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
|
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
CFL CFL '"4-amino-1-(2-deoxy-2-fluoro-5-O-pho' non-polymer 32 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CFL
#
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
CFL F F F 0.000 0.000 0.000 0.000
CFL "C2'" C CH1 0.000 -0.779 -0.824 -0.819
CFL "H2'" H H 0.000 -0.142 -1.520 -1.382
CFL "C3'" C CH1 0.000 -1.817 -1.600 0.024
CFL "H3'" H H 0.000 -1.725 -1.338 1.087
CFL "O3'" O OH1 0.000 -1.660 -3.009 -0.160
CFL "HO3'" H H 0.000 -0.804 -3.286 0.194
CFL "C4'" C CH1 0.000 -3.180 -1.131 -0.533
CFL "H4'" H H 0.000 -3.541 -1.830 -1.300
CFL "C5'" C CH2 0.000 -4.204 -1.004 0.596
CFL "H5'1" H H 0.000 -3.865 -0.253 1.312
CFL "H5'2" H H 0.000 -4.308 -1.966 1.102
CFL "O5'" O O2 0.000 -5.466 -0.612 0.053
CFL P P P 0.000 -6.490 -0.498 1.290
CFL O2P O OP -0.666 -5.923 0.443 2.330
CFL O1P O OP -0.666 -7.819 0.034 0.798
CFL O3P O OP -0.666 -6.692 -1.865 1.905
CFL "C1'" C CH1 0.000 -1.638 0.025 -1.782
CFL "H1'" H H 0.000 -1.762 -0.495 -2.742
CFL "O4'" O O2 0.000 -2.913 0.163 -1.118
CFL N1 N NR6 0.000 -1.026 1.339 -1.989
CFL C6 C CR16 0.000 -0.594 1.699 -3.230
CFL H6 H H 0.000 -0.696 1.016 -4.065
CFL C5 C CR16 0.000 -0.035 2.919 -3.409
CFL H5 H H 0.000 0.305 3.229 -4.390
CFL C4 C CR6 0.000 0.096 3.780 -2.300
CFL N4 N NH2 0.000 0.665 5.023 -2.454
CFL HN42 H H 0.000 0.997 5.327 -3.363
CFL HN41 H H 0.000 0.756 5.647 -1.660
CFL N3 N NRD6 0.000 -0.339 3.387 -1.111
CFL C2 C CR6 0.000 -0.892 2.186 -0.951
CFL O2 O O 0.000 -1.284 1.848 0.154
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
CFL F n/a "C2'" START
CFL "C2'" F "C1'" .
CFL "H2'" "C2'" . .
CFL "C3'" "C2'" "C4'" .
CFL "H3'" "C3'" . .
CFL "O3'" "C3'" "HO3'" .
CFL "HO3'" "O3'" . .
CFL "C4'" "C3'" "C5'" .
CFL "H4'" "C4'" . .
CFL "C5'" "C4'" "O5'" .
CFL "H5'1" "C5'" . .
CFL "H5'2" "C5'" . .
CFL "O5'" "C5'" P .
CFL P "O5'" O3P .
CFL O2P P . .
CFL O1P P . .
CFL O3P P . .
CFL "C1'" "C2'" N1 .
CFL "H1'" "C1'" . .
CFL "O4'" "C1'" . .
CFL N1 "C1'" C6 .
CFL C6 N1 C5 .
CFL H6 C6 . .
CFL C5 C6 C4 .
CFL H5 C5 . .
CFL C4 C5 N3 .
CFL N4 C4 HN41 .
CFL HN42 N4 . .
CFL HN41 N4 . .
CFL N3 C4 C2 .
CFL C2 N3 O2 .
CFL O2 C2 . END
CFL "C4'" "O4'" . ADD
CFL N1 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
CFL O3P P deloc 1.510 0.020
CFL O1P P deloc 1.510 0.020
CFL O2P P deloc 1.510 0.020
CFL P "O5'" single 1.610 0.020
CFL "O5'" "C5'" single 1.426 0.020
CFL "C5'" "C4'" single 1.524 0.020
CFL "H5'1" "C5'" single 1.092 0.020
CFL "H5'2" "C5'" single 1.092 0.020
CFL "C4'" "O4'" single 1.426 0.020
CFL "C4'" "C3'" single 1.524 0.020
CFL "H4'" "C4'" single 1.099 0.020
CFL "O4'" "C1'" single 1.426 0.020
CFL "O3'" "C3'" single 1.432 0.020
CFL "C3'" "C2'" single 1.524 0.020
CFL "H3'" "C3'" single 1.099 0.020
CFL "HO3'" "O3'" single 0.967 0.020
CFL "C1'" "C2'" single 1.524 0.020
CFL "C2'" F single 1.370 0.020
CFL "H2'" "C2'" single 1.099 0.020
CFL N1 "C1'" single 1.465 0.020
CFL "H1'" "C1'" single 1.099 0.020
CFL N1 C2 single 1.410 0.020
CFL C6 N1 single 1.337 0.020
CFL O2 C2 double 1.250 0.020
CFL C2 N3 single 1.350 0.020
CFL N3 C4 double 1.350 0.020
CFL N4 C4 single 1.355 0.020
CFL C4 C5 single 1.390 0.020
CFL HN41 N4 single 1.010 0.020
CFL HN42 N4 single 1.010 0.020
CFL C5 C6 double 1.390 0.020
CFL H5 C5 single 1.083 0.020
CFL H6 C6 single 1.083 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
CFL F "C2'" "H2'" 109.500 3.000
CFL F "C2'" "C3'" 109.500 3.000
CFL F "C2'" "C1'" 109.500 3.000
CFL "H2'" "C2'" "C3'" 108.340 3.000
CFL "H2'" "C2'" "C1'" 108.340 3.000
CFL "C3'" "C2'" "C1'" 111.000 3.000
CFL "C2'" "C3'" "H3'" 108.340 3.000
CFL "C2'" "C3'" "O3'" 109.470 3.000
CFL "C2'" "C3'" "C4'" 111.000 3.000
CFL "H3'" "C3'" "O3'" 109.470 3.000
CFL "H3'" "C3'" "C4'" 108.340 3.000
CFL "O3'" "C3'" "C4'" 109.470 3.000
CFL "C3'" "O3'" "HO3'" 109.470 3.000
CFL "C3'" "C4'" "H4'" 108.340 3.000
CFL "C3'" "C4'" "C5'" 111.000 3.000
CFL "C3'" "C4'" "O4'" 109.470 3.000
CFL "H4'" "C4'" "C5'" 108.340 3.000
CFL "H4'" "C4'" "O4'" 109.470 3.000
CFL "C5'" "C4'" "O4'" 109.470 3.000
CFL "C4'" "C5'" "H5'1" 109.470 3.000
CFL "C4'" "C5'" "H5'2" 109.470 3.000
CFL "C4'" "C5'" "O5'" 109.470 3.000
CFL "H5'1" "C5'" "H5'2" 107.900 3.000
CFL "H5'1" "C5'" "O5'" 109.470 3.000
CFL "H5'2" "C5'" "O5'" 109.470 3.000
CFL "C5'" "O5'" P 120.500 3.000
CFL "O5'" P O2P 108.200 3.000
CFL "O5'" P O1P 108.200 3.000
CFL "O5'" P O3P 108.200 3.000
CFL O2P P O1P 119.900 3.000
CFL O2P P O3P 119.900 3.000
CFL O1P P O3P 119.900 3.000
CFL "C2'" "C1'" "H1'" 108.340 3.000
CFL "C2'" "C1'" "O4'" 109.470 3.000
CFL "C2'" "C1'" N1 109.470 3.000
CFL "H1'" "C1'" "O4'" 109.470 3.000
CFL "H1'" "C1'" N1 109.470 3.000
CFL "O4'" "C1'" N1 109.470 3.000
CFL "C1'" "O4'" "C4'" 111.800 3.000
CFL "C1'" N1 C6 120.000 3.000
CFL "C1'" N1 C2 120.000 3.000
CFL C6 N1 C2 120.000 3.000
CFL N1 C6 H6 120.000 3.000
CFL N1 C6 C5 120.000 3.000
CFL H6 C6 C5 120.000 3.000
CFL C6 C5 H5 120.000 3.000
CFL C6 C5 C4 120.000 3.000
CFL H5 C5 C4 120.000 3.000
CFL C5 C4 N4 120.000 3.000
CFL C5 C4 N3 120.000 3.000
CFL N4 C4 N3 120.000 3.000
CFL C4 N4 HN42 120.000 3.000
CFL C4 N4 HN41 120.000 3.000
CFL HN42 N4 HN41 120.000 3.000
CFL C4 N3 C2 120.000 3.000
CFL N3 C2 O2 120.000 3.000
CFL N3 C2 N1 120.000 3.000
CFL O2 C2 N1 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
CFL var_1 F "C2'" "C3'" "C4'" 120.000 20.000 3
CFL var_2 "C2'" "C3'" "O3'" "HO3'" 65.347 20.000 1
CFL var_3 "C2'" "C3'" "C4'" "C5'" -150.000 20.000 3
CFL var_4 "C3'" "C4'" "O4'" "C1'" 30.000 20.000 1
CFL var_5 "C3'" "C4'" "C5'" "O5'" -178.100 20.000 3
CFL var_6 "C4'" "C5'" "O5'" P -179.967 20.000 1
CFL var_7 "C5'" "O5'" P O3P -64.991 20.000 1
CFL var_8 F "C2'" "C1'" N1 30.000 20.000 3
CFL var_9 "C2'" "C1'" "O4'" "C4'" -30.000 20.000 1
CFL var_10 "C2'" "C1'" N1 C6 116.517 20.000 1
CFL CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
CFL CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
CFL CONST_3 N1 C6 C5 C4 0.000 0.000 0
CFL CONST_4 C6 C5 C4 N3 0.000 0.000 0
CFL CONST_5 C5 C4 N4 HN41 179.713 0.000 0
CFL CONST_6 C5 C4 N3 C2 0.000 0.000 0
CFL CONST_7 C4 N3 C2 O2 180.000 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
CFL chir_01 "C4'" "C5'" "O4'" "C3'" negativ
CFL chir_02 "C3'" "C4'" "O3'" "C2'" negativ
CFL chir_03 "C2'" "C3'" "C1'" F negativ
CFL chir_04 "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
CFL plan-1 N1 0.020
CFL plan-1 "C1'" 0.020
CFL plan-1 C2 0.020
CFL plan-1 C6 0.020
CFL plan-1 N3 0.020
CFL plan-1 C4 0.020
CFL plan-1 C5 0.020
CFL plan-1 O2 0.020
CFL plan-1 N4 0.020
CFL plan-1 H5 0.020
CFL plan-1 H6 0.020
CFL plan-1 HN42 0.020
CFL plan-1 HN41 0.020
CFL plan-2 N4 0.020
CFL plan-2 C4 0.020
CFL plan-2 HN41 0.020
CFL plan-2 HN42 0.020
# ------------------------------------------------------
|
