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
|
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
AF2 AF2 '. ' DNA 34 23 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AF2
#
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
AF2 OP3 O OP -0.666 0.000 0.000 0.000
AF2 P P P 0.000 -1.025 0.391 1.042
AF2 OP2 O OP -0.666 -0.558 1.634 1.767
AF2 OP1 O OP -0.666 -1.189 -0.739 2.035
AF2 "O5'" O O2 0.000 -2.435 0.685 0.324
AF2 "C5'" C CH2 0.000 -3.631 0.976 1.049
AF2 "H5'" H H 0.000 -3.482 1.875 1.650
AF2 "H5'A" H H 0.000 -3.872 0.136 1.704
AF2 "C4'" C CH1 0.000 -4.781 1.203 0.065
AF2 "H4'" H H 0.000 -4.501 1.948 -0.693
AF2 "O4'" O O2 0.000 -5.168 -0.039 -0.560
AF2 "C1'" C CH1 0.000 -6.510 0.135 -1.044
AF2 "H1'" H H 0.000 -6.490 0.470 -2.091
AF2 N9 N NR5 0.000 -7.246 -1.128 -0.938
AF2 C4 C CR56 0.000 -8.352 -1.487 -1.665
AF2 N3 N NRD6 0.000 -9.080 -0.907 -2.614
AF2 C2 C CR16 0.000 -10.118 -1.526 -3.135
AF2 H2 H H 0.000 -10.690 -1.025 -3.907
AF2 C8 C CR15 0.000 -6.956 -2.161 -0.098
AF2 H8 H H 0.000 -6.133 -2.178 0.606
AF2 N7 N NRD5 0.000 -7.814 -3.124 -0.266
AF2 C5 C CR56 0.000 -8.706 -2.772 -1.223
AF2 C6 C CR6 0.000 -9.822 -3.392 -1.810
AF2 N1 N NRD6 0.000 -10.489 -2.734 -2.753
AF2 N6 N NH2 0.000 -10.219 -4.657 -1.414
AF2 HN6A H H 0.000 -11.026 -5.102 -1.840
AF2 HN6 H H 0.000 -9.707 -5.156 -0.693
AF2 "C3'" C CH1 0.000 -6.063 1.644 0.816
AF2 "H3'" H H 0.000 -6.156 1.116 1.776
AF2 "C2'" C CH1 0.000 -7.179 1.207 -0.164
AF2 "H2'" H H 0.000 -8.028 0.778 0.386
AF2 F F F 0.000 -7.597 2.291 -0.944
AF2 "O3'" O OH1 0.000 -6.080 3.060 1.010
AF2 "HO3'" H H 0.000 -6.902 3.394 1.396
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
AF2 OP3 n/a P START
AF2 P OP3 "O5'" .
AF2 OP2 P . .
AF2 OP1 P . .
AF2 "O5'" P "C5'" .
AF2 "C5'" "O5'" "C4'" .
AF2 "H5'" "C5'" . .
AF2 "H5'A" "C5'" . .
AF2 "C4'" "C5'" "C3'" .
AF2 "H4'" "C4'" . .
AF2 "O4'" "C4'" "C1'" .
AF2 "C1'" "O4'" N9 .
AF2 "H1'" "C1'" . .
AF2 N9 "C1'" C8 .
AF2 C4 N9 N3 .
AF2 N3 C4 C2 .
AF2 C2 N3 H2 .
AF2 H2 C2 . .
AF2 C8 N9 N7 .
AF2 H8 C8 . .
AF2 N7 C8 C5 .
AF2 C5 N7 C6 .
AF2 C6 C5 N6 .
AF2 N1 C6 . .
AF2 N6 C6 HN6 .
AF2 HN6A N6 . .
AF2 HN6 N6 . .
AF2 "C3'" "C4'" "O3'" .
AF2 "H3'" "C3'" . .
AF2 "C2'" "C3'" F .
AF2 "H2'" "C2'" . .
AF2 F "C2'" . .
AF2 "O3'" "C3'" . END
AF2 "HO3'" "O3'" . .
AF2 N1 C2 . ADD
AF2 C4 C5 . ADD
AF2 "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
AF2 F "C2'" single 1.370 0.020
AF2 OP1 P deloc 1.510 0.020
AF2 OP2 P deloc 1.510 0.020
AF2 N1 C6 single 1.350 0.020
AF2 N1 C2 double 1.337 0.020
AF2 C2 N3 single 1.337 0.020
AF2 N3 C4 double 1.355 0.020
AF2 C4 N9 single 1.337 0.020
AF2 C4 C5 single 1.490 0.020
AF2 C5 N7 single 1.350 0.020
AF2 C6 C5 double 1.490 0.020
AF2 N6 C6 single 1.355 0.020
AF2 HN6A N6 single 1.010 0.020
AF2 N7 C8 double 1.350 0.020
AF2 H8 C8 single 1.083 0.020
AF2 C8 N9 single 1.337 0.020
AF2 N9 "C1'" single 1.485 0.020
AF2 "C1'" "C2'" single 1.524 0.020
AF2 "H2'" "C2'" single 1.099 0.020
AF2 "C2'" "C3'" single 1.524 0.020
AF2 "H3'" "C3'" single 1.099 0.020
AF2 "O3'" "C3'" single 1.432 0.020
AF2 "HO3'" "O3'" single 0.967 0.020
AF2 "C3'" "C4'" single 1.524 0.020
AF2 "C4'" "C5'" single 1.524 0.020
AF2 "C1'" "O4'" single 1.426 0.020
AF2 "O4'" "C4'" single 1.426 0.020
AF2 "C5'" "O5'" single 1.426 0.020
AF2 "H5'A" "C5'" single 1.092 0.020
AF2 "O5'" P single 1.610 0.020
AF2 H2 C2 single 1.083 0.020
AF2 "H5'" "C5'" single 1.092 0.020
AF2 "H1'" "C1'" single 1.099 0.020
AF2 "H4'" "C4'" single 1.099 0.020
AF2 HN6 N6 single 1.010 0.020
AF2 P OP3 deloc 1.510 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
AF2 OP3 P OP2 119.900 3.000
AF2 OP3 P OP1 119.900 3.000
AF2 OP3 P "O5'" 108.200 3.000
AF2 OP2 P OP1 119.900 3.000
AF2 OP2 P "O5'" 108.200 3.000
AF2 OP1 P "O5'" 108.200 3.000
AF2 P "O5'" "C5'" 120.500 3.000
AF2 "O5'" "C5'" "H5'" 109.470 3.000
AF2 "O5'" "C5'" "H5'A" 109.470 3.000
AF2 "O5'" "C5'" "C4'" 109.470 3.000
AF2 "H5'" "C5'" "H5'A" 107.900 3.000
AF2 "H5'" "C5'" "C4'" 109.470 3.000
AF2 "H5'A" "C5'" "C4'" 109.470 3.000
AF2 "C5'" "C4'" "H4'" 108.340 3.000
AF2 "C5'" "C4'" "O4'" 109.470 3.000
AF2 "C5'" "C4'" "C3'" 111.000 3.000
AF2 "H4'" "C4'" "O4'" 109.470 3.000
AF2 "H4'" "C4'" "C3'" 108.340 3.000
AF2 "O4'" "C4'" "C3'" 109.470 3.000
AF2 "C4'" "O4'" "C1'" 111.800 3.000
AF2 "O4'" "C1'" "H1'" 109.470 3.000
AF2 "O4'" "C1'" N9 109.470 3.000
AF2 "O4'" "C1'" "C2'" 109.470 3.000
AF2 "H1'" "C1'" N9 109.470 3.000
AF2 "H1'" "C1'" "C2'" 108.340 3.000
AF2 N9 "C1'" "C2'" 109.470 3.000
AF2 "C1'" N9 C4 126.000 3.000
AF2 "C1'" N9 C8 126.000 3.000
AF2 C4 N9 C8 108.000 3.000
AF2 N9 C4 N3 132.000 3.000
AF2 N9 C4 C5 108.000 3.000
AF2 N3 C4 C5 120.000 3.000
AF2 C4 N3 C2 120.000 3.000
AF2 N3 C2 H2 120.000 3.000
AF2 N3 C2 N1 120.000 3.000
AF2 H2 C2 N1 120.000 3.000
AF2 N9 C8 H8 126.000 3.000
AF2 N9 C8 N7 108.000 3.000
AF2 H8 C8 N7 126.000 3.000
AF2 C8 N7 C5 108.000 3.000
AF2 N7 C5 C6 132.000 3.000
AF2 N7 C5 C4 108.000 3.000
AF2 C6 C5 C4 120.000 3.000
AF2 C5 C6 N1 120.000 3.000
AF2 C5 C6 N6 120.000 3.000
AF2 N1 C6 N6 120.000 3.000
AF2 C6 N1 C2 120.000 3.000
AF2 C6 N6 HN6A 120.000 3.000
AF2 C6 N6 HN6 120.000 3.000
AF2 HN6A N6 HN6 120.000 3.000
AF2 "C4'" "C3'" "H3'" 108.340 3.000
AF2 "C4'" "C3'" "C2'" 111.000 3.000
AF2 "C4'" "C3'" "O3'" 109.470 3.000
AF2 "H3'" "C3'" "C2'" 108.340 3.000
AF2 "H3'" "C3'" "O3'" 109.470 3.000
AF2 "C2'" "C3'" "O3'" 109.470 3.000
AF2 "C3'" "C2'" "H2'" 108.340 3.000
AF2 "C3'" "C2'" F 109.500 3.000
AF2 "C3'" "C2'" "C1'" 111.000 3.000
AF2 "H2'" "C2'" F 109.500 3.000
AF2 "H2'" "C2'" "C1'" 108.340 3.000
AF2 F "C2'" "C1'" 109.500 3.000
AF2 "C3'" "O3'" "HO3'" 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
AF2 var_1 OP3 P "O5'" "C5'" 174.976 20.000 1
AF2 var_2 P "O5'" "C5'" "C4'" 179.984 20.000 1
AF2 var_3 "O5'" "C5'" "C4'" "C3'" -175.003 20.000 3
AF2 var_4 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
AF2 var_5 "C4'" "O4'" "C1'" N9 -150.000 20.000 1
AF2 var_6 "O4'" "C1'" "C2'" "C3'" 0.000 20.000 3
AF2 var_7 "O4'" "C1'" N9 C8 22.874 20.000 1
AF2 CONST_1 "C1'" N9 C4 N3 0.000 0.000 0
AF2 CONST_2 N9 C4 C5 N7 0.000 0.000 0
AF2 CONST_3 N9 C4 N3 C2 180.000 0.000 0
AF2 CONST_4 C4 N3 C2 N1 0.000 0.000 0
AF2 CONST_5 "C1'" N9 C8 N7 180.000 0.000 0
AF2 CONST_6 N9 C8 N7 C5 0.000 0.000 0
AF2 CONST_7 C8 N7 C5 C6 180.000 0.000 0
AF2 CONST_8 N7 C5 C6 N6 0.000 0.000 0
AF2 CONST_9 C5 C6 N1 C2 0.000 0.000 0
AF2 CONST_10 C6 N1 C2 N3 0.000 0.000 0
AF2 CONST_11 C5 C6 N6 HN6 -0.024 0.000 0
AF2 var_8 "C5'" "C4'" "C3'" "O3'" 90.000 20.000 3
AF2 var_9 "C4'" "C3'" "C2'" F -90.000 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
AF2 chir_01 "C1'" N9 "C2'" "O4'" negativ
AF2 chir_02 "C2'" "C1'" "C3'" F negativ
AF2 chir_03 "C3'" "C2'" "O3'" "C4'" positiv
AF2 chir_04 "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
AF2 plan-1 N1 0.020
AF2 plan-1 C2 0.020
AF2 plan-1 C6 0.020
AF2 plan-1 N3 0.020
AF2 plan-1 H2 0.020
AF2 plan-1 C4 0.020
AF2 plan-1 C5 0.020
AF2 plan-1 N9 0.020
AF2 plan-1 N7 0.020
AF2 plan-1 C8 0.020
AF2 plan-1 N6 0.020
AF2 plan-1 H8 0.020
AF2 plan-1 "C1'" 0.020
AF2 plan-1 HN6A 0.020
AF2 plan-1 HN6 0.020
AF2 plan-2 N6 0.020
AF2 plan-2 C6 0.020
AF2 plan-2 HN6 0.020
AF2 plan-2 HN6A 0.020
# ------------------------------------------------------
|
