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
|
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
AHX AHX 'SERYL-HYDROXAMATE-ADENOSINE MONOPHOS' non-polymer 49 30 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AHX
#
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
AHX O2A O OP -0.500 0.000 0.000 0.000
AHX PA P P 0.000 -1.003 -0.058 1.091
AHX O1A O OP -0.500 -1.274 1.313 1.586
AHX O3A O O2 0.000 -0.434 -0.961 2.295
AHX N8 N NH1 0.000 0.759 -0.344 2.742
AHX HN8 H H 0.000 1.084 0.505 2.301
AHX C9 C C 0.000 1.460 -0.888 3.756
AHX O9 O O 0.000 1.069 -1.905 4.286
AHX CA C CH1 0.000 2.730 -0.231 4.231
AHX HA H H 0.000 2.663 0.854 4.070
AHX CB C CH2 0.000 3.919 -0.790 3.447
AHX HB1 H H 0.000 3.780 -0.588 2.383
AHX HB2 H H 0.000 3.984 -1.869 3.606
AHX OG O OH1 0.000 5.123 -0.167 3.899
AHX HOG H H 0.000 5.874 -0.522 3.404
AHX N10 N NH2 0.000 2.916 -0.502 5.663
AHX HN12 H H 0.000 2.194 -0.977 6.191
AHX HN11 H H 0.000 3.768 -0.216 6.131
AHX "O5'" O O2 0.000 -2.367 -0.704 0.532
AHX "C5'" C CH2 0.000 -2.820 0.137 -0.530
AHX "H5'1" H H 0.000 -2.059 0.177 -1.312
AHX "H5'2" H H 0.000 -2.997 1.144 -0.145
AHX "C4'" C CH1 0.000 -4.119 -0.424 -1.109
AHX "H4'" H H 0.000 -3.950 -1.442 -1.487
AHX "C3'" C CH1 0.000 -4.620 0.482 -2.249
AHX "H3'" H H 0.000 -3.963 1.356 -2.361
AHX "O3'" O OH1 0.000 -4.698 -0.244 -3.477
AHX "HO3'" H H 0.000 -5.070 0.325 -4.164
AHX "C2'" C CH1 0.000 -6.034 0.922 -1.788
AHX "H2'" H H 0.000 -6.001 1.912 -1.313
AHX "O2'" O OH1 0.000 -6.953 0.912 -2.882
AHX "HO2'" H H 0.000 -6.709 1.604 -3.513
AHX "C1'" C CH1 0.000 -6.394 -0.175 -0.754
AHX "H1'" H H 0.000 -6.764 -1.077 -1.261
AHX "O4'" O O2 0.000 -5.138 -0.442 -0.095
AHX N9 N NR5 0.000 -7.385 0.320 0.203
AHX C4 C CR56 0.000 -8.746 0.170 0.113
AHX C5 C CR56 0.000 -9.281 0.798 1.250
AHX N7 N NRD5 0.000 -8.239 1.297 1.957
AHX C8 C CR15 0.000 -7.125 1.017 1.345
AHX H8 H H 0.000 -6.137 1.296 1.691
AHX N3 N NRD6 0.000 -9.572 -0.411 -0.750
AHX C2 C CR16 0.000 -10.873 -0.392 -0.553
AHX H2 H H 0.000 -11.518 -0.871 -1.279
AHX N1 N NRD6 0.000 -11.421 0.191 0.497
AHX C6 C CR6 0.000 -10.676 0.793 1.417
AHX N6 N NH2 0.000 -11.260 1.402 2.515
AHX HN62 H H 0.000 -10.687 1.862 3.215
AHX HN61 H H 0.000 -12.269 1.395 2.633
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
AHX O2A n/a PA START
AHX PA O2A "O5'" .
AHX O1A PA . .
AHX O3A PA N8 .
AHX N8 O3A C9 .
AHX HN8 N8 . .
AHX C9 N8 CA .
AHX O9 C9 . .
AHX CA C9 N10 .
AHX HA CA . .
AHX CB CA OG .
AHX HB1 CB . .
AHX HB2 CB . .
AHX OG CB HOG .
AHX HOG OG . .
AHX N10 CA HN11 .
AHX HN12 N10 . .
AHX HN11 N10 . .
AHX "O5'" PA "C5'" .
AHX "C5'" "O5'" "C4'" .
AHX "H5'1" "C5'" . .
AHX "H5'2" "C5'" . .
AHX "C4'" "C5'" "C3'" .
AHX "H4'" "C4'" . .
AHX "C3'" "C4'" "C2'" .
AHX "H3'" "C3'" . .
AHX "O3'" "C3'" "HO3'" .
AHX "HO3'" "O3'" . .
AHX "C2'" "C3'" "C1'" .
AHX "H2'" "C2'" . .
AHX "O2'" "C2'" "HO2'" .
AHX "HO2'" "O2'" . .
AHX "C1'" "C2'" N9 .
AHX "H1'" "C1'" . .
AHX "O4'" "C1'" . .
AHX N9 "C1'" C4 .
AHX C4 N9 N3 .
AHX C5 C4 N7 .
AHX N7 C5 C8 .
AHX C8 N7 H8 .
AHX H8 C8 . .
AHX N3 C4 C2 .
AHX C2 N3 N1 .
AHX H2 C2 . .
AHX N1 C2 C6 .
AHX C6 N1 N6 .
AHX N6 C6 HN61 .
AHX HN62 N6 . .
AHX HN61 N6 . END
AHX "C4'" "O4'" . ADD
AHX N9 C8 . ADD
AHX C5 C6 . 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
AHX N10 CA single 1.450 0.020
AHX HN11 N10 single 1.010 0.020
AHX HN12 N10 single 1.010 0.020
AHX CB CA single 1.524 0.020
AHX CA C9 single 1.500 0.020
AHX HA CA single 1.099 0.020
AHX OG CB single 1.432 0.020
AHX HB1 CB single 1.092 0.020
AHX HB2 CB single 1.092 0.020
AHX HOG OG single 0.967 0.020
AHX O9 C9 double 1.220 0.020
AHX C9 N8 single 1.330 0.020
AHX N8 O3A single 1.335 0.020
AHX HN8 N8 single 1.010 0.020
AHX O1A PA deloc 1.510 0.020
AHX PA O2A deloc 1.510 0.020
AHX O3A PA single 1.610 0.020
AHX "O5'" PA single 1.610 0.020
AHX "C5'" "O5'" single 1.426 0.020
AHX "C4'" "C5'" single 1.524 0.020
AHX "H5'1" "C5'" single 1.092 0.020
AHX "H5'2" "C5'" single 1.092 0.020
AHX "C4'" "O4'" single 1.426 0.020
AHX "C3'" "C4'" single 1.524 0.020
AHX "H4'" "C4'" single 1.099 0.020
AHX "O4'" "C1'" single 1.426 0.020
AHX "O3'" "C3'" single 1.432 0.020
AHX "C2'" "C3'" single 1.524 0.020
AHX "H3'" "C3'" single 1.099 0.020
AHX "HO3'" "O3'" single 0.967 0.020
AHX "O2'" "C2'" single 1.432 0.020
AHX "C1'" "C2'" single 1.524 0.020
AHX "H2'" "C2'" single 1.099 0.020
AHX "HO2'" "O2'" single 0.967 0.020
AHX N9 "C1'" single 1.485 0.020
AHX "H1'" "C1'" single 1.099 0.020
AHX N9 C8 single 1.337 0.020
AHX C4 N9 single 1.337 0.020
AHX C8 N7 double 1.350 0.020
AHX H8 C8 single 1.083 0.020
AHX N7 C5 single 1.350 0.020
AHX C5 C6 single 1.490 0.020
AHX C5 C4 double 1.490 0.020
AHX N6 C6 single 1.355 0.020
AHX C6 N1 double 1.350 0.020
AHX HN61 N6 single 1.010 0.020
AHX HN62 N6 single 1.010 0.020
AHX N1 C2 single 1.337 0.020
AHX C2 N3 double 1.337 0.020
AHX H2 C2 single 1.083 0.020
AHX N3 C4 single 1.355 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
AHX O2A PA O1A 119.900 3.000
AHX O2A PA O3A 108.200 3.000
AHX O2A PA "O5'" 108.200 3.000
AHX O1A PA O3A 108.200 3.000
AHX O1A PA "O5'" 108.200 3.000
AHX O3A PA "O5'" 102.600 3.000
AHX PA O3A N8 120.000 3.000
AHX O3A N8 HN8 120.000 3.000
AHX O3A N8 C9 120.000 3.000
AHX HN8 N8 C9 120.000 3.000
AHX N8 C9 O9 123.000 3.000
AHX N8 C9 CA 116.500 3.000
AHX O9 C9 CA 120.500 3.000
AHX C9 CA HA 108.810 3.000
AHX C9 CA CB 109.470 3.000
AHX C9 CA N10 109.470 3.000
AHX HA CA CB 108.340 3.000
AHX HA CA N10 109.470 3.000
AHX CB CA N10 109.470 3.000
AHX CA CB HB1 109.470 3.000
AHX CA CB HB2 109.470 3.000
AHX CA CB OG 109.470 3.000
AHX HB1 CB HB2 107.900 3.000
AHX HB1 CB OG 109.470 3.000
AHX HB2 CB OG 109.470 3.000
AHX CB OG HOG 109.470 3.000
AHX CA N10 HN12 120.000 3.000
AHX CA N10 HN11 120.000 3.000
AHX HN12 N10 HN11 120.000 3.000
AHX PA "O5'" "C5'" 120.500 3.000
AHX "O5'" "C5'" "H5'1" 109.470 3.000
AHX "O5'" "C5'" "H5'2" 109.470 3.000
AHX "O5'" "C5'" "C4'" 109.470 3.000
AHX "H5'1" "C5'" "H5'2" 107.900 3.000
AHX "H5'1" "C5'" "C4'" 109.470 3.000
AHX "H5'2" "C5'" "C4'" 109.470 3.000
AHX "C5'" "C4'" "H4'" 108.340 3.000
AHX "C5'" "C4'" "C3'" 111.000 3.000
AHX "C5'" "C4'" "O4'" 109.470 3.000
AHX "H4'" "C4'" "C3'" 108.340 3.000
AHX "H4'" "C4'" "O4'" 109.470 3.000
AHX "C3'" "C4'" "O4'" 109.470 3.000
AHX "C4'" "C3'" "H3'" 108.340 3.000
AHX "C4'" "C3'" "O3'" 109.470 3.000
AHX "C4'" "C3'" "C2'" 111.000 3.000
AHX "H3'" "C3'" "O3'" 109.470 3.000
AHX "H3'" "C3'" "C2'" 108.340 3.000
AHX "O3'" "C3'" "C2'" 109.470 3.000
AHX "C3'" "O3'" "HO3'" 109.470 3.000
AHX "C3'" "C2'" "H2'" 108.340 3.000
AHX "C3'" "C2'" "O2'" 109.470 3.000
AHX "C3'" "C2'" "C1'" 111.000 3.000
AHX "H2'" "C2'" "O2'" 109.470 3.000
AHX "H2'" "C2'" "C1'" 108.340 3.000
AHX "O2'" "C2'" "C1'" 109.470 3.000
AHX "C2'" "O2'" "HO2'" 109.470 3.000
AHX "C2'" "C1'" "H1'" 108.340 3.000
AHX "C2'" "C1'" "O4'" 109.470 3.000
AHX "C2'" "C1'" N9 109.470 3.000
AHX "H1'" "C1'" "O4'" 109.470 3.000
AHX "H1'" "C1'" N9 109.470 3.000
AHX "O4'" "C1'" N9 109.470 3.000
AHX "C1'" "O4'" "C4'" 111.800 3.000
AHX "C1'" N9 C4 126.000 3.000
AHX "C1'" N9 C8 126.000 3.000
AHX C4 N9 C8 108.000 3.000
AHX N9 C4 C5 108.000 3.000
AHX N9 C4 N3 132.000 3.000
AHX C5 C4 N3 120.000 3.000
AHX C4 C5 N7 108.000 3.000
AHX C4 C5 C6 120.000 3.000
AHX N7 C5 C6 132.000 3.000
AHX C5 N7 C8 108.000 3.000
AHX N7 C8 H8 126.000 3.000
AHX N7 C8 N9 108.000 3.000
AHX H8 C8 N9 126.000 3.000
AHX C4 N3 C2 120.000 3.000
AHX N3 C2 H2 120.000 3.000
AHX N3 C2 N1 120.000 3.000
AHX H2 C2 N1 120.000 3.000
AHX C2 N1 C6 120.000 3.000
AHX N1 C6 N6 120.000 3.000
AHX N1 C6 C5 120.000 3.000
AHX N6 C6 C5 120.000 3.000
AHX C6 N6 HN62 120.000 3.000
AHX C6 N6 HN61 120.000 3.000
AHX HN62 N6 HN61 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
AHX var_1 O2A PA O3A N8 59.992 20.000 1
AHX var_2 PA O3A N8 C9 179.985 20.000 1
AHX CONST_1 O3A N8 C9 CA 180.000 0.000 0
AHX var_3 N8 C9 CA N10 149.985 20.000 3
AHX var_4 C9 CA CB OG -179.991 20.000 3
AHX var_5 CA CB OG HOG 179.924 20.000 1
AHX var_6 C9 CA N10 HN11 173.819 20.000 1
AHX var_7 O2A PA "O5'" "C5'" -59.959 20.000 1
AHX var_8 PA "O5'" "C5'" "C4'" 179.966 20.000 1
AHX var_9 "O5'" "C5'" "C4'" "C3'" 179.678 20.000 3
AHX var_10 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
AHX var_11 "C5'" "C4'" "C3'" "C2'" -120.000 20.000 3
AHX var_12 "C4'" "C3'" "O3'" "HO3'" 176.244 20.000 1
AHX var_13 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
AHX var_14 "C3'" "C2'" "O2'" "HO2'" -67.337 20.000 1
AHX var_15 "C3'" "C2'" "C1'" N9 150.000 20.000 3
AHX var_16 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
AHX var_17 "C2'" "C1'" N9 C4 94.142 20.000 1
AHX CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
AHX CONST_3 "C1'" N9 C4 N3 0.000 0.000 0
AHX CONST_4 N9 C4 C5 N7 0.000 0.000 0
AHX CONST_5 C4 C5 C6 N1 0.000 0.000 0
AHX CONST_6 C4 C5 N7 C8 0.000 0.000 0
AHX CONST_7 C5 N7 C8 N9 0.000 0.000 0
AHX CONST_8 N9 C4 N3 C2 180.000 0.000 0
AHX CONST_9 C4 N3 C2 N1 0.000 0.000 0
AHX CONST_10 N3 C2 N1 C6 0.000 0.000 0
AHX CONST_11 C2 N1 C6 N6 180.000 0.000 0
AHX CONST_12 N1 C6 N6 HN61 0.113 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
AHX chir_01 CA N10 CB C9 negativ
AHX chir_02 "C4'" "C5'" "O4'" "C3'" negativ
AHX chir_03 "C3'" "C4'" "O3'" "C2'" negativ
AHX chir_04 "C2'" "C3'" "O2'" "C1'" negativ
AHX 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
AHX plan-1 N10 0.020
AHX plan-1 CA 0.020
AHX plan-1 HN11 0.020
AHX plan-1 HN12 0.020
AHX plan-2 C9 0.020
AHX plan-2 CA 0.020
AHX plan-2 O9 0.020
AHX plan-2 N8 0.020
AHX plan-2 HN8 0.020
AHX plan-3 N8 0.020
AHX plan-3 C9 0.020
AHX plan-3 O3A 0.020
AHX plan-3 HN8 0.020
AHX plan-4 N9 0.020
AHX plan-4 "C1'" 0.020
AHX plan-4 C8 0.020
AHX plan-4 C4 0.020
AHX plan-4 N7 0.020
AHX plan-4 H8 0.020
AHX plan-4 C5 0.020
AHX plan-4 C6 0.020
AHX plan-4 N1 0.020
AHX plan-4 C2 0.020
AHX plan-4 N3 0.020
AHX plan-4 N6 0.020
AHX plan-4 H2 0.020
AHX plan-4 HN62 0.020
AHX plan-4 HN61 0.020
AHX plan-5 N6 0.020
AHX plan-5 C6 0.020
AHX plan-5 HN61 0.020
AHX plan-5 HN62 0.020
# ------------------------------------------------------
|
