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
|
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
AQP AQP 'ADENOSINE-5'-TETRAPHOSPHATE ' non-polymer 47 35 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AQP
#
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
AQP O3D O OP -0.666 0.000 0.000 0.000
AQP PD P P 0.000 0.200 0.986 1.130
AQP O2D O OP -0.666 0.633 2.321 0.564
AQP O1D O OP -0.666 1.267 0.469 2.069
AQP O3G O O2 0.000 -1.183 1.168 1.935
AQP PG P P 0.000 -2.360 1.194 0.838
AQP O2G O OP -0.500 -2.357 2.503 0.141
AQP O1G O OP -0.500 -2.141 0.108 -0.148
AQP O3B O O2 0.000 -3.778 0.978 1.568
AQP PB P P 0.000 -4.814 0.488 0.437
AQP O2B O OP -0.500 -5.198 1.639 -0.415
AQP O1B O OP -0.500 -4.174 -0.556 -0.400
AQP O3A O O2 0.000 -6.129 -0.121 1.141
AQP PA P P 0.000 -6.856 -1.048 0.043
AQP O1A O OP -0.500 -6.173 -2.363 -0.022
AQP O2A O OP -0.500 -6.790 -0.389 -1.284
AQP "O5'" O O2 0.000 -8.397 -1.265 0.460
AQP "C5'" C CH2 0.000 -9.014 -1.990 -0.604
AQP "H5'1" H H 0.000 -8.507 -2.950 -0.731
AQP "H5'2" H H 0.000 -8.937 -1.415 -1.529
AQP "C4'" C CH1 0.000 -10.488 -2.230 -0.272
AQP "H4'" H H 0.000 -10.583 -2.743 0.696
AQP "O4'" O O2 0.000 -11.207 -0.979 -0.248
AQP "C3'" C CH1 0.000 -11.167 -3.056 -1.386
AQP "H3'" H H 0.000 -10.629 -2.934 -2.337
AQP "O3'" O OH1 0.000 -11.230 -4.436 -1.020
AQP H1 H H 0.000 -11.657 -4.937 -1.727
AQP "C2'" C CH1 0.000 -12.588 -2.455 -1.487
AQP "H2'" H H 0.000 -12.757 -2.034 -2.488
AQP "O2'" O OH1 0.000 -13.573 -3.446 -1.188
AQP H3 H H 0.000 -13.511 -4.165 -1.830
AQP "C1'" C CH1 0.000 -12.597 -1.335 -0.422
AQP "H1'" H H 0.000 -13.017 -1.708 0.522
AQP N9 N NR5 0.000 -13.363 -0.182 -0.901
AQP C8 C CR15 0.000 -12.861 0.908 -1.546
AQP H8 H H 0.000 -11.817 1.060 -1.790
AQP N7 N NRD5 0.000 -13.821 1.740 -1.827
AQP C5 C CR56 0.000 -14.998 1.235 -1.386
AQP C6 C CR6 0.000 -16.332 1.679 -1.400
AQP N6 N NH2 0.000 -16.669 2.891 -1.976
AQP HN62 H H 0.000 -15.954 3.479 -2.394
AQP HN61 H H 0.000 -17.634 3.206 -1.987
AQP C4 C CR56 0.000 -14.717 -0.002 -0.781
AQP N3 N NRD6 0.000 -15.716 -0.706 -0.258
AQP C2 C CR16 0.000 -16.951 -0.253 -0.299
AQP H2 H H 0.000 -17.741 -0.852 0.135
AQP N1 N NRD6 0.000 -17.263 0.905 -0.851
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
AQP O3D n/a PD START
AQP PD O3D O3G .
AQP O2D PD . .
AQP O1D PD . .
AQP O3G PD PG .
AQP PG O3G O3B .
AQP O2G PG . .
AQP O1G PG . .
AQP O3B PG PB .
AQP PB O3B O3A .
AQP O2B PB . .
AQP O1B PB . .
AQP O3A PB PA .
AQP PA O3A "O5'" .
AQP O1A PA . .
AQP O2A PA . .
AQP "O5'" PA "C5'" .
AQP "C5'" "O5'" "C4'" .
AQP "H5'1" "C5'" . .
AQP "H5'2" "C5'" . .
AQP "C4'" "C5'" "C3'" .
AQP "H4'" "C4'" . .
AQP "O4'" "C4'" . .
AQP "C3'" "C4'" "C2'" .
AQP "H3'" "C3'" . .
AQP "O3'" "C3'" H1 .
AQP H1 "O3'" . .
AQP "C2'" "C3'" "C1'" .
AQP "H2'" "C2'" . .
AQP "O2'" "C2'" H3 .
AQP H3 "O2'" . .
AQP "C1'" "C2'" N9 .
AQP "H1'" "C1'" . .
AQP N9 "C1'" C8 .
AQP C8 N9 N7 .
AQP H8 C8 . .
AQP N7 C8 C5 .
AQP C5 N7 C4 .
AQP C6 C5 N6 .
AQP N6 C6 HN61 .
AQP HN62 N6 . .
AQP HN61 N6 . .
AQP C4 C5 N3 .
AQP N3 C4 C2 .
AQP C2 N3 N1 .
AQP H2 C2 . .
AQP N1 C2 . END
AQP C6 N1 . ADD
AQP C4 N9 . ADD
AQP "C1'" "O4'" . 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
AQP N6 C6 single 1.355 0.020
AQP HN61 N6 single 1.010 0.020
AQP HN62 N6 single 1.010 0.020
AQP C6 N1 double 1.350 0.020
AQP C6 C5 single 1.490 0.020
AQP N1 C2 single 1.337 0.020
AQP C2 N3 double 1.337 0.020
AQP H2 C2 single 1.083 0.020
AQP N3 C4 single 1.355 0.020
AQP C4 N9 single 1.337 0.020
AQP C4 C5 double 1.490 0.020
AQP C8 N9 single 1.337 0.020
AQP N9 "C1'" single 1.485 0.020
AQP N7 C8 double 1.350 0.020
AQP H8 C8 single 1.083 0.020
AQP C5 N7 single 1.350 0.020
AQP "C1'" "O4'" single 1.426 0.020
AQP "C1'" "C2'" single 1.524 0.020
AQP "H1'" "C1'" single 1.099 0.020
AQP "O4'" "C4'" single 1.426 0.020
AQP "C4'" "C5'" single 1.524 0.020
AQP "C3'" "C4'" single 1.524 0.020
AQP "H4'" "C4'" single 1.099 0.020
AQP "C5'" "O5'" single 1.426 0.020
AQP "H5'1" "C5'" single 1.092 0.020
AQP "H5'2" "C5'" single 1.092 0.020
AQP "O5'" PA single 1.610 0.020
AQP O1A PA deloc 1.510 0.020
AQP O2A PA deloc 1.510 0.020
AQP PA O3A single 1.610 0.020
AQP O3A PB single 1.610 0.020
AQP O2B PB deloc 1.510 0.020
AQP O1B PB deloc 1.510 0.020
AQP PB O3B single 1.610 0.020
AQP O3B PG single 1.610 0.020
AQP O2G PG deloc 1.510 0.020
AQP O1G PG deloc 1.510 0.020
AQP PG O3G single 1.610 0.020
AQP O3G PD single 1.610 0.020
AQP O2D PD deloc 1.510 0.020
AQP O1D PD deloc 1.510 0.020
AQP PD O3D deloc 1.510 0.020
AQP "O3'" "C3'" single 1.432 0.020
AQP "C2'" "C3'" single 1.524 0.020
AQP "H3'" "C3'" single 1.099 0.020
AQP H1 "O3'" single 0.967 0.020
AQP "O2'" "C2'" single 1.432 0.020
AQP "H2'" "C2'" single 1.099 0.020
AQP H3 "O2'" 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
AQP O3D PD O2D 119.900 3.000
AQP O3D PD O1D 119.900 3.000
AQP O3D PD O3G 108.200 3.000
AQP O2D PD O1D 119.900 3.000
AQP O2D PD O3G 108.200 3.000
AQP O1D PD O3G 108.200 3.000
AQP PD O3G PG 120.500 3.000
AQP O3G PG O2G 108.200 3.000
AQP O3G PG O1G 108.200 3.000
AQP O3G PG O3B 102.600 3.000
AQP O2G PG O1G 119.900 3.000
AQP O2G PG O3B 108.200 3.000
AQP O1G PG O3B 108.200 3.000
AQP PG O3B PB 120.500 3.000
AQP O3B PB O2B 108.200 3.000
AQP O3B PB O1B 108.200 3.000
AQP O3B PB O3A 102.600 3.000
AQP O2B PB O1B 119.900 3.000
AQP O2B PB O3A 108.200 3.000
AQP O1B PB O3A 108.200 3.000
AQP PB O3A PA 120.500 3.000
AQP O3A PA O1A 108.200 3.000
AQP O3A PA O2A 108.200 3.000
AQP O3A PA "O5'" 102.600 3.000
AQP O1A PA O2A 119.900 3.000
AQP O1A PA "O5'" 108.200 3.000
AQP O2A PA "O5'" 108.200 3.000
AQP PA "O5'" "C5'" 120.500 3.000
AQP "O5'" "C5'" "H5'1" 109.470 3.000
AQP "O5'" "C5'" "H5'2" 109.470 3.000
AQP "O5'" "C5'" "C4'" 109.470 3.000
AQP "H5'1" "C5'" "H5'2" 107.900 3.000
AQP "H5'1" "C5'" "C4'" 109.470 3.000
AQP "H5'2" "C5'" "C4'" 109.470 3.000
AQP "C5'" "C4'" "H4'" 108.340 3.000
AQP "C5'" "C4'" "O4'" 109.470 3.000
AQP "C5'" "C4'" "C3'" 111.000 3.000
AQP "H4'" "C4'" "O4'" 109.470 3.000
AQP "H4'" "C4'" "C3'" 108.340 3.000
AQP "O4'" "C4'" "C3'" 109.470 3.000
AQP "C4'" "O4'" "C1'" 111.800 3.000
AQP "C4'" "C3'" "H3'" 108.340 3.000
AQP "C4'" "C3'" "O3'" 109.470 3.000
AQP "C4'" "C3'" "C2'" 111.000 3.000
AQP "H3'" "C3'" "O3'" 109.470 3.000
AQP "H3'" "C3'" "C2'" 108.340 3.000
AQP "O3'" "C3'" "C2'" 109.470 3.000
AQP "C3'" "O3'" H1 109.470 3.000
AQP "C3'" "C2'" "H2'" 108.340 3.000
AQP "C3'" "C2'" "O2'" 109.470 3.000
AQP "C3'" "C2'" "C1'" 111.000 3.000
AQP "H2'" "C2'" "O2'" 109.470 3.000
AQP "H2'" "C2'" "C1'" 108.340 3.000
AQP "O2'" "C2'" "C1'" 109.470 3.000
AQP "C2'" "O2'" H3 109.470 3.000
AQP "C2'" "C1'" "H1'" 108.340 3.000
AQP "C2'" "C1'" N9 109.470 3.000
AQP "C2'" "C1'" "O4'" 109.470 3.000
AQP "H1'" "C1'" N9 109.470 3.000
AQP "H1'" "C1'" "O4'" 109.470 3.000
AQP N9 "C1'" "O4'" 109.470 3.000
AQP "C1'" N9 C8 126.000 3.000
AQP "C1'" N9 C4 126.000 3.000
AQP C8 N9 C4 108.000 3.000
AQP N9 C8 H8 126.000 3.000
AQP N9 C8 N7 108.000 3.000
AQP H8 C8 N7 126.000 3.000
AQP C8 N7 C5 108.000 3.000
AQP N7 C5 C6 132.000 3.000
AQP N7 C5 C4 108.000 3.000
AQP C6 C5 C4 120.000 3.000
AQP C5 C6 N6 120.000 3.000
AQP C5 C6 N1 120.000 3.000
AQP N6 C6 N1 120.000 3.000
AQP C6 N6 HN62 120.000 3.000
AQP C6 N6 HN61 120.000 3.000
AQP HN62 N6 HN61 120.000 3.000
AQP C5 C4 N3 120.000 3.000
AQP C5 C4 N9 108.000 3.000
AQP N3 C4 N9 132.000 3.000
AQP C4 N3 C2 120.000 3.000
AQP N3 C2 H2 120.000 3.000
AQP N3 C2 N1 120.000 3.000
AQP H2 C2 N1 120.000 3.000
AQP C2 N1 C6 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
AQP var_1 O3D PD O3G PG -40.003 20.000 1
AQP var_2 PD O3G PG O3B 164.995 20.000 1
AQP var_3 O3G PG O3B PB -159.992 20.000 1
AQP var_4 PG O3B PB O3A 164.981 20.000 1
AQP var_5 O3B PB O3A PA -160.009 20.000 1
AQP var_6 PB O3A PA "O5'" -160.024 20.000 1
AQP var_7 O3A PA "O5'" "C5'" 175.008 20.000 1
AQP var_8 PA "O5'" "C5'" "C4'" -179.944 20.000 1
AQP var_9 "O5'" "C5'" "C4'" "C3'" -178.077 20.000 3
AQP var_10 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
AQP var_11 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
AQP var_12 "C4'" "C3'" "O3'" H1 -180.000 20.000 1
AQP var_13 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
AQP var_14 "C3'" "C2'" "O2'" H3 -61.425 20.000 1
AQP var_15 "C3'" "C2'" "C1'" N9 150.000 20.000 3
AQP var_16 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
AQP var_17 "C2'" "C1'" N9 C8 -93.421 20.000 1
AQP CONST_1 "C1'" N9 C8 N7 180.000 0.000 0
AQP CONST_2 N9 C8 N7 C5 0.000 0.000 0
AQP CONST_3 C8 N7 C5 C4 0.000 0.000 0
AQP CONST_4 N7 C5 C6 N6 0.000 0.000 0
AQP CONST_5 C5 C6 N1 C2 0.000 0.000 0
AQP CONST_6 C5 C6 N6 HN61 179.795 0.000 0
AQP CONST_7 N7 C5 C4 N3 180.000 0.000 0
AQP CONST_8 C5 C4 N9 "C1'" 180.000 0.000 0
AQP CONST_9 C5 C4 N3 C2 0.000 0.000 0
AQP CONST_10 C4 N3 C2 N1 0.000 0.000 0
AQP CONST_11 N3 C2 N1 C6 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
AQP chir_01 "C1'" N9 "O4'" "C2'" positiv
AQP chir_02 "C4'" "O4'" "C5'" "C3'" positiv
AQP chir_03 "C3'" "C4'" "O3'" "C2'" negativ
AQP chir_04 "C2'" "C1'" "C3'" "O2'" negativ
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
AQP plan-1 N6 0.020
AQP plan-1 C6 0.020
AQP plan-1 HN61 0.020
AQP plan-1 HN62 0.020
AQP plan-2 C6 0.020
AQP plan-2 N6 0.020
AQP plan-2 N1 0.020
AQP plan-2 C5 0.020
AQP plan-2 C2 0.020
AQP plan-2 N3 0.020
AQP plan-2 H2 0.020
AQP plan-2 C4 0.020
AQP plan-2 N9 0.020
AQP plan-2 C8 0.020
AQP plan-2 N7 0.020
AQP plan-2 "C1'" 0.020
AQP plan-2 H8 0.020
AQP plan-2 HN62 0.020
AQP plan-2 HN61 0.020
# ------------------------------------------------------
|
