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
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
|
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
VRA VRA 'N-{3,4-difluoro-2-[(2-fluoro-4-iodop' non-polymer 51 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VRA
#
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
VRA O21 O OS 0.000 0.000 0.000 0.000
VRA S19 S ST 0.000 -0.447 0.540 -1.236
VRA O20 O OS 0.000 -0.126 1.872 -1.611
VRA C22 C CT 0.000 -0.096 -0.607 -2.597
VRA C25 C CH2 0.000 -1.171 -0.691 -3.682
VRA H25 H H 0.000 -0.794 -1.278 -4.523
VRA H25A H H 0.000 -1.421 0.315 -4.025
VRA C26 C CH1 0.000 -2.422 -1.362 -3.110
VRA H26 H H 0.000 -2.877 -0.706 -2.355
VRA O29 O OH1 0.000 -2.061 -2.606 -2.506
VRA HO29 H H 0.000 -1.662 -3.183 -3.171
VRA C27 C CH2 0.000 -3.425 -1.614 -4.237
VRA H27 H H 0.000 -3.007 -2.335 -4.942
VRA H27A H H 0.000 -3.632 -0.676 -4.757
VRA O28 O OH1 0.000 -4.638 -2.133 -3.687
VRA HO28 H H 0.000 -5.272 -2.292 -4.399
VRA C24 C CH2 0.000 0.672 -1.886 -2.261
VRA H24 H H 0.000 0.672 -2.796 -2.866
VRA H24A H H 0.000 1.208 -2.071 -1.328
VRA C23 C CH2 0.000 1.363 -0.760 -3.033
VRA H23A H H 0.000 1.428 -0.692 -4.121
VRA H23 H H 0.000 1.963 0.033 -2.583
VRA N18 N NH1 0.000 -2.098 0.538 -1.109
VRA HN18 H H 0.000 -2.628 1.346 -1.402
VRA C9 C CR6 0.000 -2.761 -0.587 -0.593
VRA C10 C CR6 0.000 -2.041 -1.729 -0.257
VRA O30 O O2 0.000 -0.690 -1.755 -0.427
VRA C31 C CH3 0.000 0.047 -2.670 0.385
VRA H31B H H 0.000 1.085 -2.522 0.233
VRA H31A H H 0.000 -0.186 -2.506 1.405
VRA H31 H H 0.000 -0.209 -3.664 0.121
VRA C11 C CR16 0.000 -2.697 -2.838 0.251
VRA H11 H H 0.000 -2.134 -3.725 0.514
VRA C12 C CR6 0.000 -4.071 -2.814 0.424
VRA F17 F F 0.000 -4.706 -3.899 0.920
VRA C13 C CR6 0.000 -4.794 -1.679 0.096
VRA F16 F F 0.000 -6.133 -1.657 0.272
VRA C8 C CR6 0.000 -4.142 -0.565 -0.418
VRA N7 N NH1 0.000 -4.875 0.583 -0.756
VRA HN7 H H 0.000 -4.478 1.268 -1.383
VRA C2 C CR6 0.000 -6.154 0.778 -0.226
VRA C3 C CR16 0.000 -7.262 0.764 -1.061
VRA H3 H H 0.000 -7.138 0.602 -2.124
VRA C4 C CR16 0.000 -8.525 0.956 -0.534
VRA H4 H H 0.000 -9.390 0.946 -1.186
VRA C5 C CR6 0.000 -8.686 1.163 0.824
VRA I14 I I 0.000 -10.604 1.455 1.616
VRA C6 C CR16 0.000 -7.583 1.178 1.661
VRA H6 H H 0.000 -7.713 1.341 2.724
VRA C1 C CR6 0.000 -6.318 0.985 1.140
VRA F15 F F 0.000 -5.241 0.994 1.958
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
VRA O21 n/a S19 START
VRA S19 O21 N18 .
VRA O20 S19 . .
VRA C22 S19 C24 .
VRA C25 C22 C26 .
VRA H25 C25 . .
VRA H25A C25 . .
VRA C26 C25 C27 .
VRA H26 C26 . .
VRA O29 C26 HO29 .
VRA HO29 O29 . .
VRA C27 C26 O28 .
VRA H27 C27 . .
VRA H27A C27 . .
VRA O28 C27 HO28 .
VRA HO28 O28 . .
VRA C24 C22 C23 .
VRA H24 C24 . .
VRA H24A C24 . .
VRA C23 C24 H23 .
VRA H23A C23 . .
VRA H23 C23 . .
VRA N18 S19 C9 .
VRA HN18 N18 . .
VRA C9 N18 C10 .
VRA C10 C9 C11 .
VRA O30 C10 C31 .
VRA C31 O30 H31 .
VRA H31B C31 . .
VRA H31A C31 . .
VRA H31 C31 . .
VRA C11 C10 C12 .
VRA H11 C11 . .
VRA C12 C11 C13 .
VRA F17 C12 . .
VRA C13 C12 C8 .
VRA F16 C13 . .
VRA C8 C13 N7 .
VRA N7 C8 C2 .
VRA HN7 N7 . .
VRA C2 N7 C3 .
VRA C3 C2 C4 .
VRA H3 C3 . .
VRA C4 C3 C5 .
VRA H4 C4 . .
VRA C5 C4 C6 .
VRA I14 C5 . .
VRA C6 C5 C1 .
VRA H6 C6 . .
VRA C1 C6 F15 .
VRA F15 C1 . END
VRA C1 C2 . ADD
VRA C8 C9 . ADD
VRA C22 C23 . 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
VRA C1 C6 double 1.390 0.020
VRA F15 C1 single 1.345 0.020
VRA C1 C2 single 1.487 0.020
VRA C3 C2 double 1.390 0.020
VRA C4 C3 single 1.390 0.020
VRA H3 C3 single 1.083 0.020
VRA C5 C4 double 1.390 0.020
VRA H4 C4 single 1.083 0.020
VRA I14 C5 single 2.090 0.020
VRA C6 C5 single 1.390 0.020
VRA H6 C6 single 1.083 0.020
VRA C2 N7 single 1.350 0.020
VRA HN7 N7 single 1.010 0.020
VRA N7 C8 single 1.350 0.020
VRA C8 C13 single 1.487 0.020
VRA C8 C9 double 1.487 0.020
VRA C10 C9 single 1.487 0.020
VRA C11 C10 double 1.390 0.020
VRA C12 C11 single 1.390 0.020
VRA H11 C11 single 1.083 0.020
VRA F17 C12 single 1.345 0.020
VRA C13 C12 double 1.487 0.020
VRA F16 C13 single 1.345 0.020
VRA C9 N18 single 1.350 0.020
VRA N18 S19 single 1.600 0.020
VRA HN18 N18 single 1.010 0.020
VRA S19 O21 double 1.436 0.020
VRA O20 S19 double 1.436 0.020
VRA C22 S19 single 1.662 0.020
VRA C22 C23 single 1.524 0.020
VRA C24 C22 single 1.524 0.020
VRA C23 C24 single 1.524 0.020
VRA H23 C23 single 1.092 0.020
VRA H23A C23 single 1.092 0.020
VRA H24 C24 single 1.092 0.020
VRA H24A C24 single 1.092 0.020
VRA C25 C22 single 1.524 0.020
VRA H25 C25 single 1.092 0.020
VRA H25A C25 single 1.092 0.020
VRA C26 C25 single 1.524 0.020
VRA O29 C26 single 1.432 0.020
VRA H26 C26 single 1.099 0.020
VRA C27 C26 single 1.524 0.020
VRA H27 C27 single 1.092 0.020
VRA H27A C27 single 1.092 0.020
VRA O28 C27 single 1.432 0.020
VRA HO28 O28 single 0.967 0.020
VRA HO29 O29 single 0.967 0.020
VRA O30 C10 single 1.370 0.020
VRA C31 O30 single 1.426 0.020
VRA H31 C31 single 1.059 0.020
VRA H31A C31 single 1.059 0.020
VRA H31B C31 single 1.059 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
VRA O21 S19 O20 109.500 3.000
VRA O21 S19 C22 109.500 3.000
VRA O21 S19 N18 109.500 3.000
VRA O20 S19 C22 109.500 3.000
VRA O20 S19 N18 109.500 3.000
VRA C22 S19 N18 109.500 3.000
VRA S19 C22 C25 109.500 3.000
VRA S19 C22 C24 109.500 3.000
VRA S19 C22 C23 109.500 3.000
VRA C25 C22 C24 111.000 3.000
VRA C25 C22 C23 111.000 3.000
VRA C24 C22 C23 60.000 3.000
VRA C22 C25 H25 109.470 3.000
VRA C22 C25 H25A 109.470 3.000
VRA C22 C25 C26 111.000 3.000
VRA H25 C25 H25A 107.900 3.000
VRA H25 C25 C26 109.470 3.000
VRA H25A C25 C26 109.470 3.000
VRA C25 C26 H26 108.340 3.000
VRA C25 C26 O29 109.470 3.000
VRA C25 C26 C27 109.470 3.000
VRA H26 C26 O29 109.470 3.000
VRA H26 C26 C27 108.340 3.000
VRA O29 C26 C27 109.470 3.000
VRA C26 O29 HO29 109.470 3.000
VRA C26 C27 H27 109.470 3.000
VRA C26 C27 H27A 109.470 3.000
VRA C26 C27 O28 109.470 3.000
VRA H27 C27 H27A 107.900 3.000
VRA H27 C27 O28 109.470 3.000
VRA H27A C27 O28 109.470 3.000
VRA C27 O28 HO28 109.470 3.000
VRA C22 C24 H24 109.470 3.000
VRA C22 C24 H24A 109.470 3.000
VRA C22 C24 C23 60.000 3.000
VRA H24 C24 H24A 107.900 3.000
VRA H24 C24 C23 109.470 3.000
VRA H24A C24 C23 109.470 3.000
VRA C24 C23 H23A 109.470 3.000
VRA C24 C23 H23 109.470 3.000
VRA C24 C23 C22 60.000 3.000
VRA H23A C23 H23 107.900 3.000
VRA H23A C23 C22 109.470 3.000
VRA H23 C23 C22 109.470 3.000
VRA S19 N18 HN18 120.000 3.000
VRA S19 N18 C9 120.000 3.000
VRA HN18 N18 C9 120.000 3.000
VRA N18 C9 C10 120.000 3.000
VRA N18 C9 C8 120.000 3.000
VRA C10 C9 C8 120.000 3.000
VRA C9 C10 O30 120.000 3.000
VRA C9 C10 C11 120.000 3.000
VRA O30 C10 C11 120.000 3.000
VRA C10 O30 C31 120.000 3.000
VRA O30 C31 H31B 109.470 3.000
VRA O30 C31 H31A 109.470 3.000
VRA O30 C31 H31 109.470 3.000
VRA H31B C31 H31A 109.470 3.000
VRA H31B C31 H31 109.470 3.000
VRA H31A C31 H31 109.470 3.000
VRA C10 C11 H11 120.000 3.000
VRA C10 C11 C12 120.000 3.000
VRA H11 C11 C12 120.000 3.000
VRA C11 C12 F17 120.000 3.000
VRA C11 C12 C13 120.000 3.000
VRA F17 C12 C13 120.000 3.000
VRA C12 C13 F16 120.000 3.000
VRA C12 C13 C8 120.000 3.000
VRA F16 C13 C8 120.000 3.000
VRA C13 C8 N7 120.000 3.000
VRA C13 C8 C9 120.000 3.000
VRA N7 C8 C9 120.000 3.000
VRA C8 N7 HN7 120.000 3.000
VRA C8 N7 C2 120.000 3.000
VRA HN7 N7 C2 120.000 3.000
VRA N7 C2 C3 120.000 3.000
VRA N7 C2 C1 120.000 3.000
VRA C3 C2 C1 120.000 3.000
VRA C2 C3 H3 120.000 3.000
VRA C2 C3 C4 120.000 3.000
VRA H3 C3 C4 120.000 3.000
VRA C3 C4 H4 120.000 3.000
VRA C3 C4 C5 120.000 3.000
VRA H4 C4 C5 120.000 3.000
VRA C4 C5 I14 120.000 3.000
VRA C4 C5 C6 120.000 3.000
VRA I14 C5 C6 120.000 3.000
VRA C5 C6 H6 120.000 3.000
VRA C5 C6 C1 120.000 3.000
VRA H6 C6 C1 120.000 3.000
VRA C6 C1 F15 120.000 3.000
VRA C6 C1 C2 120.000 3.000
VRA F15 C1 C2 120.000 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
VRA var_1 O21 S19 C22 C24 -3.702 20.000 1
VRA var_2 S19 C22 C23 C24 107.485 20.000 1
VRA var_3 S19 C22 C25 C26 -68.991 20.000 1
VRA var_4 C22 C25 C26 C27 -172.567 20.000 3
VRA var_5 C25 C26 O29 HO29 -60.034 20.000 1
VRA var_6 C25 C26 C27 O28 -174.981 20.000 3
VRA var_7 C26 C27 O28 HO28 -179.985 20.000 1
VRA var_8 S19 C22 C24 C23 -107.474 20.000 1
VRA var_9 O21 S19 N18 C9 -44.482 20.000 1
VRA var_10 S19 N18 C9 C10 -3.513 20.000 1
VRA CONST_1 N18 C9 C10 C11 180.000 0.000 0
VRA var_11 C9 C10 O30 C31 155.777 20.000 1
VRA var_12 C10 O30 C31 H31 65.958 20.000 1
VRA CONST_2 C9 C10 C11 C12 0.000 0.000 0
VRA CONST_3 C10 C11 C12 C13 0.000 0.000 0
VRA CONST_4 C11 C12 C13 C8 0.000 0.000 0
VRA CONST_5 C12 C13 C8 N7 180.000 0.000 0
VRA CONST_6 C13 C8 C9 N18 180.000 0.000 0
VRA var_13 C13 C8 N7 C2 19.199 20.000 1
VRA var_14 C8 N7 C2 C3 -113.872 20.000 1
VRA CONST_7 N7 C2 C3 C4 180.000 0.000 0
VRA CONST_8 C2 C3 C4 C5 0.000 0.000 0
VRA CONST_9 C3 C4 C5 C6 0.000 0.000 0
VRA CONST_10 C4 C5 C6 C1 0.000 0.000 0
VRA CONST_11 C5 C6 C1 F15 180.000 0.000 0
VRA CONST_12 C6 C1 C2 N7 180.000 0.000 0
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
VRA chir_01 S19 N18 O20 O21 negativ
VRA chir_02 C22 S19 C23 C24 negativ
VRA chir_03 C26 C25 C27 O29 negativ
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
VRA plan-1 C1 0.020
VRA plan-1 C2 0.020
VRA plan-1 C6 0.020
VRA plan-1 F15 0.020
VRA plan-1 C3 0.020
VRA plan-1 C4 0.020
VRA plan-1 C5 0.020
VRA plan-1 N7 0.020
VRA plan-1 H3 0.020
VRA plan-1 H4 0.020
VRA plan-1 I14 0.020
VRA plan-1 H6 0.020
VRA plan-1 HN7 0.020
VRA plan-2 N7 0.020
VRA plan-2 C2 0.020
VRA plan-2 C8 0.020
VRA plan-2 HN7 0.020
VRA plan-3 C8 0.020
VRA plan-3 N7 0.020
VRA plan-3 C9 0.020
VRA plan-3 C13 0.020
VRA plan-3 C10 0.020
VRA plan-3 C11 0.020
VRA plan-3 C12 0.020
VRA plan-3 N18 0.020
VRA plan-3 O30 0.020
VRA plan-3 H11 0.020
VRA plan-3 F17 0.020
VRA plan-3 F16 0.020
VRA plan-3 HN7 0.020
VRA plan-3 HN18 0.020
VRA plan-4 N18 0.020
VRA plan-4 C9 0.020
VRA plan-4 S19 0.020
VRA plan-4 HN18 0.020
# ------------------------------------------------------
|
