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
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
|
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
VB1 VB1 '"N^6^-[(1R)-2-{[(1S)-1-carboxypropyl' non-polymer 44 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VB1
#
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
VB1 O43 O OC -0.500 0.000 0.000 0.000
VB1 C31 C C 0.000 -1.182 -0.385 0.141
VB1 O42 O OC -0.500 -1.679 -1.192 -0.676
VB1 CAV C CH1 0.000 -2.007 0.123 1.295
VB1 HAV H H 0.000 -2.090 1.217 1.233
VB1 C33 C CH2 0.000 -1.333 -0.263 2.613
VB1 H331 H H 0.000 -0.305 0.104 2.617
VB1 H332 H H 0.000 -1.330 -1.351 2.715
VB1 C32 C CH3 0.000 -2.103 0.358 3.781
VB1 H323 H H 0.000 -1.638 0.092 4.696
VB1 H322 H H 0.000 -2.107 1.413 3.684
VB1 H321 H H 0.000 -3.102 0.002 3.779
VB1 N29 N NH1 0.000 -3.345 -0.473 1.238
VB1 H29 H H 0.000 -3.550 -1.305 1.772
VB1 C13 C C 0.000 -4.301 0.092 0.474
VB1 O18 O O 0.000 -4.055 1.091 -0.166
VB1 C12 C CH1 0.000 -5.678 -0.521 0.415
VB1 H12 H H 0.000 -6.116 -0.534 1.423
VB1 C16 C CH2 0.000 -5.576 -1.953 -0.116
VB1 H161 H H 0.000 -4.941 -2.543 0.549
VB1 H162 H H 0.000 -5.139 -1.940 -1.117
VB1 S17 S SH1 0.000 -7.232 -2.690 -0.186
VB1 H17 H H 0.000 -6.839 -3.869 -0.660
VB1 N11 N NH1 0.000 -6.527 0.271 -0.477
VB1 H11 H H 0.000 -6.109 0.828 -1.209
VB1 C10 C C 0.000 -7.865 0.256 -0.322
VB1 O15 O O 0.000 -8.367 -0.412 0.557
VB1 C7 C CH2 0.000 -8.739 1.072 -1.239
VB1 H7C1 H H 0.000 -8.588 0.745 -2.270
VB1 H7C2 H H 0.000 -8.473 2.127 -1.151
VB1 C4 C CH2 0.000 -10.207 0.880 -0.851
VB1 H4C1 H H 0.000 -10.355 1.206 0.180
VB1 H4C2 H H 0.000 -10.470 -0.177 -0.939
VB1 C3 C CH2 0.000 -11.094 1.707 -1.783
VB1 H3C1 H H 0.000 -10.943 1.380 -2.814
VB1 H3C2 H H 0.000 -10.829 2.763 -1.695
VB1 C2 C CH1 0.000 -12.561 1.514 -1.395
VB1 H2 H H 0.000 -12.693 1.758 -0.331
VB1 N14 N NH2 0.000 -12.950 0.117 -1.628
VB1 H142 H H 0.000 -13.280 -0.457 -0.860
VB1 H141 H H 0.000 -12.892 -0.282 -2.557
VB1 C1 C C 0.000 -13.426 2.423 -2.230
VB1 O19 O OC -0.500 -13.534 3.633 -1.932
VB1 O20 O OC -0.500 -14.031 1.967 -3.226
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
VB1 O43 n/a C31 START
VB1 C31 O43 CAV .
VB1 O42 C31 . .
VB1 CAV C31 N29 .
VB1 HAV CAV . .
VB1 C33 CAV C32 .
VB1 H331 C33 . .
VB1 H332 C33 . .
VB1 C32 C33 H321 .
VB1 H323 C32 . .
VB1 H322 C32 . .
VB1 H321 C32 . .
VB1 N29 CAV C13 .
VB1 H29 N29 . .
VB1 C13 N29 C12 .
VB1 O18 C13 . .
VB1 C12 C13 N11 .
VB1 H12 C12 . .
VB1 C16 C12 S17 .
VB1 H161 C16 . .
VB1 H162 C16 . .
VB1 S17 C16 H17 .
VB1 H17 S17 . .
VB1 N11 C12 C10 .
VB1 H11 N11 . .
VB1 C10 N11 C7 .
VB1 O15 C10 . .
VB1 C7 C10 C4 .
VB1 H7C1 C7 . .
VB1 H7C2 C7 . .
VB1 C4 C7 C3 .
VB1 H4C1 C4 . .
VB1 H4C2 C4 . .
VB1 C3 C4 C2 .
VB1 H3C1 C3 . .
VB1 H3C2 C3 . .
VB1 C2 C3 C1 .
VB1 H2 C2 . .
VB1 N14 C2 H141 .
VB1 H142 N14 . .
VB1 H141 N14 . .
VB1 C1 C2 O20 .
VB1 O19 C1 . .
VB1 O20 C1 . END
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
VB1 C32 C33 single 1.513 0.020
VB1 C33 CAV single 1.524 0.020
VB1 CAV C31 single 1.500 0.020
VB1 N29 CAV single 1.450 0.020
VB1 C31 O43 deloc 1.250 0.020
VB1 O42 C31 deloc 1.250 0.020
VB1 C13 N29 single 1.330 0.020
VB1 O18 C13 double 1.220 0.020
VB1 C12 C13 single 1.500 0.020
VB1 C16 C12 single 1.524 0.020
VB1 N11 C12 single 1.450 0.020
VB1 S17 C16 single 1.810 0.020
VB1 C10 N11 single 1.330 0.020
VB1 O15 C10 double 1.220 0.020
VB1 C7 C10 single 1.510 0.020
VB1 C4 C7 single 1.524 0.020
VB1 C3 C4 single 1.524 0.020
VB1 C2 C3 single 1.524 0.020
VB1 C1 C2 single 1.500 0.020
VB1 N14 C2 single 1.450 0.020
VB1 O20 C1 deloc 1.250 0.020
VB1 O19 C1 deloc 1.250 0.020
VB1 H321 C32 single 1.059 0.020
VB1 H322 C32 single 1.059 0.020
VB1 H323 C32 single 1.059 0.020
VB1 H331 C33 single 1.092 0.020
VB1 H332 C33 single 1.092 0.020
VB1 HAV CAV single 1.099 0.020
VB1 H29 N29 single 1.010 0.020
VB1 H12 C12 single 1.099 0.020
VB1 H161 C16 single 1.092 0.020
VB1 H162 C16 single 1.092 0.020
VB1 H11 N11 single 1.010 0.020
VB1 H17 S17 single 1.330 0.020
VB1 H7C1 C7 single 1.092 0.020
VB1 H7C2 C7 single 1.092 0.020
VB1 H4C1 C4 single 1.092 0.020
VB1 H4C2 C4 single 1.092 0.020
VB1 H3C1 C3 single 1.092 0.020
VB1 H3C2 C3 single 1.092 0.020
VB1 H2 C2 single 1.099 0.020
VB1 H141 N14 single 1.010 0.020
VB1 H142 N14 single 1.010 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
VB1 O43 C31 O42 123.000 3.000
VB1 O43 C31 CAV 118.500 3.000
VB1 O42 C31 CAV 118.500 3.000
VB1 C31 CAV HAV 108.810 3.000
VB1 C31 CAV C33 109.470 3.000
VB1 C31 CAV N29 111.600 3.000
VB1 HAV CAV C33 108.340 3.000
VB1 HAV CAV N29 108.550 3.000
VB1 C33 CAV N29 110.000 3.000
VB1 CAV C33 H331 109.470 3.000
VB1 CAV C33 H332 109.470 3.000
VB1 CAV C33 C32 111.000 3.000
VB1 H331 C33 H332 107.900 3.000
VB1 H331 C33 C32 109.470 3.000
VB1 H332 C33 C32 109.470 3.000
VB1 C33 C32 H323 109.470 3.000
VB1 C33 C32 H322 109.470 3.000
VB1 C33 C32 H321 109.470 3.000
VB1 H323 C32 H322 109.470 3.000
VB1 H323 C32 H321 109.470 3.000
VB1 H322 C32 H321 109.470 3.000
VB1 CAV N29 H29 118.500 3.000
VB1 CAV N29 C13 121.500 3.000
VB1 H29 N29 C13 120.000 3.000
VB1 N29 C13 O18 123.000 3.000
VB1 N29 C13 C12 116.500 3.000
VB1 O18 C13 C12 120.500 3.000
VB1 C13 C12 H12 108.810 3.000
VB1 C13 C12 C16 109.470 3.000
VB1 C13 C12 N11 111.600 3.000
VB1 H12 C12 C16 108.340 3.000
VB1 H12 C12 N11 108.550 3.000
VB1 C16 C12 N11 110.000 3.000
VB1 C12 C16 H161 109.470 3.000
VB1 C12 C16 H162 109.470 3.000
VB1 C12 C16 S17 112.500 3.000
VB1 H161 C16 H162 107.900 3.000
VB1 H161 C16 S17 109.470 3.000
VB1 H162 C16 S17 109.470 3.000
VB1 C16 S17 H17 96.000 3.000
VB1 C12 N11 H11 118.500 3.000
VB1 C12 N11 C10 121.500 3.000
VB1 H11 N11 C10 120.000 3.000
VB1 N11 C10 O15 123.000 3.000
VB1 N11 C10 C7 116.500 3.000
VB1 O15 C10 C7 120.500 3.000
VB1 C10 C7 H7C1 109.470 3.000
VB1 C10 C7 H7C2 109.470 3.000
VB1 C10 C7 C4 109.470 3.000
VB1 H7C1 C7 H7C2 107.900 3.000
VB1 H7C1 C7 C4 109.470 3.000
VB1 H7C2 C7 C4 109.470 3.000
VB1 C7 C4 H4C1 109.470 3.000
VB1 C7 C4 H4C2 109.470 3.000
VB1 C7 C4 C3 111.000 3.000
VB1 H4C1 C4 H4C2 107.900 3.000
VB1 H4C1 C4 C3 109.470 3.000
VB1 H4C2 C4 C3 109.470 3.000
VB1 C4 C3 H3C1 109.470 3.000
VB1 C4 C3 H3C2 109.470 3.000
VB1 C4 C3 C2 111.000 3.000
VB1 H3C1 C3 H3C2 107.900 3.000
VB1 H3C1 C3 C2 109.470 3.000
VB1 H3C2 C3 C2 109.470 3.000
VB1 C3 C2 H2 108.340 3.000
VB1 C3 C2 N14 109.470 3.000
VB1 C3 C2 C1 109.470 3.000
VB1 H2 C2 N14 109.470 3.000
VB1 H2 C2 C1 108.810 3.000
VB1 N14 C2 C1 109.470 3.000
VB1 C2 N14 H142 120.000 3.000
VB1 C2 N14 H141 120.000 3.000
VB1 H142 N14 H141 120.000 3.000
VB1 C2 C1 O19 118.500 3.000
VB1 C2 C1 O20 118.500 3.000
VB1 O19 C1 O20 123.000 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
VB1 var_1 O43 C31 CAV N29 -179.960 20.000 3
VB1 var_2 C31 CAV C33 C32 174.998 20.000 3
VB1 var_3 CAV C33 C32 H321 59.981 20.000 3
VB1 var_4 C31 CAV N29 C13 -84.987 20.000 3
VB1 CONST_1 CAV N29 C13 C12 180.000 0.000 0
VB1 var_5 N29 C13 C12 N11 -179.961 20.000 3
VB1 var_6 C13 C12 C16 S17 179.999 20.000 3
VB1 var_7 C12 C16 S17 H17 179.987 20.000 1
VB1 var_8 C13 C12 N11 C10 -155.012 20.000 3
VB1 CONST_2 C12 N11 C10 C7 180.000 0.000 0
VB1 var_9 N11 C10 C7 C4 -179.972 20.000 3
VB1 var_10 C10 C7 C4 C3 -179.966 20.000 3
VB1 var_11 C7 C4 C3 C2 179.972 20.000 3
VB1 var_12 C4 C3 C2 C1 174.969 20.000 3
VB1 var_13 C3 C2 N14 H141 -59.974 20.000 1
VB1 var_14 C3 C2 C1 O20 99.996 20.000 3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
VB1 chir_01 C2 C1 C3 N14 positiv
VB1 chir_02 CAV N29 C31 C33 positiv
VB1 chir_03 C12 N11 C13 C16 positiv
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
VB1 plan-1 C1 0.020
VB1 plan-1 C2 0.020
VB1 plan-1 O19 0.020
VB1 plan-1 O20 0.020
VB1 plan-2 C10 0.020
VB1 plan-2 C7 0.020
VB1 plan-2 N11 0.020
VB1 plan-2 O15 0.020
VB1 plan-2 H11 0.020
VB1 plan-3 N11 0.020
VB1 plan-3 C10 0.020
VB1 plan-3 C12 0.020
VB1 plan-3 H11 0.020
VB1 plan-4 C13 0.020
VB1 plan-4 C12 0.020
VB1 plan-4 O18 0.020
VB1 plan-4 N29 0.020
VB1 plan-4 H29 0.020
VB1 plan-5 N14 0.020
VB1 plan-5 C2 0.020
VB1 plan-5 H141 0.020
VB1 plan-5 H142 0.020
VB1 plan-6 N29 0.020
VB1 plan-6 CAV 0.020
VB1 plan-6 C13 0.020
VB1 plan-6 H29 0.020
VB1 plan-7 C31 0.020
VB1 plan-7 CAV 0.020
VB1 plan-7 O42 0.020
VB1 plan-7 O43 0.020
# ------------------------------------------------------
|
