1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
|
global_
_lib_name ?
_lib_version ?
_lib_update ?
# ------------------------------------------------
#
# --- LIST OF MONOMERS ---
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
VM1 VM1 '5-(2-thienyl)nicotinic acid ' non-polymer 20 14 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VM1
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
VM1 O1C O OC -0.500 0.000 0.000 0.000
VM1 C1B C C 0.000 -1.147 -0.500 0.005
VM1 O1A O OC -0.500 -1.286 -1.744 0.005
VM1 C1G C CR6 0.000 -2.336 0.376 0.002
VM1 C1L C CR16 0.000 -2.191 1.766 0.007
VM1 H1L H H 0.000 -1.199 2.201 0.012
VM1 N1M N NRD6 0.000 -3.246 2.554 0.005
VM1 C1N C CR16 0.000 -4.474 2.079 -0.001
VM1 H1N H H 0.000 -5.312 2.765 -0.007
VM1 C1I C CR6 0.000 -4.711 0.703 0.000
VM1 C1H C CR16 0.000 -3.621 -0.172 0.001
VM1 H1H H H 0.000 -3.768 -1.245 0.003
VM1 C1J C CR5 0.000 -6.094 0.179 -0.002
VM1 S1D S S2 0.000 -6.535 -1.523 0.000
VM1 C1K C CR15 0.000 -7.212 0.932 -0.003
VM1 H1K H H 0.000 -7.187 2.015 -0.002
VM1 C1F C CR15 0.000 -8.390 0.216 -0.004
VM1 H1F H H 0.000 -9.361 0.694 -0.005
VM1 C1E C CR15 0.000 -8.244 -1.113 -0.003
VM1 H1E H H 0.000 -9.057 -1.829 -0.003
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
VM1 O1C n/a C1B START
VM1 C1B O1C C1G .
VM1 O1A C1B . .
VM1 C1G C1B C1L .
VM1 C1L C1G N1M .
VM1 H1L C1L . .
VM1 N1M C1L C1N .
VM1 C1N N1M C1I .
VM1 H1N C1N . .
VM1 C1I C1N C1J .
VM1 C1H C1I H1H .
VM1 H1H C1H . .
VM1 C1J C1I C1K .
VM1 S1D C1J . .
VM1 C1K C1J C1F .
VM1 H1K C1K . .
VM1 C1F C1K C1E .
VM1 H1F C1F . .
VM1 C1E C1F H1E .
VM1 H1E C1E . END
VM1 S1D C1E . ADD
VM1 C1G C1H . ADD
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
VM1 O1A C1B deloc 1.250 0.020
VM1 C1G C1B single 1.500 0.020
VM1 C1B O1C deloc 1.250 0.020
VM1 S1D C1E single 1.745 0.020
VM1 S1D C1J single 1.745 0.020
VM1 C1E C1F double 1.380 0.020
VM1 H1E C1E single 1.083 0.020
VM1 C1F C1K single 1.380 0.020
VM1 H1F C1F single 1.083 0.020
VM1 C1G C1H double 1.390 0.020
VM1 C1L C1G single 1.390 0.020
VM1 C1H C1I single 1.390 0.020
VM1 H1H C1H single 1.083 0.020
VM1 C1J C1I single 1.490 0.020
VM1 C1I C1N double 1.390 0.020
VM1 C1K C1J double 1.387 0.020
VM1 H1K C1K single 1.083 0.020
VM1 N1M C1L double 1.337 0.020
VM1 H1L C1L single 1.083 0.020
VM1 C1N N1M single 1.337 0.020
VM1 H1N C1N single 1.083 0.020
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
VM1 O1C C1B O1A 123.000 3.000
VM1 O1C C1B C1G 120.000 3.000
VM1 O1A C1B C1G 120.000 3.000
VM1 C1B C1G C1L 120.000 3.000
VM1 C1B C1G C1H 120.000 3.000
VM1 C1L C1G C1H 120.000 3.000
VM1 C1G C1L H1L 120.000 3.000
VM1 C1G C1L N1M 120.000 3.000
VM1 H1L C1L N1M 120.000 3.000
VM1 C1L N1M C1N 120.000 3.000
VM1 N1M C1N H1N 120.000 3.000
VM1 N1M C1N C1I 120.000 3.000
VM1 H1N C1N C1I 120.000 3.000
VM1 C1N C1I C1H 120.000 3.000
VM1 C1N C1I C1J 120.000 3.000
VM1 C1H C1I C1J 120.000 3.000
VM1 C1I C1H H1H 120.000 3.000
VM1 C1I C1H C1G 120.000 3.000
VM1 H1H C1H C1G 120.000 3.000
VM1 C1I C1J S1D 108.000 3.000
VM1 C1I C1J C1K 126.000 3.000
VM1 S1D C1J C1K 108.000 3.000
VM1 C1J S1D C1E 91.031 3.000
VM1 C1J C1K H1K 126.000 3.000
VM1 C1J C1K C1F 108.000 3.000
VM1 H1K C1K C1F 126.000 3.000
VM1 C1K C1F H1F 126.000 3.000
VM1 C1K C1F C1E 108.000 3.000
VM1 H1F C1F C1E 126.000 3.000
VM1 C1F C1E H1E 126.000 3.000
VM1 C1F C1E S1D 108.000 3.000
VM1 H1E C1E S1D 108.000 3.000
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
VM1 var_1 O1C C1B C1G C1L -0.625 20.000 1
VM1 CONST_1 C1B C1G C1H C1I 180.000 0.000 0
VM1 CONST_2 C1B C1G C1L N1M 180.000 0.000 0
VM1 CONST_3 C1G C1L N1M C1N 0.000 0.000 0
VM1 CONST_4 C1L N1M C1N C1I 0.000 0.000 0
VM1 CONST_5 N1M C1N C1I C1J 180.000 0.000 0
VM1 CONST_6 C1N C1I C1H C1G 0.000 0.000 0
VM1 var_2 C1N C1I C1J C1K -0.048 20.000 1
VM1 CONST_7 C1I C1J S1D C1E 180.000 0.000 0
VM1 CONST_8 C1J S1D C1E C1F 0.000 0.000 0
VM1 CONST_9 C1I C1J C1K C1F 180.000 0.000 0
VM1 CONST_10 C1J C1K C1F C1E 0.000 0.000 0
VM1 CONST_11 C1K C1F C1E S1D 0.000 0.000 0
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
VM1 plan-1 C1B 0.020
VM1 plan-1 O1A 0.020
VM1 plan-1 O1C 0.020
VM1 plan-1 C1G 0.020
VM1 plan-2 C1E 0.020
VM1 plan-2 S1D 0.020
VM1 plan-2 C1F 0.020
VM1 plan-2 H1E 0.020
VM1 plan-2 C1J 0.020
VM1 plan-2 C1K 0.020
VM1 plan-2 H1F 0.020
VM1 plan-2 C1I 0.020
VM1 plan-2 H1K 0.020
VM1 plan-3 C1G 0.020
VM1 plan-3 C1B 0.020
VM1 plan-3 C1H 0.020
VM1 plan-3 C1L 0.020
VM1 plan-3 C1I 0.020
VM1 plan-3 N1M 0.020
VM1 plan-3 C1N 0.020
VM1 plan-3 H1H 0.020
VM1 plan-3 C1J 0.020
VM1 plan-3 H1L 0.020
VM1 plan-3 H1N 0.020
# ------------------------------------------------------
|
