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
|
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
VAR VAR '9-amino-5-(2-aminopyrimidin-4-yl)pyr' non-polymer 33 22 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_VAR
#
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
VAR O1 O OH1 0.000 0.000 0.000 0.000
VAR HO1 H H 0.000 0.260 -0.274 0.890
VAR C1 C CR6 0.000 -1.074 0.828 0.078
VAR C10 C CR56 0.000 -2.380 0.321 0.038
VAR C4 C CR56 0.000 -3.468 1.206 0.126
VAR N1 N NRD6 0.000 -3.248 2.512 0.236
VAR C3 C CR16 0.000 -2.031 3.012 0.272
VAR H3 H H 0.000 -1.903 4.083 0.364
VAR C2 C CR16 0.000 -0.911 2.201 0.195
VAR H2 H H 0.000 0.082 2.634 0.226
VAR C9 C CR5 0.000 -2.945 -1.030 -0.070
VAR C11 C CR6 0.000 -2.197 -2.292 -0.183
VAR N5 N NRD6 0.000 -1.186 -2.408 -1.049
VAR C12 C CR6 0.000 -0.513 -3.543 -1.144
VAR N6 N NH2 0.000 0.535 -3.634 -2.045
VAR HN6A H H 0.000 0.789 -2.838 -2.623
VAR HN6 H H 0.000 1.062 -4.497 -2.138
VAR N7 N NRD6 0.000 -0.820 -4.597 -0.401
VAR C13 C CR16 0.000 -1.815 -4.551 0.474
VAR H13 H H 0.000 -2.054 -5.420 1.075
VAR C14 C CR16 0.000 -2.538 -3.397 0.613
VAR H14 H H 0.000 -3.355 -3.338 1.321
VAR C8 C CR56 0.000 -4.329 -0.877 -0.048
VAR N2 N NR56 0.000 -4.632 0.464 0.069
VAR C7 C CR16 0.000 -5.387 -1.807 -0.122
VAR H7 H H 0.000 -5.183 -2.867 -0.213
VAR C6 C CR16 0.000 -6.668 -1.349 -0.075
VAR H6 H H 0.000 -7.492 -2.049 -0.132
VAR N4 N NRD6 0.000 -6.914 -0.042 0.039
VAR C5 C CR6 0.000 -5.949 0.845 0.110
VAR N3 N NH2 0.000 -6.262 2.176 0.225
VAR HN3A H H 0.000 -7.230 2.473 0.256
VAR HN3 H H 0.000 -5.527 2.871 0.281
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
VAR O1 n/a C1 START
VAR HO1 O1 . .
VAR C1 O1 C10 .
VAR C10 C1 C9 .
VAR C4 C10 N1 .
VAR N1 C4 C3 .
VAR C3 N1 C2 .
VAR H3 C3 . .
VAR C2 C3 H2 .
VAR H2 C2 . .
VAR C9 C10 C8 .
VAR C11 C9 N5 .
VAR N5 C11 C12 .
VAR C12 N5 N7 .
VAR N6 C12 HN6 .
VAR HN6A N6 . .
VAR HN6 N6 . .
VAR N7 C12 C13 .
VAR C13 N7 C14 .
VAR H13 C13 . .
VAR C14 C13 H14 .
VAR H14 C14 . .
VAR C8 C9 C7 .
VAR N2 C8 . .
VAR C7 C8 C6 .
VAR H7 C7 . .
VAR C6 C7 N4 .
VAR H6 C6 . .
VAR N4 C6 C5 .
VAR C5 N4 N3 .
VAR N3 C5 HN3 .
VAR HN3A N3 . .
VAR HN3 N3 . END
VAR C1 C2 . ADD
VAR C4 N2 . ADD
VAR N2 C5 . ADD
VAR C11 C14 . 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
VAR C1 O1 single 1.362 0.020
VAR C1 C2 single 1.390 0.020
VAR C10 C1 double 1.490 0.020
VAR C2 C3 double 1.390 0.020
VAR C3 N1 single 1.337 0.020
VAR N1 C4 double 1.355 0.020
VAR C4 N2 single 1.337 0.020
VAR C4 C10 single 1.490 0.020
VAR N2 C5 single 1.337 0.020
VAR N2 C8 single 1.337 0.020
VAR N3 C5 single 1.355 0.020
VAR C5 N4 double 1.350 0.020
VAR N4 C6 single 1.337 0.020
VAR C6 C7 double 1.390 0.020
VAR C7 C8 single 1.390 0.020
VAR C8 C9 double 1.490 0.020
VAR C9 C10 single 1.490 0.020
VAR C11 C9 single 1.490 0.020
VAR C11 C14 single 1.390 0.020
VAR N5 C11 double 1.350 0.020
VAR C14 C13 double 1.390 0.020
VAR C13 N7 single 1.337 0.020
VAR N7 C12 double 1.350 0.020
VAR C12 N5 single 1.350 0.020
VAR N6 C12 single 1.355 0.020
VAR HO1 O1 single 0.967 0.020
VAR H2 C2 single 1.083 0.020
VAR H3 C3 single 1.083 0.020
VAR HN3 N3 single 1.010 0.020
VAR HN3A N3 single 1.010 0.020
VAR H6 C6 single 1.083 0.020
VAR H7 C7 single 1.083 0.020
VAR H14 C14 single 1.083 0.020
VAR H13 C13 single 1.083 0.020
VAR HN6 N6 single 1.010 0.020
VAR HN6A 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
VAR HO1 O1 C1 109.470 3.000
VAR O1 C1 C10 120.000 3.000
VAR O1 C1 C2 120.000 3.000
VAR C10 C1 C2 120.000 3.000
VAR C1 C10 C4 120.000 3.000
VAR C1 C10 C9 132.000 3.000
VAR C4 C10 C9 108.000 3.000
VAR C10 C4 N1 120.000 3.000
VAR C10 C4 N2 120.000 3.000
VAR N1 C4 N2 120.000 3.000
VAR C4 N1 C3 120.000 3.000
VAR N1 C3 H3 120.000 3.000
VAR N1 C3 C2 120.000 3.000
VAR H3 C3 C2 120.000 3.000
VAR C3 C2 H2 120.000 3.000
VAR C3 C2 C1 120.000 3.000
VAR H2 C2 C1 120.000 3.000
VAR C10 C9 C11 126.000 3.000
VAR C10 C9 C8 108.000 3.000
VAR C11 C9 C8 126.000 3.000
VAR C9 C11 N5 120.000 3.000
VAR C9 C11 C14 120.000 3.000
VAR N5 C11 C14 120.000 3.000
VAR C11 N5 C12 120.000 3.000
VAR N5 C12 N6 120.000 3.000
VAR N5 C12 N7 120.000 3.000
VAR N6 C12 N7 120.000 3.000
VAR C12 N6 HN6A 120.000 3.000
VAR C12 N6 HN6 120.000 3.000
VAR HN6A N6 HN6 120.000 3.000
VAR C12 N7 C13 120.000 3.000
VAR N7 C13 H13 120.000 3.000
VAR N7 C13 C14 120.000 3.000
VAR H13 C13 C14 120.000 3.000
VAR C13 C14 H14 120.000 3.000
VAR C13 C14 C11 120.000 3.000
VAR H14 C14 C11 120.000 3.000
VAR C9 C8 N2 108.000 3.000
VAR C9 C8 C7 126.000 3.000
VAR N2 C8 C7 120.000 3.000
VAR C8 N2 C4 108.000 3.000
VAR C8 N2 C5 120.000 3.000
VAR C4 N2 C5 120.000 3.000
VAR C8 C7 H7 120.000 3.000
VAR C8 C7 C6 120.000 3.000
VAR H7 C7 C6 120.000 3.000
VAR C7 C6 H6 120.000 3.000
VAR C7 C6 N4 120.000 3.000
VAR H6 C6 N4 120.000 3.000
VAR C6 N4 C5 120.000 3.000
VAR N4 C5 N3 120.000 3.000
VAR N4 C5 N2 120.000 3.000
VAR N3 C5 N2 120.000 3.000
VAR C5 N3 HN3A 120.000 3.000
VAR C5 N3 HN3 120.000 3.000
VAR HN3A N3 HN3 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
VAR var_1 HO1 O1 C1 C10 -90.253 20.000 1
VAR CONST_1 O1 C1 C2 C3 180.000 0.000 0
VAR CONST_2 O1 C1 C10 C9 0.000 0.000 0
VAR CONST_3 C1 C10 C4 N1 0.000 0.000 0
VAR CONST_4 C10 C4 N2 C8 0.000 0.000 0
VAR CONST_5 C10 C4 N1 C3 0.000 0.000 0
VAR CONST_6 C4 N1 C3 C2 0.000 0.000 0
VAR CONST_7 N1 C3 C2 C1 0.000 0.000 0
VAR CONST_8 C1 C10 C9 C8 180.000 0.000 0
VAR var_2 C10 C9 C11 N5 -47.185 20.000 1
VAR CONST_9 C9 C11 C14 C13 180.000 0.000 0
VAR CONST_10 C9 C11 N5 C12 180.000 0.000 0
VAR CONST_11 C11 N5 C12 N7 0.000 0.000 0
VAR CONST_12 N5 C12 N6 HN6 -179.649 0.000 0
VAR CONST_13 N5 C12 N7 C13 0.000 0.000 0
VAR CONST_14 C12 N7 C13 C14 0.000 0.000 0
VAR CONST_15 N7 C13 C14 C11 0.000 0.000 0
VAR CONST_16 C10 C9 C8 C7 180.000 0.000 0
VAR CONST_17 C9 C8 N2 C4 0.000 0.000 0
VAR CONST_18 C8 N2 C5 N4 0.000 0.000 0
VAR CONST_19 C9 C8 C7 C6 180.000 0.000 0
VAR CONST_20 C8 C7 C6 N4 0.000 0.000 0
VAR CONST_21 C7 C6 N4 C5 0.000 0.000 0
VAR CONST_22 C6 N4 C5 N3 180.000 0.000 0
VAR CONST_23 N4 C5 N3 HN3 -179.965 0.000 0
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
VAR plan-1 C1 0.020
VAR plan-1 O1 0.020
VAR plan-1 C2 0.020
VAR plan-1 C10 0.020
VAR plan-1 C3 0.020
VAR plan-1 N1 0.020
VAR plan-1 H2 0.020
VAR plan-1 H3 0.020
VAR plan-1 C4 0.020
VAR plan-1 N2 0.020
VAR plan-1 C9 0.020
VAR plan-1 C5 0.020
VAR plan-1 C8 0.020
VAR plan-1 N4 0.020
VAR plan-1 C6 0.020
VAR plan-1 C7 0.020
VAR plan-1 N3 0.020
VAR plan-1 H6 0.020
VAR plan-1 H7 0.020
VAR plan-1 C11 0.020
VAR plan-1 HN3A 0.020
VAR plan-1 HN3 0.020
VAR plan-2 N3 0.020
VAR plan-2 C5 0.020
VAR plan-2 HN3 0.020
VAR plan-2 HN3A 0.020
VAR plan-3 C11 0.020
VAR plan-3 C9 0.020
VAR plan-3 C14 0.020
VAR plan-3 N5 0.020
VAR plan-3 C13 0.020
VAR plan-3 N7 0.020
VAR plan-3 C12 0.020
VAR plan-3 H14 0.020
VAR plan-3 H13 0.020
VAR plan-3 N6 0.020
VAR plan-3 HN6A 0.020
VAR plan-3 HN6 0.020
VAR plan-4 N6 0.020
VAR plan-4 C12 0.020
VAR plan-4 HN6 0.020
VAR plan-4 HN6A 0.020
# ------------------------------------------------------
|
