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
|
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
VGA VGA '1-[(3S)-5-PHENYL-3-THIOPHEN-2-YL-3H-' non-polymer 46 27 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VGA
#
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
VGA O27 O OH1 0.000 0.000 0.000 0.000
VGA H27 H H 0.000 0.675 0.247 -0.646
VGA C15 C CH1 0.000 -0.578 -1.253 -0.372
VGA H15 H H 0.000 0.161 -2.021 -0.641
VGA C14 C CH2 0.000 -1.669 -1.751 0.585
VGA H142 H H 0.000 -1.670 -1.393 1.616
VGA H141 H H 0.000 -1.943 -2.808 0.568
VGA C16 C CH2 0.000 -1.748 -1.143 -1.362
VGA H161 H H 0.000 -2.044 -2.029 -1.929
VGA H162 H H 0.000 -1.816 -0.262 -2.003
VGA N13 N N 0.000 -2.641 -0.979 -0.205
VGA C2 C C 0.000 -3.845 -0.379 0.032
VGA C3 C CH1 0.000 -4.533 0.336 -1.097
VGA H3 H H 0.000 -3.959 0.199 -2.025
VGA C22 C CR5 0.000 -5.922 -0.220 -1.275
VGA C26 C CR15 0.000 -6.961 0.452 -1.774
VGA H26 H H 0.000 -6.887 1.482 -2.099
VGA C25 C CR15 0.000 -8.142 -0.268 -1.845
VGA H25 H H 0.000 -9.059 0.154 -2.237
VGA C24 C CR15 0.000 -8.063 -1.520 -1.394
VGA H24 H H 0.000 -8.884 -2.226 -1.367
VGA S23 S S2 0.000 -6.424 -1.850 -0.848
VGA N5 N N 0.000 -4.612 1.761 -0.775
VGA C4 C C 0.000 -5.279 2.183 0.244
VGA C12 C CR6 0.000 -5.294 3.641 0.507
VGA C21 C CR16 0.000 -5.046 4.542 -0.528
VGA H21 H H 0.000 -4.837 4.177 -1.526
VGA C20 C CR16 0.000 -5.066 5.899 -0.279
VGA H20 H H 0.000 -4.883 6.599 -1.085
VGA C19 C CR16 0.000 -5.321 6.366 0.998
VGA H19 H H 0.000 -5.331 7.432 1.190
VGA C18 C CR16 0.000 -5.562 5.477 2.031
VGA H18 H H 0.000 -5.759 5.849 3.028
VGA C17 C CR16 0.000 -5.550 4.118 1.792
VGA H17 H H 0.000 -5.740 3.424 2.602
VGA C6 C CR6 0.000 -6.027 1.311 1.163
VGA C11 C CR16 0.000 -7.273 1.762 1.621
VGA H11 H H 0.000 -7.646 2.727 1.300
VGA C10 C CR16 0.000 -8.026 0.988 2.474
VGA H10 H H 0.000 -8.987 1.347 2.822
VGA C9 C CR16 0.000 -7.559 -0.248 2.890
VGA H9 H H 0.000 -8.158 -0.855 3.558
VGA C8 C CR16 0.000 -6.336 -0.708 2.456
VGA H8 H H 0.000 -5.979 -1.676 2.787
VGA C7 C CR6 0.000 -5.550 0.065 1.590
VGA N1 N N 0.000 -4.349 -0.444 1.212
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
VGA O27 n/a C15 START
VGA H27 O27 . .
VGA C15 O27 C16 .
VGA H15 C15 . .
VGA C14 C15 H141 .
VGA H142 C14 . .
VGA H141 C14 . .
VGA C16 C15 N13 .
VGA H161 C16 . .
VGA H162 C16 . .
VGA N13 C16 C2 .
VGA C2 N13 C3 .
VGA C3 C2 N5 .
VGA H3 C3 . .
VGA C22 C3 C26 .
VGA C26 C22 C25 .
VGA H26 C26 . .
VGA C25 C26 C24 .
VGA H25 C25 . .
VGA C24 C25 S23 .
VGA H24 C24 . .
VGA S23 C24 . .
VGA N5 C3 C4 .
VGA C4 N5 C6 .
VGA C12 C4 C21 .
VGA C21 C12 C20 .
VGA H21 C21 . .
VGA C20 C21 C19 .
VGA H20 C20 . .
VGA C19 C20 C18 .
VGA H19 C19 . .
VGA C18 C19 C17 .
VGA H18 C18 . .
VGA C17 C18 H17 .
VGA H17 C17 . .
VGA C6 C4 C11 .
VGA C11 C6 C10 .
VGA H11 C11 . .
VGA C10 C11 C9 .
VGA H10 C10 . .
VGA C9 C10 C8 .
VGA H9 C9 . .
VGA C8 C9 C7 .
VGA H8 C8 . .
VGA C7 C8 N1 .
VGA N1 C7 . END
VGA N1 C2 . ADD
VGA C6 C7 . ADD
VGA C12 C17 . ADD
VGA N13 C14 . ADD
VGA C22 S23 . 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
VGA N1 C2 double 1.260 0.020
VGA N1 C7 single 1.400 0.020
VGA C3 C2 single 1.500 0.020
VGA C2 N13 single 1.330 0.020
VGA N5 C3 single 1.455 0.020
VGA C22 C3 single 1.480 0.020
VGA C4 N5 double 1.260 0.020
VGA C6 C4 single 1.500 0.020
VGA C12 C4 single 1.500 0.020
VGA C6 C7 single 1.487 0.020
VGA C11 C6 double 1.390 0.020
VGA C7 C8 double 1.390 0.020
VGA C8 C9 single 1.390 0.020
VGA C9 C10 double 1.390 0.020
VGA C10 C11 single 1.390 0.020
VGA C12 C17 single 1.390 0.020
VGA C21 C12 double 1.390 0.020
VGA N13 C14 single 1.455 0.020
VGA N13 C16 single 1.455 0.020
VGA C14 C15 single 1.524 0.020
VGA C16 C15 single 1.524 0.020
VGA C15 O27 single 1.432 0.020
VGA C17 C18 double 1.390 0.020
VGA C18 C19 single 1.390 0.020
VGA C19 C20 double 1.390 0.020
VGA C20 C21 single 1.390 0.020
VGA C22 S23 single 1.745 0.020
VGA C26 C22 double 1.387 0.020
VGA S23 C24 single 1.745 0.020
VGA C24 C25 double 1.380 0.020
VGA C25 C26 single 1.380 0.020
VGA H3 C3 single 1.099 0.020
VGA H11 C11 single 1.083 0.020
VGA H8 C8 single 1.083 0.020
VGA H9 C9 single 1.083 0.020
VGA H10 C10 single 1.083 0.020
VGA H17 C17 single 1.083 0.020
VGA H21 C21 single 1.083 0.020
VGA H141 C14 single 1.092 0.020
VGA H142 C14 single 1.092 0.020
VGA H161 C16 single 1.092 0.020
VGA H162 C16 single 1.092 0.020
VGA H15 C15 single 1.099 0.020
VGA H27 O27 single 0.967 0.020
VGA H18 C18 single 1.083 0.020
VGA H19 C19 single 1.083 0.020
VGA H20 C20 single 1.083 0.020
VGA H26 C26 single 1.083 0.020
VGA H24 C24 single 1.083 0.020
VGA H25 C25 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
VGA H27 O27 C15 109.470 3.000
VGA O27 C15 H15 109.470 3.000
VGA O27 C15 C14 109.470 3.000
VGA O27 C15 C16 109.470 3.000
VGA H15 C15 C14 108.340 3.000
VGA H15 C15 C16 108.340 3.000
VGA C14 C15 C16 109.470 3.000
VGA C15 C14 H142 109.470 3.000
VGA C15 C14 H141 109.470 3.000
VGA C15 C14 N13 105.000 3.000
VGA H142 C14 H141 107.900 3.000
VGA H142 C14 N13 109.470 3.000
VGA H141 C14 N13 109.470 3.000
VGA C15 C16 H161 109.470 3.000
VGA C15 C16 H162 109.470 3.000
VGA C15 C16 N13 105.000 3.000
VGA H161 C16 H162 107.900 3.000
VGA H161 C16 N13 109.470 3.000
VGA H162 C16 N13 109.470 3.000
VGA C16 N13 C2 127.000 3.000
VGA C16 N13 C14 120.000 3.000
VGA C2 N13 C14 127.000 3.000
VGA N13 C2 C3 116.500 3.000
VGA N13 C2 N1 120.000 3.000
VGA C3 C2 N1 116.500 3.000
VGA C2 C3 H3 108.810 3.000
VGA C2 C3 C22 109.500 3.000
VGA C2 C3 N5 111.600 3.000
VGA H3 C3 C22 109.470 3.000
VGA H3 C3 N5 109.470 3.000
VGA C22 C3 N5 109.500 3.000
VGA C3 C22 C26 108.000 3.000
VGA C3 C22 S23 108.000 3.000
VGA C26 C22 S23 108.000 3.000
VGA C22 C26 H26 126.000 3.000
VGA C22 C26 C25 108.000 3.000
VGA H26 C26 C25 126.000 3.000
VGA C26 C25 H25 126.000 3.000
VGA C26 C25 C24 108.000 3.000
VGA H25 C25 C24 126.000 3.000
VGA C25 C24 H24 126.000 3.000
VGA C25 C24 S23 108.000 3.000
VGA H24 C24 S23 108.000 3.000
VGA C24 S23 C22 90.972 3.000
VGA C3 N5 C4 121.000 3.000
VGA N5 C4 C12 120.000 3.000
VGA N5 C4 C6 120.000 3.000
VGA C12 C4 C6 120.000 3.000
VGA C4 C12 C21 120.000 3.000
VGA C4 C12 C17 120.000 3.000
VGA C21 C12 C17 120.000 3.000
VGA C12 C21 H21 120.000 3.000
VGA C12 C21 C20 120.000 3.000
VGA H21 C21 C20 120.000 3.000
VGA C21 C20 H20 120.000 3.000
VGA C21 C20 C19 120.000 3.000
VGA H20 C20 C19 120.000 3.000
VGA C20 C19 H19 120.000 3.000
VGA C20 C19 C18 120.000 3.000
VGA H19 C19 C18 120.000 3.000
VGA C19 C18 H18 120.000 3.000
VGA C19 C18 C17 120.000 3.000
VGA H18 C18 C17 120.000 3.000
VGA C18 C17 H17 120.000 3.000
VGA C18 C17 C12 120.000 3.000
VGA H17 C17 C12 120.000 3.000
VGA C4 C6 C11 120.000 3.000
VGA C4 C6 C7 120.000 3.000
VGA C11 C6 C7 120.000 3.000
VGA C6 C11 H11 120.000 3.000
VGA C6 C11 C10 120.000 3.000
VGA H11 C11 C10 120.000 3.000
VGA C11 C10 H10 120.000 3.000
VGA C11 C10 C9 120.000 3.000
VGA H10 C10 C9 120.000 3.000
VGA C10 C9 H9 120.000 3.000
VGA C10 C9 C8 120.000 3.000
VGA H9 C9 C8 120.000 3.000
VGA C9 C8 H8 120.000 3.000
VGA C9 C8 C7 120.000 3.000
VGA H8 C8 C7 120.000 3.000
VGA C8 C7 N1 120.000 3.000
VGA C8 C7 C6 120.000 3.000
VGA N1 C7 C6 120.000 3.000
VGA C7 N1 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
VGA var_1 H27 O27 C15 C16 -86.394 20.000 1
VGA var_2 O27 C15 C14 N13 87.534 20.000 3
VGA var_3 O27 C15 C16 N13 -87.347 20.000 3
VGA var_4 C15 C16 N13 C2 152.974 20.000 1
VGA var_5 C16 N13 C14 C15 27.315 20.000 1
VGA CONST_1 C16 N13 C2 C3 0.000 0.000 0
VGA var_6 N13 C2 C3 N5 -115.564 20.000 3
VGA var_7 C2 C3 C22 C26 152.675 20.000 1
VGA CONST_2 C3 C22 S23 C24 180.000 0.000 0
VGA CONST_3 C3 C22 C26 C25 180.000 0.000 0
VGA CONST_4 C22 C26 C25 C24 0.000 0.000 0
VGA CONST_5 C26 C25 C24 S23 0.000 0.000 0
VGA CONST_6 C25 C24 S23 C22 0.000 0.000 0
VGA var_8 C2 C3 N5 C4 -62.794 20.000 3
VGA CONST_7 C3 N5 C4 C6 0.000 0.000 0
VGA var_9 N5 C4 C12 C21 23.223 20.000 1
VGA CONST_8 C4 C12 C17 C18 180.000 0.000 0
VGA CONST_9 C4 C12 C21 C20 180.000 0.000 0
VGA CONST_10 C12 C21 C20 C19 0.000 0.000 0
VGA CONST_11 C21 C20 C19 C18 0.000 0.000 0
VGA CONST_12 C20 C19 C18 C17 0.000 0.000 0
VGA CONST_13 C19 C18 C17 C12 0.000 0.000 0
VGA var_10 N5 C4 C6 C11 -140.104 20.000 1
VGA CONST_14 C4 C6 C7 C8 180.000 0.000 0
VGA CONST_15 C4 C6 C11 C10 180.000 0.000 0
VGA CONST_16 C6 C11 C10 C9 0.000 0.000 0
VGA CONST_17 C11 C10 C9 C8 0.000 0.000 0
VGA CONST_18 C10 C9 C8 C7 0.000 0.000 0
VGA CONST_19 C9 C8 C7 N1 180.000 0.000 0
VGA var_11 C8 C7 N1 C2 139.266 20.000 1
VGA CONST_20 C7 N1 C2 N13 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
VGA chir_01 C3 C2 N5 C22 positiv
VGA chir_02 C15 C14 C16 O27 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
VGA plan-1 N1 0.020
VGA plan-1 C2 0.020
VGA plan-1 C7 0.020
VGA plan-1 C3 0.020
VGA plan-1 N13 0.020
VGA plan-2 C4 0.020
VGA plan-2 N5 0.020
VGA plan-2 C6 0.020
VGA plan-2 C12 0.020
VGA plan-2 C3 0.020
VGA plan-3 C6 0.020
VGA plan-3 C4 0.020
VGA plan-3 C7 0.020
VGA plan-3 C11 0.020
VGA plan-3 C8 0.020
VGA plan-3 C9 0.020
VGA plan-3 C10 0.020
VGA plan-3 N1 0.020
VGA plan-3 H8 0.020
VGA plan-3 H9 0.020
VGA plan-3 H10 0.020
VGA plan-3 H11 0.020
VGA plan-4 C12 0.020
VGA plan-4 C4 0.020
VGA plan-4 C17 0.020
VGA plan-4 C21 0.020
VGA plan-4 C18 0.020
VGA plan-4 C19 0.020
VGA plan-4 C20 0.020
VGA plan-4 H17 0.020
VGA plan-4 H18 0.020
VGA plan-4 H19 0.020
VGA plan-4 H20 0.020
VGA plan-4 H21 0.020
VGA plan-5 N13 0.020
VGA plan-5 C2 0.020
VGA plan-5 C14 0.020
VGA plan-5 C16 0.020
VGA plan-6 C22 0.020
VGA plan-6 C3 0.020
VGA plan-6 S23 0.020
VGA plan-6 C26 0.020
VGA plan-6 C24 0.020
VGA plan-6 C25 0.020
VGA plan-6 H24 0.020
VGA plan-6 H25 0.020
VGA plan-6 H26 0.020
# ------------------------------------------------------
|
