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
|
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
3GP 3GP 'GUANOSINE-3'-MONOPHOSPHATE ' non-polymer 36 24 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_3GP
#
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
3GP O6 O O 0.000 0.000 0.000 0.000
3GP C6 C CR6 0.000 -0.976 -0.497 0.535
3GP N1 N NR16 0.000 -0.838 -1.348 1.574
3GP HN1 H H 0.000 0.111 -1.581 1.929
3GP C2 C CR6 0.000 -1.937 -1.903 2.161
3GP N2 N NH2 0.000 -1.765 -2.769 3.212
3GP HN22 H H 0.000 -0.834 -2.994 3.542
3GP HN21 H H 0.000 -2.568 -3.189 3.665
3GP N3 N NRD6 0.000 -3.156 -1.627 1.754
3GP C4 C CR56 0.000 -3.371 -0.788 0.734
3GP C5 C CR56 0.000 -2.283 -0.192 0.086
3GP N7 N NRD5 0.000 -2.784 0.598 -0.894
3GP C8 C CR15 0.000 -4.082 0.524 -0.887
3GP H8 H H 0.000 -4.740 1.054 -1.564
3GP N9 N NR5 0.000 -4.491 -0.322 0.103
3GP "C1'" C CH1 0.000 -5.878 -0.667 0.429
3GP "H1'" H H 0.000 -5.933 -1.689 0.829
3GP "O4'" O O2 0.000 -6.715 -0.540 -0.739
3GP "C2'" C CH1 0.000 -6.456 0.339 1.446
3GP "H2'" H H 0.000 -5.919 1.296 1.387
3GP "O2'" O OH1 0.000 -6.395 -0.187 2.772
3GP "HO2'" H H 0.000 -5.471 -0.290 3.035
3GP "C3'" C CH1 0.000 -7.927 0.516 1.001
3GP "H3'" H H 0.000 -8.121 1.561 0.721
3GP "O3'" O O2 0.000 -8.818 0.102 2.036
3GP P P P 0.000 -9.782 1.353 2.351
3GP O3P O OP -0.666 -8.946 2.531 2.801
3GP O2P O OP -0.666 -10.755 0.977 3.447
3GP O1P O OP -0.666 -10.548 1.725 1.101
3GP "C4'" C CH1 0.000 -8.060 -0.407 -0.230
3GP "H4'" H H 0.000 -8.454 -1.388 0.069
3GP "C5'" C CH2 0.000 -8.968 0.231 -1.283
3GP "H5'1" H H 0.000 -8.572 1.211 -1.558
3GP "H5'2" H H 0.000 -9.973 0.348 -0.872
3GP "O5'" O OH1 0.000 -9.018 -0.606 -2.440
3GP "HO5'" H H 0.000 -9.592 -0.202 -3.104
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
3GP O6 n/a C6 START
3GP C6 O6 N1 .
3GP N1 C6 C2 .
3GP HN1 N1 . .
3GP C2 N1 N3 .
3GP N2 C2 HN21 .
3GP HN22 N2 . .
3GP HN21 N2 . .
3GP N3 C2 C4 .
3GP C4 N3 N9 .
3GP C5 C4 N7 .
3GP N7 C5 C8 .
3GP C8 N7 H8 .
3GP H8 C8 . .
3GP N9 C4 "C1'" .
3GP "C1'" N9 "C2'" .
3GP "H1'" "C1'" . .
3GP "O4'" "C1'" . .
3GP "C2'" "C1'" "C3'" .
3GP "H2'" "C2'" . .
3GP "O2'" "C2'" "HO2'" .
3GP "HO2'" "O2'" . .
3GP "C3'" "C2'" "C4'" .
3GP "H3'" "C3'" . .
3GP "O3'" "C3'" P .
3GP P "O3'" O1P .
3GP O3P P . .
3GP O2P P . .
3GP O1P P . .
3GP "C4'" "C3'" "C5'" .
3GP "H4'" "C4'" . .
3GP "C5'" "C4'" "O5'" .
3GP "H5'1" "C5'" . .
3GP "H5'2" "C5'" . .
3GP "O5'" "C5'" "HO5'" .
3GP "HO5'" "O5'" . END
3GP "C4'" "O4'" . ADD
3GP N9 C8 . ADD
3GP 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
3GP O1P P deloc 1.510 0.020
3GP O2P P deloc 1.510 0.020
3GP O3P P deloc 1.510 0.020
3GP P "O3'" single 1.610 0.020
3GP "O5'" "C5'" single 1.432 0.020
3GP "HO5'" "O5'" single 0.967 0.020
3GP "C5'" "C4'" single 1.524 0.020
3GP "H5'1" "C5'" single 1.092 0.020
3GP "H5'2" "C5'" single 1.092 0.020
3GP "C4'" "O4'" single 1.426 0.020
3GP "C4'" "C3'" single 1.524 0.020
3GP "H4'" "C4'" single 1.099 0.020
3GP "O4'" "C1'" single 1.426 0.020
3GP "O3'" "C3'" single 1.426 0.020
3GP "C3'" "C2'" single 1.524 0.020
3GP "H3'" "C3'" single 1.099 0.020
3GP "O2'" "C2'" single 1.432 0.020
3GP "C2'" "C1'" single 1.524 0.020
3GP "H2'" "C2'" single 1.099 0.020
3GP "HO2'" "O2'" single 0.967 0.020
3GP "C1'" N9 single 1.485 0.020
3GP "H1'" "C1'" single 1.099 0.020
3GP N9 C8 single 1.337 0.020
3GP N9 C4 single 1.337 0.020
3GP C8 N7 double 1.350 0.020
3GP H8 C8 single 1.083 0.020
3GP N7 C5 single 1.350 0.020
3GP C5 C6 single 1.490 0.020
3GP C5 C4 double 1.490 0.020
3GP C6 O6 double 1.250 0.020
3GP N1 C6 single 1.337 0.020
3GP C2 N1 single 1.337 0.020
3GP HN1 N1 single 1.040 0.020
3GP N2 C2 single 1.355 0.020
3GP N3 C2 double 1.350 0.020
3GP HN21 N2 single 1.010 0.020
3GP HN22 N2 single 1.010 0.020
3GP C4 N3 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
3GP O6 C6 N1 120.000 3.000
3GP O6 C6 C5 120.000 3.000
3GP N1 C6 C5 120.000 3.000
3GP C6 N1 HN1 120.000 3.000
3GP C6 N1 C2 120.000 3.000
3GP HN1 N1 C2 120.000 3.000
3GP N1 C2 N2 120.000 3.000
3GP N1 C2 N3 120.000 3.000
3GP N2 C2 N3 120.000 3.000
3GP C2 N2 HN22 120.000 3.000
3GP C2 N2 HN21 120.000 3.000
3GP HN22 N2 HN21 120.000 3.000
3GP C2 N3 C4 120.000 3.000
3GP N3 C4 C5 120.000 3.000
3GP N3 C4 N9 132.000 3.000
3GP C5 C4 N9 108.000 3.000
3GP C4 C5 N7 108.000 3.000
3GP C4 C5 C6 120.000 3.000
3GP N7 C5 C6 132.000 3.000
3GP C5 N7 C8 108.000 3.000
3GP N7 C8 H8 126.000 3.000
3GP N7 C8 N9 108.000 3.000
3GP H8 C8 N9 126.000 3.000
3GP C4 N9 "C1'" 126.000 3.000
3GP C4 N9 C8 108.000 3.000
3GP "C1'" N9 C8 126.000 3.000
3GP N9 "C1'" "H1'" 109.470 3.000
3GP N9 "C1'" "O4'" 109.470 3.000
3GP N9 "C1'" "C2'" 109.470 3.000
3GP "H1'" "C1'" "O4'" 109.470 3.000
3GP "H1'" "C1'" "C2'" 108.340 3.000
3GP "O4'" "C1'" "C2'" 109.470 3.000
3GP "C1'" "O4'" "C4'" 111.800 3.000
3GP "C1'" "C2'" "H2'" 108.340 3.000
3GP "C1'" "C2'" "O2'" 109.470 3.000
3GP "C1'" "C2'" "C3'" 111.000 3.000
3GP "H2'" "C2'" "O2'" 109.470 3.000
3GP "H2'" "C2'" "C3'" 108.340 3.000
3GP "O2'" "C2'" "C3'" 109.470 3.000
3GP "C2'" "O2'" "HO2'" 109.470 3.000
3GP "C2'" "C3'" "H3'" 108.340 3.000
3GP "C2'" "C3'" "O3'" 109.470 3.000
3GP "C2'" "C3'" "C4'" 111.000 3.000
3GP "H3'" "C3'" "O3'" 109.470 3.000
3GP "H3'" "C3'" "C4'" 108.340 3.000
3GP "O3'" "C3'" "C4'" 109.470 3.000
3GP "C3'" "O3'" P 120.500 3.000
3GP "O3'" P O3P 108.200 3.000
3GP "O3'" P O2P 108.200 3.000
3GP "O3'" P O1P 108.200 3.000
3GP O3P P O2P 119.900 3.000
3GP O3P P O1P 119.900 3.000
3GP O2P P O1P 119.900 3.000
3GP "C3'" "C4'" "H4'" 108.340 3.000
3GP "C3'" "C4'" "C5'" 111.000 3.000
3GP "C3'" "C4'" "O4'" 109.470 3.000
3GP "H4'" "C4'" "C5'" 108.340 3.000
3GP "H4'" "C4'" "O4'" 109.470 3.000
3GP "C5'" "C4'" "O4'" 109.470 3.000
3GP "C4'" "C5'" "H5'1" 109.470 3.000
3GP "C4'" "C5'" "H5'2" 109.470 3.000
3GP "C4'" "C5'" "O5'" 109.470 3.000
3GP "H5'1" "C5'" "H5'2" 107.900 3.000
3GP "H5'1" "C5'" "O5'" 109.470 3.000
3GP "H5'2" "C5'" "O5'" 109.470 3.000
3GP "C5'" "O5'" "HO5'" 109.470 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
3GP CONST_1 O6 C6 N1 C2 180.000 0.000 0
3GP CONST_2 C6 N1 C2 N3 0.000 0.000 0
3GP CONST_3 N1 C2 N2 HN21 179.704 0.000 0
3GP CONST_4 N1 C2 N3 C4 0.000 0.000 0
3GP CONST_5 C2 N3 C4 N9 180.000 0.000 0
3GP CONST_6 N3 C4 C5 N7 180.000 0.000 0
3GP CONST_7 C4 C5 C6 O6 180.000 0.000 0
3GP CONST_8 C4 C5 N7 C8 0.000 0.000 0
3GP CONST_9 C5 N7 C8 N9 0.000 0.000 0
3GP CONST_10 N3 C4 N9 "C1'" 0.000 0.000 0
3GP CONST_11 C4 N9 C8 N7 0.000 0.000 0
3GP var_1 C4 N9 "C1'" "C2'" 91.465 20.000 1
3GP var_2 N9 "C1'" "O4'" "C4'" -150.000 20.000 1
3GP var_3 N9 "C1'" "C2'" "C3'" 150.000 20.000 3
3GP var_4 "C1'" "C2'" "O2'" "HO2'" 65.335 20.000 1
3GP var_5 "C1'" "C2'" "C3'" "C4'" 0.000 20.000 3
3GP var_6 "C2'" "C3'" "O3'" P 123.888 20.000 1
3GP var_7 "C3'" "O3'" P O1P 60.012 20.000 1
3GP var_8 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
3GP var_9 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
3GP var_10 "C3'" "C4'" "C5'" "O5'" 176.900 20.000 3
3GP var_11 "C4'" "C5'" "O5'" "HO5'" 179.991 20.000 1
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
3GP chir_01 "C4'" "C5'" "O4'" "C3'" negativ
3GP chir_02 "C3'" "C4'" "O3'" "C2'" negativ
3GP chir_03 "C2'" "C3'" "O2'" "C1'" negativ
3GP chir_04 "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
3GP plan-1 N9 0.020
3GP plan-1 "C1'" 0.020
3GP plan-1 C8 0.020
3GP plan-1 C4 0.020
3GP plan-1 N7 0.020
3GP plan-1 H8 0.020
3GP plan-1 C5 0.020
3GP plan-1 C6 0.020
3GP plan-1 N1 0.020
3GP plan-1 C2 0.020
3GP plan-1 N3 0.020
3GP plan-1 O6 0.020
3GP plan-1 HN1 0.020
3GP plan-1 N2 0.020
3GP plan-1 HN22 0.020
3GP plan-1 HN21 0.020
3GP plan-2 N2 0.020
3GP plan-2 C2 0.020
3GP plan-2 HN21 0.020
3GP plan-2 HN22 0.020
# ------------------------------------------------------
|
