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
|
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
O2C O2C '3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE ' non-polymer 32 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_O2C
#
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
O2C O3P O OP -0.666 0.000 0.000 0.000
O2C P P P 0.000 -0.532 0.533 1.312
O2C O1P O OP -0.666 0.241 0.099 2.539
O2C O2P O OP -0.666 -0.592 2.027 1.083
O2C "O5'" O O2 0.000 -2.084 0.075 1.284
O2C "C5'" C CH2 0.000 -2.876 0.444 0.167
O2C "H5'1" H H 0.000 -2.448 0.021 -0.744
O2C "H5'2" H H 0.000 -2.908 1.532 0.081
O2C "C4'" C CH1 0.000 -4.288 -0.094 0.364
O2C "H4'" H H 0.000 -4.253 -1.185 0.490
O2C "C3'" C CH2 0.000 -5.225 0.258 -0.776
O2C "H3'1" H H 0.000 -6.047 -0.453 -0.882
O2C "H3'2" H H 0.000 -4.707 0.358 -1.732
O2C "C2'" C CH1 0.000 -5.771 1.602 -0.354
O2C "H2'" H H 0.000 -5.063 2.402 -0.613
O2C "O2'" O OH1 0.000 -7.039 1.862 -0.922
O2C "HO'2" H H 0.000 -7.198 1.240 -1.644
O2C "C1'" C CH1 0.000 -5.865 1.444 1.154
O2C "H1'" H H 0.000 -6.851 1.038 1.417
O2C "O4'" O O2 0.000 -4.846 0.511 1.544
O2C N1 N NR6 0.000 -5.658 2.681 1.853
O2C C2 C CR6 0.000 -6.737 3.512 2.243
O2C O2 O O 0.000 -7.902 3.199 1.991
O2C N3 N NRD6 0.000 -6.463 4.691 2.914
O2C C4 C CR6 0.000 -5.233 5.041 3.189
O2C N4 N NH2 0.000 -4.982 6.217 3.857
O2C HN42 H H 0.000 -5.282 7.103 3.466
O2C HN41 H H 0.000 -4.495 6.207 4.746
O2C C5 C CR16 0.000 -4.075 4.195 2.797
O2C H5 H H 0.000 -3.056 4.481 3.024
O2C C6 C CR16 0.000 -4.360 3.066 2.152
O2C H6 H H 0.000 -3.545 2.421 1.848
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
O2C O3P n/a P START
O2C P O3P "O5'" .
O2C O1P P . .
O2C O2P P . .
O2C "O5'" P "C5'" .
O2C "C5'" "O5'" "C4'" .
O2C "H5'1" "C5'" . .
O2C "H5'2" "C5'" . .
O2C "C4'" "C5'" "C3'" .
O2C "H4'" "C4'" . .
O2C "C3'" "C4'" "C2'" .
O2C "H3'1" "C3'" . .
O2C "H3'2" "C3'" . .
O2C "C2'" "C3'" "C1'" .
O2C "H2'" "C2'" . .
O2C "O2'" "C2'" "HO'2" .
O2C "HO'2" "O2'" . .
O2C "C1'" "C2'" N1 .
O2C "H1'" "C1'" . .
O2C "O4'" "C1'" . .
O2C N1 "C1'" C2 .
O2C C2 N1 N3 .
O2C O2 C2 . .
O2C N3 C2 C4 .
O2C C4 N3 C5 .
O2C N4 C4 HN41 .
O2C HN42 N4 . .
O2C HN41 N4 . .
O2C C5 C4 C6 .
O2C H5 C5 . .
O2C C6 C5 H6 .
O2C H6 C6 . END
O2C "C4'" "O4'" . ADD
O2C N1 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
O2C O1P P deloc 1.510 0.020
O2C O2P P deloc 1.510 0.020
O2C "O5'" P single 1.610 0.020
O2C P O3P deloc 1.510 0.020
O2C "C5'" "O5'" single 1.426 0.020
O2C "C4'" "C5'" single 1.524 0.020
O2C "H5'1" "C5'" single 1.092 0.020
O2C "H5'2" "C5'" single 1.092 0.020
O2C "C4'" "O4'" single 1.426 0.020
O2C "C3'" "C4'" single 1.524 0.020
O2C "H4'" "C4'" single 1.099 0.020
O2C "O4'" "C1'" single 1.426 0.020
O2C N1 "C1'" single 1.465 0.020
O2C "C1'" "C2'" single 1.524 0.020
O2C "H1'" "C1'" single 1.099 0.020
O2C N1 C6 single 1.337 0.020
O2C C2 N1 single 1.410 0.020
O2C C6 C5 double 1.390 0.020
O2C H6 C6 single 1.083 0.020
O2C O2 C2 double 1.250 0.020
O2C N3 C2 single 1.350 0.020
O2C C4 N3 double 1.350 0.020
O2C N4 C4 single 1.355 0.020
O2C C5 C4 single 1.390 0.020
O2C HN41 N4 single 1.010 0.020
O2C HN42 N4 single 1.010 0.020
O2C H5 C5 single 1.083 0.020
O2C "O2'" "C2'" single 1.432 0.020
O2C "C2'" "C3'" single 1.524 0.020
O2C "H2'" "C2'" single 1.099 0.020
O2C "HO'2" "O2'" single 0.967 0.020
O2C "H3'1" "C3'" single 1.092 0.020
O2C "H3'2" "C3'" single 1.092 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
O2C O3P P O1P 119.900 3.000
O2C O3P P O2P 119.900 3.000
O2C O3P P "O5'" 108.200 3.000
O2C O1P P O2P 119.900 3.000
O2C O1P P "O5'" 108.200 3.000
O2C O2P P "O5'" 108.200 3.000
O2C P "O5'" "C5'" 120.500 3.000
O2C "O5'" "C5'" "H5'1" 109.470 3.000
O2C "O5'" "C5'" "H5'2" 109.470 3.000
O2C "O5'" "C5'" "C4'" 109.470 3.000
O2C "H5'1" "C5'" "H5'2" 107.900 3.000
O2C "H5'1" "C5'" "C4'" 109.470 3.000
O2C "H5'2" "C5'" "C4'" 109.470 3.000
O2C "C5'" "C4'" "H4'" 108.340 3.000
O2C "C5'" "C4'" "C3'" 109.470 3.000
O2C "C5'" "C4'" "O4'" 109.470 3.000
O2C "H4'" "C4'" "C3'" 108.340 3.000
O2C "H4'" "C4'" "O4'" 109.470 3.000
O2C "C3'" "C4'" "O4'" 109.470 3.000
O2C "C4'" "C3'" "H3'1" 109.470 3.000
O2C "C4'" "C3'" "H3'2" 109.470 3.000
O2C "C4'" "C3'" "C2'" 111.000 3.000
O2C "H3'1" "C3'" "H3'2" 107.900 3.000
O2C "H3'1" "C3'" "C2'" 109.470 3.000
O2C "H3'2" "C3'" "C2'" 109.470 3.000
O2C "C3'" "C2'" "H2'" 108.340 3.000
O2C "C3'" "C2'" "O2'" 109.470 3.000
O2C "C3'" "C2'" "C1'" 111.000 3.000
O2C "H2'" "C2'" "O2'" 109.470 3.000
O2C "H2'" "C2'" "C1'" 108.340 3.000
O2C "O2'" "C2'" "C1'" 109.470 3.000
O2C "C2'" "O2'" "HO'2" 109.470 3.000
O2C "C2'" "C1'" "H1'" 108.340 3.000
O2C "C2'" "C1'" "O4'" 109.470 3.000
O2C "C2'" "C1'" N1 109.470 3.000
O2C "H1'" "C1'" "O4'" 109.470 3.000
O2C "H1'" "C1'" N1 109.470 3.000
O2C "O4'" "C1'" N1 109.470 3.000
O2C "C1'" "O4'" "C4'" 111.800 3.000
O2C "C1'" N1 C2 120.000 3.000
O2C "C1'" N1 C6 120.000 3.000
O2C C2 N1 C6 120.000 3.000
O2C N1 C2 O2 120.000 3.000
O2C N1 C2 N3 120.000 3.000
O2C O2 C2 N3 120.000 3.000
O2C C2 N3 C4 120.000 3.000
O2C N3 C4 N4 120.000 3.000
O2C N3 C4 C5 120.000 3.000
O2C N4 C4 C5 120.000 3.000
O2C C4 N4 HN42 120.000 3.000
O2C C4 N4 HN41 120.000 3.000
O2C HN42 N4 HN41 120.000 3.000
O2C C4 C5 H5 120.000 3.000
O2C C4 C5 C6 120.000 3.000
O2C H5 C5 C6 120.000 3.000
O2C C5 C6 H6 120.000 3.000
O2C C5 C6 N1 120.000 3.000
O2C H6 C6 N1 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
O2C var_1 O3P P "O5'" "C5'" -54.231 20.000 1
O2C var_2 P "O5'" "C5'" "C4'" -179.999 20.000 1
O2C var_3 "O5'" "C5'" "C4'" "C3'" 179.506 20.000 3
O2C var_4 "C5'" "C4'" "O4'" "C1'" 120.000 20.000 1
O2C var_5 "C5'" "C4'" "C3'" "C2'" -90.000 20.000 3
O2C var_6 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
O2C var_7 "C3'" "C2'" "O2'" "HO'2" -14.912 20.000 1
O2C var_8 "C3'" "C2'" "C1'" N1 150.000 20.000 3
O2C var_9 "C2'" "C1'" "O4'" "C4'" 0.000 20.000 1
O2C var_10 "C2'" "C1'" N1 C2 94.027 20.000 1
O2C CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
O2C CONST_2 "C1'" N1 C2 N3 180.000 0.000 0
O2C CONST_3 N1 C2 N3 C4 0.000 0.000 0
O2C CONST_4 C2 N3 C4 C5 0.000 0.000 0
O2C CONST_5 N3 C4 N4 HN41 120.568 0.000 0
O2C CONST_6 N3 C4 C5 C6 0.000 0.000 0
O2C CONST_7 C4 C5 C6 N1 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
O2C chir_01 "C4'" "C5'" "O4'" "C3'" negativ
O2C chir_02 "C1'" "O4'" N1 "C2'" negativ
O2C chir_03 "C2'" "C1'" "O2'" "C3'" 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
O2C plan-1 N1 0.020
O2C plan-1 "C1'" 0.020
O2C plan-1 C6 0.020
O2C plan-1 C2 0.020
O2C plan-1 N3 0.020
O2C plan-1 C4 0.020
O2C plan-1 C5 0.020
O2C plan-1 H6 0.020
O2C plan-1 O2 0.020
O2C plan-1 N4 0.020
O2C plan-1 H5 0.020
O2C plan-1 HN42 0.020
O2C plan-1 HN41 0.020
O2C plan-2 N4 0.020
O2C plan-2 C4 0.020
O2C plan-2 HN41 0.020
O2C plan-2 HN42 0.020
# ------------------------------------------------------
|
