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
|
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
DCZ DCZ '2'-DEOXYCYTIDINE ' non-polymer 29 16 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DCZ
#
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
DCZ O2 O O 0.000 0.000 0.000 0.000
DCZ C2 C CR6 0.000 -0.494 -0.679 0.885
DCZ N3 N NRD6 0.000 0.197 -0.905 2.000
DCZ C4 C CR6 0.000 -0.316 -1.638 2.978
DCZ N4 N NH2 0.000 0.408 -1.866 4.126
DCZ HN42 H H 0.000 0.017 -2.426 4.876
DCZ HN41 H H 0.000 1.337 -1.476 4.233
DCZ C5 C CR16 0.000 -1.604 -2.190 2.832
DCZ H5 H H 0.000 -2.033 -2.800 3.617
DCZ C6 C CR16 0.000 -2.297 -1.947 1.695
DCZ H6 H H 0.000 -3.293 -2.352 1.564
DCZ N1 N NR6 0.000 -1.728 -1.186 0.718
DCZ "C1'" C CH1 0.000 -2.465 -0.921 -0.520
DCZ "H1'" H H 0.000 -3.443 -1.420 -0.488
DCZ "O4'" O O2 0.000 -1.711 -1.394 -1.648
DCZ "C4'" C CH1 0.000 -1.972 -0.482 -2.739
DCZ "H4'" H H 0.000 -2.948 -0.696 -3.196
DCZ "C5'" C CH2 0.000 -0.861 -0.559 -3.788
DCZ "H5'1" H H 0.000 0.105 -0.392 -3.306
DCZ "H5'2" H H 0.000 -1.025 0.208 -4.548
DCZ "O5'" O OH1 0.000 -0.871 -1.848 -4.401
DCZ HO51 H H 0.000 -0.168 -1.895 -5.062
DCZ "C3'" C CH1 0.000 -1.984 0.908 -2.056
DCZ "H3'" H H 0.000 -0.960 1.281 -1.909
DCZ "O3'" O OH1 0.000 -2.762 1.840 -2.811
DCZ "HO3'" H H 0.000 -2.831 2.671 -2.322
DCZ "C2'" C CH2 0.000 -2.657 0.598 -0.698
DCZ "H2'2" H H 0.000 -3.724 0.832 -0.707
DCZ "H2'1" H H 0.000 -2.176 1.126 0.128
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
DCZ O2 n/a C2 START
DCZ C2 O2 N3 .
DCZ N3 C2 C4 .
DCZ C4 N3 C5 .
DCZ N4 C4 HN41 .
DCZ HN42 N4 . .
DCZ HN41 N4 . .
DCZ C5 C4 C6 .
DCZ H5 C5 . .
DCZ C6 C5 N1 .
DCZ H6 C6 . .
DCZ N1 C6 "C1'" .
DCZ "C1'" N1 "O4'" .
DCZ "H1'" "C1'" . .
DCZ "O4'" "C1'" "C4'" .
DCZ "C4'" "O4'" "C3'" .
DCZ "H4'" "C4'" . .
DCZ "C5'" "C4'" "O5'" .
DCZ "H5'1" "C5'" . .
DCZ "H5'2" "C5'" . .
DCZ "O5'" "C5'" HO51 .
DCZ HO51 "O5'" . .
DCZ "C3'" "C4'" "C2'" .
DCZ "H3'" "C3'" . .
DCZ "O3'" "C3'" "HO3'" .
DCZ "HO3'" "O3'" . .
DCZ "C2'" "C3'" "H2'1" .
DCZ "H2'2" "C2'" . .
DCZ "H2'1" "C2'" . END
DCZ N1 C2 . ADD
DCZ "C1'" "C2'" . 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
DCZ N1 C2 single 1.410 0.020
DCZ N1 C6 single 1.337 0.020
DCZ "C1'" N1 single 1.465 0.020
DCZ N3 C2 single 1.350 0.020
DCZ C2 O2 double 1.250 0.020
DCZ C4 N3 double 1.350 0.020
DCZ C5 C4 single 1.390 0.020
DCZ N4 C4 single 1.355 0.020
DCZ C6 C5 double 1.390 0.020
DCZ H5 C5 single 1.083 0.020
DCZ H6 C6 single 1.083 0.020
DCZ HN41 N4 single 1.010 0.020
DCZ HN42 N4 single 1.010 0.020
DCZ "C1'" "C2'" single 1.524 0.020
DCZ "O4'" "C1'" single 1.426 0.020
DCZ "H1'" "C1'" single 1.099 0.020
DCZ "C2'" "C3'" single 1.524 0.020
DCZ "H2'1" "C2'" single 1.092 0.020
DCZ "H2'2" "C2'" single 1.092 0.020
DCZ "C3'" "C4'" single 1.524 0.020
DCZ "O3'" "C3'" single 1.432 0.020
DCZ "H3'" "C3'" single 1.099 0.020
DCZ "C4'" "O4'" single 1.426 0.020
DCZ "C5'" "C4'" single 1.524 0.020
DCZ "H4'" "C4'" single 1.099 0.020
DCZ "HO3'" "O3'" single 0.967 0.020
DCZ "O5'" "C5'" single 1.432 0.020
DCZ "H5'1" "C5'" single 1.092 0.020
DCZ "H5'2" "C5'" single 1.092 0.020
DCZ HO51 "O5'" 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
DCZ O2 C2 N3 120.000 3.000
DCZ O2 C2 N1 120.000 3.000
DCZ N3 C2 N1 120.000 3.000
DCZ C2 N3 C4 120.000 3.000
DCZ N3 C4 N4 120.000 3.000
DCZ N3 C4 C5 120.000 3.000
DCZ N4 C4 C5 120.000 3.000
DCZ C4 N4 HN42 120.000 3.000
DCZ C4 N4 HN41 120.000 3.000
DCZ HN42 N4 HN41 120.000 3.000
DCZ C4 C5 H5 120.000 3.000
DCZ C4 C5 C6 120.000 3.000
DCZ H5 C5 C6 120.000 3.000
DCZ C5 C6 H6 120.000 3.000
DCZ C5 C6 N1 120.000 3.000
DCZ H6 C6 N1 120.000 3.000
DCZ C6 N1 "C1'" 120.000 3.000
DCZ C6 N1 C2 120.000 3.000
DCZ "C1'" N1 C2 120.000 3.000
DCZ N1 "C1'" "H1'" 109.470 3.000
DCZ N1 "C1'" "O4'" 109.470 3.000
DCZ N1 "C1'" "C2'" 109.470 3.000
DCZ "H1'" "C1'" "O4'" 109.470 3.000
DCZ "H1'" "C1'" "C2'" 108.340 3.000
DCZ "O4'" "C1'" "C2'" 109.470 3.000
DCZ "C1'" "O4'" "C4'" 111.800 3.000
DCZ "O4'" "C4'" "H4'" 109.470 3.000
DCZ "O4'" "C4'" "C5'" 109.470 3.000
DCZ "O4'" "C4'" "C3'" 109.470 3.000
DCZ "H4'" "C4'" "C5'" 108.340 3.000
DCZ "H4'" "C4'" "C3'" 108.340 3.000
DCZ "C5'" "C4'" "C3'" 111.000 3.000
DCZ "C4'" "C5'" "H5'1" 109.470 3.000
DCZ "C4'" "C5'" "H5'2" 109.470 3.000
DCZ "C4'" "C5'" "O5'" 109.470 3.000
DCZ "H5'1" "C5'" "H5'2" 107.900 3.000
DCZ "H5'1" "C5'" "O5'" 109.470 3.000
DCZ "H5'2" "C5'" "O5'" 109.470 3.000
DCZ "C5'" "O5'" HO51 109.470 3.000
DCZ "C4'" "C3'" "H3'" 108.340 3.000
DCZ "C4'" "C3'" "O3'" 109.470 3.000
DCZ "C4'" "C3'" "C2'" 111.000 3.000
DCZ "H3'" "C3'" "O3'" 109.470 3.000
DCZ "H3'" "C3'" "C2'" 108.340 3.000
DCZ "O3'" "C3'" "C2'" 109.470 3.000
DCZ "C3'" "O3'" "HO3'" 109.470 3.000
DCZ "C3'" "C2'" "H2'2" 109.470 3.000
DCZ "C3'" "C2'" "H2'1" 109.470 3.000
DCZ "C3'" "C2'" "C1'" 111.000 3.000
DCZ "H2'2" "C2'" "H2'1" 107.900 3.000
DCZ "H2'2" "C2'" "C1'" 109.470 3.000
DCZ "H2'1" "C2'" "C1'" 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
DCZ CONST_1 O2 C2 N3 C4 180.000 0.000 0
DCZ CONST_2 C2 N3 C4 C5 0.000 0.000 0
DCZ CONST_3 N3 C4 N4 HN41 -0.036 0.000 0
DCZ CONST_4 N3 C4 C5 C6 0.000 0.000 0
DCZ CONST_5 C4 C5 C6 N1 0.000 0.000 0
DCZ CONST_6 C5 C6 N1 "C1'" 180.000 0.000 0
DCZ CONST_7 C6 N1 C2 O2 180.000 0.000 0
DCZ var_1 C6 N1 "C1'" "O4'" -121.719 20.000 1
DCZ var_2 N1 "C1'" "C2'" "C3'" 120.000 20.000 3
DCZ var_3 N1 "C1'" "O4'" "C4'" -150.000 20.000 1
DCZ var_4 "C1'" "O4'" "C4'" "C3'" 30.000 20.000 1
DCZ var_5 "O4'" "C4'" "C5'" "O5'" 65.683 20.000 3
DCZ var_6 "C4'" "C5'" "O5'" HO51 -179.942 20.000 1
DCZ var_7 "O4'" "C4'" "C3'" "C2'" -30.000 20.000 3
DCZ var_8 "C4'" "C3'" "O3'" "HO3'" 174.182 20.000 1
DCZ var_9 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
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
DCZ chir_01 "C1'" N1 "C2'" "O4'" negativ
DCZ chir_02 "C3'" "C2'" "C4'" "O3'" negativ
DCZ chir_03 "C4'" "C3'" "O4'" "C5'" 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
DCZ plan-1 N1 0.020
DCZ plan-1 C2 0.020
DCZ plan-1 C6 0.020
DCZ plan-1 "C1'" 0.020
DCZ plan-1 N3 0.020
DCZ plan-1 C4 0.020
DCZ plan-1 C5 0.020
DCZ plan-1 O2 0.020
DCZ plan-1 N4 0.020
DCZ plan-1 H5 0.020
DCZ plan-1 H6 0.020
DCZ plan-1 HN42 0.020
DCZ plan-1 HN41 0.020
DCZ plan-2 N4 0.020
DCZ plan-2 C4 0.020
DCZ plan-2 HN41 0.020
DCZ plan-2 HN42 0.020
# ------------------------------------------------------
|
