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
|
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
PSD PSD '5'-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE' non-polymer 52 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PSD
#
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
PSD O1P O O 0.000 0.000 0.000 0.000
PSD P P P 0.000 -0.994 -0.622 0.902
PSD O2P O OH1 0.000 -0.394 -1.994 1.496
PSD HOP2 H H 0.000 -0.921 -2.528 2.107
PSD N10 N NH1 0.000 -1.334 0.404 2.134
PSD HN01 H H 0.000 -0.879 1.304 2.181
PSD C C C 0.000 -2.220 0.047 3.083
PSD O O O 0.000 -2.766 -1.034 3.028
PSD CA C CH1 0.000 -2.532 0.990 4.216
PSD HCA H H 0.000 -2.434 2.033 3.884
PSD N N NH1 0.000 -3.900 0.740 4.739
PSD HN H H 0.000 -4.671 0.290 4.267
PSD CD C CH2 0.000 -3.874 1.302 6.114
PSD HCD1 H H 0.000 -4.648 0.862 6.746
PSD HCD2 H H 0.000 -3.982 2.388 6.109
PSD CG C CH2 0.000 -2.482 0.924 6.664
PSD HCG2 H H 0.000 -2.516 -0.001 7.243
PSD HCG1 H H 0.000 -2.063 1.722 7.281
PSD CB C CH2 0.000 -1.599 0.719 5.416
PSD HCB2 H H 0.000 -0.762 1.420 5.442
PSD HCB1 H H 0.000 -1.216 -0.303 5.404
PSD "O5'" O O2 0.000 -2.342 -0.938 0.079
PSD "C5'" C CH2 0.000 -2.823 0.310 -0.420
PSD "H5'1" H H 0.000 -2.066 0.756 -1.069
PSD "H5'2" H H 0.000 -3.026 0.982 0.416
PSD "C4'" C CH1 0.000 -4.109 0.080 -1.216
PSD "HC'4" H H 0.000 -3.916 -0.584 -2.071
PSD "C3'" C CH1 0.000 -4.692 1.426 -1.702
PSD "HC'3" H H 0.000 -4.353 2.248 -1.055
PSD "O3'" O OH1 0.000 -4.320 1.671 -3.059
PSD "HO'3" H H 0.000 -4.692 2.516 -3.347
PSD "C2'" C CH1 0.000 -6.222 1.237 -1.583
PSD "HC'2" H H 0.000 -6.646 1.966 -0.877
PSD "O2'" O OH1 0.000 -6.843 1.363 -2.863
PSD "HO'2" H H 0.000 -6.680 2.250 -3.213
PSD "C1'" C CH1 0.000 -6.380 -0.198 -1.037
PSD "HC'1" H H 0.000 -6.538 -0.906 -1.862
PSD "O4'" O O2 0.000 -5.133 -0.480 -0.366
PSD N9 N NR5 0.000 -7.495 -0.263 -0.088
PSD C8 C CR15 0.000 -7.427 -0.033 1.252
PSD HC8 H H 0.000 -6.526 0.231 1.792
PSD N7 N NRD5 0.000 -8.603 -0.178 1.789
PSD C5 C CR56 0.000 -9.501 -0.502 0.827
PSD C4 C CR56 0.000 -8.798 -0.568 -0.389
PSD C6 C CR6 0.000 -10.878 -0.782 0.813
PSD N6 N NH2 0.000 -11.620 -0.739 1.981
PSD HN62 H H 0.000 -11.178 -0.507 2.865
PSD HN61 H H 0.000 -12.616 -0.937 1.966
PSD N1 N NRD6 0.000 -11.451 -1.083 -0.347
PSD C2 C CR16 0.000 -10.751 -1.126 -1.465
PSD HC2 H H 0.000 -11.258 -1.376 -2.389
PSD N3 N NRD6 0.000 -9.459 -0.878 -1.499
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
PSD O1P n/a P START
PSD P O1P "O5'" .
PSD O2P P HOP2 .
PSD HOP2 O2P . .
PSD N10 P C .
PSD HN01 N10 . .
PSD C N10 CA .
PSD O C . .
PSD CA C CB .
PSD HCA CA . .
PSD N CA CD .
PSD HN N . .
PSD CD N CG .
PSD HCD1 CD . .
PSD HCD2 CD . .
PSD CG CD HCG1 .
PSD HCG2 CG . .
PSD HCG1 CG . .
PSD CB CA HCB1 .
PSD HCB2 CB . .
PSD HCB1 CB . .
PSD "O5'" P "C5'" .
PSD "C5'" "O5'" "C4'" .
PSD "H5'1" "C5'" . .
PSD "H5'2" "C5'" . .
PSD "C4'" "C5'" "C3'" .
PSD "HC'4" "C4'" . .
PSD "C3'" "C4'" "C2'" .
PSD "HC'3" "C3'" . .
PSD "O3'" "C3'" "HO'3" .
PSD "HO'3" "O3'" . .
PSD "C2'" "C3'" "C1'" .
PSD "HC'2" "C2'" . .
PSD "O2'" "C2'" "HO'2" .
PSD "HO'2" "O2'" . .
PSD "C1'" "C2'" N9 .
PSD "HC'1" "C1'" . .
PSD "O4'" "C1'" . .
PSD N9 "C1'" C8 .
PSD C8 N9 N7 .
PSD HC8 C8 . .
PSD N7 C8 C5 .
PSD C5 N7 C6 .
PSD C4 C5 . .
PSD C6 C5 N1 .
PSD N6 C6 HN61 .
PSD HN62 N6 . .
PSD HN61 N6 . .
PSD N1 C6 C2 .
PSD C2 N1 N3 .
PSD HC2 C2 . .
PSD N3 C2 . END
PSD CB CG . ADD
PSD "C4'" "O4'" . ADD
PSD N9 C4 . ADD
PSD C4 N3 . 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
PSD CB CG single 1.524 0.020
PSD CB CA single 1.524 0.020
PSD HCB1 CB single 1.092 0.020
PSD HCB2 CB single 1.092 0.020
PSD CG CD single 1.524 0.020
PSD HCG1 CG single 1.092 0.020
PSD HCG2 CG single 1.092 0.020
PSD O C double 1.220 0.020
PSD CA C single 1.500 0.020
PSD C N10 single 1.330 0.020
PSD CD N single 1.450 0.020
PSD N CA single 1.450 0.020
PSD HN N single 1.010 0.020
PSD HCD1 CD single 1.092 0.020
PSD HCD2 CD single 1.092 0.020
PSD HCA CA single 1.099 0.020
PSD N10 P single 1.750 0.020
PSD HN01 N10 single 1.010 0.020
PSD P O1P double 1.480 0.020
PSD O2P P single 1.610 0.020
PSD "O5'" P single 1.610 0.020
PSD HOP2 O2P single 0.967 0.020
PSD "C5'" "O5'" single 1.426 0.020
PSD "C4'" "C5'" single 1.524 0.020
PSD "H5'1" "C5'" single 1.092 0.020
PSD "H5'2" "C5'" single 1.092 0.020
PSD "C4'" "O4'" single 1.426 0.020
PSD "C3'" "C4'" single 1.524 0.020
PSD "HC'4" "C4'" single 1.099 0.020
PSD "O4'" "C1'" single 1.426 0.020
PSD N9 "C1'" single 1.485 0.020
PSD "C1'" "C2'" single 1.524 0.020
PSD "HC'1" "C1'" single 1.099 0.020
PSD N9 C4 single 1.337 0.020
PSD C8 N9 single 1.337 0.020
PSD C4 N3 double 1.355 0.020
PSD C4 C5 single 1.490 0.020
PSD N3 C2 single 1.337 0.020
PSD C2 N1 double 1.337 0.020
PSD HC2 C2 single 1.083 0.020
PSD N1 C6 single 1.350 0.020
PSD N6 C6 single 1.355 0.020
PSD C6 C5 double 1.490 0.020
PSD HN61 N6 single 1.010 0.020
PSD HN62 N6 single 1.010 0.020
PSD C5 N7 single 1.350 0.020
PSD N7 C8 double 1.350 0.020
PSD HC8 C8 single 1.083 0.020
PSD "O2'" "C2'" single 1.432 0.020
PSD "C2'" "C3'" single 1.524 0.020
PSD "HC'2" "C2'" single 1.099 0.020
PSD "HO'2" "O2'" single 0.967 0.020
PSD "O3'" "C3'" single 1.432 0.020
PSD "HC'3" "C3'" single 1.099 0.020
PSD "HO'3" "O3'" single 0.967 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
PSD O1P P O2P 109.500 3.000
PSD O1P P N10 109.500 3.000
PSD O1P P "O5'" 109.500 3.000
PSD O2P P N10 109.500 3.000
PSD O2P P "O5'" 109.500 3.000
PSD N10 P "O5'" 109.500 3.000
PSD P O2P HOP2 120.000 3.000
PSD P N10 HN01 120.000 3.000
PSD P N10 C 120.000 3.000
PSD HN01 N10 C 120.000 3.000
PSD N10 C O 123.000 3.000
PSD N10 C CA 116.500 3.000
PSD O C CA 120.500 3.000
PSD C CA HCA 108.810 3.000
PSD C CA N 111.600 3.000
PSD C CA CB 109.470 3.000
PSD HCA CA N 108.550 3.000
PSD HCA CA CB 108.340 3.000
PSD N CA CB 110.000 3.000
PSD CA N HN 118.500 3.000
PSD CA N CD 120.000 3.000
PSD HN N CD 118.500 3.000
PSD N CD HCD1 109.470 3.000
PSD N CD HCD2 109.470 3.000
PSD N CD CG 112.000 3.000
PSD HCD1 CD HCD2 107.900 3.000
PSD HCD1 CD CG 109.470 3.000
PSD HCD2 CD CG 109.470 3.000
PSD CD CG HCG2 109.470 3.000
PSD CD CG HCG1 109.470 3.000
PSD CD CG CB 111.000 3.000
PSD HCG2 CG HCG1 107.900 3.000
PSD HCG2 CG CB 109.470 3.000
PSD HCG1 CG CB 109.470 3.000
PSD CA CB HCB2 109.470 3.000
PSD CA CB HCB1 109.470 3.000
PSD CA CB CG 111.000 3.000
PSD HCB2 CB HCB1 107.900 3.000
PSD HCB2 CB CG 109.470 3.000
PSD HCB1 CB CG 109.470 3.000
PSD P "O5'" "C5'" 120.500 3.000
PSD "O5'" "C5'" "H5'1" 109.470 3.000
PSD "O5'" "C5'" "H5'2" 109.470 3.000
PSD "O5'" "C5'" "C4'" 109.470 3.000
PSD "H5'1" "C5'" "H5'2" 107.900 3.000
PSD "H5'1" "C5'" "C4'" 109.470 3.000
PSD "H5'2" "C5'" "C4'" 109.470 3.000
PSD "C5'" "C4'" "HC'4" 108.340 3.000
PSD "C5'" "C4'" "C3'" 111.000 3.000
PSD "C5'" "C4'" "O4'" 109.470 3.000
PSD "HC'4" "C4'" "C3'" 108.340 3.000
PSD "HC'4" "C4'" "O4'" 109.470 3.000
PSD "C3'" "C4'" "O4'" 109.470 3.000
PSD "C4'" "C3'" "HC'3" 108.340 3.000
PSD "C4'" "C3'" "O3'" 109.470 3.000
PSD "C4'" "C3'" "C2'" 111.000 3.000
PSD "HC'3" "C3'" "O3'" 109.470 3.000
PSD "HC'3" "C3'" "C2'" 108.340 3.000
PSD "O3'" "C3'" "C2'" 109.470 3.000
PSD "C3'" "O3'" "HO'3" 109.470 3.000
PSD "C3'" "C2'" "HC'2" 108.340 3.000
PSD "C3'" "C2'" "O2'" 109.470 3.000
PSD "C3'" "C2'" "C1'" 111.000 3.000
PSD "HC'2" "C2'" "O2'" 109.470 3.000
PSD "HC'2" "C2'" "C1'" 108.340 3.000
PSD "O2'" "C2'" "C1'" 109.470 3.000
PSD "C2'" "O2'" "HO'2" 109.470 3.000
PSD "C2'" "C1'" "HC'1" 108.340 3.000
PSD "C2'" "C1'" "O4'" 109.470 3.000
PSD "C2'" "C1'" N9 109.470 3.000
PSD "HC'1" "C1'" "O4'" 109.470 3.000
PSD "HC'1" "C1'" N9 109.470 3.000
PSD "O4'" "C1'" N9 109.470 3.000
PSD "C1'" "O4'" "C4'" 111.800 3.000
PSD "C1'" N9 C8 126.000 3.000
PSD "C1'" N9 C4 126.000 3.000
PSD C8 N9 C4 108.000 3.000
PSD N9 C8 HC8 126.000 3.000
PSD N9 C8 N7 108.000 3.000
PSD HC8 C8 N7 126.000 3.000
PSD C8 N7 C5 108.000 3.000
PSD N7 C5 C4 108.000 3.000
PSD N7 C5 C6 132.000 3.000
PSD C4 C5 C6 120.000 3.000
PSD C5 C4 N9 108.000 3.000
PSD C5 C4 N3 120.000 3.000
PSD N9 C4 N3 132.000 3.000
PSD C5 C6 N6 120.000 3.000
PSD C5 C6 N1 120.000 3.000
PSD N6 C6 N1 120.000 3.000
PSD C6 N6 HN62 120.000 3.000
PSD C6 N6 HN61 120.000 3.000
PSD HN62 N6 HN61 120.000 3.000
PSD C6 N1 C2 120.000 3.000
PSD N1 C2 HC2 120.000 3.000
PSD N1 C2 N3 120.000 3.000
PSD HC2 C2 N3 120.000 3.000
PSD C2 N3 C4 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
PSD var_1 O1P P O2P HOP2 179.985 20.000 1
PSD var_2 O1P P N10 C 179.989 20.000 1
PSD CONST_1 P N10 C CA 180.000 0.000 0
PSD var_3 N10 C CA CB -91.614 20.000 3
PSD var_4 C CA N CD 150.000 20.000 3
PSD var_5 CA N CD CG -30.000 20.000 3
PSD var_6 N CD CG CB 30.000 20.000 3
PSD var_7 C CA CB CG -150.000 20.000 3
PSD var_8 CA CB CG CD 0.000 20.000 3
PSD var_9 O1P P "O5'" "C5'" -59.994 20.000 1
PSD var_10 P "O5'" "C5'" "C4'" 179.989 20.000 1
PSD var_11 "O5'" "C5'" "C4'" "C3'" 176.859 20.000 3
PSD var_12 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
PSD var_13 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
PSD var_14 "C4'" "C3'" "O3'" "HO'3" 179.998 20.000 1
PSD var_15 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
PSD var_16 "C3'" "C2'" "O2'" "HO'2" -61.478 20.000 1
PSD var_17 "C3'" "C2'" "C1'" N9 150.000 20.000 3
PSD var_18 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
PSD var_19 "C2'" "C1'" N9 C8 -88.515 20.000 1
PSD CONST_2 "C1'" N9 C4 C5 180.000 0.000 0
PSD CONST_3 "C1'" N9 C8 N7 180.000 0.000 0
PSD CONST_4 N9 C8 N7 C5 0.000 0.000 0
PSD CONST_5 C8 N7 C5 C6 180.000 0.000 0
PSD CONST_6 N7 C5 C4 N9 0.000 0.000 0
PSD CONST_7 C5 C4 N3 C2 0.000 0.000 0
PSD CONST_8 N7 C5 C6 N1 180.000 0.000 0
PSD CONST_9 C5 C6 N6 HN61 179.759 0.000 0
PSD CONST_10 C5 C6 N1 C2 0.000 0.000 0
PSD CONST_11 C6 N1 C2 N3 0.000 0.000 0
PSD CONST_12 N1 C2 N3 C4 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
PSD chir_01 CA CB C N negativ
PSD chir_02 "C4'" "C5'" "O4'" "C3'" negativ
PSD chir_03 "C1'" "O4'" N9 "C2'" negativ
PSD chir_04 "C2'" "C1'" "O2'" "C3'" positiv
PSD chir_05 "C3'" "C4'" "C2'" "O3'" 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
PSD plan-1 C 0.020
PSD plan-1 O 0.020
PSD plan-1 CA 0.020
PSD plan-1 N10 0.020
PSD plan-1 HN01 0.020
PSD plan-2 N 0.020
PSD plan-2 CD 0.020
PSD plan-2 CA 0.020
PSD plan-2 HN 0.020
PSD plan-3 N10 0.020
PSD plan-3 C 0.020
PSD plan-3 P 0.020
PSD plan-3 HN01 0.020
PSD plan-4 N9 0.020
PSD plan-4 "C1'" 0.020
PSD plan-4 C4 0.020
PSD plan-4 C8 0.020
PSD plan-4 N7 0.020
PSD plan-4 N3 0.020
PSD plan-4 C5 0.020
PSD plan-4 C2 0.020
PSD plan-4 N1 0.020
PSD plan-4 C6 0.020
PSD plan-4 HC2 0.020
PSD plan-4 N6 0.020
PSD plan-4 HC8 0.020
PSD plan-4 HN62 0.020
PSD plan-4 HN61 0.020
PSD plan-5 N6 0.020
PSD plan-5 C6 0.020
PSD plan-5 HN61 0.020
PSD plan-5 HN62 0.020
# ------------------------------------------------------
|
