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
|
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
APK APK '5'-O-[(S)-{[(5S)-5-AMINO-6-OXOHEXYL]' non-polymer 57 31 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_APK
#
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
APK O1P O O 0.000 0.000 0.000 0.000
APK P P P 0.000 -0.499 0.633 -1.241
APK O2P O OH1 0.000 0.157 -0.097 -2.517
APK HO2P H H 0.000 -0.066 0.198 -3.411
APK NZ N NH1 0.000 -0.077 2.262 -1.248
APK HZ H H 0.000 0.435 2.755 -0.531
APK CE C CH2 0.000 -0.599 2.828 -2.499
APK HE2 H H 0.000 -1.323 2.137 -2.937
APK HE3 H H 0.000 0.225 2.983 -3.199
APK CD C CH2 0.000 -1.281 4.167 -2.208
APK HD2 H H 0.000 -0.556 4.856 -1.769
APK HD3 H H 0.000 -2.103 4.010 -1.506
APK CG C CH2 0.000 -1.825 4.756 -3.512
APK HG2 H H 0.000 -2.548 4.065 -3.949
APK HG3 H H 0.000 -1.002 4.910 -4.212
APK CB C CH2 0.000 -2.507 6.094 -3.220
APK HB2 H H 0.000 -1.782 6.783 -2.782
APK HB3 H H 0.000 -3.330 5.938 -2.519
APK CA C CH1 0.000 -3.050 6.683 -4.523
APK HA H H 0.000 -3.710 5.951 -5.009
APK N N NH2 0.000 -1.932 7.004 -5.420
APK H2 H H 0.000 -1.865 6.565 -6.331
APK H H H 0.000 -1.220 7.666 -5.134
APK C C C1 0.000 -3.827 7.939 -4.221
APK HC H H 0.000 -4.688 7.897 -3.575
APK O O O 0.000 -3.485 8.992 -4.703
APK "O5'" O O2 0.000 -2.102 0.494 -1.308
APK "C5'" C CH2 0.000 -2.608 0.944 -0.050
APK "H5'1" H H 0.000 -2.314 1.984 0.109
APK "H5'2" H H 0.000 -2.196 0.325 0.750
APK "C4'" C CH1 0.000 -4.134 0.836 -0.046
APK "H4'" H H 0.000 -4.548 1.375 -0.910
APK "C3'" C CH1 0.000 -4.698 1.428 1.260
APK "H3'" H H 0.000 -3.881 1.749 1.921
APK "O3'" O OH1 0.000 -5.576 2.522 0.983
APK "HO3'" H H 0.000 -5.965 2.840 1.809
APK "C2'" C CH1 0.000 -5.483 0.252 1.898
APK "H2'" H H 0.000 -4.872 -0.262 2.654
APK "O2'" O OH1 0.000 -6.714 0.708 2.462
APK "HO2'" H H 0.000 -6.529 1.278 3.220
APK "C1'" C CH1 0.000 -5.740 -0.668 0.678
APK "H1'" H H 0.000 -6.605 -0.312 0.101
APK "O4'" O O2 0.000 -4.527 -0.545 -0.098
APK N9 N NR5 0.000 -5.940 -2.055 1.105
APK C4 C CR56 0.000 -7.136 -2.633 1.448
APK N3 N NRD6 0.000 -8.398 -2.218 1.503
APK C2 C CR16 0.000 -9.358 -3.039 1.876
APK HC2 H H 0.000 -10.375 -2.669 1.914
APK N1 N NRD6 0.000 -9.127 -4.297 2.205
APK C6 C CR6 0.000 -7.898 -4.801 2.176
APK N6 N NH2 0.000 -7.666 -6.121 2.524
APK HN62 H H 0.000 -8.434 -6.722 2.807
APK HN61 H H 0.000 -6.725 -6.503 2.500
APK C5 C CR56 0.000 -6.839 -3.965 1.784
APK N7 N NRD5 0.000 -5.502 -4.124 1.640
APK C8 C CR15 0.000 -4.972 -3.005 1.241
APK H8 H H 0.000 -3.918 -2.851 1.046
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
APK O1P n/a P START
APK P O1P "O5'" .
APK O2P P HO2P .
APK HO2P O2P . .
APK NZ P CE .
APK HZ NZ . .
APK CE NZ CD .
APK HE2 CE . .
APK HE3 CE . .
APK CD CE CG .
APK HD2 CD . .
APK HD3 CD . .
APK CG CD CB .
APK HG2 CG . .
APK HG3 CG . .
APK CB CG CA .
APK HB2 CB . .
APK HB3 CB . .
APK CA CB C .
APK HA CA . .
APK N CA H .
APK H2 N . .
APK H N . .
APK C CA O .
APK HC C . .
APK O C . .
APK "O5'" P "C5'" .
APK "C5'" "O5'" "C4'" .
APK "H5'1" "C5'" . .
APK "H5'2" "C5'" . .
APK "C4'" "C5'" "C3'" .
APK "H4'" "C4'" . .
APK "C3'" "C4'" "C2'" .
APK "H3'" "C3'" . .
APK "O3'" "C3'" "HO3'" .
APK "HO3'" "O3'" . .
APK "C2'" "C3'" "C1'" .
APK "H2'" "C2'" . .
APK "O2'" "C2'" "HO2'" .
APK "HO2'" "O2'" . .
APK "C1'" "C2'" N9 .
APK "H1'" "C1'" . .
APK "O4'" "C1'" . .
APK N9 "C1'" C4 .
APK C4 N9 N3 .
APK N3 C4 C2 .
APK C2 N3 N1 .
APK HC2 C2 . .
APK N1 C2 C6 .
APK C6 N1 C5 .
APK N6 C6 HN61 .
APK HN62 N6 . .
APK HN61 N6 . .
APK C5 C6 N7 .
APK N7 C5 C8 .
APK C8 N7 H8 .
APK H8 C8 . END
APK "C4'" "O4'" . ADD
APK N9 C8 . ADD
APK C5 C4 . 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
APK O C double 1.220 0.020
APK C CA single 1.510 0.020
APK HC C single 1.077 0.020
APK N CA single 1.450 0.020
APK CA CB single 1.524 0.020
APK HA CA single 1.099 0.020
APK H N single 1.010 0.020
APK H2 N single 1.010 0.020
APK CB CG single 1.524 0.020
APK HB2 CB single 1.092 0.020
APK HB3 CB single 1.092 0.020
APK CG CD single 1.524 0.020
APK HG2 CG single 1.092 0.020
APK HG3 CG single 1.092 0.020
APK CD CE single 1.524 0.020
APK HD2 CD single 1.092 0.020
APK HD3 CD single 1.092 0.020
APK CE NZ single 1.450 0.020
APK HE2 CE single 1.092 0.020
APK HE3 CE single 1.092 0.020
APK NZ P single 1.750 0.020
APK HZ NZ single 1.010 0.020
APK P O1P double 1.480 0.020
APK O2P P single 1.610 0.020
APK "O5'" P single 1.610 0.020
APK HO2P O2P single 0.967 0.020
APK "C5'" "O5'" single 1.426 0.020
APK "C4'" "C5'" single 1.524 0.020
APK "H5'1" "C5'" single 1.092 0.020
APK "H5'2" "C5'" single 1.092 0.020
APK "C4'" "O4'" single 1.426 0.020
APK "C3'" "C4'" single 1.524 0.020
APK "H4'" "C4'" single 1.099 0.020
APK "O4'" "C1'" single 1.426 0.020
APK "O3'" "C3'" single 1.432 0.020
APK "C2'" "C3'" single 1.524 0.020
APK "H3'" "C3'" single 1.099 0.020
APK "HO3'" "O3'" single 0.967 0.020
APK "O2'" "C2'" single 1.432 0.020
APK "C1'" "C2'" single 1.524 0.020
APK "H2'" "C2'" single 1.099 0.020
APK "HO2'" "O2'" single 0.967 0.020
APK N9 "C1'" single 1.485 0.020
APK "H1'" "C1'" single 1.099 0.020
APK N9 C8 single 1.337 0.020
APK C4 N9 single 1.337 0.020
APK C8 N7 double 1.350 0.020
APK H8 C8 single 1.083 0.020
APK N7 C5 single 1.350 0.020
APK C5 C4 double 1.490 0.020
APK C5 C6 single 1.490 0.020
APK N3 C4 single 1.355 0.020
APK C2 N3 double 1.337 0.020
APK N1 C2 single 1.337 0.020
APK HC2 C2 single 1.083 0.020
APK C6 N1 double 1.350 0.020
APK N6 C6 single 1.355 0.020
APK HN61 N6 single 1.010 0.020
APK HN62 N6 single 1.010 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
APK O1P P O2P 109.500 3.000
APK O1P P NZ 109.500 3.000
APK O1P P "O5'" 109.500 3.000
APK O2P P NZ 109.500 3.000
APK O2P P "O5'" 109.500 3.000
APK NZ P "O5'" 109.500 3.000
APK P O2P HO2P 120.000 3.000
APK P NZ HZ 120.000 3.000
APK P NZ CE 120.000 3.000
APK HZ NZ CE 118.500 3.000
APK NZ CE HE2 109.470 3.000
APK NZ CE HE3 109.470 3.000
APK NZ CE CD 112.000 3.000
APK HE2 CE HE3 107.900 3.000
APK HE2 CE CD 109.470 3.000
APK HE3 CE CD 109.470 3.000
APK CE CD HD2 109.470 3.000
APK CE CD HD3 109.470 3.000
APK CE CD CG 111.000 3.000
APK HD2 CD HD3 107.900 3.000
APK HD2 CD CG 109.470 3.000
APK HD3 CD CG 109.470 3.000
APK CD CG HG2 109.470 3.000
APK CD CG HG3 109.470 3.000
APK CD CG CB 111.000 3.000
APK HG2 CG HG3 107.900 3.000
APK HG2 CG CB 109.470 3.000
APK HG3 CG CB 109.470 3.000
APK CG CB HB2 109.470 3.000
APK CG CB HB3 109.470 3.000
APK CG CB CA 111.000 3.000
APK HB2 CB HB3 107.900 3.000
APK HB2 CB CA 109.470 3.000
APK HB3 CB CA 109.470 3.000
APK CB CA HA 108.340 3.000
APK CB CA N 109.470 3.000
APK CB CA C 109.470 3.000
APK HA CA N 109.470 3.000
APK HA CA C 108.810 3.000
APK N CA C 109.470 3.000
APK CA N H2 120.000 3.000
APK CA N H 120.000 3.000
APK H2 N H 120.000 3.000
APK CA C HC 120.000 3.000
APK CA C O 120.500 3.000
APK HC C O 123.000 3.000
APK P "O5'" "C5'" 120.500 3.000
APK "O5'" "C5'" "H5'1" 109.470 3.000
APK "O5'" "C5'" "H5'2" 109.470 3.000
APK "O5'" "C5'" "C4'" 109.470 3.000
APK "H5'1" "C5'" "H5'2" 107.900 3.000
APK "H5'1" "C5'" "C4'" 109.470 3.000
APK "H5'2" "C5'" "C4'" 109.470 3.000
APK "C5'" "C4'" "H4'" 108.340 3.000
APK "C5'" "C4'" "C3'" 111.000 3.000
APK "C5'" "C4'" "O4'" 109.470 3.000
APK "H4'" "C4'" "C3'" 108.340 3.000
APK "H4'" "C4'" "O4'" 109.470 3.000
APK "C3'" "C4'" "O4'" 109.470 3.000
APK "C4'" "C3'" "H3'" 108.340 3.000
APK "C4'" "C3'" "O3'" 109.470 3.000
APK "C4'" "C3'" "C2'" 111.000 3.000
APK "H3'" "C3'" "O3'" 109.470 3.000
APK "H3'" "C3'" "C2'" 108.340 3.000
APK "O3'" "C3'" "C2'" 109.470 3.000
APK "C3'" "O3'" "HO3'" 109.470 3.000
APK "C3'" "C2'" "H2'" 108.340 3.000
APK "C3'" "C2'" "O2'" 109.470 3.000
APK "C3'" "C2'" "C1'" 111.000 3.000
APK "H2'" "C2'" "O2'" 109.470 3.000
APK "H2'" "C2'" "C1'" 108.340 3.000
APK "O2'" "C2'" "C1'" 109.470 3.000
APK "C2'" "O2'" "HO2'" 109.470 3.000
APK "C2'" "C1'" "H1'" 108.340 3.000
APK "C2'" "C1'" "O4'" 109.470 3.000
APK "C2'" "C1'" N9 109.470 3.000
APK "H1'" "C1'" "O4'" 109.470 3.000
APK "H1'" "C1'" N9 109.470 3.000
APK "O4'" "C1'" N9 109.470 3.000
APK "C1'" "O4'" "C4'" 111.800 3.000
APK "C1'" N9 C4 126.000 3.000
APK "C1'" N9 C8 126.000 3.000
APK C4 N9 C8 108.000 3.000
APK N9 C4 N3 132.000 3.000
APK N9 C4 C5 108.000 3.000
APK N3 C4 C5 120.000 3.000
APK C4 N3 C2 120.000 3.000
APK N3 C2 HC2 120.000 3.000
APK N3 C2 N1 120.000 3.000
APK HC2 C2 N1 120.000 3.000
APK C2 N1 C6 120.000 3.000
APK N1 C6 N6 120.000 3.000
APK N1 C6 C5 120.000 3.000
APK N6 C6 C5 120.000 3.000
APK C6 N6 HN62 120.000 3.000
APK C6 N6 HN61 120.000 3.000
APK HN62 N6 HN61 120.000 3.000
APK C6 C5 N7 132.000 3.000
APK C6 C5 C4 120.000 3.000
APK N7 C5 C4 108.000 3.000
APK C5 N7 C8 108.000 3.000
APK N7 C8 H8 126.000 3.000
APK N7 C8 N9 108.000 3.000
APK H8 C8 N9 126.000 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
APK var_1 O1P P O2P HO2P -179.990 20.000 1
APK var_2 O1P P NZ CE 179.975 20.000 1
APK var_3 P NZ CE CD 134.977 20.000 3
APK var_4 NZ CE CD CG -179.976 20.000 3
APK var_5 CE CD CG CB 180.000 20.000 3
APK var_6 CD CG CB CA 179.970 20.000 3
APK var_7 CG CB CA C 175.010 20.000 3
APK var_8 CB CA N H -59.969 20.000 1
APK var_9 CB CA C O 120.041 20.000 1
APK var_10 O1P P "O5'" "C5'" 49.972 20.000 1
APK var_11 P "O5'" "C5'" "C4'" -179.969 20.000 1
APK var_12 "O5'" "C5'" "C4'" "C3'" -175.307 20.000 3
APK var_13 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
APK var_14 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
APK var_15 "C4'" "C3'" "O3'" "HO3'" 176.179 20.000 1
APK var_16 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
APK var_17 "C3'" "C2'" "O2'" "HO2'" -67.288 20.000 1
APK var_18 "C3'" "C2'" "C1'" N9 150.000 20.000 3
APK var_19 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
APK var_20 "C2'" "C1'" N9 C4 89.091 20.000 1
APK CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
APK CONST_2 "C1'" N9 C4 N3 0.000 0.000 0
APK CONST_3 N9 C4 N3 C2 180.000 0.000 0
APK CONST_4 C4 N3 C2 N1 0.000 0.000 0
APK CONST_5 N3 C2 N1 C6 0.000 0.000 0
APK CONST_6 C2 N1 C6 C5 0.000 0.000 0
APK CONST_7 N1 C6 N6 HN61 179.962 0.000 0
APK CONST_8 N1 C6 C5 N7 180.000 0.000 0
APK CONST_9 C6 C5 C4 N9 180.000 0.000 0
APK CONST_10 C6 C5 N7 C8 180.000 0.000 0
APK CONST_11 C5 N7 C8 N9 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
APK chir_01 CA C N CB negativ
APK chir_02 "C4'" "C5'" "O4'" "C3'" negativ
APK chir_03 "C3'" "C4'" "O3'" "C2'" negativ
APK chir_04 "C2'" "C3'" "O2'" "C1'" negativ
APK chir_05 "C1'" "O4'" "C2'" N9 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
APK plan-1 C 0.020
APK plan-1 O 0.020
APK plan-1 CA 0.020
APK plan-1 HC 0.020
APK plan-2 N 0.020
APK plan-2 CA 0.020
APK plan-2 H 0.020
APK plan-2 H2 0.020
APK plan-3 NZ 0.020
APK plan-3 CE 0.020
APK plan-3 P 0.020
APK plan-3 HZ 0.020
APK plan-4 N9 0.020
APK plan-4 "C1'" 0.020
APK plan-4 C8 0.020
APK plan-4 C4 0.020
APK plan-4 N7 0.020
APK plan-4 H8 0.020
APK plan-4 C5 0.020
APK plan-4 C6 0.020
APK plan-4 N3 0.020
APK plan-4 C2 0.020
APK plan-4 N1 0.020
APK plan-4 HC2 0.020
APK plan-4 N6 0.020
APK plan-4 HN62 0.020
APK plan-4 HN61 0.020
APK plan-5 N6 0.020
APK plan-5 C6 0.020
APK plan-5 HN61 0.020
APK plan-5 HN62 0.020
# ------------------------------------------------------
|
