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
|
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
P2P P2P 'N7-(5'-PHOSPHO-ALPHA-RIBOSYL)-2-HYDR' non-polymer 34 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_P2P
#
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
P2P O3P O OP -0.666 0.000 0.000 0.000
P2P P P P 0.000 -0.851 -1.174 -0.433
P2P O1P O OP -0.666 -0.515 -2.381 0.415
P2P O2P O OP -0.666 -0.575 -1.488 -1.887
P2P "O6'" O O2 0.000 -2.407 -0.804 -0.250
P2P "C5'" C CH2 0.000 -2.604 -0.521 1.137
P2P "H5'1" H H 0.000 -1.968 0.317 1.430
P2P "H5'2" H H 0.000 -2.341 -1.400 1.728
P2P "C4'" C CH1 0.000 -4.070 -0.160 1.380
P2P "H4'" H H 0.000 -4.346 0.731 0.800
P2P "C3'" C CH1 0.000 -4.330 0.077 2.884
P2P "H3'" H H 0.000 -3.583 -0.452 3.492
P2P "O3'" O OH1 0.000 -4.316 1.475 3.180
P2P "HO3'" H H 0.000 -4.510 1.608 4.118
P2P "C2'" C CH1 0.000 -5.737 -0.512 3.123
P2P "H2'" H H 0.000 -5.690 -1.337 3.847
P2P "O2'" O OH1 0.000 -6.635 0.502 3.577
P2P "HO2'" H H 0.000 -6.319 0.859 4.418
P2P "C1'" C CH1 0.000 -6.165 -1.037 1.734
P2P "H1'" H H 0.000 -6.730 -1.973 1.836
P2P "O5'" O O2 0.000 -4.927 -1.272 1.031
P2P N7 N NR5 0.000 -6.967 -0.030 1.035
P2P C8 C CR15 0.000 -6.532 0.822 0.081
P2P H8 H H 0.000 -5.516 0.868 -0.292
P2P C5 C CR56 0.000 -8.312 0.221 1.222
P2P C6 C CR16 0.000 -9.304 -0.294 2.042
P2P H6 H H 0.000 -9.084 -1.093 2.738
P2P N1 N NRD6 0.000 -10.526 0.211 1.956
P2P C2 C CR6 0.000 -10.806 1.191 1.111
P2P O11 O OH1 0.000 -12.073 1.671 1.063
P2P HO11 H H 0.000 -12.580 1.172 0.409
P2P N3 N NRD6 0.000 -9.894 1.717 0.315
P2P C4 C CR56 0.000 -8.638 1.267 0.339
P2P N9 N NRD5 0.000 -7.511 1.581 -0.326
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
P2P O3P n/a P START
P2P P O3P "O6'" .
P2P O1P P . .
P2P O2P P . .
P2P "O6'" P "C5'" .
P2P "C5'" "O6'" "C4'" .
P2P "H5'1" "C5'" . .
P2P "H5'2" "C5'" . .
P2P "C4'" "C5'" "C3'" .
P2P "H4'" "C4'" . .
P2P "C3'" "C4'" "C2'" .
P2P "H3'" "C3'" . .
P2P "O3'" "C3'" "HO3'" .
P2P "HO3'" "O3'" . .
P2P "C2'" "C3'" "C1'" .
P2P "H2'" "C2'" . .
P2P "O2'" "C2'" "HO2'" .
P2P "HO2'" "O2'" . .
P2P "C1'" "C2'" N7 .
P2P "H1'" "C1'" . .
P2P "O5'" "C1'" . .
P2P N7 "C1'" C5 .
P2P C8 N7 H8 .
P2P H8 C8 . .
P2P C5 N7 C6 .
P2P C6 C5 N1 .
P2P H6 C6 . .
P2P N1 C6 C2 .
P2P C2 N1 N3 .
P2P O11 C2 HO11 .
P2P HO11 O11 . .
P2P N3 C2 C4 .
P2P C4 N3 N9 .
P2P N9 C4 . END
P2P "C4'" "O5'" . ADD
P2P C8 N9 . ADD
P2P C4 C5 . 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
P2P O1P P deloc 1.510 0.020
P2P O2P P deloc 1.510 0.020
P2P P O3P deloc 1.510 0.020
P2P "O6'" P single 1.610 0.020
P2P "C5'" "O6'" single 1.426 0.020
P2P "C4'" "C5'" single 1.524 0.020
P2P "H5'1" "C5'" single 1.092 0.020
P2P "H5'2" "C5'" single 1.092 0.020
P2P "C4'" "O5'" single 1.426 0.020
P2P "C3'" "C4'" single 1.524 0.020
P2P "H4'" "C4'" single 1.099 0.020
P2P "O5'" "C1'" single 1.426 0.020
P2P "O3'" "C3'" single 1.432 0.020
P2P "C2'" "C3'" single 1.524 0.020
P2P "H3'" "C3'" single 1.099 0.020
P2P "HO3'" "O3'" single 0.967 0.020
P2P "O2'" "C2'" single 1.432 0.020
P2P "C1'" "C2'" single 1.524 0.020
P2P "H2'" "C2'" single 1.099 0.020
P2P "HO2'" "O2'" single 0.967 0.020
P2P N7 "C1'" single 1.485 0.020
P2P "H1'" "C1'" single 1.099 0.020
P2P C8 N9 double 1.350 0.020
P2P C8 N7 single 1.337 0.020
P2P H8 C8 single 1.083 0.020
P2P N9 C4 single 1.350 0.020
P2P C4 C5 double 1.490 0.020
P2P C4 N3 single 1.355 0.020
P2P C5 N7 single 1.337 0.020
P2P C6 C5 single 1.390 0.020
P2P N3 C2 double 1.350 0.020
P2P C2 N1 single 1.350 0.020
P2P O11 C2 single 1.362 0.020
P2P N1 C6 double 1.337 0.020
P2P H6 C6 single 1.083 0.020
P2P HO11 O11 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
P2P O3P P O1P 119.900 3.000
P2P O3P P O2P 119.900 3.000
P2P O3P P "O6'" 108.200 3.000
P2P O1P P O2P 119.900 3.000
P2P O1P P "O6'" 108.200 3.000
P2P O2P P "O6'" 108.200 3.000
P2P P "O6'" "C5'" 120.500 3.000
P2P "O6'" "C5'" "H5'1" 109.470 3.000
P2P "O6'" "C5'" "H5'2" 109.470 3.000
P2P "O6'" "C5'" "C4'" 109.470 3.000
P2P "H5'1" "C5'" "H5'2" 107.900 3.000
P2P "H5'1" "C5'" "C4'" 109.470 3.000
P2P "H5'2" "C5'" "C4'" 109.470 3.000
P2P "C5'" "C4'" "H4'" 108.340 3.000
P2P "C5'" "C4'" "C3'" 111.000 3.000
P2P "C5'" "C4'" "O5'" 109.470 3.000
P2P "H4'" "C4'" "C3'" 108.340 3.000
P2P "H4'" "C4'" "O5'" 109.470 3.000
P2P "C3'" "C4'" "O5'" 109.470 3.000
P2P "C4'" "C3'" "H3'" 108.340 3.000
P2P "C4'" "C3'" "O3'" 109.470 3.000
P2P "C4'" "C3'" "C2'" 111.000 3.000
P2P "H3'" "C3'" "O3'" 109.470 3.000
P2P "H3'" "C3'" "C2'" 108.340 3.000
P2P "O3'" "C3'" "C2'" 109.470 3.000
P2P "C3'" "O3'" "HO3'" 109.470 3.000
P2P "C3'" "C2'" "H2'" 108.340 3.000
P2P "C3'" "C2'" "O2'" 109.470 3.000
P2P "C3'" "C2'" "C1'" 111.000 3.000
P2P "H2'" "C2'" "O2'" 109.470 3.000
P2P "H2'" "C2'" "C1'" 108.340 3.000
P2P "O2'" "C2'" "C1'" 109.470 3.000
P2P "C2'" "O2'" "HO2'" 109.470 3.000
P2P "C2'" "C1'" "H1'" 108.340 3.000
P2P "C2'" "C1'" "O5'" 109.470 3.000
P2P "C2'" "C1'" N7 109.470 3.000
P2P "H1'" "C1'" "O5'" 109.470 3.000
P2P "H1'" "C1'" N7 109.470 3.000
P2P "O5'" "C1'" N7 109.470 3.000
P2P "C1'" "O5'" "C4'" 111.800 3.000
P2P "C1'" N7 C8 126.000 3.000
P2P "C1'" N7 C5 126.000 3.000
P2P C8 N7 C5 108.000 3.000
P2P N7 C8 H8 126.000 3.000
P2P N7 C8 N9 108.000 3.000
P2P H8 C8 N9 126.000 3.000
P2P N7 C5 C6 132.000 3.000
P2P N7 C5 C4 108.000 3.000
P2P C6 C5 C4 120.000 3.000
P2P C5 C6 H6 120.000 3.000
P2P C5 C6 N1 120.000 3.000
P2P H6 C6 N1 120.000 3.000
P2P C6 N1 C2 120.000 3.000
P2P N1 C2 O11 120.000 3.000
P2P N1 C2 N3 120.000 3.000
P2P O11 C2 N3 120.000 3.000
P2P C2 O11 HO11 109.470 3.000
P2P C2 N3 C4 120.000 3.000
P2P N3 C4 N9 120.000 3.000
P2P N3 C4 C5 120.000 3.000
P2P N9 C4 C5 108.000 3.000
P2P C4 N9 C8 108.000 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
P2P var_1 O3P P "O6'" "C5'" -60.078 20.000 1
P2P var_2 P "O6'" "C5'" "C4'" -179.997 20.000 1
P2P var_3 "O6'" "C5'" "C4'" "C3'" 176.930 20.000 3
P2P var_4 "C5'" "C4'" "O5'" "C1'" 150.000 20.000 1
P2P var_5 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
P2P var_6 "C4'" "C3'" "O3'" "HO3'" 178.098 20.000 1
P2P var_7 "C4'" "C3'" "C2'" "C1'" 0.000 20.000 3
P2P var_8 "C3'" "C2'" "O2'" "HO2'" -61.475 20.000 1
P2P var_9 "C3'" "C2'" "C1'" N7 -90.000 20.000 3
P2P var_10 "C2'" "C1'" "O5'" "C4'" -30.000 20.000 1
P2P var_11 "C2'" "C1'" N7 C5 -80.827 20.000 1
P2P CONST_1 "C1'" N7 C8 N9 180.000 0.000 0
P2P CONST_2 N7 C8 N9 C4 0.000 0.000 0
P2P CONST_3 "C1'" N7 C5 C6 0.000 0.000 0
P2P CONST_4 N7 C5 C6 N1 180.000 0.000 0
P2P CONST_5 C5 C6 N1 C2 0.000 0.000 0
P2P CONST_6 C6 N1 C2 N3 0.000 0.000 0
P2P var_12 N1 C2 O11 HO11 -90.048 20.000 1
P2P CONST_7 N1 C2 N3 C4 0.000 0.000 0
P2P CONST_8 C2 N3 C4 N9 180.000 0.000 0
P2P CONST_9 N3 C4 C5 N7 180.000 0.000 0
P2P CONST_10 N3 C4 N9 C8 180.000 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
P2P chir_01 "C4'" "C5'" "O5'" "C3'" negativ
P2P chir_02 "C3'" "C4'" "O3'" "C2'" negativ
P2P chir_03 "C2'" "C3'" "O2'" "C1'" negativ
P2P chir_04 "C1'" "O5'" "C2'" N7 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
P2P plan-1 C8 0.020
P2P plan-1 N9 0.020
P2P plan-1 N7 0.020
P2P plan-1 H8 0.020
P2P plan-1 C4 0.020
P2P plan-1 C5 0.020
P2P plan-1 N3 0.020
P2P plan-1 C2 0.020
P2P plan-1 N1 0.020
P2P plan-1 C6 0.020
P2P plan-1 "C1'" 0.020
P2P plan-1 O11 0.020
P2P plan-1 H6 0.020
# ------------------------------------------------------
|
