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
|
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
2FA 2FA '2-(6-AMINO-2-FLUORO-PURIN-9-YL)-5-HY' non-polymer 32 20 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2FA
#
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
2FA F F F 0.000 0.000 0.000 0.000
2FA C2 C CR6 0.000 -1.037 0.809 0.309
2FA N3 N NRD6 0.000 -2.263 0.396 0.053
2FA N1 N NRD6 0.000 -0.785 1.986 0.858
2FA C6 C CR6 0.000 -1.770 2.819 1.181
2FA N6 N NH2 0.000 -1.497 4.047 1.756
2FA HN62 H H 0.000 -2.252 4.681 2.001
2FA HN61 H H 0.000 -0.539 4.330 1.939
2FA C5 C CR56 0.000 -3.094 2.419 0.933
2FA C4 C CR56 0.000 -3.310 1.163 0.344
2FA N7 N NRD5 0.000 -4.311 2.988 1.118
2FA C8 C CR15 0.000 -5.237 2.176 0.698
2FA H8 H H 0.000 -6.300 2.376 0.731
2FA N9 N NR5 0.000 -4.669 1.036 0.210
2FA "C1'" C CH1 0.000 -5.381 -0.115 -0.352
2FA "H1'" H H 0.000 -4.807 -0.552 -1.180
2FA "O4'" O O2 0.000 -6.695 0.279 -0.804
2FA "C2'" C CH1 0.000 -5.639 -1.175 0.742
2FA "H2'" H H 0.000 -5.643 -0.707 1.736
2FA "O2'" O OH1 0.000 -4.659 -2.213 0.683
2FA H1 H H 0.000 -4.874 -2.895 1.334
2FA "C3'" C CH1 0.000 -7.041 -1.732 0.400
2FA "H3'" H H 0.000 -7.743 -1.541 1.224
2FA "O3'" O OH1 0.000 -6.969 -3.130 0.116
2FA H2 H H 0.000 -7.841 -3.448 -0.154
2FA "C4'" C CH1 0.000 -7.461 -0.944 -0.862
2FA "H4'" H H 0.000 -7.208 -1.511 -1.768
2FA "C5'" C CH2 0.000 -8.958 -0.636 -0.827
2FA "H5'1" H H 0.000 -9.181 -0.010 0.039
2FA "H5'2" H H 0.000 -9.520 -1.570 -0.753
2FA "O5'" O OH1 0.000 -9.331 0.052 -2.022
2FA "H5'" H H 0.000 -10.278 0.246 -1.999
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
2FA F n/a C2 START
2FA C2 F N1 .
2FA N3 C2 . .
2FA N1 C2 C6 .
2FA C6 N1 C5 .
2FA N6 C6 HN61 .
2FA HN62 N6 . .
2FA HN61 N6 . .
2FA C5 C6 N7 .
2FA C4 C5 . .
2FA N7 C5 C8 .
2FA C8 N7 N9 .
2FA H8 C8 . .
2FA N9 C8 "C1'" .
2FA "C1'" N9 "C2'" .
2FA "H1'" "C1'" . .
2FA "O4'" "C1'" . .
2FA "C2'" "C1'" "C3'" .
2FA "H2'" "C2'" . .
2FA "O2'" "C2'" H1 .
2FA H1 "O2'" . .
2FA "C3'" "C2'" "C4'" .
2FA "H3'" "C3'" . .
2FA "O3'" "C3'" H2 .
2FA H2 "O3'" . .
2FA "C4'" "C3'" "C5'" .
2FA "H4'" "C4'" . .
2FA "C5'" "C4'" "O5'" .
2FA "H5'1" "C5'" . .
2FA "H5'2" "C5'" . .
2FA "O5'" "C5'" "H5'" .
2FA "H5'" "O5'" . END
2FA "C4'" "O4'" . ADD
2FA N9 C4 . ADD
2FA C4 N3 . 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
2FA "O5'" "C5'" single 1.432 0.020
2FA "H5'" "O5'" single 0.967 0.020
2FA "C5'" "C4'" single 1.524 0.020
2FA "H5'1" "C5'" single 1.092 0.020
2FA "H5'2" "C5'" single 1.092 0.020
2FA "C4'" "O4'" single 1.426 0.020
2FA "C4'" "C3'" single 1.524 0.020
2FA "H4'" "C4'" single 1.099 0.020
2FA "O4'" "C1'" single 1.426 0.020
2FA "C1'" N9 single 1.485 0.020
2FA "C2'" "C1'" single 1.524 0.020
2FA "H1'" "C1'" single 1.099 0.020
2FA N9 C4 single 1.337 0.020
2FA N9 C8 single 1.337 0.020
2FA C4 N3 double 1.355 0.020
2FA C4 C5 single 1.490 0.020
2FA N3 C2 single 1.350 0.020
2FA C2 F single 1.345 0.020
2FA N1 C2 double 1.350 0.020
2FA C6 N1 single 1.350 0.020
2FA N6 C6 single 1.355 0.020
2FA C5 C6 double 1.490 0.020
2FA HN61 N6 single 1.010 0.020
2FA HN62 N6 single 1.010 0.020
2FA N7 C5 single 1.350 0.020
2FA C8 N7 double 1.350 0.020
2FA H8 C8 single 1.083 0.020
2FA "O2'" "C2'" single 1.432 0.020
2FA "C3'" "C2'" single 1.524 0.020
2FA "H2'" "C2'" single 1.099 0.020
2FA H1 "O2'" single 0.967 0.020
2FA "O3'" "C3'" single 1.432 0.020
2FA "H3'" "C3'" single 1.099 0.020
2FA H2 "O3'" 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
2FA F C2 N3 120.000 3.000
2FA F C2 N1 120.000 3.000
2FA N3 C2 N1 120.000 3.000
2FA C2 N3 C4 120.000 3.000
2FA C2 N1 C6 120.000 3.000
2FA N1 C6 N6 120.000 3.000
2FA N1 C6 C5 120.000 3.000
2FA N6 C6 C5 120.000 3.000
2FA C6 N6 HN62 120.000 3.000
2FA C6 N6 HN61 120.000 3.000
2FA HN62 N6 HN61 120.000 3.000
2FA C6 C5 C4 120.000 3.000
2FA C6 C5 N7 132.000 3.000
2FA C4 C5 N7 108.000 3.000
2FA C5 C4 N9 108.000 3.000
2FA C5 C4 N3 120.000 3.000
2FA N9 C4 N3 132.000 3.000
2FA C5 N7 C8 108.000 3.000
2FA N7 C8 H8 126.000 3.000
2FA N7 C8 N9 108.000 3.000
2FA H8 C8 N9 126.000 3.000
2FA C8 N9 "C1'" 126.000 3.000
2FA C8 N9 C4 108.000 3.000
2FA "C1'" N9 C4 126.000 3.000
2FA N9 "C1'" "H1'" 109.470 3.000
2FA N9 "C1'" "O4'" 109.470 3.000
2FA N9 "C1'" "C2'" 109.470 3.000
2FA "H1'" "C1'" "O4'" 109.470 3.000
2FA "H1'" "C1'" "C2'" 108.340 3.000
2FA "O4'" "C1'" "C2'" 109.470 3.000
2FA "C1'" "O4'" "C4'" 111.800 3.000
2FA "C1'" "C2'" "H2'" 108.340 3.000
2FA "C1'" "C2'" "O2'" 109.470 3.000
2FA "C1'" "C2'" "C3'" 111.000 3.000
2FA "H2'" "C2'" "O2'" 109.470 3.000
2FA "H2'" "C2'" "C3'" 108.340 3.000
2FA "O2'" "C2'" "C3'" 109.470 3.000
2FA "C2'" "O2'" H1 109.470 3.000
2FA "C2'" "C3'" "H3'" 108.340 3.000
2FA "C2'" "C3'" "O3'" 109.470 3.000
2FA "C2'" "C3'" "C4'" 111.000 3.000
2FA "H3'" "C3'" "O3'" 109.470 3.000
2FA "H3'" "C3'" "C4'" 108.340 3.000
2FA "O3'" "C3'" "C4'" 109.470 3.000
2FA "C3'" "O3'" H2 109.470 3.000
2FA "C3'" "C4'" "H4'" 108.340 3.000
2FA "C3'" "C4'" "C5'" 111.000 3.000
2FA "C3'" "C4'" "O4'" 109.470 3.000
2FA "H4'" "C4'" "C5'" 108.340 3.000
2FA "H4'" "C4'" "O4'" 109.470 3.000
2FA "C5'" "C4'" "O4'" 109.470 3.000
2FA "C4'" "C5'" "H5'1" 109.470 3.000
2FA "C4'" "C5'" "H5'2" 109.470 3.000
2FA "C4'" "C5'" "O5'" 109.470 3.000
2FA "H5'1" "C5'" "H5'2" 107.900 3.000
2FA "H5'1" "C5'" "O5'" 109.470 3.000
2FA "H5'2" "C5'" "O5'" 109.470 3.000
2FA "C5'" "O5'" "H5'" 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
2FA CONST_1 F C2 N3 C4 180.000 0.000 0
2FA CONST_2 F C2 N1 C6 180.000 0.000 0
2FA CONST_3 C2 N1 C6 C5 0.000 0.000 0
2FA CONST_4 N1 C6 N6 HN61 -0.007 0.000 0
2FA CONST_5 N1 C6 C5 N7 180.000 0.000 0
2FA CONST_6 C6 C5 C4 N9 180.000 0.000 0
2FA CONST_7 C5 C4 N3 C2 0.000 0.000 0
2FA CONST_8 C6 C5 N7 C8 180.000 0.000 0
2FA CONST_9 C5 N7 C8 N9 0.000 0.000 0
2FA CONST_10 N7 C8 N9 "C1'" 180.000 0.000 0
2FA CONST_11 C8 N9 C4 C5 0.000 0.000 0
2FA var_1 C8 N9 "C1'" "C2'" -93.436 20.000 1
2FA var_2 N9 "C1'" "O4'" "C4'" -150.000 20.000 1
2FA var_3 N9 "C1'" "C2'" "C3'" 150.000 20.000 3
2FA var_4 "C1'" "C2'" "O2'" H1 -176.160 20.000 1
2FA var_5 "C1'" "C2'" "C3'" "C4'" 0.000 20.000 3
2FA var_6 "C2'" "C3'" "O3'" H2 -176.136 20.000 1
2FA var_7 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
2FA var_8 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
2FA var_9 "C3'" "C4'" "C5'" "O5'" -178.090 20.000 3
2FA var_10 "C4'" "C5'" "O5'" "H5'" -179.996 20.000 1
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
2FA chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2FA chir_02 "C1'" "O4'" N9 "C2'" negativ
2FA chir_03 "C2'" "C1'" "O2'" "C3'" positiv
2FA chir_04 "C3'" "C4'" "C2'" "O3'" 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
2FA plan-1 N9 0.020
2FA plan-1 "C1'" 0.020
2FA plan-1 C4 0.020
2FA plan-1 C8 0.020
2FA plan-1 N7 0.020
2FA plan-1 N3 0.020
2FA plan-1 C5 0.020
2FA plan-1 C2 0.020
2FA plan-1 N1 0.020
2FA plan-1 C6 0.020
2FA plan-1 F 0.020
2FA plan-1 N6 0.020
2FA plan-1 H8 0.020
2FA plan-1 HN62 0.020
2FA plan-1 HN61 0.020
2FA plan-2 N6 0.020
2FA plan-2 C6 0.020
2FA plan-2 HN61 0.020
2FA plan-2 HN62 0.020
# ------------------------------------------------------
|
