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
|
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
2FD 2FD '5-(6-AMINO-2-FLUORO-PURIN-9-YL)-2-HY' non-polymer 31 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_2FD
#
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
2FD F F F 0.000 0.000 0.000 0.000
2FD C2 C CR6 0.000 -1.084 0.767 0.254
2FD N3 N NRD6 0.000 -2.281 0.280 -0.007
2FD N1 N NRD6 0.000 -0.905 1.978 0.755
2FD C6 C CR6 0.000 -1.937 2.770 1.023
2FD N6 N NH2 0.000 -1.739 4.036 1.547
2FD HN62 H H 0.000 -2.530 4.639 1.750
2FD HN61 H H 0.000 -0.801 4.376 1.735
2FD C5 C CR56 0.000 -3.233 2.293 0.766
2FD C4 C CR56 0.000 -3.371 1.002 0.228
2FD N7 N NRD5 0.000 -4.480 2.805 0.903
2FD C8 C CR15 0.000 -5.355 1.929 0.501
2FD H8 H H 0.000 -6.428 2.075 0.504
2FD N9 N NR5 0.000 -4.720 0.799 0.075
2FD "C1'" C CH1 0.000 -5.360 -0.410 -0.449
2FD "H1'" H H 0.000 -4.740 -0.846 -1.246
2FD "O4'" O O2 0.000 -6.662 -0.088 -0.965
2FD "C2'" C CH2 0.000 -5.552 -1.435 0.685
2FD "H2'1" H H 0.000 -5.230 -1.041 1.651
2FD "H2'2" H H 0.000 -5.031 -2.372 0.483
2FD "C3'" C CH1 0.000 -7.080 -1.687 0.713
2FD "H3'" H H 0.000 -7.564 -1.075 1.486
2FD "O3'" O OH1 0.000 -7.364 -3.074 0.910
2FD H1 H H 0.000 -7.005 -3.358 1.762
2FD "C4'" C CH1 0.000 -7.510 -1.230 -0.704
2FD "H4'" H H 0.000 -7.324 -2.025 -1.439
2FD "C5'" C CH2 0.000 -8.986 -0.824 -0.714
2FD "H5'1" H H 0.000 -9.126 0.054 -0.081
2FD "H5'2" H H 0.000 -9.592 -1.648 -0.330
2FD "O5'" O OH1 0.000 -9.387 -0.519 -2.052
2FD "H5'" H H 0.000 -10.319 -0.263 -2.058
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
2FD F n/a C2 START
2FD C2 F N1 .
2FD N3 C2 . .
2FD N1 C2 C6 .
2FD C6 N1 C5 .
2FD N6 C6 HN61 .
2FD HN62 N6 . .
2FD HN61 N6 . .
2FD C5 C6 N7 .
2FD C4 C5 . .
2FD N7 C5 C8 .
2FD C8 N7 N9 .
2FD H8 C8 . .
2FD N9 C8 "C1'" .
2FD "C1'" N9 "C2'" .
2FD "H1'" "C1'" . .
2FD "O4'" "C1'" . .
2FD "C2'" "C1'" "C3'" .
2FD "H2'1" "C2'" . .
2FD "H2'2" "C2'" . .
2FD "C3'" "C2'" "C4'" .
2FD "H3'" "C3'" . .
2FD "O3'" "C3'" H1 .
2FD H1 "O3'" . .
2FD "C4'" "C3'" "C5'" .
2FD "H4'" "C4'" . .
2FD "C5'" "C4'" "O5'" .
2FD "H5'1" "C5'" . .
2FD "H5'2" "C5'" . .
2FD "O5'" "C5'" "H5'" .
2FD "H5'" "O5'" . END
2FD "C4'" "O4'" . ADD
2FD N9 C4 . ADD
2FD 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
2FD "O5'" "C5'" single 1.432 0.020
2FD "H5'" "O5'" single 0.967 0.020
2FD "C5'" "C4'" single 1.524 0.020
2FD "H5'1" "C5'" single 1.092 0.020
2FD "H5'2" "C5'" single 1.092 0.020
2FD "C4'" "O4'" single 1.426 0.020
2FD "C4'" "C3'" single 1.524 0.020
2FD "H4'" "C4'" single 1.099 0.020
2FD "O4'" "C1'" single 1.426 0.020
2FD "C1'" N9 single 1.485 0.020
2FD "C2'" "C1'" single 1.524 0.020
2FD "H1'" "C1'" single 1.099 0.020
2FD N9 C4 single 1.337 0.020
2FD N9 C8 single 1.337 0.020
2FD C4 N3 double 1.355 0.020
2FD C4 C5 single 1.490 0.020
2FD N3 C2 single 1.350 0.020
2FD C2 F single 1.345 0.020
2FD N1 C2 double 1.350 0.020
2FD C6 N1 single 1.350 0.020
2FD N6 C6 single 1.355 0.020
2FD C5 C6 double 1.490 0.020
2FD HN61 N6 single 1.010 0.020
2FD HN62 N6 single 1.010 0.020
2FD N7 C5 single 1.350 0.020
2FD C8 N7 double 1.350 0.020
2FD H8 C8 single 1.083 0.020
2FD "C3'" "C2'" single 1.524 0.020
2FD "H2'1" "C2'" single 1.092 0.020
2FD "H2'2" "C2'" single 1.092 0.020
2FD "O3'" "C3'" single 1.432 0.020
2FD "H3'" "C3'" single 1.099 0.020
2FD H1 "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
2FD F C2 N3 120.000 3.000
2FD F C2 N1 120.000 3.000
2FD N3 C2 N1 120.000 3.000
2FD C2 N3 C4 120.000 3.000
2FD C2 N1 C6 120.000 3.000
2FD N1 C6 N6 120.000 3.000
2FD N1 C6 C5 120.000 3.000
2FD N6 C6 C5 120.000 3.000
2FD C6 N6 HN62 120.000 3.000
2FD C6 N6 HN61 120.000 3.000
2FD HN62 N6 HN61 120.000 3.000
2FD C6 C5 C4 120.000 3.000
2FD C6 C5 N7 132.000 3.000
2FD C4 C5 N7 108.000 3.000
2FD C5 C4 N9 108.000 3.000
2FD C5 C4 N3 120.000 3.000
2FD N9 C4 N3 132.000 3.000
2FD C5 N7 C8 108.000 3.000
2FD N7 C8 H8 126.000 3.000
2FD N7 C8 N9 108.000 3.000
2FD H8 C8 N9 126.000 3.000
2FD C8 N9 "C1'" 126.000 3.000
2FD C8 N9 C4 108.000 3.000
2FD "C1'" N9 C4 126.000 3.000
2FD N9 "C1'" "H1'" 109.470 3.000
2FD N9 "C1'" "O4'" 109.470 3.000
2FD N9 "C1'" "C2'" 109.470 3.000
2FD "H1'" "C1'" "O4'" 109.470 3.000
2FD "H1'" "C1'" "C2'" 108.340 3.000
2FD "O4'" "C1'" "C2'" 109.470 3.000
2FD "C1'" "O4'" "C4'" 111.800 3.000
2FD "C1'" "C2'" "H2'1" 109.470 3.000
2FD "C1'" "C2'" "H2'2" 109.470 3.000
2FD "C1'" "C2'" "C3'" 111.000 3.000
2FD "H2'1" "C2'" "H2'2" 107.900 3.000
2FD "H2'1" "C2'" "C3'" 109.470 3.000
2FD "H2'2" "C2'" "C3'" 109.470 3.000
2FD "C2'" "C3'" "H3'" 108.340 3.000
2FD "C2'" "C3'" "O3'" 109.470 3.000
2FD "C2'" "C3'" "C4'" 111.000 3.000
2FD "H3'" "C3'" "O3'" 109.470 3.000
2FD "H3'" "C3'" "C4'" 108.340 3.000
2FD "O3'" "C3'" "C4'" 109.470 3.000
2FD "C3'" "O3'" H1 109.470 3.000
2FD "C3'" "C4'" "H4'" 108.340 3.000
2FD "C3'" "C4'" "C5'" 111.000 3.000
2FD "C3'" "C4'" "O4'" 109.470 3.000
2FD "H4'" "C4'" "C5'" 108.340 3.000
2FD "H4'" "C4'" "O4'" 109.470 3.000
2FD "C5'" "C4'" "O4'" 109.470 3.000
2FD "C4'" "C5'" "H5'1" 109.470 3.000
2FD "C4'" "C5'" "H5'2" 109.470 3.000
2FD "C4'" "C5'" "O5'" 109.470 3.000
2FD "H5'1" "C5'" "H5'2" 107.900 3.000
2FD "H5'1" "C5'" "O5'" 109.470 3.000
2FD "H5'2" "C5'" "O5'" 109.470 3.000
2FD "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
2FD CONST_1 F C2 N3 C4 180.000 0.000 0
2FD CONST_2 F C2 N1 C6 180.000 0.000 0
2FD CONST_3 C2 N1 C6 C5 0.000 0.000 0
2FD CONST_4 N1 C6 N6 HN61 -0.015 0.000 0
2FD CONST_5 N1 C6 C5 N7 180.000 0.000 0
2FD CONST_6 C6 C5 C4 N9 180.000 0.000 0
2FD CONST_7 C5 C4 N3 C2 0.000 0.000 0
2FD CONST_8 C6 C5 N7 C8 180.000 0.000 0
2FD CONST_9 C5 N7 C8 N9 0.000 0.000 0
2FD CONST_10 N7 C8 N9 "C1'" 180.000 0.000 0
2FD CONST_11 C8 N9 C4 C5 0.000 0.000 0
2FD var_1 C8 N9 "C1'" "C2'" -94.718 20.000 1
2FD var_2 N9 "C1'" "O4'" "C4'" -150.000 20.000 1
2FD var_3 N9 "C1'" "C2'" "C3'" 120.000 20.000 3
2FD var_4 "C1'" "C2'" "C3'" "C4'" 30.000 20.000 3
2FD var_5 "C2'" "C3'" "O3'" H1 61.454 20.000 1
2FD var_6 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
2FD var_7 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
2FD var_8 "C3'" "C4'" "C5'" "O5'" -175.003 20.000 3
2FD var_9 "C4'" "C5'" "O5'" "H5'" 179.990 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
2FD chir_01 "C4'" "C5'" "O4'" "C3'" negativ
2FD chir_02 "C1'" "O4'" N9 "C2'" negativ
2FD chir_03 "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
2FD plan-1 N9 0.020
2FD plan-1 "C1'" 0.020
2FD plan-1 C4 0.020
2FD plan-1 C8 0.020
2FD plan-1 N7 0.020
2FD plan-1 N3 0.020
2FD plan-1 C5 0.020
2FD plan-1 C2 0.020
2FD plan-1 N1 0.020
2FD plan-1 C6 0.020
2FD plan-1 F 0.020
2FD plan-1 N6 0.020
2FD plan-1 H8 0.020
2FD plan-1 HN62 0.020
2FD plan-1 HN61 0.020
2FD plan-2 N6 0.020
2FD plan-2 C6 0.020
2FD plan-2 HN61 0.020
2FD plan-2 HN62 0.020
# ------------------------------------------------------
|
