Ticket #9710: MGD.xml

File MGD.xml, 10.2 KB (added by Tristan Croll, 2 years ago)

Corrected parameterisation of ligand MGD

Line 
1<ForceField>
2 <Info>
3 <DateGenerated>2023-09-06</DateGenerated>
4 </Info>
5 <Residues>
6 <Residue name="MGD">
7 <Atom name="C1" type="c3" charge="0.2168"/>
8 <Atom name="C2" type="c3" charge="0.1724"/>
9 <Atom name="C3" type="c3" charge="0.1743"/>
10 <Atom name="C4" type="c2" charge="0.0134"/>
11 <Atom name="C5" type="c2" charge="-0.0986"/>
12 <Atom name="C6" type="c3" charge="0.0352"/>
13 <Atom name="C7" type="cc" charge="-0.147"/>
14 <Atom name="C8" type="c" charge="0.6242"/>
15 <Atom name="C9" type="cc" charge="0.48"/>
16 <Atom name="C10" type="cc" charge="0.4973"/>
17 <Atom name="C11" type="c3" charge="0.1141"/>
18 <Atom name="C12" type="c2" charge="0.3701"/>
19 <Atom name="C13" type="c3" charge="0.2138"/>
20 <Atom name="C14" type="c3" charge="0.1001"/>
21 <Atom name="C15" type="cd" charge="0.0588"/>
22 <Atom name="C16" type="c3" charge="0.0791"/>
23 <Atom name="C17" type="cc" charge="0.2018"/>
24 <Atom name="C18" type="c3" charge="0.1654"/>
25 <Atom name="C19" type="c" charge="0.645"/>
26 <Atom name="C20" type="cd" charge="0.4554"/>
27 <Atom name="H1" type="h2" charge="0.0857"/>
28 <Atom name="H2" type="h1" charge="0.0517"/>
29 <Atom name="H3" type="h1" charge="0.0517"/>
30 <Atom name="H4" type="h1" charge="0.1047"/>
31 <Atom name="H5" type="hs" charge="0.1838"/>
32 <Atom name="H6" type="hs" charge="0.2088"/>
33 <Atom name="H7" type="h1" charge="0.0517"/>
34 <Atom name="H8" type="hn" charge="0.2227"/>
35 <Atom name="H9" type="hn" charge="0.3875"/>
36 <Atom name="H10" type="hn" charge="0.2762"/>
37 <Atom name="H11" type="hn" charge="0.2762"/>
38 <Atom name="H12" type="h1" charge="0.1207"/>
39 <Atom name="H13" type="hn" charge="0.2607"/>
40 <Atom name="H14" type="h2" charge="0.0657"/>
41 <Atom name="H15" type="h1" charge="0.1297"/>
42 <Atom name="H16" type="h1" charge="0.0747"/>
43 <Atom name="H17" type="h1" charge="0.0552"/>
44 <Atom name="H18" type="h1" charge="0.0552"/>
45 <Atom name="H19" type="h5" charge="0.1721"/>
46 <Atom name="H20" type="hn" charge="0.3215"/>
47 <Atom name="H21" type="hn" charge="0.2267"/>
48 <Atom name="H22" type="hn" charge="0.2267"/>
49 <Atom name="H23" type="ho" charge="0.419"/>
50 <Atom name="H24" type="ho" charge="0.475"/>
51 <Atom name="N1" type="n" charge="-0.4994"/>
52 <Atom name="N2" type="nh" charge="-0.2831"/>
53 <Atom name="N3" type="n" charge="-0.4554"/>
54 <Atom name="N4" type="nh" charge="-0.4541"/>
55 <Atom name="N5" type="nh" charge="-0.4591"/>
56 <Atom name="N6" type="n1" charge="-0.6258"/>
57 <Atom name="N7" type="nh" charge="-0.3431"/>
58 <Atom name="N8" type="nd" charge="-0.6221"/>
59 <Atom name="N9" type="nc" charge="-0.632"/>
60 <Atom name="N10" type="na" charge="-0.1909"/>
61 <Atom name="O1" type="os" charge="-0.4276"/>
62 <Atom name="O2" type="o" charge="-0.6885"/>
63 <Atom name="O3" type="o" charge="-0.8705"/>
64 <Atom name="O4" type="o" charge="-0.8895"/>
65 <Atom name="O5" type="oh" charge="-0.6048"/>
66 <Atom name="O6" type="o" charge="-0.8705"/>
67 <Atom name="O7" type="o" charge="-0.8895"/>
68 <Atom name="O8" type="oh" charge="-0.6538"/>
69 <Atom name="O9" type="os" charge="-0.5772"/>
70 <Atom name="O10" type="os" charge="-0.8278"/>
71 <Atom name="O11" type="os" charge="-0.4256"/>
72 <Atom name="O12" type="os" charge="-0.6162"/>
73 <Atom name="O13" type="o" charge="-0.6415"/>
74 <Atom name="P1" type="p5" charge="1.6048"/>
75 <Atom name="P2" type="p5" charge="1.6248"/>
76 <Atom name="S1" type="sh" charge="-0.2054"/>
77 <Atom name="S2" type="sh" charge="-0.3534"/>
78 <Bond atomName1="C1" atomName2="C11"/>
79 <Bond atomName1="C1" atomName2="H1"/>
80 <Bond atomName1="C1" atomName2="N10"/>
81 <Bond atomName1="C1" atomName2="O11"/>
82 <Bond atomName1="C2" atomName2="C3"/>
83 <Bond atomName1="C2" atomName2="H2"/>
84 <Bond atomName1="C2" atomName2="H3"/>
85 <Bond atomName1="C2" atomName2="O9"/>
86 <Bond atomName1="C3" atomName2="C4"/>
87 <Bond atomName1="C3" atomName2="H4"/>
88 <Bond atomName1="C3" atomName2="O1"/>
89 <Bond atomName1="C4" atomName2="C5"/>
90 <Bond atomName1="C4" atomName2="S1"/>
91 <Bond atomName1="C5" atomName2="C6"/>
92 <Bond atomName1="C5" atomName2="S2"/>
93 <Bond atomName1="C6" atomName2="C13"/>
94 <Bond atomName1="C6" atomName2="H7"/>
95 <Bond atomName1="C6" atomName2="N2"/>
96 <Bond atomName1="C7" atomName2="C8"/>
97 <Bond atomName1="C7" atomName2="C12"/>
98 <Bond atomName1="C7" atomName2="N2"/>
99 <Bond atomName1="C8" atomName2="N3"/>
100 <Bond atomName1="C8" atomName2="O2"/>
101 <Bond atomName1="C9" atomName2="N3"/>
102 <Bond atomName1="C9" atomName2="N4"/>
103 <Bond atomName1="C9" atomName2="N6"/>
104 <Bond atomName1="C10" atomName2="N1"/>
105 <Bond atomName1="C10" atomName2="N5"/>
106 <Bond atomName1="C10" atomName2="N8"/>
107 <Bond atomName1="C11" atomName2="C14"/>
108 <Bond atomName1="C11" atomName2="H12"/>
109 <Bond atomName1="C11" atomName2="O5"/>
110 <Bond atomName1="C12" atomName2="N6"/>
111 <Bond atomName1="C12" atomName2="N7"/>
112 <Bond atomName1="C13" atomName2="H14"/>
113 <Bond atomName1="C13" atomName2="N7"/>
114 <Bond atomName1="C13" atomName2="O1"/>
115 <Bond atomName1="C14" atomName2="C16"/>
116 <Bond atomName1="C14" atomName2="H15"/>
117 <Bond atomName1="C14" atomName2="O8"/>
118 <Bond atomName1="C15" atomName2="C17"/>
119 <Bond atomName1="C15" atomName2="N8"/>
120 <Bond atomName1="C15" atomName2="N10"/>
121 <Bond atomName1="C16" atomName2="C18"/>
122 <Bond atomName1="C16" atomName2="H16"/>
123 <Bond atomName1="C16" atomName2="O11"/>
124 <Bond atomName1="C17" atomName2="C19"/>
125 <Bond atomName1="C17" atomName2="N9"/>
126 <Bond atomName1="C18" atomName2="H17"/>
127 <Bond atomName1="C18" atomName2="H18"/>
128 <Bond atomName1="C18" atomName2="O12"/>
129 <Bond atomName1="C19" atomName2="N1"/>
130 <Bond atomName1="C19" atomName2="O13"/>
131 <Bond atomName1="C20" atomName2="H19"/>
132 <Bond atomName1="C20" atomName2="N9"/>
133 <Bond atomName1="C20" atomName2="N10"/>
134 <Bond atomName1="H5" atomName2="S1"/>
135 <Bond atomName1="H6" atomName2="S2"/>
136 <Bond atomName1="H8" atomName2="N2"/>
137 <Bond atomName1="H9" atomName2="N3"/>
138 <Bond atomName1="H10" atomName2="N4"/>
139 <Bond atomName1="H11" atomName2="N4"/>
140 <Bond atomName1="H13" atomName2="N7"/>
141 <Bond atomName1="H20" atomName2="N1"/>
142 <Bond atomName1="H21" atomName2="N5"/>
143 <Bond atomName1="H22" atomName2="N5"/>
144 <Bond atomName1="H23" atomName2="O5"/>
145 <Bond atomName1="H24" atomName2="O8"/>
146 <Bond atomName1="O3" atomName2="P1"/>
147 <Bond atomName1="O4" atomName2="P2"/>
148 <Bond atomName1="O6" atomName2="P1"/>
149 <Bond atomName1="O7" atomName2="P2"/>
150 <Bond atomName1="O9" atomName2="P1"/>
151 <Bond atomName1="O10" atomName2="P1"/>
152 <Bond atomName1="O10" atomName2="P2"/>
153 <Bond atomName1="O12" atomName2="P2"/>
154 </Residue>
155 </Residues>
156 <HarmonicBondForce>
157 <Bond class1="cc" class2="n1" length="0.1311" k="386266.87999999995"/>
158 </HarmonicBondForce>
159 <HarmonicAngleForce>
160 <Angle class1="c3" class2="c2" class3="sh" angle="2.0884609829364145" k="531.368"/>
161 <Angle class1="cc" class2="c2" class3="n1" angle="2.1464059141026266" k="753.9567999999999"/>
162 <Angle class1="c" class2="cc" class3="nh" angle="2.15146736893341" k="725.5056000000001"/>
163 <Angle class1="c2" class2="n1" class3="cc" angle="0.0" k="0.0"/>
164 <Angle class1="c2" class2="cc" class3="nh" angle="2.1315706154606744" k="705.4224"/>
165 <Angle class1="n" class2="cc" class3="n1" angle="2.077029076335852" k="603.550368"/>
166 <Angle class1="n1" class2="cc" class3="nh" angle="2.077029076335852" k="603.550368"/>
167 <Angle class1="n1" class2="c2" class3="nh" angle="2.0679533642254815" k="610.48744"/>
168 </HarmonicAngleForce>
169 <PeriodicTorsionForce>
170 <Proper class1="n1" class2="c2" class3="cc" class4="c" periodicity1="2" phase1="3.141592653589793" k1="27.823600000000003"/>
171 <Proper class1="nh" class2="c2" class3="cc" class4="c" periodicity1="2" phase1="3.141592653589793" k1="27.823600000000003"/>
172 <Proper class1="n1" class2="c2" class3="cc" class4="nh" periodicity1="2" phase1="3.141592653589793" k1="27.823600000000003"/>
173 <Proper class1="nh" class2="c2" class3="cc" class4="nh" periodicity1="2" phase1="3.141592653589793" k1="27.823600000000003"/>
174 <Improper class1="c2" class2="c2" class3="c3" class4="sh" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
175 <Improper class1="cc" class2="c" class3="c2" class4="nh" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
176 <Improper class1="c" class2="cc" class3="n" class4="o" periodicity1="2" phase1="3.141592653589793" k1="43.932"/>
177 <Improper class1="cc" class2="n" class3="n1" class4="nh" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
178 <Improper class1="cc" class2="n" class3="nd" class4="nh" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
179 <Improper class1="c2" class2="cc" class3="n1" class4="nh" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
180 <Improper class1="cd" class2="cc" class3="na" class4="nd" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
181 <Improper class1="cc" class2="c" class3="cd" class4="nc" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
182 <Improper class1="cd" class2="h5" class3="na" class4="nc" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
183 <Improper class1="n" class2="c" class3="cc" class4="hn" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
184 <Improper class1="nh" class2="c3" class3="cc" class4="hn" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
185 <Improper class1="nh" class2="cc" class3="hn" class4="hn" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
186 <Improper class1="nh" class2="c2" class3="c3" class4="hn" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
187 <Improper class1="na" class2="c3" class3="cd" class4="cd" periodicity1="2" phase1="3.141592653589793" k1="4.6024"/>
188 </PeriodicTorsionForce>
189</ForceField>