HD2 -0.347 3.107
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CD1 -0.352 3.662
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 CZ -0.358 3.478
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 CB -0.364 3.524
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 CB -0.372 3.682
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A ARG 84 NH1 -0.385 3.890
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A TYR 93 CA -0.392 3.552
1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 C 1BJ8.pdbqt #1/A TRP 94 O -0.399 3.489
46 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1BJ8.pdbqt
2.1 1BJ8--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1BJ8.pdbqt #1/A ARG 84 NH1 1BJ8--WRM-16.result.pdbqt #2.1/? UNL 1 O 1BJ8.pdbqt #1/A ARG 84 1HH1 3.013 2.235
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -6.1 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1BJ8 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1BJ8--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/2LX7.pdbqt
Chain information for 2LX7.pdbqt #1
---
Chain | Description
A | No description available
Opened 2LX7.pdbqt containing 1 structures (931 atoms, 945 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 2LX7.pdbqt #1
---
notes | No usable SEQRES records for 2LX7.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LEU 60
Chain-final residues that are not actual C termini:
24 hydrogen bonds
0 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LX7--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/2LX7--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.2 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 2LX7--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
35 contacts
atom1 atom2 overlap distance
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2LX7.pdbqt #1/A TRP 39 HH2 0.191 2.689
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 HH 0.132 1.888
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 HZ 0.130 2.750
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 HH2 0.115 2.645
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 O 0.112 3.128
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HE2 0.053 2.707
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 HG3 0.042 2.718
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HH 0.010 2.600
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 CL 2LX7.pdbqt #1/A TRP 39 CH2 -0.011 3.591
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 HG3 -0.060 2.820
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 CH2 -0.068 3.528
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 HA3 -0.079 2.959
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CZ -0.105 3.685
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLU 15 O -0.118 3.058
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 CA -0.132 3.712
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 CE2 -0.179 3.639
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 CZ3 -0.207 3.787
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 HH2 -0.232 2.842
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 51 CH2 -0.241 3.821
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 HA2 -0.243 3.003
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLU 15 O -0.254 3.154
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CZ -0.296 3.606
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 OH -0.300 2.820
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 CG -0.319 3.779
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PRO 53 CG -0.323 3.783
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 OH -0.323 3.583
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 HE1 -0.324 2.934
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 C -0.328 3.908
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TRP 39 CZ3 -0.350 3.810
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLY 14 H -0.369 2.389
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A GLY 20 CA -0.372 3.832
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A SER 13 CB -0.376 3.496
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 OH -0.387 3.497
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A PHE 52 CE1 -0.391 3.701
2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 C 2LX7.pdbqt #1/A TYR 56 HE2 -0.398 3.008
35 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 2LX7.pdbqt
2.1 2LX7--WRM-16.result.pdbqt
2 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
2LX7.pdbqt #1/A GLY 14 N 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A GLY 14 H 3.315 2.389
2LX7.pdbqt #1/A TYR 56 OH 2LX7--WRM-16.result.pdbqt #2.1/? UNL 1 O 2LX7.pdbqt #1/A TYR 56 HH 2.820 1.888
2 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.2 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "2LX7 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/2LX7--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1SM3.pdbqt
Chain information for 1SM3.pdbqt #1
---
Chain | Description
H | No description available
L | No description available
P | No description available
Opened 1SM3.pdbqt containing 1 structures (6388 atoms, 6469 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1SM3.pdbqt #1
---
warnings | Not adding hydrogens to /L ASP 41 CB because it is missing heavy-
atom bond partners
Not adding hydrogens to /L GLU 123 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /L GLN 163 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /H GLN 1 CB because it is missing heavy-atom bond
partners
Not adding hydrogens to /H GLU 42 CB because it is missing heavy-atom bond
partners
7 messages similar to the above omitted
notes | No usable SEQRES records for 1SM3.pdbqt (#1) chain H; guessing termini
instead
No usable SEQRES records for 1SM3.pdbqt (#1) chain L; guessing termini instead
No usable SEQRES records for 1SM3.pdbqt (#1) chain P; guessing termini instead
Chain-initial residues that are actual N termini: /H GLN 1, /L ILE 3, /P SER 2
Chain-initial residues that are not actual N termini: /H SER 134
Chain-final residues that are actual C termini: /H ARG 213, /L ARG 208, /P PRO
10
Chain-final residues that are not actual C termini: /H GLY 127
327 hydrogen bonds
Adding 'H' to /H SER 134
/H GLY 127 is not terminus, removing H atom from 'C'
6 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1SM3--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1SM3--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1SM3--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
44 contacts
atom1 atom2 overlap distance
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H LEU 45 O 0.370 2.990
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN 0.367 2.393
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 0.353 2.257
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 3HG2 0.128 2.632
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 N 0.075 3.310
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 2HG1 0.056 2.404
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN 0.000 2.610
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H ALA 60 HB1 -0.008 2.428
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H ALA 60 HA -0.009 2.769
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H TRP 47 HN -0.048 2.068
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG1 -0.053 3.363
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 3HG2 -0.115 2.995
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.116 3.501
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 HD1 -0.124 3.004
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H GLU 46 HA -0.129 2.549
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 -0.148 2.758
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 3HG2 -0.173 2.933
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L ILE 3 O -0.179 3.419
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CG -0.185 3.645
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 HN -0.187 2.797
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 HA -0.215 2.635
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L ILE 3 O -0.217 3.457
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 2HG1 -0.234 2.844
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CE1 -0.246 3.706
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L VAL 97 CG1 -0.256 3.416
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CG -0.264 3.724
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 HA -0.282 2.892
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 CG2 -0.283 3.743
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H ALA 60 CA -0.291 3.751
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 CE1 -0.319 3.779
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H ALA 60 CB -0.325 3.445
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/L PHE 98 O -0.325 3.265
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.328 3.713
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 HG1 -0.347 2.957
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 CG -0.354 3.664
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H TRP 47 HN -0.354 2.964
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 46 HG2 -0.363 3.243
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.366 3.601
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L HIS 95 ND1 -0.369 3.874
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG1 -0.375 3.685
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 4 HA -0.380 3.140
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/H GLU 61 N -0.390 3.625
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 C 1SM3.pdbqt #1/L VAL 97 CG2 -0.393 3.973
1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H GLU 46 CA -0.398 3.518
44 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1SM3.pdbqt
2.1 1SM3--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1SM3.pdbqt #1/H TRP 47 N 1SM3--WRM-16.result.pdbqt #2.1/? UNL 1 O 1SM3.pdbqt #1/H TRP 47 HN 3.052 2.068
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.7 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1SM3 WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1SM3--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1RRP.pdbqt
Chain information for 1RRP.pdbqt #1
---
Chain | Description
A | No description available
B D | No description available
C | No description available
Opened 1RRP.pdbqt containing 1 structures (10655 atoms, 10785 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1RRP.pdbqt #1
---
notes | No usable SEQRES records for 1RRP.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1RRP.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 1RRP.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 1RRP.pdbqt (#1) chain D; guessing termini instead
Chain-initial residues that are actual N termini: /A GLN 8, /B HIS 17, /C GLN
8, /D HIS 17
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A ASP 211, /B ILE 150, /C VAL
187, /D ILE 150
Chain-final residues that are not actual C termini:
454 hydrogen bonds
12 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RRP--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1RRP--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -7.9 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1RRP--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
73 contacts
atom1 atom2 overlap distance
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 0.550 2.210
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ALA 151 HB2 0.329 2.431
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 HA2 0.286 2.594
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 ND2 0.178 3.207
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 CA 0.103 3.477
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ 0.101 2.509
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 0.066 2.694
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HE1 0.052 2.708
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 0.026 2.734
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ 0.015 2.745
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C ILE 126 1HD1 0.006 2.454
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C THR 25 HG1 -0.002 2.882
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HD2 -0.018 2.898
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1RRP.pdbqt #1/C ILE 126 1HG2 -0.020 2.900
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HB2 -0.024 2.784
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ALA 151 CB -0.043 3.503
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.053 2.663
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.087 2.847
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.100 2.710
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.113 2.723
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HG2 -0.115 2.875
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.120 2.730
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CE1 -0.126 3.586
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HA -0.140 2.900
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.150 3.030
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1RRP.pdbqt #1/C ILE 126 CG2 -0.172 3.752
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 CD -0.173 3.753
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ1 -0.173 3.053
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HZ3 -0.182 3.062
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 HB2 -0.189 2.949
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.193 3.073
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C THR 25 HG1 -0.195 2.255
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CE1 -0.197 3.657
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C THR 25 OG1 -0.198 3.578
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.208 3.668
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.213 2.973
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CE -0.220 3.800
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.220 3.680
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.221 3.726
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.225 3.685
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.232 2.992
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASP 125 OD1 -0.239 3.479
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 1HD2 -0.242 3.002
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.254 3.564
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.263 3.498
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.264 3.724
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.270 3.730
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HZ2 -0.272 2.882
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASN 122 ND2 -0.275 3.660
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HE1 -0.275 3.035
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.277 3.587
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CE -0.281 3.591
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 CB -0.282 3.742
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HG2 -0.293 3.053
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.294 3.754
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 NZ -0.297 3.802
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.298 3.058
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 22 N -0.311 3.816
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 2HD1 -0.319 3.079
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 152 N -0.321 3.706
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CG -0.336 3.796
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 1HG2 -0.341 2.951
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ILE 126 CD1 -0.346 3.656
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 37 O -0.351 3.441
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CG -0.355 3.815
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C ASP 125 OD1 -0.356 3.596
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 HZ -0.358 3.118
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C GLY 20 O -0.362 3.722
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C ILE 126 CD1 -0.365 3.525
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C PHE 35 CZ -0.372 3.832
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 CD -0.385 3.845
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 NZ -0.393 3.628
1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 C 1RRP.pdbqt #1/C LYS 123 HE2 -0.399 3.009
73 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1RRP.pdbqt
2.1 1RRP--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1RRP.pdbqt #1/C THR 25 OG1 1RRP--WRM-16.result.pdbqt #2.1/? UNL 1 O 1RRP.pdbqt #1/C THR 25 HG1 3.164 2.255
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -7.9 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1RRP WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1RRP--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1OQD.pdbqt
Chain information for 1OQD.pdbqt #1
---
Chain | Description
A B C D E F G H I J | No description available
K L M O P Q R | No description available
N | No description available
Opened 1OQD.pdbqt containing 1 structures (27310 atoms, 27575 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1OQD.pdbqt #1
---
notes | No usable SEQRES records for 1OQD.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1OQD.pdbqt (#1) chain B; guessing termini instead
No usable SEQRES records for 1OQD.pdbqt (#1) chain C; guessing termini instead
No usable SEQRES records for 1OQD.pdbqt (#1) chain D; guessing termini instead
No usable SEQRES records for 1OQD.pdbqt (#1) chain E; guessing termini instead
13 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A VAL 1, /B VAL 1, /C VAL
1, /D VAL 1, /E VAL 1, /F VAL 1, /G VAL 1, /H VAL 1, /I VAL 1, /J VAL 1, /K
CYS 1, /L CYS 1, /M CYS 1, /N CYS 1, /O CYS 1, /P CYS 1, /Q CYS 1, /R CYS 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LEU 144, /B LEU 144, /C LEU
144, /D LEU 144, /E LEU 144, /F LEU 144, /G LEU 144, /H LEU 144, /I LEU 144,
/J LEU 144, /K THR 39, /L THR 39, /M THR 39, /N CYS 21, /O THR 39, /P THR 39,
/Q THR 39, /R THR 39
Chain-final residues that are not actual C termini:
1396 hydrogen bonds
76 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OQD--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1OQD--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -8.0 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1OQD--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
59 contacts
atom1 atom2 overlap distance
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HB2 0.581 2.179
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 2HD2 0.325 2.555
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CB 0.263 3.197
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 HB1 0.221 2.659
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 ND2 0.083 3.422
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/B PRO 96 HA 0.046 2.374
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 0.043 2.717
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 HG1 0.040 2.720
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 HG1 0.021 2.739
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 O 0.012 3.348
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 HB2 0.008 2.872
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 OG1 -0.005 3.265
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.011 3.101
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/C GLU 97 HB2 -0.026 2.486
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.055 2.665
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HB2 -0.060 2.820
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 HB1 -0.061 2.821
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/A ASN 94 CB -0.062 3.642
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.072 2.682
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 HG1 -0.076 2.956
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CB -0.091 3.551
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.093 2.853
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.135 3.495
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 OD1 -0.141 3.501
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 C -0.144 3.724
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 HB1 -0.150 2.610
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C GLU 97 HN -0.158 2.768
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CA -0.160 3.620
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.168 2.778
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.196 2.956
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/B PRO 96 CA -0.202 3.322
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 HA -0.204 2.964
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.212 3.452
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A ASN 94 HB2 -0.215 2.975
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 CB -0.218 3.798
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.248 3.338
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 CB -0.254 3.414
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B ASN 94 O -0.260 3.500
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C PRO 96 HA -0.262 3.142
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A ASN 94 CB -0.270 3.730
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1OQD.pdbqt #1/B ASN 102 CG -0.275 3.855
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 O -0.277 3.517
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A THR 98 OG1 -0.281 3.541
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CA -0.285 3.745
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C ASN 94 HB2 -0.287 3.047
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CG -0.291 3.751
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C TYR 65 CB -0.306 3.766
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HG2 -0.316 3.076
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.318 3.778
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 HA -0.322 3.082
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/A PRO 96 CG -0.332 3.912
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.340 3.800
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C MET 95 O -0.340 3.430
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/C GLU 97 CB -0.345 3.465
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 CG -0.346 3.506
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/C GLU 97 OE1 -0.350 3.710
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 O 1OQD.pdbqt #1/A PRO 96 HG1 -0.351 2.811
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B MET 95 C -0.360 3.820
1OQD--WRM-16.result.pdbqt #2.1/? UNL 1 C 1OQD.pdbqt #1/B PRO 96 CG -0.383 3.843
59 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1OQD.pdbqt
2.1 1OQD--WRM-16.result.pdbqt
0 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
0 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -8.0 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1OQD WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1OQD--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1S9J.pdbqt
Chain information for 1S9J.pdbqt #1
---
Chain | Description
A | No description available
Opened 1S9J.pdbqt containing 1 structures (4567 atoms, 4613 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1S9J.pdbqt #1
---
notes | No usable SEQRES records for 1S9J.pdbqt (#1) chain A; guessing termini
instead
Chain-initial residues that are actual N termini: /A MET 61
Chain-initial residues that are not actual N termini: /A VAL 224, /A PRO 306
Chain-final residues that are actual C termini: /A ASN 382
Chain-final residues that are not actual C termini: /A ALA 220, /A PHE 275
207 hydrogen bonds
Adding 'H' to /A VAL 224
/A ALA 220 is not terminus, removing H atom from 'C'
/A PHE 275 is not terminus, removing H atom from 'C'
-1 hydrogens added
> wait 5
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1S9J--
> WRM-16.result.pdbqt
Summary of feedback from opening
/home/vishalkumarsahu/Desktop/DGE8-2-Docking/docking/1S9J--WRM-16.result.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -9.2 0.000 0.000
Ignored bad PDB record found on line 3
REMARK 5 active torsions:
Ignored bad PDB record found on line 4
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 5
REMARK 1 A between atoms: C_9 and O_15
Ignored bad PDB record found on line 6
REMARK 2 A between atoms: C_10 and O_17
184 messages similar to the above omitted
Opened 1S9J--WRM-16.result.pdbqt containing 9 structures (252 atoms, 279
bonds)
> wait 5
> close #2.2-9
> wait 5
> contacts :UNL radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
> WRM-16.contacts.txt
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
47 contacts
atom1 atom2 overlap distance
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 146 HN 0.179 2.581
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 1HG1 0.131 2.329
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A ASN 78 HB1 0.073 2.807
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 149 HA1 0.062 2.818
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 0.042 2.718
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 HB2 0.034 2.846
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ALA 95 CB 0.029 3.431
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLN 153 OE1 0.015 3.345
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.055 2.815
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 HE1 -0.069 2.949
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.092 3.552
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 O -0.118 3.478
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LYS 97 HE1 -0.119 2.999
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A VAL 82 1HG2 -0.133 2.743
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.148 3.608
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A GLY 149 HA1 -0.156 2.616
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 CE -0.158 3.278
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ASP 208 OD2 -0.164 3.524
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 149 CA -0.173 3.753
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 146 N -0.179 3.564
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 CE -0.181 3.761
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A CYS 207 SG -0.191 3.853
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A MET 143 SD -0.205 3.747
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A SER 194 HG -0.211 2.971
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 HG -0.219 2.979
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 CG1 -0.246 3.406
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.247 3.707
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.262 3.022
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A SER 150 OG -0.269 2.789
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A ASN 78 CB -0.271 3.851
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 O -0.279 3.519
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A ASP 208 OD1 -0.291 3.651
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A VAL 82 1HG2 -0.310 2.920
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 HE2 -0.310 2.730
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LYS 97 CE -0.316 3.896
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A GLY 149 CA -0.320 3.480
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 -0.323 3.083
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 HA2 -0.326 2.936
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 CD2 -0.341 3.801
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 74 CB -0.348 3.928
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A GLY 77 CA -0.350 3.810
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 CL 1S9J.pdbqt #1/A LYS 192 NZ -0.352 3.857
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 1HD2 -0.353 2.963
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 2HD2 -0.368 3.128
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A SER 194 HB2 -0.376 3.136
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 C 1S9J.pdbqt #1/A LEU 197 2HD2 -0.385 3.145
1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A VAL 82 1HG2 -0.389 2.849
47 contacts
> hbonds :UNL showDist true radius 0.05 log true saveFile
> /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
> WRM-16.hbonds.txt
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 1S9J.pdbqt
2.1 1S9J--WRM-16.result.pdbqt
1 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
1S9J.pdbqt #1/A LYS 97 NZ 1S9J--WRM-16.result.pdbqt #2.1/? UNL 1 O 1S9J.pdbqt #1/A LYS 97 HZ1 3.189 2.451
1 hydrogen bonds found
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> label sel text "Ligand "
> label height 1
> ~select
Nothing selected
> 2dlabels text "Binding Energy: -9.2 kcal/mol" color red size 18 xpos .03
> ypos .95
> 2dlabels text "1S9J WRM-16 Complex" color gray size 18 xpos .03 ypos .91
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
> WRM-16.complex.png width 1200 height 838 supersample 4 transparentBackground
> true
> select :UNL
28 atoms, 31 bonds, 1 residue, 1 model selected
> view sel
> save /home/vishalkumarsahu/Desktop/DGE8-2-Docking/analysis/1S9J--
> WRM-16.ligand.png width 1200 height 838 supersample 4 transparentBackground
> true
> close
> wait 5
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/1XJV.pdbqt
Chain information for 1XJV.pdbqt #1
---
Chain | Description
A | No description available
B | No description available
Opened 1XJV.pdbqt containing 1 structures (4991 atoms, 5066 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to 1XJV.pdbqt #1
---
notes | No usable SEQRES records for 1XJV.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1XJV.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: /A ALA 6, /B DT 1
Chain-initial residues that are not actual N termini: /A THR 149
Chain-final residues that are actual C termini: /A ALA 299, /B DG 10
Chain-final residues that are not actual C termini: /A SER 145
244 hydrogen bonds
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 404, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 37, in open
return open_command_script(session, data, file_name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/scripting.py", line 161, in open_command_script
run(session, text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 447, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 1098, in _try_finish
pos = at_pos + nearest * h_len
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 1098, in _try_finish
pos = at_pos + nearest * h_len
See log for complete Python traceback.
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/ucsf-commands.cxc
> set bgColor white
> open /home/vishalkumarsahu/Desktop/DGE8-2-Docking/proteins-pdbqt/3EI4.pdbqt
Chain information for 3EI4.pdbqt #2
---
Chain | Description
A C E | No description available
B D F | No description available
Opened 3EI4.pdbqt containing 1 structures (70284 atoms, 71031 bonds)
> wait 5
> hide surfaces
> hide atoms
> show cartoons
> wait 5
> addh
Summary of feedback from adding hydrogens to multiple structures
---
notes | No usable SEQRES records for 1XJV.pdbqt (#1) chain A; guessing termini
instead
No usable SEQRES records for 1XJV.pdbqt (#1) chain B; guessing termini instead
Chain-initial residues that are actual N termini: 1XJV.pdbqt #1/A ALA 6,
1XJV.pdbqt #1/B DT 1
Chain-initial residues that are not actual N termini: 1XJV.pdbqt #1/A THR 149
Chain-final residues that are actual C termini: 1XJV.pdbqt #1/A ALA 299,
1XJV.pdbqt #1/B DG 10
Chain-final residues that are not actual C termini: 1XJV.pdbqt #1/A SER 145
244 hydrogen bonds
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute
cmd.run(cmd_text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 179, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 404, in collated_open
return func(*func_args, **func_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core_formats/__init__.py", line 37, in open
return open_command_script(session, data, file_name)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/scripting.py", line 161, in open_command_script
run(session, text)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 63, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 162, in hbond_add_hydrogens
hbond_add_hydrogens(session, [struct], unknowns_info=unknowns_info,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 447, in add_hydrogens
did_finish = _try_finish(end, hbond_info, finished, aro_amines, pruned_by,
processed)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 1098, in _try_finish
pos = at_pos + nearest * h_len
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-
packages/chimerax/addh/hbond.py", line 1098, in _try_finish
pos = at_pos + nearest * h_len
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 20.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel
Manufacturer: HP
Model: HP Desktop Pro G1 MT
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
Cache Size: 9216 KB
Memory:
total used free shared buff/cache available
Mem: 11Gi 5.2Gi 2.7Gi 401Mi 3.7Gi 5.7Gi
Swap: 31Gi 5.2Gi 26Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop) [8086:3e92]
DeviceName: Onboard - Video
Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop) [103c:843c]
Locale: ('en_IN', 'ISO8859-1')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.5.0
chardet: 3.0.4
ChimeraX-AddCharge: 1.0.1
ChimeraX-AddH: 2.1.6
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.13.2
ChimeraX-AtomicLibrary: 3.1.3
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.4
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.5
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.3
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.2.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0.1
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.1
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4.1
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.1
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.6
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 5.0.9
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 2.0.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
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