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
|
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
PDS PDS '3-{1-[3-(DIMETHYLAMINO)PROPYL]-2-MET' non-polymer 61 33 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PDS
#
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
PDS O20 O O 0.000 0.000 0.000 0.000
PDS C12 C CR5 0.000 -1.128 0.191 0.424
PDS N13 N NR15 0.000 -2.126 0.925 -0.145
PDS HN13 H H 0.000 -2.039 1.423 -1.054
PDS C5 C CR5 0.000 -1.673 -0.339 1.700
PDS C11 C CR5 0.000 -0.903 -1.151 2.589
PDS C19 C CR5 0.000 -0.853 -2.527 2.553
PDS C26 C CH3 0.000 -1.517 -3.506 1.670
PDS H263 H H 0.000 -1.455 -3.168 0.671
PDS H262 H H 0.000 -1.032 -4.440 1.764
PDS H261 H H 0.000 -2.530 -3.597 1.955
PDS N25 N NR15 0.000 -0.016 -2.943 3.554
PDS HN25 H H 0.000 0.211 -3.936 3.765
PDS C23 C CR56 0.000 0.482 -1.858 4.239
PDS C28 C CR16 0.000 1.364 -1.802 5.325
PDS H28 H H 0.000 1.772 -2.704 5.763
PDS C31 C CR16 0.000 1.697 -0.539 5.822
PDS H31 H H 0.000 2.377 -0.458 6.661
PDS C29 C CR16 0.000 1.169 0.619 5.254
PDS H29 H H 0.000 1.444 1.586 5.658
PDS C24 C CR16 0.000 0.288 0.547 4.169
PDS H24 H H 0.000 -0.119 1.451 3.733
PDS C18 C CR56 0.000 -0.063 -0.715 3.650
PDS C2 C CR5 0.000 -2.939 0.103 1.821
PDS C6 C CR5 0.000 -3.251 0.925 0.625
PDS O14 O O 0.000 -4.318 1.471 0.398
PDS C1 C CR5 0.000 -3.892 -0.142 2.860
PDS C4 C CR5 0.000 -4.048 0.634 3.988
PDS C10 C CH3 0.000 -3.329 1.854 4.419
PDS H103 H H 0.000 -3.327 2.554 3.627
PDS H102 H H 0.000 -3.818 2.267 5.260
PDS H101 H H 0.000 -2.335 1.599 4.673
PDS N9 N NR5 0.000 -5.052 0.089 4.742
PDS C17 C CH2 0.000 -5.520 0.615 6.009
PDS H171 H H 0.000 -4.678 1.097 6.508
PDS H172 H H 0.000 -5.871 -0.222 6.615
PDS C22 C CH2 0.000 -6.653 1.626 5.827
PDS H221 H H 0.000 -7.476 1.120 5.317
PDS H222 H H 0.000 -6.282 2.438 5.198
PDS C27 C CH2 0.000 -7.147 2.192 7.153
PDS H271 H H 0.000 -6.297 2.659 7.656
PDS H272 H H 0.000 -7.514 1.361 7.758
PDS N30 N NT 0.000 -8.195 3.160 6.979
PDS C33 C CH3 0.000 -9.367 2.568 6.314
PDS H333 H H 0.000 -9.255 1.516 6.271
PDS H332 H H 0.000 -10.242 2.808 6.861
PDS H331 H H 0.000 -9.448 2.955 5.331
PDS C32 C CH3 0.000 -8.605 3.745 8.266
PDS H323 H H 0.000 -8.279 4.751 8.317
PDS H322 H H 0.000 -9.660 3.712 8.348
PDS H321 H H 0.000 -8.172 3.193 9.059
PDS C7 C CR56 0.000 -5.556 -1.033 4.123
PDS C3 C CR56 0.000 -4.842 -1.201 2.935
PDS C15 C CR16 0.000 -6.578 -1.903 4.520
PDS H15 H H 0.000 -7.117 -1.751 5.447
PDS C21 C CR16 0.000 -6.877 -2.975 3.676
PDS H21 H H 0.000 -7.663 -3.668 3.953
PDS C16 C CR16 0.000 -6.182 -3.169 2.485
PDS H16 H H 0.000 -6.434 -4.008 1.848
PDS C8 C CR16 0.000 -5.162 -2.291 2.100
PDS H8 H H 0.000 -4.625 -2.447 1.173
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
PDS O20 n/a C12 START
PDS C12 O20 C5 .
PDS N13 C12 HN13 .
PDS HN13 N13 . .
PDS C5 C12 C2 .
PDS C11 C5 C19 .
PDS C19 C11 N25 .
PDS C26 C19 H261 .
PDS H263 C26 . .
PDS H262 C26 . .
PDS H261 C26 . .
PDS N25 C19 C23 .
PDS HN25 N25 . .
PDS C23 N25 C18 .
PDS C28 C23 C31 .
PDS H28 C28 . .
PDS C31 C28 C29 .
PDS H31 C31 . .
PDS C29 C31 C24 .
PDS H29 C29 . .
PDS C24 C29 H24 .
PDS H24 C24 . .
PDS C18 C23 . .
PDS C2 C5 C1 .
PDS C6 C2 O14 .
PDS O14 C6 . .
PDS C1 C2 C4 .
PDS C4 C1 N9 .
PDS C10 C4 H101 .
PDS H103 C10 . .
PDS H102 C10 . .
PDS H101 C10 . .
PDS N9 C4 C7 .
PDS C17 N9 C22 .
PDS H171 C17 . .
PDS H172 C17 . .
PDS C22 C17 C27 .
PDS H221 C22 . .
PDS H222 C22 . .
PDS C27 C22 N30 .
PDS H271 C27 . .
PDS H272 C27 . .
PDS N30 C27 C32 .
PDS C33 N30 H331 .
PDS H333 C33 . .
PDS H332 C33 . .
PDS H331 C33 . .
PDS C32 N30 H321 .
PDS H323 C32 . .
PDS H322 C32 . .
PDS H321 C32 . .
PDS C7 N9 C15 .
PDS C3 C7 . .
PDS C15 C7 C21 .
PDS H15 C15 . .
PDS C21 C15 C16 .
PDS H21 C21 . .
PDS C16 C21 C8 .
PDS H16 C16 . .
PDS C8 C16 H8 .
PDS H8 C8 . END
PDS C6 N13 . ADD
PDS C11 C18 . ADD
PDS C18 C24 . ADD
PDS C1 C3 . ADD
PDS C3 C8 . 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
PDS O14 C6 double 1.285 0.020
PDS C6 C2 single 1.490 0.020
PDS C6 N13 single 1.340 0.020
PDS N13 C12 single 1.340 0.020
PDS HN13 N13 single 1.040 0.020
PDS C5 C12 single 1.490 0.020
PDS C12 O20 double 1.285 0.020
PDS C1 C2 single 1.490 0.020
PDS C2 C5 double 1.490 0.020
PDS C11 C5 single 1.490 0.020
PDS C11 C18 single 1.490 0.020
PDS C19 C11 double 1.490 0.020
PDS C18 C24 double 1.390 0.020
PDS C18 C23 single 1.490 0.020
PDS C24 C29 single 1.390 0.020
PDS H24 C24 single 1.083 0.020
PDS C29 C31 double 1.390 0.020
PDS H29 C29 single 1.083 0.020
PDS C31 C28 single 1.390 0.020
PDS H31 C31 single 1.083 0.020
PDS C28 C23 double 1.390 0.020
PDS H28 C28 single 1.083 0.020
PDS C23 N25 single 1.340 0.020
PDS N25 C19 single 1.340 0.020
PDS HN25 N25 single 1.040 0.020
PDS C26 C19 single 1.506 0.020
PDS H261 C26 single 1.059 0.020
PDS H262 C26 single 1.059 0.020
PDS H263 C26 single 1.059 0.020
PDS C1 C3 single 1.490 0.020
PDS C4 C1 double 1.490 0.020
PDS C3 C7 double 1.490 0.020
PDS C3 C8 single 1.390 0.020
PDS C8 C16 double 1.390 0.020
PDS H8 C8 single 1.083 0.020
PDS C16 C21 single 1.390 0.020
PDS H16 C16 single 1.083 0.020
PDS C15 C7 single 1.390 0.020
PDS C7 N9 single 1.337 0.020
PDS C21 C15 double 1.390 0.020
PDS H15 C15 single 1.083 0.020
PDS H21 C21 single 1.083 0.020
PDS C17 N9 single 1.462 0.020
PDS N9 C4 single 1.337 0.020
PDS C10 C4 single 1.506 0.020
PDS H101 C10 single 1.059 0.020
PDS H102 C10 single 1.059 0.020
PDS H103 C10 single 1.059 0.020
PDS C22 C17 single 1.524 0.020
PDS H171 C17 single 1.092 0.020
PDS H172 C17 single 1.092 0.020
PDS C27 C22 single 1.524 0.020
PDS H221 C22 single 1.092 0.020
PDS H222 C22 single 1.092 0.020
PDS N30 C27 single 1.469 0.020
PDS H271 C27 single 1.092 0.020
PDS H272 C27 single 1.092 0.020
PDS C33 N30 single 1.469 0.020
PDS C32 N30 single 1.469 0.020
PDS H321 C32 single 1.059 0.020
PDS H322 C32 single 1.059 0.020
PDS H323 C32 single 1.059 0.020
PDS H331 C33 single 1.059 0.020
PDS H332 C33 single 1.059 0.020
PDS H333 C33 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
PDS O20 C12 N13 108.000 3.000
PDS O20 C12 C5 108.000 3.000
PDS N13 C12 C5 108.000 3.000
PDS C12 N13 HN13 126.000 3.000
PDS C12 N13 C6 108.000 3.000
PDS HN13 N13 C6 126.000 3.000
PDS C12 C5 C11 108.000 3.000
PDS C12 C5 C2 108.000 3.000
PDS C11 C5 C2 108.000 3.000
PDS C5 C11 C19 108.000 3.000
PDS C5 C11 C18 108.000 3.000
PDS C19 C11 C18 108.000 3.000
PDS C11 C19 C26 126.000 3.000
PDS C11 C19 N25 108.000 3.000
PDS C26 C19 N25 126.000 3.000
PDS C19 C26 H263 109.470 3.000
PDS C19 C26 H262 109.470 3.000
PDS C19 C26 H261 109.470 3.000
PDS H263 C26 H262 109.470 3.000
PDS H263 C26 H261 109.470 3.000
PDS H262 C26 H261 109.470 3.000
PDS C19 N25 HN25 126.000 3.000
PDS C19 N25 C23 108.000 3.000
PDS HN25 N25 C23 126.000 3.000
PDS N25 C23 C28 132.000 3.000
PDS N25 C23 C18 108.000 3.000
PDS C28 C23 C18 120.000 3.000
PDS C23 C28 H28 120.000 3.000
PDS C23 C28 C31 120.000 3.000
PDS H28 C28 C31 120.000 3.000
PDS C28 C31 H31 120.000 3.000
PDS C28 C31 C29 120.000 3.000
PDS H31 C31 C29 120.000 3.000
PDS C31 C29 H29 120.000 3.000
PDS C31 C29 C24 120.000 3.000
PDS H29 C29 C24 120.000 3.000
PDS C29 C24 H24 120.000 3.000
PDS C29 C24 C18 120.000 3.000
PDS H24 C24 C18 120.000 3.000
PDS C23 C18 C11 108.000 3.000
PDS C23 C18 C24 120.000 3.000
PDS C11 C18 C24 126.000 3.000
PDS C5 C2 C6 108.000 3.000
PDS C5 C2 C1 108.000 3.000
PDS C6 C2 C1 108.000 3.000
PDS C2 C6 O14 108.000 3.000
PDS C2 C6 N13 108.000 3.000
PDS O14 C6 N13 108.000 3.000
PDS C2 C1 C4 108.000 3.000
PDS C2 C1 C3 108.000 3.000
PDS C4 C1 C3 108.000 3.000
PDS C1 C4 C10 126.000 3.000
PDS C1 C4 N9 108.000 3.000
PDS C10 C4 N9 126.000 3.000
PDS C4 C10 H103 109.470 3.000
PDS C4 C10 H102 109.470 3.000
PDS C4 C10 H101 109.470 3.000
PDS H103 C10 H102 109.470 3.000
PDS H103 C10 H101 109.470 3.000
PDS H102 C10 H101 109.470 3.000
PDS C4 N9 C17 126.000 3.000
PDS C4 N9 C7 108.000 3.000
PDS C17 N9 C7 126.000 3.000
PDS N9 C17 H171 109.500 3.000
PDS N9 C17 H172 109.500 3.000
PDS N9 C17 C22 109.500 3.000
PDS H171 C17 H172 107.900 3.000
PDS H171 C17 C22 109.470 3.000
PDS H172 C17 C22 109.470 3.000
PDS C17 C22 H221 109.470 3.000
PDS C17 C22 H222 109.470 3.000
PDS C17 C22 C27 111.000 3.000
PDS H221 C22 H222 107.900 3.000
PDS H221 C22 C27 109.470 3.000
PDS H222 C22 C27 109.470 3.000
PDS C22 C27 H271 109.470 3.000
PDS C22 C27 H272 109.470 3.000
PDS C22 C27 N30 109.470 3.000
PDS H271 C27 H272 107.900 3.000
PDS H271 C27 N30 109.470 3.000
PDS H272 C27 N30 109.470 3.000
PDS C27 N30 C33 109.470 3.000
PDS C27 N30 C32 109.470 3.000
PDS C33 N30 C32 109.470 3.000
PDS N30 C33 H333 109.470 3.000
PDS N30 C33 H332 109.470 3.000
PDS N30 C33 H331 109.470 3.000
PDS H333 C33 H332 109.470 3.000
PDS H333 C33 H331 109.470 3.000
PDS H332 C33 H331 109.470 3.000
PDS N30 C32 H323 109.470 3.000
PDS N30 C32 H322 109.470 3.000
PDS N30 C32 H321 109.470 3.000
PDS H323 C32 H322 109.470 3.000
PDS H323 C32 H321 109.470 3.000
PDS H322 C32 H321 109.470 3.000
PDS N9 C7 C3 108.000 3.000
PDS N9 C7 C15 132.000 3.000
PDS C3 C7 C15 120.000 3.000
PDS C7 C3 C1 108.000 3.000
PDS C7 C3 C8 120.000 3.000
PDS C1 C3 C8 126.000 3.000
PDS C7 C15 H15 120.000 3.000
PDS C7 C15 C21 120.000 3.000
PDS H15 C15 C21 120.000 3.000
PDS C15 C21 H21 120.000 3.000
PDS C15 C21 C16 120.000 3.000
PDS H21 C21 C16 120.000 3.000
PDS C21 C16 H16 120.000 3.000
PDS C21 C16 C8 120.000 3.000
PDS H16 C16 C8 120.000 3.000
PDS C16 C8 H8 120.000 3.000
PDS C16 C8 C3 120.000 3.000
PDS H8 C8 C3 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
PDS CONST_1 O20 C12 N13 C6 180.000 0.000 0
PDS CONST_2 O20 C12 C5 C2 180.000 0.000 0
PDS CONST_3 C12 C5 C11 C19 180.000 0.000 0
PDS CONST_4 C5 C11 C18 C23 180.000 0.000 0
PDS CONST_5 C5 C11 C19 N25 180.000 0.000 0
PDS var_1 C11 C19 C26 H261 -75.975 20.000 1
PDS CONST_6 C11 C19 N25 C23 0.000 0.000 0
PDS CONST_7 C19 N25 C23 C18 0.000 0.000 0
PDS CONST_8 N25 C23 C28 C31 180.000 0.000 0
PDS CONST_9 C23 C28 C31 C29 0.000 0.000 0
PDS CONST_10 C28 C31 C29 C24 0.000 0.000 0
PDS CONST_11 C31 C29 C24 C18 0.000 0.000 0
PDS CONST_12 N25 C23 C18 C11 0.000 0.000 0
PDS CONST_13 C23 C18 C24 C29 0.000 0.000 0
PDS CONST_14 C12 C5 C2 C1 180.000 0.000 0
PDS CONST_15 C5 C2 C6 O14 180.000 0.000 0
PDS CONST_16 C2 C6 N13 C12 0.000 0.000 0
PDS CONST_17 C5 C2 C1 C4 180.000 0.000 0
PDS CONST_18 C2 C1 C3 C7 180.000 0.000 0
PDS CONST_19 C2 C1 C4 N9 180.000 0.000 0
PDS var_2 C1 C4 C10 H101 -69.036 20.000 1
PDS CONST_20 C1 C4 N9 C7 0.000 0.000 0
PDS var_3 C4 N9 C17 C22 89.944 20.000 1
PDS var_4 N9 C17 C22 C27 -179.623 20.000 3
PDS var_5 C17 C22 C27 N30 178.930 20.000 3
PDS var_6 C22 C27 N30 C32 -176.978 20.000 1
PDS var_7 C27 N30 C33 H331 -109.468 20.000 1
PDS var_8 C27 N30 C32 H321 -10.877 20.000 1
PDS CONST_21 C4 N9 C7 C15 180.000 0.000 0
PDS CONST_22 N9 C7 C3 C1 0.000 0.000 0
PDS CONST_23 C7 C3 C8 C16 0.000 0.000 0
PDS CONST_24 N9 C7 C15 C21 180.000 0.000 0
PDS CONST_25 C7 C15 C21 C16 0.000 0.000 0
PDS CONST_26 C15 C21 C16 C8 0.000 0.000 0
PDS CONST_27 C21 C16 C8 C3 0.000 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
PDS chir_01 N30 C27 C32 C33 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
PDS plan-1 C6 0.020
PDS plan-1 O14 0.020
PDS plan-1 N13 0.020
PDS plan-1 C2 0.020
PDS plan-1 C12 0.020
PDS plan-1 C5 0.020
PDS plan-1 HN13 0.020
PDS plan-1 O20 0.020
PDS plan-1 C1 0.020
PDS plan-1 C11 0.020
PDS plan-2 C11 0.020
PDS plan-2 C5 0.020
PDS plan-2 C18 0.020
PDS plan-2 C19 0.020
PDS plan-2 N25 0.020
PDS plan-2 C24 0.020
PDS plan-2 C23 0.020
PDS plan-2 C29 0.020
PDS plan-2 C31 0.020
PDS plan-2 C28 0.020
PDS plan-2 H24 0.020
PDS plan-2 H29 0.020
PDS plan-2 H31 0.020
PDS plan-2 H28 0.020
PDS plan-2 HN25 0.020
PDS plan-2 C26 0.020
PDS plan-3 C1 0.020
PDS plan-3 C2 0.020
PDS plan-3 C3 0.020
PDS plan-3 C4 0.020
PDS plan-3 N9 0.020
PDS plan-3 C8 0.020
PDS plan-3 C7 0.020
PDS plan-3 C16 0.020
PDS plan-3 C15 0.020
PDS plan-3 C21 0.020
PDS plan-3 H8 0.020
PDS plan-3 H16 0.020
PDS plan-3 H15 0.020
PDS plan-3 H21 0.020
PDS plan-3 C17 0.020
PDS plan-3 C10 0.020
# ------------------------------------------------------
|
