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
|
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
PS4 PS4 'N-({(2S)-1-[(3R)-3-amino-4-(3-chloro' non-polymer 60 32 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PS4
#
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
PS4 CL6 CL CL 0.000 0.000 0.000 0.000
PS4 C9 C CR6 0.000 -0.707 1.342 0.844
PS4 C7 C CR16 0.000 -1.779 2.021 0.291
PS4 H7 H H 0.000 -2.177 1.715 -0.668
PS4 C11 C CR16 0.000 -0.200 1.734 2.070
PS4 H11 H H 0.000 0.639 1.203 2.504
PS4 C12 C CR16 0.000 -0.763 2.802 2.741
PS4 H12 H H 0.000 -0.364 3.110 3.700
PS4 C10 C CR16 0.000 -1.834 3.479 2.189
PS4 H10 H H 0.000 -2.277 4.315 2.716
PS4 C8 C CR6 0.000 -2.342 3.088 0.964
PS4 C13 C CH2 0.000 -3.509 3.827 0.362
PS4 H13 H H 0.000 -3.445 3.784 -0.727
PS4 H13A H H 0.000 -3.485 4.870 0.685
PS4 C14 C CH1 0.000 -4.816 3.178 0.824
PS4 H14 H H 0.000 -4.800 2.107 0.577
PS4 N21 N NH2 0.000 -4.959 3.343 2.276
PS4 HN2A H H 0.000 -5.721 3.892 2.656
PS4 HN21 H H 0.000 -4.296 2.909 2.908
PS4 C15 C CH2 0.000 -5.995 3.848 0.115
PS4 H15 H H 0.000 -5.843 3.803 -0.965
PS4 H15A H H 0.000 -6.063 4.891 0.430
PS4 C16 C C 0.000 -7.271 3.129 0.475
PS4 O5 O O 0.000 -7.239 2.175 1.225
PS4 N17 N N 0.000 -8.446 3.546 -0.035
PS4 C22 C CH2 0.000 -8.644 4.748 -0.867
PS4 H22 H H 0.000 -8.456 4.544 -1.923
PS4 H22A H H 0.000 -8.011 5.575 -0.539
PS4 C23 C CH2 0.000 -10.133 5.126 -0.669
PS4 H23A H H 0.000 -10.551 5.684 -1.509
PS4 H23 H H 0.000 -10.319 5.672 0.258
PS4 C18 C CH1 0.000 -9.744 2.880 0.147
PS4 H18 H H 0.000 -9.989 2.822 1.217
PS4 C24 C CH2 0.000 -10.803 3.728 -0.590
PS4 H24A H H 0.000 -11.741 3.803 -0.036
PS4 H24 H H 0.000 -11.005 3.362 -1.599
PS4 C19 C CH2 0.000 -9.695 1.473 -0.453
PS4 H19 H H 0.000 -8.885 0.908 0.012
PS4 H19A H H 0.000 -9.518 1.543 -1.528
PS4 N20 N NH1 0.000 -10.969 0.793 -0.210
PS4 HN20 H H 0.000 -11.733 1.292 0.224
PS4 C25 C C 0.000 -11.123 -0.498 -0.564
PS4 O32 O O 0.000 -10.203 -1.099 -1.085
PS4 C28 C CR6 0.000 -12.409 -1.184 -0.318
PS4 C26 C CR16 0.000 -13.467 -0.497 0.280
PS4 H26 H H 0.000 -13.347 0.540 0.567
PS4 C27 C CR16 0.000 -14.665 -1.144 0.505
PS4 H27 H H 0.000 -15.487 -0.612 0.968
PS4 C30 C CR16 0.000 -12.571 -2.522 -0.684
PS4 H30 H H 0.000 -11.755 -3.060 -1.149
PS4 C31 C CR6 0.000 -13.774 -3.156 -0.453
PS4 C29 C CR16 0.000 -14.819 -2.468 0.141
PS4 H29 H H 0.000 -15.762 -2.971 0.321
PS4 S4 S ST 0.000 -13.981 -4.844 -0.914
PS4 O2 O OS 0.000 -13.059 -5.032 -1.977
PS4 O3 O OS 0.000 -15.380 -4.980 -1.125
PS4 C1 C CH3 0.000 -13.465 -5.780 0.552
PS4 H1B H H 0.000 -13.549 -6.834 0.386
PS4 H1A H H 0.000 -12.446 -5.570 0.804
PS4 H1 H H 0.000 -14.069 -5.533 1.400
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
PS4 CL6 n/a C9 START
PS4 C9 CL6 C11 .
PS4 C7 C9 H7 .
PS4 H7 C7 . .
PS4 C11 C9 C12 .
PS4 H11 C11 . .
PS4 C12 C11 C10 .
PS4 H12 C12 . .
PS4 C10 C12 C8 .
PS4 H10 C10 . .
PS4 C8 C10 C13 .
PS4 C13 C8 C14 .
PS4 H13 C13 . .
PS4 H13A C13 . .
PS4 C14 C13 C15 .
PS4 H14 C14 . .
PS4 N21 C14 HN21 .
PS4 HN2A N21 . .
PS4 HN21 N21 . .
PS4 C15 C14 C16 .
PS4 H15 C15 . .
PS4 H15A C15 . .
PS4 C16 C15 N17 .
PS4 O5 C16 . .
PS4 N17 C16 C18 .
PS4 C22 N17 C23 .
PS4 H22 C22 . .
PS4 H22A C22 . .
PS4 C23 C22 H23 .
PS4 H23A C23 . .
PS4 H23 C23 . .
PS4 C18 N17 C19 .
PS4 H18 C18 . .
PS4 C24 C18 H24 .
PS4 H24A C24 . .
PS4 H24 C24 . .
PS4 C19 C18 N20 .
PS4 H19 C19 . .
PS4 H19A C19 . .
PS4 N20 C19 C25 .
PS4 HN20 N20 . .
PS4 C25 N20 C28 .
PS4 O32 C25 . .
PS4 C28 C25 C30 .
PS4 C26 C28 C27 .
PS4 H26 C26 . .
PS4 C27 C26 H27 .
PS4 H27 C27 . .
PS4 C30 C28 C31 .
PS4 H30 C30 . .
PS4 C31 C30 S4 .
PS4 C29 C31 H29 .
PS4 H29 C29 . .
PS4 S4 C31 C1 .
PS4 O2 S4 . .
PS4 O3 S4 . .
PS4 C1 S4 H1 .
PS4 H1B C1 . .
PS4 H1A C1 . .
PS4 H1 C1 . END
PS4 C7 C8 . ADD
PS4 C23 C24 . ADD
PS4 C27 C29 . 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
PS4 C1 S4 single 1.662 0.020
PS4 C7 C8 double 1.390 0.020
PS4 C7 C9 single 1.390 0.020
PS4 C13 C8 single 1.511 0.020
PS4 C8 C10 single 1.390 0.020
PS4 C12 C11 single 1.390 0.020
PS4 C11 C9 double 1.390 0.020
PS4 C10 C12 double 1.390 0.020
PS4 C16 C15 single 1.510 0.020
PS4 C15 C14 single 1.524 0.020
PS4 N17 C16 single 1.330 0.020
PS4 O5 C16 double 1.220 0.020
PS4 C19 C18 single 1.524 0.020
PS4 C24 C18 single 1.524 0.020
PS4 C18 N17 single 1.455 0.020
PS4 N20 C19 single 1.450 0.020
PS4 C23 C24 single 1.524 0.020
PS4 C23 C22 single 1.524 0.020
PS4 C27 C29 double 1.390 0.020
PS4 C27 C26 single 1.390 0.020
PS4 C31 C30 double 1.390 0.020
PS4 C30 C28 single 1.390 0.020
PS4 C29 C31 single 1.390 0.020
PS4 S4 C31 single 1.595 0.020
PS4 O32 C25 double 1.220 0.020
PS4 C28 C25 single 1.500 0.020
PS4 C25 N20 single 1.330 0.020
PS4 C26 C28 double 1.390 0.020
PS4 O2 S4 double 1.436 0.020
PS4 O3 S4 double 1.436 0.020
PS4 C22 N17 single 1.455 0.020
PS4 N21 C14 single 1.450 0.020
PS4 C14 C13 single 1.524 0.020
PS4 C9 CL6 single 1.795 0.020
PS4 H1 C1 single 1.059 0.020
PS4 H1A C1 single 1.059 0.020
PS4 H1B C1 single 1.059 0.020
PS4 H7 C7 single 1.083 0.020
PS4 H11 C11 single 1.083 0.020
PS4 H12 C12 single 1.083 0.020
PS4 H15 C15 single 1.092 0.020
PS4 H15A C15 single 1.092 0.020
PS4 H18 C18 single 1.099 0.020
PS4 H19 C19 single 1.092 0.020
PS4 H19A C19 single 1.092 0.020
PS4 H23 C23 single 1.092 0.020
PS4 H23A C23 single 1.092 0.020
PS4 H24 C24 single 1.092 0.020
PS4 H24A C24 single 1.092 0.020
PS4 H27 C27 single 1.083 0.020
PS4 H30 C30 single 1.083 0.020
PS4 H29 C29 single 1.083 0.020
PS4 H26 C26 single 1.083 0.020
PS4 HN20 N20 single 1.010 0.020
PS4 H22 C22 single 1.092 0.020
PS4 H22A C22 single 1.092 0.020
PS4 H14 C14 single 1.099 0.020
PS4 HN21 N21 single 1.010 0.020
PS4 HN2A N21 single 1.010 0.020
PS4 H13 C13 single 1.092 0.020
PS4 H13A C13 single 1.092 0.020
PS4 H10 C10 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
PS4 CL6 C9 C7 120.000 3.000
PS4 CL6 C9 C11 120.000 3.000
PS4 C7 C9 C11 120.000 3.000
PS4 C9 C7 H7 120.000 3.000
PS4 C9 C7 C8 120.000 3.000
PS4 H7 C7 C8 120.000 3.000
PS4 C9 C11 H11 120.000 3.000
PS4 C9 C11 C12 120.000 3.000
PS4 H11 C11 C12 120.000 3.000
PS4 C11 C12 H12 120.000 3.000
PS4 C11 C12 C10 120.000 3.000
PS4 H12 C12 C10 120.000 3.000
PS4 C12 C10 H10 120.000 3.000
PS4 C12 C10 C8 120.000 3.000
PS4 H10 C10 C8 120.000 3.000
PS4 C10 C8 C13 120.000 3.000
PS4 C10 C8 C7 120.000 3.000
PS4 C13 C8 C7 120.000 3.000
PS4 C8 C13 H13 109.470 3.000
PS4 C8 C13 H13A 109.470 3.000
PS4 C8 C13 C14 109.470 3.000
PS4 H13 C13 H13A 107.900 3.000
PS4 H13 C13 C14 109.470 3.000
PS4 H13A C13 C14 109.470 3.000
PS4 C13 C14 H14 108.340 3.000
PS4 C13 C14 N21 109.470 3.000
PS4 C13 C14 C15 109.470 3.000
PS4 H14 C14 N21 109.470 3.000
PS4 H14 C14 C15 108.340 3.000
PS4 N21 C14 C15 109.470 3.000
PS4 C14 N21 HN2A 120.000 3.000
PS4 C14 N21 HN21 120.000 3.000
PS4 HN2A N21 HN21 120.000 3.000
PS4 C14 C15 H15 109.470 3.000
PS4 C14 C15 H15A 109.470 3.000
PS4 C14 C15 C16 109.470 3.000
PS4 H15 C15 H15A 107.900 3.000
PS4 H15 C15 C16 109.470 3.000
PS4 H15A C15 C16 109.470 3.000
PS4 C15 C16 O5 120.500 3.000
PS4 C15 C16 N17 116.500 3.000
PS4 O5 C16 N17 123.000 3.000
PS4 C16 N17 C22 127.000 3.000
PS4 C16 N17 C18 121.000 3.000
PS4 C22 N17 C18 112.000 3.000
PS4 N17 C22 H22 109.470 3.000
PS4 N17 C22 H22A 109.470 3.000
PS4 N17 C22 C23 105.000 3.000
PS4 H22 C22 H22A 107.900 3.000
PS4 H22 C22 C23 109.470 3.000
PS4 H22A C22 C23 109.470 3.000
PS4 C22 C23 H23A 109.470 3.000
PS4 C22 C23 H23 109.470 3.000
PS4 C22 C23 C24 111.000 3.000
PS4 H23A C23 H23 107.900 3.000
PS4 H23A C23 C24 109.470 3.000
PS4 H23 C23 C24 109.470 3.000
PS4 N17 C18 H18 109.470 3.000
PS4 N17 C18 C24 105.000 3.000
PS4 N17 C18 C19 105.000 3.000
PS4 H18 C18 C24 108.340 3.000
PS4 H18 C18 C19 108.340 3.000
PS4 C24 C18 C19 109.470 3.000
PS4 C18 C24 H24A 109.470 3.000
PS4 C18 C24 H24 109.470 3.000
PS4 C18 C24 C23 111.000 3.000
PS4 H24A C24 H24 107.900 3.000
PS4 H24A C24 C23 109.470 3.000
PS4 H24 C24 C23 109.470 3.000
PS4 C18 C19 H19 109.470 3.000
PS4 C18 C19 H19A 109.470 3.000
PS4 C18 C19 N20 110.000 3.000
PS4 H19 C19 H19A 107.900 3.000
PS4 H19 C19 N20 109.470 3.000
PS4 H19A C19 N20 109.470 3.000
PS4 C19 N20 HN20 118.500 3.000
PS4 C19 N20 C25 121.500 3.000
PS4 HN20 N20 C25 120.000 3.000
PS4 N20 C25 O32 123.000 3.000
PS4 N20 C25 C28 120.000 3.000
PS4 O32 C25 C28 120.500 3.000
PS4 C25 C28 C26 120.000 3.000
PS4 C25 C28 C30 120.000 3.000
PS4 C26 C28 C30 120.000 3.000
PS4 C28 C26 H26 120.000 3.000
PS4 C28 C26 C27 120.000 3.000
PS4 H26 C26 C27 120.000 3.000
PS4 C26 C27 H27 120.000 3.000
PS4 C26 C27 C29 120.000 3.000
PS4 H27 C27 C29 120.000 3.000
PS4 C28 C30 H30 120.000 3.000
PS4 C28 C30 C31 120.000 3.000
PS4 H30 C30 C31 120.000 3.000
PS4 C30 C31 C29 120.000 3.000
PS4 C30 C31 S4 120.000 3.000
PS4 C29 C31 S4 120.000 3.000
PS4 C31 C29 H29 120.000 3.000
PS4 C31 C29 C27 120.000 3.000
PS4 H29 C29 C27 120.000 3.000
PS4 C31 S4 O2 109.500 3.000
PS4 C31 S4 O3 109.500 3.000
PS4 C31 S4 C1 109.500 3.000
PS4 O2 S4 O3 109.500 3.000
PS4 O2 S4 C1 109.500 3.000
PS4 O3 S4 C1 109.500 3.000
PS4 S4 C1 H1B 109.500 3.000
PS4 S4 C1 H1A 109.500 3.000
PS4 S4 C1 H1 109.500 3.000
PS4 H1B C1 H1A 109.470 3.000
PS4 H1B C1 H1 109.470 3.000
PS4 H1A C1 H1 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
PS4 CONST_1 CL6 C9 C7 C8 180.000 0.000 0
PS4 CONST_2 C9 C7 C8 C10 0.000 0.000 0
PS4 CONST_3 CL6 C9 C11 C12 180.000 0.000 0
PS4 CONST_4 C9 C11 C12 C10 0.000 0.000 0
PS4 CONST_5 C11 C12 C10 C8 0.000 0.000 0
PS4 CONST_6 C12 C10 C8 C13 180.000 0.000 0
PS4 var_1 C10 C8 C13 C14 -89.980 20.000 2
PS4 var_2 C8 C13 C14 C15 -174.966 20.000 3
PS4 var_3 C13 C14 N21 HN21 -63.958 20.000 1
PS4 var_4 C13 C14 C15 C16 174.989 20.000 3
PS4 var_5 C14 C15 C16 N17 179.976 20.000 3
PS4 CONST_7 C15 C16 N17 C18 180.000 0.000 0
PS4 var_6 C16 N17 C22 C23 -150.000 20.000 1
PS4 var_7 N17 C22 C23 C24 -30.000 20.000 3
PS4 var_8 C22 C23 C24 C18 30.000 20.000 3
PS4 var_9 C16 N17 C18 C19 -60.000 20.000 3
PS4 var_10 N17 C18 C24 C23 -30.000 20.000 3
PS4 var_11 N17 C18 C19 N20 177.243 20.000 3
PS4 var_12 C18 C19 N20 C25 -175.129 20.000 3
PS4 CONST_8 C19 N20 C25 C28 180.000 0.000 0
PS4 var_13 N20 C25 C28 C30 -179.990 20.000 1
PS4 CONST_9 C25 C28 C26 C27 180.000 0.000 0
PS4 CONST_10 C28 C26 C27 C29 0.000 0.000 0
PS4 CONST_11 C26 C27 C29 C31 0.000 0.000 0
PS4 CONST_12 C25 C28 C30 C31 180.000 0.000 0
PS4 CONST_13 C28 C30 C31 S4 180.000 0.000 0
PS4 CONST_14 C30 C31 C29 C27 0.000 0.000 0
PS4 var_14 C30 C31 S4 C1 89.994 20.000 1
PS4 var_15 C31 S4 C1 H1 60.010 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
PS4 chir_01 C18 C19 C24 N17 positiv
PS4 chir_02 S4 C1 C31 O2 negativ
PS4 chir_03 C14 C15 N21 C13 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
PS4 plan-1 C7 0.020
PS4 plan-1 C8 0.020
PS4 plan-1 C9 0.020
PS4 plan-1 H7 0.020
PS4 plan-1 C11 0.020
PS4 plan-1 C12 0.020
PS4 plan-1 C10 0.020
PS4 plan-1 C13 0.020
PS4 plan-1 H11 0.020
PS4 plan-1 H12 0.020
PS4 plan-1 H10 0.020
PS4 plan-1 CL6 0.020
PS4 plan-2 C16 0.020
PS4 plan-2 C15 0.020
PS4 plan-2 N17 0.020
PS4 plan-2 O5 0.020
PS4 plan-3 C27 0.020
PS4 plan-3 C29 0.020
PS4 plan-3 C26 0.020
PS4 plan-3 H27 0.020
PS4 plan-3 C30 0.020
PS4 plan-3 C31 0.020
PS4 plan-3 C28 0.020
PS4 plan-3 H30 0.020
PS4 plan-3 S4 0.020
PS4 plan-3 C25 0.020
PS4 plan-3 H29 0.020
PS4 plan-3 H26 0.020
PS4 plan-4 C25 0.020
PS4 plan-4 O32 0.020
PS4 plan-4 C28 0.020
PS4 plan-4 N20 0.020
PS4 plan-4 HN20 0.020
PS4 plan-5 N20 0.020
PS4 plan-5 C19 0.020
PS4 plan-5 C25 0.020
PS4 plan-5 HN20 0.020
PS4 plan-6 N17 0.020
PS4 plan-6 C16 0.020
PS4 plan-6 C18 0.020
PS4 plan-6 C22 0.020
PS4 plan-7 N21 0.020
PS4 plan-7 C14 0.020
PS4 plan-7 HN21 0.020
PS4 plan-7 HN2A 0.020
# ------------------------------------------------------
|
