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
|
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
SON SON 'ADENOSINE PHOSPHONOACETIC ACID ' non-polymer 42 26 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_SON
#
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
SON OA O O -0.500 0.000 0.000 0.000
SON CA C C 0.000 -0.849 0.202 0.896
SON CB C CH2 0.000 -0.576 1.217 1.976
SON HB1 H H 0.000 0.470 1.150 2.282
SON HB2 H H 0.000 -1.219 1.016 2.835
SON PB P P 0.000 -0.919 2.890 1.337
SON O2B O OH1 0.000 -2.488 3.029 1.009
SON H2B H H 0.000 -3.142 2.909 1.712
SON O3B O OH1 0.000 -0.504 3.983 2.445
SON H3B H H 0.000 -0.622 4.925 2.263
SON O1B O O 0.000 -0.134 3.117 0.103
SON "O5'" O O2 -0.500 -1.924 -0.438 0.896
SON "C5'" C CH2 0.000 -2.264 -1.463 -0.145
SON "H5'1" H H 0.000 -1.494 -2.237 -0.118
SON "H5'2" H H 0.000 -2.249 -0.970 -1.119
SON "C4'" C CH1 0.000 -3.637 -2.098 0.087
SON "H4'" H H 0.000 -3.692 -2.533 1.095
SON "C3'" C CH1 0.000 -3.920 -3.177 -0.982
SON "H3'" H H 0.000 -3.334 -2.982 -1.890
SON "O3'" O OH1 0.000 -3.630 -4.478 -0.468
SON H1 H H 0.000 -3.812 -5.141 -1.148
SON "C2'" C CH1 0.000 -5.432 -3.033 -1.271
SON "H2'" H H 0.000 -5.598 -2.766 -2.325
SON "O2'" O OH1 0.000 -6.123 -4.241 -0.948
SON H3 H H 0.000 -5.784 -4.962 -1.496
SON "C1'" C CH1 0.000 -5.881 -1.880 -0.346
SON "H1'" H H 0.000 -6.283 -2.280 0.596
SON "O4'" O O2 0.000 -4.681 -1.116 -0.095
SON N9 N NR5 0.000 -6.884 -1.049 -1.016
SON C8 C CR15 0.000 -6.643 0.083 -1.735
SON H8 H H 0.000 -5.665 0.516 -1.904
SON N7 N NRD5 0.000 -7.762 0.568 -2.190
SON C5 C CR56 0.000 -8.789 -0.223 -1.796
SON C4 C CR56 0.000 -8.239 -1.267 -1.033
SON C6 C CR6 0.000 -10.183 -0.195 -1.974
SON N6 N NH2 0.000 -10.782 0.812 -2.711
SON HN62 H H 0.000 -10.221 1.547 -3.131
SON HN61 H H 0.000 -11.789 0.826 -2.841
SON N1 N NRD6 0.000 -10.911 -1.160 -1.424
SON C2 C CR16 0.000 -10.348 -2.124 -0.718
SON H2 H H 0.000 -10.979 -2.890 -0.286
SON N3 N NRD6 0.000 -9.048 -2.189 -0.521
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
SON OA n/a CA START
SON CA OA "O5'" .
SON CB CA PB .
SON HB1 CB . .
SON HB2 CB . .
SON PB CB O1B .
SON O2B PB H2B .
SON H2B O2B . .
SON O3B PB H3B .
SON H3B O3B . .
SON O1B PB . .
SON "O5'" CA "C5'" .
SON "C5'" "O5'" "C4'" .
SON "H5'1" "C5'" . .
SON "H5'2" "C5'" . .
SON "C4'" "C5'" "C3'" .
SON "H4'" "C4'" . .
SON "C3'" "C4'" "C2'" .
SON "H3'" "C3'" . .
SON "O3'" "C3'" H1 .
SON H1 "O3'" . .
SON "C2'" "C3'" "C1'" .
SON "H2'" "C2'" . .
SON "O2'" "C2'" H3 .
SON H3 "O2'" . .
SON "C1'" "C2'" N9 .
SON "H1'" "C1'" . .
SON "O4'" "C1'" . .
SON N9 "C1'" C8 .
SON C8 N9 N7 .
SON H8 C8 . .
SON N7 C8 C5 .
SON C5 N7 C6 .
SON C4 C5 . .
SON C6 C5 N1 .
SON N6 C6 HN61 .
SON HN62 N6 . .
SON HN61 N6 . .
SON N1 C6 C2 .
SON C2 N1 N3 .
SON H2 C2 . .
SON N3 C2 . END
SON "C4'" "O4'" . ADD
SON N9 C4 . ADD
SON 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
SON O1B PB double 1.480 0.020
SON O2B PB single 1.610 0.020
SON O3B PB single 1.610 0.020
SON PB CB single 1.812 0.020
SON H2B O2B single 0.967 0.020
SON H3B O3B single 0.967 0.020
SON CB CA single 1.510 0.020
SON HB1 CB single 1.092 0.020
SON HB2 CB single 1.092 0.020
SON CA OA deloc 1.220 0.020
SON "O5'" CA deloc 1.454 0.020
SON "C5'" "O5'" single 1.426 0.020
SON "C4'" "C5'" single 1.524 0.020
SON "H5'1" "C5'" single 1.092 0.020
SON "H5'2" "C5'" single 1.092 0.020
SON "C4'" "O4'" single 1.426 0.020
SON "C3'" "C4'" single 1.524 0.020
SON "H4'" "C4'" single 1.099 0.020
SON "O4'" "C1'" single 1.426 0.020
SON N9 "C1'" single 1.485 0.020
SON "C1'" "C2'" single 1.524 0.020
SON "H1'" "C1'" single 1.099 0.020
SON N9 C4 single 1.337 0.020
SON C8 N9 single 1.337 0.020
SON C4 N3 double 1.355 0.020
SON C4 C5 single 1.490 0.020
SON N3 C2 single 1.337 0.020
SON C2 N1 double 1.337 0.020
SON H2 C2 single 1.083 0.020
SON N1 C6 single 1.350 0.020
SON N6 C6 single 1.355 0.020
SON C6 C5 double 1.490 0.020
SON HN61 N6 single 1.010 0.020
SON HN62 N6 single 1.010 0.020
SON C5 N7 single 1.350 0.020
SON N7 C8 double 1.350 0.020
SON H8 C8 single 1.083 0.020
SON "O2'" "C2'" single 1.432 0.020
SON "C2'" "C3'" single 1.524 0.020
SON "H2'" "C2'" single 1.099 0.020
SON H3 "O2'" single 0.967 0.020
SON "O3'" "C3'" single 1.432 0.020
SON "H3'" "C3'" single 1.099 0.020
SON H1 "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
SON OA CA CB 120.500 3.000
SON OA CA "O5'" 119.000 3.000
SON CB CA "O5'" 120.000 3.000
SON CA CB HB1 109.470 3.000
SON CA CB HB2 109.470 3.000
SON CA CB PB 109.500 3.000
SON HB1 CB HB2 107.900 3.000
SON HB1 CB PB 109.500 3.000
SON HB2 CB PB 109.500 3.000
SON CB PB O3B 109.500 3.000
SON CB PB O2B 109.500 3.000
SON CB PB O1B 109.500 3.000
SON O3B PB O2B 109.500 3.000
SON O3B PB O1B 109.500 3.000
SON O2B PB O1B 109.500 3.000
SON PB O3B H3B 120.000 3.000
SON PB O2B H2B 120.000 3.000
SON CA "O5'" "C5'" 120.000 3.000
SON "O5'" "C5'" "H5'1" 109.470 3.000
SON "O5'" "C5'" "H5'2" 109.470 3.000
SON "O5'" "C5'" "C4'" 109.470 3.000
SON "H5'1" "C5'" "H5'2" 107.900 3.000
SON "H5'1" "C5'" "C4'" 109.470 3.000
SON "H5'2" "C5'" "C4'" 109.470 3.000
SON "C5'" "C4'" "H4'" 108.340 3.000
SON "C5'" "C4'" "C3'" 111.000 3.000
SON "C5'" "C4'" "O4'" 109.470 3.000
SON "H4'" "C4'" "C3'" 108.340 3.000
SON "H4'" "C4'" "O4'" 109.470 3.000
SON "C3'" "C4'" "O4'" 109.470 3.000
SON "C4'" "C3'" "H3'" 108.340 3.000
SON "C4'" "C3'" "O3'" 109.470 3.000
SON "C4'" "C3'" "C2'" 111.000 3.000
SON "H3'" "C3'" "O3'" 109.470 3.000
SON "H3'" "C3'" "C2'" 108.340 3.000
SON "O3'" "C3'" "C2'" 109.470 3.000
SON "C3'" "O3'" H1 109.470 3.000
SON "C3'" "C2'" "H2'" 108.340 3.000
SON "C3'" "C2'" "O2'" 109.470 3.000
SON "C3'" "C2'" "C1'" 111.000 3.000
SON "H2'" "C2'" "O2'" 109.470 3.000
SON "H2'" "C2'" "C1'" 108.340 3.000
SON "O2'" "C2'" "C1'" 109.470 3.000
SON "C2'" "O2'" H3 109.470 3.000
SON "C2'" "C1'" "H1'" 108.340 3.000
SON "C2'" "C1'" "O4'" 109.470 3.000
SON "C2'" "C1'" N9 109.470 3.000
SON "H1'" "C1'" "O4'" 109.470 3.000
SON "H1'" "C1'" N9 109.470 3.000
SON "O4'" "C1'" N9 109.470 3.000
SON "C1'" "O4'" "C4'" 111.800 3.000
SON "C1'" N9 C8 126.000 3.000
SON "C1'" N9 C4 126.000 3.000
SON C8 N9 C4 108.000 3.000
SON N9 C8 H8 126.000 3.000
SON N9 C8 N7 108.000 3.000
SON H8 C8 N7 126.000 3.000
SON C8 N7 C5 108.000 3.000
SON N7 C5 C4 108.000 3.000
SON N7 C5 C6 132.000 3.000
SON C4 C5 C6 120.000 3.000
SON C5 C4 N9 108.000 3.000
SON C5 C4 N3 120.000 3.000
SON N9 C4 N3 132.000 3.000
SON C5 C6 N6 120.000 3.000
SON C5 C6 N1 120.000 3.000
SON N6 C6 N1 120.000 3.000
SON C6 N6 HN62 120.000 3.000
SON C6 N6 HN61 120.000 3.000
SON HN62 N6 HN61 120.000 3.000
SON C6 N1 C2 120.000 3.000
SON N1 C2 H2 120.000 3.000
SON N1 C2 N3 120.000 3.000
SON H2 C2 N3 120.000 3.000
SON 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
SON var_1 OA CA CB PB 80.031 20.000 3
SON var_2 CA CB PB O1B -55.044 20.000 1
SON var_3 CB PB O3B H3B 179.997 20.000 1
SON var_4 CB PB O2B H2B 59.920 20.000 1
SON var_5 OA CA "O5'" "C5'" -0.018 20.000 1
SON var_6 CA "O5'" "C5'" "C4'" -179.980 20.000 1
SON var_7 "O5'" "C5'" "C4'" "C3'" -178.133 20.000 3
SON var_8 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
SON var_9 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
SON var_10 "C4'" "C3'" "O3'" H1 -179.983 20.000 1
SON var_11 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
SON var_12 "C3'" "C2'" "O2'" H3 -61.448 20.000 1
SON var_13 "C3'" "C2'" "C1'" N9 150.000 20.000 3
SON var_14 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
SON var_15 "C2'" "C1'" N9 C8 -93.515 20.000 1
SON CONST_1 "C1'" N9 C4 C5 180.000 0.000 0
SON CONST_2 "C1'" N9 C8 N7 180.000 0.000 0
SON CONST_3 N9 C8 N7 C5 0.000 0.000 0
SON CONST_4 C8 N7 C5 C6 180.000 0.000 0
SON CONST_5 N7 C5 C4 N9 0.000 0.000 0
SON CONST_6 C5 C4 N3 C2 0.000 0.000 0
SON CONST_7 N7 C5 C6 N1 180.000 0.000 0
SON CONST_8 C5 C6 N6 HN61 179.742 0.000 0
SON CONST_9 C5 C6 N1 C2 0.000 0.000 0
SON CONST_10 C6 N1 C2 N3 0.000 0.000 0
SON CONST_11 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
SON chir_01 "C4'" "C5'" "O4'" "C3'" negativ
SON chir_02 "C1'" "O4'" N9 "C2'" negativ
SON chir_03 "C2'" "C1'" "O2'" "C3'" positiv
SON chir_04 "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
SON plan-1 CA 0.020
SON plan-1 CB 0.020
SON plan-1 OA 0.020
SON plan-1 "O5'" 0.020
SON plan-2 N9 0.020
SON plan-2 "C1'" 0.020
SON plan-2 C4 0.020
SON plan-2 C8 0.020
SON plan-2 N7 0.020
SON plan-2 N3 0.020
SON plan-2 C5 0.020
SON plan-2 C2 0.020
SON plan-2 N1 0.020
SON plan-2 C6 0.020
SON plan-2 H2 0.020
SON plan-2 N6 0.020
SON plan-2 H8 0.020
SON plan-2 HN62 0.020
SON plan-2 HN61 0.020
SON plan-3 N6 0.020
SON plan-3 C6 0.020
SON plan-3 HN61 0.020
SON plan-3 HN62 0.020
# ------------------------------------------------------
|
