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
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
|
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
VD1 VD1 '5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-' non-polymer 61 25 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VD1
#
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
VD1 O1 O OH1 0.000 0.000 0.000 0.000
VD1 HO1 H H 0.000 0.450 -0.688 -0.508
VD1 C1 C CH1 0.000 -1.237 -0.510 0.501
VD1 H1 H H 0.000 -1.876 -0.816 -0.339
VD1 C2 C C 0.000 -0.970 -1.701 1.393
VD1 C28 C C2 0.000 0.245 -2.173 1.531
VD1 H282 H H 0.000 1.061 -1.711 1.006
VD1 H281 H H 0.000 0.420 -3.021 2.169
VD1 C10 C CH2 0.000 -1.948 0.567 1.320
VD1 H101 H H 0.000 -2.321 1.350 0.657
VD1 H102 H H 0.000 -1.253 1.003 2.041
VD1 C5 C C 0.000 -3.107 -0.067 2.057
VD1 C4 C CH2 0.000 -2.841 -1.257 2.950
VD1 H41 H H 0.000 -3.784 -1.652 3.333
VD1 H42 H H 0.000 -2.206 -0.959 3.787
VD1 C3 C CH1 0.000 -2.129 -2.337 2.125
VD1 H3 H H 0.000 -1.755 -3.125 2.794
VD1 O2 O OH1 0.000 -3.044 -2.902 1.183
VD1 HO2 H H 0.000 -2.594 -3.582 0.665
VD1 C6 C C1 0.000 -4.339 0.411 1.917
VD1 H6 H H 0.000 -5.142 0.013 2.515
VD1 C7 C C1 0.000 -4.607 1.484 0.946
VD1 H7 H H 0.000 -3.790 1.951 0.421
VD1 C8 C C 0.000 -5.855 1.875 0.716
VD1 C14 C CH1 0.000 -7.040 1.017 1.044
VD1 H14 H H 0.000 -7.675 1.502 1.798
VD1 C15 C CH2 0.000 -6.750 -0.435 1.432
VD1 H151 H H 0.000 -6.521 -0.550 2.494
VD1 H152 H H 0.000 -5.948 -0.878 0.838
VD1 C16 C CH2 0.000 -8.092 -1.151 1.109
VD1 H161 H H 0.000 -8.722 -1.220 1.998
VD1 H162 H H 0.000 -7.915 -2.153 0.712
VD1 C17 C CH1 0.000 -8.802 -0.285 0.035
VD1 H17 H H 0.000 -9.733 0.137 0.439
VD1 C20 C CH1 0.000 -9.094 -1.120 -1.213
VD1 H20 H H 0.000 -8.157 -1.544 -1.597
VD1 C22 C CH2 0.000 -9.729 -0.230 -2.283
VD1 H221 H H 0.000 -9.081 0.628 -2.474
VD1 H222 H H 0.000 -10.702 0.122 -1.934
VD1 C23 C CH3 0.000 -9.908 -1.033 -3.574
VD1 H233 H H 0.000 -10.538 -1.867 -3.391
VD1 H232 H H 0.000 -10.348 -0.419 -4.319
VD1 H231 H H 0.000 -8.964 -1.376 -3.915
VD1 C21 C CH3 0.000 -10.058 -2.252 -0.854
VD1 H213 H H 0.000 -10.262 -2.831 -1.717
VD1 H212 H H 0.000 -9.620 -2.869 -0.112
VD1 H211 H H 0.000 -10.963 -1.844 -0.482
VD1 C13 C CT 0.000 -7.817 0.827 -0.292
VD1 C18 C CH3 0.000 -6.823 0.325 -1.342
VD1 H183 H H 0.000 -6.438 -0.616 -1.044
VD1 H182 H H 0.000 -7.314 0.225 -2.275
VD1 H181 H H 0.000 -6.027 1.017 -1.435
VD1 C12 C CH2 0.000 -8.347 2.173 -0.711
VD1 H121 H H 0.000 -8.906 2.627 0.110
VD1 H122 H H 0.000 -8.999 2.066 -1.580
VD1 C11 C CH2 0.000 -7.149 3.067 -1.074
VD1 H111 H H 0.000 -7.530 4.047 -1.370
VD1 H112 H H 0.000 -6.625 2.612 -1.917
VD1 C9 C CH2 0.000 -6.185 3.228 0.100
VD1 H92 H H 0.000 -6.651 3.867 0.853
VD1 H91 H H 0.000 -5.268 3.699 -0.259
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
VD1 O1 n/a C1 START
VD1 HO1 O1 . .
VD1 C1 O1 C10 .
VD1 H1 C1 . .
VD1 C2 C1 C28 .
VD1 C28 C2 H281 .
VD1 H282 C28 . .
VD1 H281 C28 . .
VD1 C10 C1 C5 .
VD1 H101 C10 . .
VD1 H102 C10 . .
VD1 C5 C10 C6 .
VD1 C4 C5 C3 .
VD1 H41 C4 . .
VD1 H42 C4 . .
VD1 C3 C4 O2 .
VD1 H3 C3 . .
VD1 O2 C3 HO2 .
VD1 HO2 O2 . .
VD1 C6 C5 C7 .
VD1 H6 C6 . .
VD1 C7 C6 C8 .
VD1 H7 C7 . .
VD1 C8 C7 C14 .
VD1 C14 C8 C15 .
VD1 H14 C14 . .
VD1 C15 C14 C16 .
VD1 H151 C15 . .
VD1 H152 C15 . .
VD1 C16 C15 C17 .
VD1 H161 C16 . .
VD1 H162 C16 . .
VD1 C17 C16 C13 .
VD1 H17 C17 . .
VD1 C20 C17 C21 .
VD1 H20 C20 . .
VD1 C22 C20 C23 .
VD1 H221 C22 . .
VD1 H222 C22 . .
VD1 C23 C22 H231 .
VD1 H233 C23 . .
VD1 H232 C23 . .
VD1 H231 C23 . .
VD1 C21 C20 H211 .
VD1 H213 C21 . .
VD1 H212 C21 . .
VD1 H211 C21 . .
VD1 C13 C17 C12 .
VD1 C18 C13 H181 .
VD1 H183 C18 . .
VD1 H182 C18 . .
VD1 H181 C18 . .
VD1 C12 C13 C11 .
VD1 H121 C12 . .
VD1 H122 C12 . .
VD1 C11 C12 C9 .
VD1 H111 C11 . .
VD1 H112 C11 . .
VD1 C9 C11 H91 .
VD1 H92 C9 . .
VD1 H91 C9 . END
VD1 C3 C2 . ADD
VD1 C8 C9 . ADD
VD1 C13 C14 . 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
VD1 O2 C3 single 1.432 0.020
VD1 HO2 O2 single 0.967 0.020
VD1 C3 C2 single 1.500 0.020
VD1 C3 C4 single 1.524 0.020
VD1 H3 C3 single 1.099 0.020
VD1 C28 C2 double 1.320 0.020
VD1 C2 C1 single 1.500 0.020
VD1 H281 C28 single 1.077 0.020
VD1 H282 C28 single 1.077 0.020
VD1 C1 O1 single 1.432 0.020
VD1 C10 C1 single 1.524 0.020
VD1 H1 C1 single 1.099 0.020
VD1 HO1 O1 single 0.967 0.020
VD1 C4 C5 single 1.510 0.020
VD1 H41 C4 single 1.092 0.020
VD1 H42 C4 single 1.092 0.020
VD1 C5 C10 single 1.510 0.020
VD1 C6 C5 double 1.340 0.020
VD1 H101 C10 single 1.092 0.020
VD1 H102 C10 single 1.092 0.020
VD1 C7 C6 single 1.460 0.020
VD1 H6 C6 single 1.077 0.020
VD1 C8 C7 double 1.340 0.020
VD1 H7 C7 single 1.077 0.020
VD1 C8 C9 single 1.510 0.020
VD1 C14 C8 single 1.500 0.020
VD1 C9 C11 single 1.524 0.020
VD1 H91 C9 single 1.092 0.020
VD1 H92 C9 single 1.092 0.020
VD1 C11 C12 single 1.524 0.020
VD1 H111 C11 single 1.092 0.020
VD1 H112 C11 single 1.092 0.020
VD1 C12 C13 single 1.524 0.020
VD1 H121 C12 single 1.092 0.020
VD1 H122 C12 single 1.092 0.020
VD1 C18 C13 single 1.524 0.020
VD1 C13 C14 single 1.524 0.020
VD1 C13 C17 single 1.524 0.020
VD1 H181 C18 single 1.059 0.020
VD1 H182 C18 single 1.059 0.020
VD1 H183 C18 single 1.059 0.020
VD1 C15 C14 single 1.524 0.020
VD1 H14 C14 single 1.099 0.020
VD1 C16 C15 single 1.524 0.020
VD1 H151 C15 single 1.092 0.020
VD1 H152 C15 single 1.092 0.020
VD1 C17 C16 single 1.524 0.020
VD1 C20 C17 single 1.524 0.020
VD1 H17 C17 single 1.099 0.020
VD1 H161 C16 single 1.092 0.020
VD1 H162 C16 single 1.092 0.020
VD1 C21 C20 single 1.524 0.020
VD1 C22 C20 single 1.524 0.020
VD1 H20 C20 single 1.099 0.020
VD1 H211 C21 single 1.059 0.020
VD1 H212 C21 single 1.059 0.020
VD1 H213 C21 single 1.059 0.020
VD1 C23 C22 single 1.513 0.020
VD1 H221 C22 single 1.092 0.020
VD1 H222 C22 single 1.092 0.020
VD1 H231 C23 single 1.059 0.020
VD1 H232 C23 single 1.059 0.020
VD1 H233 C23 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
VD1 HO1 O1 C1 109.470 3.000
VD1 O1 C1 H1 109.470 3.000
VD1 O1 C1 C2 109.470 3.000
VD1 O1 C1 C10 109.470 3.000
VD1 H1 C1 C2 108.810 3.000
VD1 H1 C1 C10 108.340 3.000
VD1 C2 C1 C10 109.470 3.000
VD1 C1 C2 C28 120.000 3.000
VD1 C1 C2 C3 120.000 3.000
VD1 C28 C2 C3 120.000 3.000
VD1 C2 C28 H282 120.000 3.000
VD1 C2 C28 H281 120.000 3.000
VD1 H282 C28 H281 120.000 3.000
VD1 C1 C10 H101 109.470 3.000
VD1 C1 C10 H102 109.470 3.000
VD1 C1 C10 C5 109.470 3.000
VD1 H101 C10 H102 107.900 3.000
VD1 H101 C10 C5 109.470 3.000
VD1 H102 C10 C5 109.470 3.000
VD1 C10 C5 C4 120.000 3.000
VD1 C10 C5 C6 120.000 3.000
VD1 C4 C5 C6 120.000 3.000
VD1 C5 C4 H41 109.470 3.000
VD1 C5 C4 H42 109.470 3.000
VD1 C5 C4 C3 109.470 3.000
VD1 H41 C4 H42 107.900 3.000
VD1 H41 C4 C3 109.470 3.000
VD1 H42 C4 C3 109.470 3.000
VD1 C4 C3 H3 108.340 3.000
VD1 C4 C3 O2 109.470 3.000
VD1 C4 C3 C2 109.470 3.000
VD1 H3 C3 O2 109.470 3.000
VD1 H3 C3 C2 108.810 3.000
VD1 O2 C3 C2 109.470 3.000
VD1 C3 O2 HO2 109.470 3.000
VD1 C5 C6 H6 120.000 3.000
VD1 C5 C6 C7 120.000 3.000
VD1 H6 C6 C7 120.000 3.000
VD1 C6 C7 H7 120.000 3.000
VD1 C6 C7 C8 120.000 3.000
VD1 H7 C7 C8 120.000 3.000
VD1 C7 C8 C14 120.000 3.000
VD1 C7 C8 C9 120.000 3.000
VD1 C14 C8 C9 120.000 3.000
VD1 C8 C14 H14 108.810 3.000
VD1 C8 C14 C15 109.470 3.000
VD1 C8 C14 C13 109.470 3.000
VD1 H14 C14 C15 108.340 3.000
VD1 H14 C14 C13 108.340 3.000
VD1 C15 C14 C13 111.000 3.000
VD1 C14 C15 H151 109.470 3.000
VD1 C14 C15 H152 109.470 3.000
VD1 C14 C15 C16 111.000 3.000
VD1 H151 C15 H152 107.900 3.000
VD1 H151 C15 C16 109.470 3.000
VD1 H152 C15 C16 109.470 3.000
VD1 C15 C16 H161 109.470 3.000
VD1 C15 C16 H162 109.470 3.000
VD1 C15 C16 C17 111.000 3.000
VD1 H161 C16 H162 107.900 3.000
VD1 H161 C16 C17 109.470 3.000
VD1 H162 C16 C17 109.470 3.000
VD1 C16 C17 H17 108.340 3.000
VD1 C16 C17 C20 111.000 3.000
VD1 C16 C17 C13 111.000 3.000
VD1 H17 C17 C20 108.340 3.000
VD1 H17 C17 C13 108.340 3.000
VD1 C20 C17 C13 111.000 3.000
VD1 C17 C20 H20 108.340 3.000
VD1 C17 C20 C22 111.000 3.000
VD1 C17 C20 C21 111.000 3.000
VD1 H20 C20 C22 108.340 3.000
VD1 H20 C20 C21 108.340 3.000
VD1 C22 C20 C21 111.000 3.000
VD1 C20 C22 H221 109.470 3.000
VD1 C20 C22 H222 109.470 3.000
VD1 C20 C22 C23 111.000 3.000
VD1 H221 C22 H222 107.900 3.000
VD1 H221 C22 C23 109.470 3.000
VD1 H222 C22 C23 109.470 3.000
VD1 C22 C23 H233 109.470 3.000
VD1 C22 C23 H232 109.470 3.000
VD1 C22 C23 H231 109.470 3.000
VD1 H233 C23 H232 109.470 3.000
VD1 H233 C23 H231 109.470 3.000
VD1 H232 C23 H231 109.470 3.000
VD1 C20 C21 H213 109.470 3.000
VD1 C20 C21 H212 109.470 3.000
VD1 C20 C21 H211 109.470 3.000
VD1 H213 C21 H212 109.470 3.000
VD1 H213 C21 H211 109.470 3.000
VD1 H212 C21 H211 109.470 3.000
VD1 C17 C13 C18 111.000 3.000
VD1 C17 C13 C12 111.000 3.000
VD1 C17 C13 C14 111.000 3.000
VD1 C18 C13 C12 111.000 3.000
VD1 C18 C13 C14 111.000 3.000
VD1 C12 C13 C14 111.000 3.000
VD1 C13 C18 H183 109.470 3.000
VD1 C13 C18 H182 109.470 3.000
VD1 C13 C18 H181 109.470 3.000
VD1 H183 C18 H182 109.470 3.000
VD1 H183 C18 H181 109.470 3.000
VD1 H182 C18 H181 109.470 3.000
VD1 C13 C12 H121 109.470 3.000
VD1 C13 C12 H122 109.470 3.000
VD1 C13 C12 C11 111.000 3.000
VD1 H121 C12 H122 107.900 3.000
VD1 H121 C12 C11 109.470 3.000
VD1 H122 C12 C11 109.470 3.000
VD1 C12 C11 H111 109.470 3.000
VD1 C12 C11 H112 109.470 3.000
VD1 C12 C11 C9 111.000 3.000
VD1 H111 C11 H112 107.900 3.000
VD1 H111 C11 C9 109.470 3.000
VD1 H112 C11 C9 109.470 3.000
VD1 C11 C9 H92 109.470 3.000
VD1 C11 C9 H91 109.470 3.000
VD1 C11 C9 C8 109.470 3.000
VD1 H92 C9 H91 107.900 3.000
VD1 H92 C9 C8 109.470 3.000
VD1 H91 C9 C8 109.470 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
VD1 var_1 HO1 O1 C1 C10 179.334 20.000 1
VD1 var_2 O1 C1 C2 C28 0.000 20.000 3
VD1 CONST_1 C1 C2 C28 H281 179.992 0.000 0
VD1 var_3 O1 C1 C10 C5 180.000 20.000 3
VD1 var_4 C1 C10 C5 C6 -120.000 20.000 3
VD1 var_5 C10 C5 C4 C3 -60.000 20.000 3
VD1 var_6 C5 C4 C3 O2 -60.000 20.000 3
VD1 var_7 C4 C3 C2 C1 -60.000 20.000 3
VD1 var_8 C4 C3 O2 HO2 179.994 20.000 1
VD1 CONST_2 C10 C5 C6 C7 5.725 0.000 0
VD1 var_9 C5 C6 C7 C8 173.719 20.000 1
VD1 CONST_3 C6 C7 C8 C14 -20.240 0.000 0
VD1 var_10 C7 C8 C9 C11 120.000 20.000 3
VD1 var_11 C7 C8 C14 C15 0.000 20.000 3
VD1 var_12 C8 C14 C15 C16 -150.000 20.000 3
VD1 var_13 C14 C15 C16 C17 30.000 20.000 3
VD1 var_14 C15 C16 C17 C13 0.000 20.000 3
VD1 var_15 C16 C17 C20 C21 62.861 20.000 3
VD1 var_16 C17 C20 C22 C23 175.027 20.000 3
VD1 var_17 C20 C22 C23 H231 -59.996 20.000 3
VD1 var_18 C17 C20 C21 H211 59.992 20.000 3
VD1 var_19 C16 C17 C13 C12 -150.000 20.000 1
VD1 var_20 C17 C13 C14 C8 180.000 20.000 1
VD1 var_21 C17 C13 C18 H181 -168.974 20.000 1
VD1 var_22 C17 C13 C12 C11 180.000 20.000 1
VD1 var_23 C13 C12 C11 C9 -60.000 20.000 3
VD1 var_24 C12 C11 C9 C8 60.000 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
VD1 chir_01 C3 O2 C2 C4 negativ
VD1 chir_02 C1 C2 O1 C10 positiv
VD1 chir_03 C13 C12 C18 C14 negativ
VD1 chir_04 C14 C8 C13 C15 negativ
VD1 chir_05 C17 C13 C16 C20 positiv
VD1 chir_06 C20 C17 C21 C22 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
VD1 plan-1 C2 0.020
VD1 plan-1 C3 0.020
VD1 plan-1 C28 0.020
VD1 plan-1 C1 0.020
VD1 plan-1 H281 0.020
VD1 plan-1 H282 0.020
VD1 plan-2 C5 0.020
VD1 plan-2 C4 0.020
VD1 plan-2 C10 0.020
VD1 plan-2 C6 0.020
VD1 plan-2 C7 0.020
VD1 plan-2 H6 0.020
VD1 plan-2 H7 0.020
VD1 plan-3 C7 0.020
VD1 plan-3 C6 0.020
VD1 plan-3 C8 0.020
VD1 plan-3 H7 0.020
VD1 plan-3 C9 0.020
VD1 plan-3 C14 0.020
VD1 plan-3 H6 0.020
# ------------------------------------------------------
|
