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
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
|
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
O75 O75 'N-benzyl-3-(2-cyano-6-propylpyrimidi' non-polymer 64 36 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_O75
#
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
O75 O23 O O 0.000 0.000 0.000 0.000
O75 C22 C C 0.000 -0.766 0.553 -0.765
O75 N24 N N 0.000 -0.358 0.884 -2.006
O75 C32 C CH2 0.000 -1.236 1.665 -2.881
O75 H32 H H 0.000 -2.270 1.559 -2.548
O75 H32A H H 0.000 -1.145 1.299 -3.906
O75 C33 C CH2 0.000 -0.829 3.139 -2.827
O75 H33 H H 0.000 0.172 3.256 -3.248
O75 H33A H H 0.000 -0.827 3.478 -1.788
O75 N34 N NT 0.000 -1.786 3.940 -3.603
O75 C36 C CH3 0.000 -1.711 3.609 -5.032
O75 H36B H H 0.000 -2.409 4.199 -5.568
O75 H36A H H 0.000 -0.734 3.807 -5.389
O75 H36 H H 0.000 -1.936 2.584 -5.169
O75 C35 C CH3 0.000 -1.570 5.377 -3.382
O75 H35B H H 0.000 -2.271 5.930 -3.951
O75 H35A H H 0.000 -1.697 5.598 -2.354
O75 H35 H H 0.000 -0.588 5.637 -3.681
O75 C25 C CH2 0.000 0.963 0.461 -2.480
O75 H25 H H 0.000 1.648 0.393 -1.632
O75 H25A H H 0.000 1.343 1.193 -3.195
O75 C26 C CR6 0.000 0.850 -0.884 -3.148
O75 C31 C CR16 0.000 1.009 -2.040 -2.405
O75 H31 H H 0.000 1.219 -1.977 -1.344
O75 C30 C CR16 0.000 0.899 -3.275 -3.017
O75 H30 H H 0.000 1.014 -4.180 -2.433
O75 C29 C CR16 0.000 0.642 -3.354 -4.373
O75 H29 H H 0.000 0.561 -4.322 -4.853
O75 C28 C CR16 0.000 0.490 -2.198 -5.116
O75 H28 H H 0.000 0.289 -2.261 -6.178
O75 C27 C CR16 0.000 0.593 -0.964 -4.504
O75 H27 H H 0.000 0.473 -0.059 -5.086
O75 C14 C CR6 0.000 -2.145 0.865 -0.332
O75 C13 C CR16 0.000 -2.903 -0.097 0.332
O75 H13 H H 0.000 -2.483 -1.075 0.534
O75 C15 C CR16 0.000 -2.692 2.124 -0.589
O75 H15 H H 0.000 -2.106 2.874 -1.105
O75 C16 C CR6 0.000 -3.979 2.415 -0.185
O75 C18 C CT 0.000 -4.564 3.776 -0.463
O75 F21 F F 0.000 -3.620 4.560 -1.135
O75 F20 F F 0.000 -4.908 4.392 0.745
O75 F19 F F 0.000 -5.706 3.639 -1.260
O75 C17 C CR16 0.000 -4.737 1.462 0.469
O75 H17 H H 0.000 -5.750 1.694 0.775
O75 C12 C CR6 0.000 -4.201 0.203 0.735
O75 C1 C CR6 0.000 -5.013 -0.816 1.443
O75 C6 C CR16 0.000 -6.318 -0.524 1.854
O75 H6 H H 0.000 -6.756 0.447 1.659
O75 C5 C CR6 0.000 -7.037 -1.506 2.516
O75 C9 C CH2 0.000 -8.447 -1.237 2.977
O75 H9 H H 0.000 -8.763 -0.253 2.627
O75 H9A H H 0.000 -8.483 -1.263 4.068
O75 C10 C CH2 0.000 -9.381 -2.307 2.409
O75 H10 H H 0.000 -9.063 -3.291 2.759
O75 H10A H H 0.000 -9.343 -2.281 1.318
O75 C11 C CH3 0.000 -10.812 -2.036 2.878
O75 H11B H H 0.000 -11.124 -1.081 2.538
O75 H11A H H 0.000 -11.462 -2.776 2.487
O75 H11 H H 0.000 -10.851 -2.060 3.937
O75 N4 N NRD6 0.000 -6.473 -2.680 2.739
O75 C3 C CR6 0.000 -5.234 -2.930 2.339
O75 N2 N NRD6 0.000 -4.511 -2.019 1.702
O75 C7 C CSP 0.000 -4.661 -4.216 2.602
O75 N8 N NS 0.000 -4.207 -5.235 2.810
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
O75 O23 n/a C22 START
O75 C22 O23 C14 .
O75 N24 C22 C25 .
O75 C32 N24 C33 .
O75 H32 C32 . .
O75 H32A C32 . .
O75 C33 C32 N34 .
O75 H33 C33 . .
O75 H33A C33 . .
O75 N34 C33 C35 .
O75 C36 N34 H36 .
O75 H36B C36 . .
O75 H36A C36 . .
O75 H36 C36 . .
O75 C35 N34 H35 .
O75 H35B C35 . .
O75 H35A C35 . .
O75 H35 C35 . .
O75 C25 N24 C26 .
O75 H25 C25 . .
O75 H25A C25 . .
O75 C26 C25 C31 .
O75 C31 C26 C30 .
O75 H31 C31 . .
O75 C30 C31 C29 .
O75 H30 C30 . .
O75 C29 C30 C28 .
O75 H29 C29 . .
O75 C28 C29 C27 .
O75 H28 C28 . .
O75 C27 C28 H27 .
O75 H27 C27 . .
O75 C14 C22 C15 .
O75 C13 C14 H13 .
O75 H13 C13 . .
O75 C15 C14 C16 .
O75 H15 C15 . .
O75 C16 C15 C17 .
O75 C18 C16 F19 .
O75 F21 C18 . .
O75 F20 C18 . .
O75 F19 C18 . .
O75 C17 C16 C12 .
O75 H17 C17 . .
O75 C12 C17 C1 .
O75 C1 C12 C6 .
O75 C6 C1 C5 .
O75 H6 C6 . .
O75 C5 C6 N4 .
O75 C9 C5 C10 .
O75 H9 C9 . .
O75 H9A C9 . .
O75 C10 C9 C11 .
O75 H10 C10 . .
O75 H10A C10 . .
O75 C11 C10 H11 .
O75 H11B C11 . .
O75 H11A C11 . .
O75 H11 C11 . .
O75 N4 C5 C3 .
O75 C3 N4 C7 .
O75 N2 C3 . .
O75 C7 C3 N8 .
O75 N8 C7 . END
O75 C1 N2 . ADD
O75 C12 C13 . ADD
O75 C26 C27 . 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
O75 C6 C1 single 1.390 0.020
O75 C1 N2 double 1.350 0.020
O75 N2 C3 single 1.350 0.020
O75 C3 N4 double 1.350 0.020
O75 N4 C5 single 1.350 0.020
O75 C9 C5 single 1.511 0.020
O75 C5 C6 double 1.390 0.020
O75 C7 C3 single 1.285 0.020
O75 N8 C7 triple 1.158 0.020
O75 C10 C9 single 1.524 0.020
O75 C11 C10 single 1.513 0.020
O75 C1 C12 single 1.487 0.020
O75 C12 C13 single 1.390 0.020
O75 C13 C14 double 1.390 0.020
O75 C14 C22 single 1.500 0.020
O75 C15 C14 single 1.390 0.020
O75 C16 C15 double 1.390 0.020
O75 C17 C16 single 1.390 0.020
O75 C12 C17 double 1.390 0.020
O75 C18 C16 single 1.500 0.020
O75 F21 C18 single 1.320 0.020
O75 F19 C18 single 1.320 0.020
O75 F20 C18 single 1.320 0.020
O75 C22 O23 double 1.220 0.020
O75 N24 C22 single 1.330 0.020
O75 C32 N24 single 1.455 0.020
O75 C25 N24 single 1.455 0.020
O75 C26 C25 single 1.511 0.020
O75 C26 C27 single 1.390 0.020
O75 C27 C28 double 1.390 0.020
O75 C28 C29 single 1.390 0.020
O75 C29 C30 double 1.390 0.020
O75 C30 C31 single 1.390 0.020
O75 C31 C26 double 1.390 0.020
O75 C33 C32 single 1.524 0.020
O75 N34 C33 single 1.469 0.020
O75 C35 N34 single 1.469 0.020
O75 C36 N34 single 1.469 0.020
O75 H6 C6 single 1.083 0.020
O75 H9 C9 single 1.092 0.020
O75 H9A C9 single 1.092 0.020
O75 H10 C10 single 1.092 0.020
O75 H10A C10 single 1.092 0.020
O75 H11 C11 single 1.059 0.020
O75 H11A C11 single 1.059 0.020
O75 H11B C11 single 1.059 0.020
O75 H13 C13 single 1.083 0.020
O75 H15 C15 single 1.083 0.020
O75 H17 C17 single 1.083 0.020
O75 H25 C25 single 1.092 0.020
O75 H25A C25 single 1.092 0.020
O75 H27 C27 single 1.083 0.020
O75 H28 C28 single 1.083 0.020
O75 H29 C29 single 1.083 0.020
O75 H30 C30 single 1.083 0.020
O75 H31 C31 single 1.083 0.020
O75 H32 C32 single 1.092 0.020
O75 H32A C32 single 1.092 0.020
O75 H33 C33 single 1.092 0.020
O75 H33A C33 single 1.092 0.020
O75 H35 C35 single 1.059 0.020
O75 H35A C35 single 1.059 0.020
O75 H35B C35 single 1.059 0.020
O75 H36 C36 single 1.059 0.020
O75 H36A C36 single 1.059 0.020
O75 H36B C36 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
O75 O23 C22 N24 123.000 3.000
O75 O23 C22 C14 120.500 3.000
O75 N24 C22 C14 120.000 3.000
O75 C22 N24 C32 127.000 3.000
O75 C22 N24 C25 127.000 3.000
O75 C32 N24 C25 120.000 3.000
O75 N24 C32 H32 109.470 3.000
O75 N24 C32 H32A 109.470 3.000
O75 N24 C32 C33 105.000 3.000
O75 H32 C32 H32A 107.900 3.000
O75 H32 C32 C33 109.470 3.000
O75 H32A C32 C33 109.470 3.000
O75 C32 C33 H33 109.470 3.000
O75 C32 C33 H33A 109.470 3.000
O75 C32 C33 N34 109.470 3.000
O75 H33 C33 H33A 107.900 3.000
O75 H33 C33 N34 109.470 3.000
O75 H33A C33 N34 109.470 3.000
O75 C33 N34 C36 109.470 3.000
O75 C33 N34 C35 109.470 3.000
O75 C36 N34 C35 109.470 3.000
O75 N34 C36 H36B 109.470 3.000
O75 N34 C36 H36A 109.470 3.000
O75 N34 C36 H36 109.470 3.000
O75 H36B C36 H36A 109.470 3.000
O75 H36B C36 H36 109.470 3.000
O75 H36A C36 H36 109.470 3.000
O75 N34 C35 H35B 109.470 3.000
O75 N34 C35 H35A 109.470 3.000
O75 N34 C35 H35 109.470 3.000
O75 H35B C35 H35A 109.470 3.000
O75 H35B C35 H35 109.470 3.000
O75 H35A C35 H35 109.470 3.000
O75 N24 C25 H25 109.470 3.000
O75 N24 C25 H25A 109.470 3.000
O75 N24 C25 C26 109.470 3.000
O75 H25 C25 H25A 107.900 3.000
O75 H25 C25 C26 109.470 3.000
O75 H25A C25 C26 109.470 3.000
O75 C25 C26 C31 120.000 3.000
O75 C25 C26 C27 120.000 3.000
O75 C31 C26 C27 120.000 3.000
O75 C26 C31 H31 120.000 3.000
O75 C26 C31 C30 120.000 3.000
O75 H31 C31 C30 120.000 3.000
O75 C31 C30 H30 120.000 3.000
O75 C31 C30 C29 120.000 3.000
O75 H30 C30 C29 120.000 3.000
O75 C30 C29 H29 120.000 3.000
O75 C30 C29 C28 120.000 3.000
O75 H29 C29 C28 120.000 3.000
O75 C29 C28 H28 120.000 3.000
O75 C29 C28 C27 120.000 3.000
O75 H28 C28 C27 120.000 3.000
O75 C28 C27 H27 120.000 3.000
O75 C28 C27 C26 120.000 3.000
O75 H27 C27 C26 120.000 3.000
O75 C22 C14 C13 120.000 3.000
O75 C22 C14 C15 120.000 3.000
O75 C13 C14 C15 120.000 3.000
O75 C14 C13 H13 120.000 3.000
O75 C14 C13 C12 120.000 3.000
O75 H13 C13 C12 120.000 3.000
O75 C14 C15 H15 120.000 3.000
O75 C14 C15 C16 120.000 3.000
O75 H15 C15 C16 120.000 3.000
O75 C15 C16 C18 120.000 3.000
O75 C15 C16 C17 120.000 3.000
O75 C18 C16 C17 120.000 3.000
O75 C16 C18 F21 109.470 3.000
O75 C16 C18 F20 109.470 3.000
O75 C16 C18 F19 109.470 3.000
O75 F21 C18 F20 109.470 3.000
O75 F21 C18 F19 109.470 3.000
O75 F20 C18 F19 109.470 3.000
O75 C16 C17 H17 120.000 3.000
O75 C16 C17 C12 120.000 3.000
O75 H17 C17 C12 120.000 3.000
O75 C17 C12 C1 120.000 3.000
O75 C17 C12 C13 120.000 3.000
O75 C1 C12 C13 120.000 3.000
O75 C12 C1 C6 120.000 3.000
O75 C12 C1 N2 120.000 3.000
O75 C6 C1 N2 120.000 3.000
O75 C1 C6 H6 120.000 3.000
O75 C1 C6 C5 120.000 3.000
O75 H6 C6 C5 120.000 3.000
O75 C6 C5 C9 120.000 3.000
O75 C6 C5 N4 120.000 3.000
O75 C9 C5 N4 120.000 3.000
O75 C5 C9 H9 109.470 3.000
O75 C5 C9 H9A 109.470 3.000
O75 C5 C9 C10 109.470 3.000
O75 H9 C9 H9A 107.900 3.000
O75 H9 C9 C10 109.470 3.000
O75 H9A C9 C10 109.470 3.000
O75 C9 C10 H10 109.470 3.000
O75 C9 C10 H10A 109.470 3.000
O75 C9 C10 C11 111.000 3.000
O75 H10 C10 H10A 107.900 3.000
O75 H10 C10 C11 109.470 3.000
O75 H10A C10 C11 109.470 3.000
O75 C10 C11 H11B 109.470 3.000
O75 C10 C11 H11A 109.470 3.000
O75 C10 C11 H11 109.470 3.000
O75 H11B C11 H11A 109.470 3.000
O75 H11B C11 H11 109.470 3.000
O75 H11A C11 H11 109.470 3.000
O75 C5 N4 C3 120.000 3.000
O75 N4 C3 N2 120.000 3.000
O75 N4 C3 C7 120.000 3.000
O75 N2 C3 C7 120.000 3.000
O75 C3 N2 C1 120.000 3.000
O75 C3 C7 N8 180.000 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
O75 CONST_1 O23 C22 N24 C25 0.000 0.000 0
O75 var_1 C22 N24 C32 C33 98.282 20.000 1
O75 var_2 N24 C32 C33 N34 -174.687 20.000 3
O75 var_3 C32 C33 N34 C35 169.973 20.000 1
O75 var_4 C33 N34 C36 H36 59.978 20.000 1
O75 var_5 C33 N34 C35 H35 60.024 20.000 1
O75 var_6 C22 N24 C25 C26 89.945 20.000 1
O75 var_7 N24 C25 C26 C31 -90.281 20.000 2
O75 CONST_2 C25 C26 C27 C28 180.000 0.000 0
O75 CONST_3 C25 C26 C31 C30 180.000 0.000 0
O75 CONST_4 C26 C31 C30 C29 0.000 0.000 0
O75 CONST_5 C31 C30 C29 C28 0.000 0.000 0
O75 CONST_6 C30 C29 C28 C27 0.000 0.000 0
O75 CONST_7 C29 C28 C27 C26 0.000 0.000 0
O75 var_8 O23 C22 C14 C15 134.157 20.000 1
O75 CONST_8 C22 C14 C13 C12 180.000 0.000 0
O75 CONST_9 C22 C14 C15 C16 180.000 0.000 0
O75 CONST_10 C14 C15 C16 C17 0.000 0.000 0
O75 var_9 C15 C16 C18 F19 119.984 20.000 1
O75 CONST_11 C15 C16 C17 C12 0.000 0.000 0
O75 CONST_12 C16 C17 C12 C1 180.000 0.000 0
O75 CONST_13 C17 C12 C13 C14 0.000 0.000 0
O75 CONST_14 C17 C12 C1 C6 0.000 0.000 0
O75 CONST_15 C12 C1 N2 C3 180.000 0.000 0
O75 CONST_16 C12 C1 C6 C5 180.000 0.000 0
O75 CONST_17 C1 C6 C5 N4 0.000 0.000 0
O75 var_10 C6 C5 C9 C10 125.008 20.000 2
O75 var_11 C5 C9 C10 C11 179.958 20.000 3
O75 var_12 C9 C10 C11 H11 -59.923 20.000 3
O75 CONST_18 C6 C5 N4 C3 0.000 0.000 0
O75 CONST_19 C5 N4 C3 C7 180.000 0.000 0
O75 CONST_20 N4 C3 N2 C1 0.000 0.000 0
O75 var_13 N4 C3 C7 N8 -22.195 20.000 1
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
O75 chir_01 C18 C16 F19 F20 negativ
O75 chir_02 N34 C33 C35 C36 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
O75 plan-1 C1 0.020
O75 plan-1 N2 0.020
O75 plan-1 C6 0.020
O75 plan-1 C12 0.020
O75 plan-1 C3 0.020
O75 plan-1 N4 0.020
O75 plan-1 C5 0.020
O75 plan-1 C7 0.020
O75 plan-1 C9 0.020
O75 plan-1 H6 0.020
O75 plan-2 C12 0.020
O75 plan-2 C1 0.020
O75 plan-2 C13 0.020
O75 plan-2 C17 0.020
O75 plan-2 C14 0.020
O75 plan-2 C15 0.020
O75 plan-2 C16 0.020
O75 plan-2 H13 0.020
O75 plan-2 C22 0.020
O75 plan-2 H15 0.020
O75 plan-2 C18 0.020
O75 plan-2 H17 0.020
O75 plan-3 C22 0.020
O75 plan-3 C14 0.020
O75 plan-3 O23 0.020
O75 plan-3 N24 0.020
O75 plan-4 N24 0.020
O75 plan-4 C22 0.020
O75 plan-4 C25 0.020
O75 plan-4 C32 0.020
O75 plan-5 C26 0.020
O75 plan-5 C25 0.020
O75 plan-5 C27 0.020
O75 plan-5 C31 0.020
O75 plan-5 C28 0.020
O75 plan-5 C29 0.020
O75 plan-5 C30 0.020
O75 plan-5 H27 0.020
O75 plan-5 H28 0.020
O75 plan-5 H29 0.020
O75 plan-5 H30 0.020
O75 plan-5 H31 0.020
# ------------------------------------------------------
|
