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
|
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
DDY DDY '2',3'-DIDEOXYCYTOSINE-5'-DIPHOSPHATE' non-polymer 35 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DDY
#
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
DDY O2A O OP -0.500 0.000 0.000 0.000
DDY PA P P 0.000 -0.919 0.680 -0.944
DDY O1A O OP -0.500 -0.384 2.023 -1.273
DDY O3A O O2 0.000 -1.046 -0.193 -2.292
DDY PB P P 0.000 -0.080 -0.446 -3.555
DDY O2B O OP -0.666 0.966 -1.477 -3.192
DDY O1B O OP -0.666 -0.899 -0.948 -4.724
DDY O3B O OP -0.666 0.600 0.851 -3.937
DDY "O5'" O O2 0.000 -2.371 0.831 -0.265
DDY "C5'" C CH2 0.000 -2.608 1.638 0.890
DDY "H5'1" H H 0.000 -2.342 2.674 0.672
DDY "H5'2" H H 0.000 -1.998 1.273 1.720
DDY "C4'" C CH1 0.000 -4.088 1.560 1.271
DDY "H4'" H H 0.000 -4.722 1.863 0.426
DDY "C3'" C CH2 0.000 -4.379 2.436 2.515
DDY "H3'1" H H 0.000 -4.602 3.475 2.262
DDY "H3'2" H H 0.000 -3.576 2.407 3.254
DDY "C2'" C CH2 0.000 -5.645 1.763 3.099
DDY "H2'1" H H 0.000 -6.560 2.273 2.791
DDY "H2'2" H H 0.000 -5.612 1.703 4.189
DDY "C1'" C CH1 0.000 -5.624 0.340 2.504
DDY "H1'" H H 0.000 -6.510 0.185 1.873
DDY "O4'" O O2 0.000 -4.430 0.228 1.710
DDY N1 N NR6 0.000 -5.599 -0.650 3.583
DDY C6 C CR16 0.000 -6.649 -1.505 3.741
DDY H6 H H 0.000 -7.497 -1.462 3.069
DDY C5 C CR16 0.000 -6.620 -2.409 4.749
DDY H5 H H 0.000 -7.442 -3.099 4.893
DDY C2 C CR6 0.000 -4.542 -0.711 4.413
DDY O2 O O 0.000 -3.610 0.062 4.256
DDY N3 N NRD6 0.000 -4.501 -1.591 5.411
DDY C4 C CR6 0.000 -5.502 -2.440 5.608
DDY N4 N NH2 0.000 -5.447 -3.348 6.640
DDY HN42 H H 0.000 -4.644 -3.372 7.259
DDY HN41 H H 0.000 -6.208 -4.001 6.790
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
DDY O2A n/a PA START
DDY PA O2A "O5'" .
DDY O1A PA . .
DDY O3A PA PB .
DDY PB O3A O3B .
DDY O2B PB . .
DDY O1B PB . .
DDY O3B PB . .
DDY "O5'" PA "C5'" .
DDY "C5'" "O5'" "C4'" .
DDY "H5'1" "C5'" . .
DDY "H5'2" "C5'" . .
DDY "C4'" "C5'" "C3'" .
DDY "H4'" "C4'" . .
DDY "C3'" "C4'" "C2'" .
DDY "H3'1" "C3'" . .
DDY "H3'2" "C3'" . .
DDY "C2'" "C3'" "C1'" .
DDY "H2'1" "C2'" . .
DDY "H2'2" "C2'" . .
DDY "C1'" "C2'" N1 .
DDY "H1'" "C1'" . .
DDY "O4'" "C1'" . .
DDY N1 "C1'" C2 .
DDY C6 N1 C5 .
DDY H6 C6 . .
DDY C5 C6 H5 .
DDY H5 C5 . .
DDY C2 N1 N3 .
DDY O2 C2 . .
DDY N3 C2 C4 .
DDY C4 N3 N4 .
DDY N4 C4 HN41 .
DDY HN42 N4 . .
DDY HN41 N4 . END
DDY C4 C5 . ADD
DDY "C4'" "O4'" . 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
DDY C4 C5 single 1.390 0.020
DDY N4 C4 single 1.355 0.020
DDY C4 N3 double 1.350 0.020
DDY O3B PB deloc 1.510 0.020
DDY O1B PB deloc 1.510 0.020
DDY O2B PB deloc 1.510 0.020
DDY PB O3A single 1.610 0.020
DDY O3A PA single 1.610 0.020
DDY O1A PA deloc 1.510 0.020
DDY PA O2A deloc 1.510 0.020
DDY "O5'" PA single 1.610 0.020
DDY O2 C2 double 1.250 0.020
DDY C2 N1 single 1.410 0.020
DDY N3 C2 single 1.350 0.020
DDY C5 C6 double 1.390 0.020
DDY H5 C5 single 1.083 0.020
DDY "C5'" "O5'" single 1.426 0.020
DDY "C4'" "C5'" single 1.524 0.020
DDY "H5'1" "C5'" single 1.092 0.020
DDY "H5'2" "C5'" single 1.092 0.020
DDY "C4'" "O4'" single 1.426 0.020
DDY "C3'" "C4'" single 1.524 0.020
DDY "H4'" "C4'" single 1.099 0.020
DDY "O4'" "C1'" single 1.426 0.020
DDY "C2'" "C3'" single 1.524 0.020
DDY "H3'1" "C3'" single 1.092 0.020
DDY "H3'2" "C3'" single 1.092 0.020
DDY "C1'" "C2'" single 1.524 0.020
DDY "H2'1" "C2'" single 1.092 0.020
DDY "H2'2" "C2'" single 1.092 0.020
DDY N1 "C1'" single 1.465 0.020
DDY "H1'" "C1'" single 1.099 0.020
DDY C6 N1 single 1.337 0.020
DDY H6 C6 single 1.083 0.020
DDY HN41 N4 single 1.010 0.020
DDY HN42 N4 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
DDY O2A PA O1A 119.900 3.000
DDY O2A PA O3A 108.200 3.000
DDY O2A PA "O5'" 108.200 3.000
DDY O1A PA O3A 108.200 3.000
DDY O1A PA "O5'" 108.200 3.000
DDY O3A PA "O5'" 102.600 3.000
DDY PA O3A PB 120.500 3.000
DDY O3A PB O2B 108.200 3.000
DDY O3A PB O1B 108.200 3.000
DDY O3A PB O3B 108.200 3.000
DDY O2B PB O1B 119.900 3.000
DDY O2B PB O3B 119.900 3.000
DDY O1B PB O3B 119.900 3.000
DDY PA "O5'" "C5'" 120.500 3.000
DDY "O5'" "C5'" "H5'1" 109.470 3.000
DDY "O5'" "C5'" "H5'2" 109.470 3.000
DDY "O5'" "C5'" "C4'" 109.470 3.000
DDY "H5'1" "C5'" "H5'2" 107.900 3.000
DDY "H5'1" "C5'" "C4'" 109.470 3.000
DDY "H5'2" "C5'" "C4'" 109.470 3.000
DDY "C5'" "C4'" "H4'" 108.340 3.000
DDY "C5'" "C4'" "C3'" 109.470 3.000
DDY "C5'" "C4'" "O4'" 109.470 3.000
DDY "H4'" "C4'" "C3'" 108.340 3.000
DDY "H4'" "C4'" "O4'" 109.470 3.000
DDY "C3'" "C4'" "O4'" 109.470 3.000
DDY "C4'" "C3'" "H3'1" 109.470 3.000
DDY "C4'" "C3'" "H3'2" 109.470 3.000
DDY "C4'" "C3'" "C2'" 111.000 3.000
DDY "H3'1" "C3'" "H3'2" 107.900 3.000
DDY "H3'1" "C3'" "C2'" 109.470 3.000
DDY "H3'2" "C3'" "C2'" 109.470 3.000
DDY "C3'" "C2'" "H2'1" 109.470 3.000
DDY "C3'" "C2'" "H2'2" 109.470 3.000
DDY "C3'" "C2'" "C1'" 111.000 3.000
DDY "H2'1" "C2'" "H2'2" 107.900 3.000
DDY "H2'1" "C2'" "C1'" 109.470 3.000
DDY "H2'2" "C2'" "C1'" 109.470 3.000
DDY "C2'" "C1'" "H1'" 108.340 3.000
DDY "C2'" "C1'" "O4'" 109.470 3.000
DDY "C2'" "C1'" N1 109.470 3.000
DDY "H1'" "C1'" "O4'" 109.470 3.000
DDY "H1'" "C1'" N1 109.470 3.000
DDY "O4'" "C1'" N1 109.470 3.000
DDY "C1'" "O4'" "C4'" 111.800 3.000
DDY "C1'" N1 C6 120.000 3.000
DDY "C1'" N1 C2 120.000 3.000
DDY C6 N1 C2 120.000 3.000
DDY N1 C6 H6 120.000 3.000
DDY N1 C6 C5 120.000 3.000
DDY H6 C6 C5 120.000 3.000
DDY C6 C5 H5 120.000 3.000
DDY C6 C5 C4 120.000 3.000
DDY H5 C5 C4 120.000 3.000
DDY N1 C2 O2 120.000 3.000
DDY N1 C2 N3 120.000 3.000
DDY O2 C2 N3 120.000 3.000
DDY C2 N3 C4 120.000 3.000
DDY N3 C4 N4 120.000 3.000
DDY N3 C4 C5 120.000 3.000
DDY N4 C4 C5 120.000 3.000
DDY C4 N4 HN42 120.000 3.000
DDY C4 N4 HN41 120.000 3.000
DDY HN42 N4 HN41 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
DDY var_1 O2A PA O3A PB -75.012 20.000 1
DDY var_2 PA O3A PB O3B -39.960 20.000 1
DDY var_3 O2A PA "O5'" "C5'" 64.964 20.000 1
DDY var_4 PA "O5'" "C5'" "C4'" 179.979 20.000 1
DDY var_5 "O5'" "C5'" "C4'" "C3'" -179.464 20.000 3
DDY var_6 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
DDY var_7 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
DDY var_8 "C4'" "C3'" "C2'" "C1'" 30.000 20.000 3
DDY var_9 "C3'" "C2'" "C1'" N1 120.000 20.000 3
DDY var_10 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
DDY var_11 "C2'" "C1'" N1 C2 -64.287 20.000 1
DDY CONST_1 "C1'" N1 C6 C5 180.000 0.000 0
DDY CONST_2 N1 C6 C5 C4 0.000 0.000 0
DDY CONST_3 "C1'" N1 C2 N3 180.000 0.000 0
DDY CONST_4 N1 C2 N3 C4 0.000 0.000 0
DDY CONST_5 C2 N3 C4 N4 180.000 0.000 0
DDY CONST_6 N3 C4 C5 C6 0.000 0.000 0
DDY CONST_7 N3 C4 N4 HN41 -179.733 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
DDY chir_01 "C4'" "C5'" "O4'" "C3'" negativ
DDY chir_02 "C1'" "O4'" "C2'" N1 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
DDY plan-1 C4 0.020
DDY plan-1 C5 0.020
DDY plan-1 N4 0.020
DDY plan-1 N3 0.020
DDY plan-1 C2 0.020
DDY plan-1 N1 0.020
DDY plan-1 C6 0.020
DDY plan-1 O2 0.020
DDY plan-1 H5 0.020
DDY plan-1 "C1'" 0.020
DDY plan-1 H6 0.020
DDY plan-1 HN42 0.020
DDY plan-1 HN41 0.020
DDY plan-2 N4 0.020
DDY plan-2 C4 0.020
DDY plan-2 HN41 0.020
DDY plan-2 HN42 0.020
# ------------------------------------------------------
|
