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
CFZ CFZ '. ' non-polymer 32 21 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CFZ
#
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
CFZ O3P O OP -0.666 0.000 0.000 0.000
CFZ P P P 0.000 -1.106 1.005 0.237
CFZ O1P O OP -0.666 -0.721 1.918 1.381
CFZ O2P O OP -0.666 -1.317 1.828 -1.015
CFZ "O5'" O O2 0.000 -2.467 0.229 0.605
CFZ "C5'" C CH2 0.000 -3.147 -0.630 -0.314
CFZ "H5'" H H 0.000 -2.483 -1.446 -0.607
CFZ "H5'A" H H 0.000 -3.434 -0.059 -1.200
CFZ "C4'" C CH1 0.000 -4.398 -1.202 0.353
CFZ "H4'" H H 0.000 -4.140 -1.669 1.314
CFZ "C3'" C CH1 0.000 -5.081 -2.230 -0.577
CFZ "H3'" H H 0.000 -4.819 -2.035 -1.626
CFZ "O3'" O OH1 0.000 -4.713 -3.561 -0.207
CFZ "HO3'" H H 0.000 -5.195 -4.193 -0.757
CFZ "C2'" C CH1 0.000 -6.591 -2.001 -0.344
CFZ "H2'" H H 0.000 -7.083 -1.692 -1.277
CFZ "F2'" F F 0.000 -7.189 -3.160 0.165
CFZ "O4'" O O2 0.000 -5.386 -0.166 0.547
CFZ "C1'" C CH1 0.000 -6.643 -0.863 0.699
CFZ "H1'" H H 0.000 -6.732 -1.277 1.713
CFZ N1 N NR6 0.000 -7.763 0.038 0.416
CFZ C6 C CR16 0.000 -8.765 0.181 1.327
CFZ H6 H H 0.000 -8.740 -0.371 2.258
CFZ C5 C CR16 0.000 -9.791 1.021 1.056
CFZ H5 H H 0.000 -10.594 1.157 1.771
CFZ C4 C CR6 0.000 -9.800 1.716 -0.170
CFZ N4 N NH2 0.000 -10.834 2.571 -0.474
CFZ HN4A H H 0.000 -11.596 2.706 0.180
CFZ HN4 H H 0.000 -10.843 3.072 -1.356
CFZ N3 N NRD6 0.000 -8.805 1.541 -1.030
CFZ C2 C CR6 0.000 -7.798 0.716 -0.746
CFZ O2 O O 0.000 -6.895 0.572 -1.553
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
CFZ O3P n/a P START
CFZ P O3P "O5'" .
CFZ O1P P . .
CFZ O2P P . .
CFZ "O5'" P "C5'" .
CFZ "C5'" "O5'" "C4'" .
CFZ "H5'" "C5'" . .
CFZ "H5'A" "C5'" . .
CFZ "C4'" "C5'" "O4'" .
CFZ "H4'" "C4'" . .
CFZ "C3'" "C4'" "C2'" .
CFZ "H3'" "C3'" . .
CFZ "O3'" "C3'" "HO3'" .
CFZ "HO3'" "O3'" . .
CFZ "C2'" "C3'" "F2'" .
CFZ "H2'" "C2'" . .
CFZ "F2'" "C2'" . .
CFZ "O4'" "C4'" "C1'" .
CFZ "C1'" "O4'" N1 .
CFZ "H1'" "C1'" . .
CFZ N1 "C1'" C6 .
CFZ C6 N1 C5 .
CFZ H6 C6 . .
CFZ C5 C6 C4 .
CFZ H5 C5 . .
CFZ C4 C5 N3 .
CFZ N4 C4 HN4 .
CFZ HN4A N4 . .
CFZ HN4 N4 . .
CFZ N3 C4 C2 .
CFZ C2 N3 O2 .
CFZ O2 C2 . END
CFZ N1 C2 . ADD
CFZ "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
CFZ O2P P deloc 1.510 0.020
CFZ "O5'" P single 1.610 0.020
CFZ O1P P deloc 1.510 0.020
CFZ P O3P deloc 1.510 0.020
CFZ C6 N1 single 1.337 0.020
CFZ N1 C2 single 1.410 0.020
CFZ N1 "C1'" single 1.465 0.020
CFZ C2 N3 single 1.350 0.020
CFZ O2 C2 double 1.250 0.020
CFZ N3 C4 double 1.350 0.020
CFZ N4 C4 single 1.355 0.020
CFZ C4 C5 single 1.390 0.020
CFZ HN4 N4 single 1.010 0.020
CFZ HN4A N4 single 1.010 0.020
CFZ C5 C6 double 1.390 0.020
CFZ H5 C5 single 1.083 0.020
CFZ H6 C6 single 1.083 0.020
CFZ "C1'" "C2'" single 1.524 0.020
CFZ "C1'" "O4'" single 1.426 0.020
CFZ "H1'" "C1'" single 1.099 0.020
CFZ "C2'" "C3'" single 1.524 0.020
CFZ "F2'" "C2'" single 1.370 0.020
CFZ "H2'" "C2'" single 1.099 0.020
CFZ "O3'" "C3'" single 1.432 0.020
CFZ "C3'" "C4'" single 1.524 0.020
CFZ "H3'" "C3'" single 1.099 0.020
CFZ "HO3'" "O3'" single 0.967 0.020
CFZ "O4'" "C4'" single 1.426 0.020
CFZ "C4'" "C5'" single 1.524 0.020
CFZ "H4'" "C4'" single 1.099 0.020
CFZ "C5'" "O5'" single 1.426 0.020
CFZ "H5'" "C5'" single 1.092 0.020
CFZ "H5'A" "C5'" single 1.092 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
CFZ O3P P O1P 119.900 3.000
CFZ O3P P O2P 119.900 3.000
CFZ O3P P "O5'" 108.200 3.000
CFZ O1P P O2P 119.900 3.000
CFZ O1P P "O5'" 108.200 3.000
CFZ O2P P "O5'" 108.200 3.000
CFZ P "O5'" "C5'" 120.500 3.000
CFZ "O5'" "C5'" "H5'" 109.470 3.000
CFZ "O5'" "C5'" "H5'A" 109.470 3.000
CFZ "O5'" "C5'" "C4'" 109.470 3.000
CFZ "H5'" "C5'" "H5'A" 107.900 3.000
CFZ "H5'" "C5'" "C4'" 109.470 3.000
CFZ "H5'A" "C5'" "C4'" 109.470 3.000
CFZ "C5'" "C4'" "H4'" 108.340 3.000
CFZ "C5'" "C4'" "C3'" 111.000 3.000
CFZ "C5'" "C4'" "O4'" 109.470 3.000
CFZ "H4'" "C4'" "C3'" 108.340 3.000
CFZ "H4'" "C4'" "O4'" 109.470 3.000
CFZ "C3'" "C4'" "O4'" 109.470 3.000
CFZ "C4'" "C3'" "H3'" 108.340 3.000
CFZ "C4'" "C3'" "O3'" 109.470 3.000
CFZ "C4'" "C3'" "C2'" 111.000 3.000
CFZ "H3'" "C3'" "O3'" 109.470 3.000
CFZ "H3'" "C3'" "C2'" 108.340 3.000
CFZ "O3'" "C3'" "C2'" 109.470 3.000
CFZ "C3'" "O3'" "HO3'" 109.470 3.000
CFZ "C3'" "C2'" "H2'" 108.340 3.000
CFZ "C3'" "C2'" "F2'" 109.500 3.000
CFZ "C3'" "C2'" "C1'" 111.000 3.000
CFZ "H2'" "C2'" "F2'" 109.500 3.000
CFZ "H2'" "C2'" "C1'" 108.340 3.000
CFZ "F2'" "C2'" "C1'" 109.500 3.000
CFZ "C4'" "O4'" "C1'" 111.800 3.000
CFZ "O4'" "C1'" "H1'" 109.470 3.000
CFZ "O4'" "C1'" N1 109.470 3.000
CFZ "O4'" "C1'" "C2'" 109.470 3.000
CFZ "H1'" "C1'" N1 109.470 3.000
CFZ "H1'" "C1'" "C2'" 108.340 3.000
CFZ N1 "C1'" "C2'" 109.470 3.000
CFZ "C1'" N1 C6 120.000 3.000
CFZ "C1'" N1 C2 120.000 3.000
CFZ C6 N1 C2 120.000 3.000
CFZ N1 C6 H6 120.000 3.000
CFZ N1 C6 C5 120.000 3.000
CFZ H6 C6 C5 120.000 3.000
CFZ C6 C5 H5 120.000 3.000
CFZ C6 C5 C4 120.000 3.000
CFZ H5 C5 C4 120.000 3.000
CFZ C5 C4 N4 120.000 3.000
CFZ C5 C4 N3 120.000 3.000
CFZ N4 C4 N3 120.000 3.000
CFZ C4 N4 HN4A 120.000 3.000
CFZ C4 N4 HN4 120.000 3.000
CFZ HN4A N4 HN4 120.000 3.000
CFZ C4 N3 C2 120.000 3.000
CFZ N3 C2 O2 120.000 3.000
CFZ N3 C2 N1 120.000 3.000
CFZ 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
CFZ var_1 O3P P "O5'" "C5'" -64.988 20.000 1
CFZ var_2 P "O5'" "C5'" "C4'" 179.991 20.000 1
CFZ var_3 "O5'" "C5'" "C4'" "O4'" 69.568 20.000 3
CFZ var_4 "C5'" "C4'" "C3'" "C2'" -150.000 20.000 3
CFZ var_5 "C4'" "C3'" "O3'" "HO3'" 176.103 20.000 1
CFZ var_6 "C4'" "C3'" "C2'" "F2'" -120.000 20.000 3
CFZ var_7 "C5'" "C4'" "O4'" "C1'" 150.000 20.000 1
CFZ var_8 "C4'" "O4'" "C1'" N1 -150.000 20.000 1
CFZ var_9 "O4'" "C1'" "C2'" "C3'" 30.000 20.000 3
CFZ var_10 "O4'" "C1'" N1 C6 -126.737 20.000 1
CFZ CONST_1 "C1'" N1 C2 N3 180.000 0.000 0
CFZ CONST_2 "C1'" N1 C6 C5 180.000 0.000 0
CFZ CONST_3 N1 C6 C5 C4 0.000 0.000 0
CFZ CONST_4 C6 C5 C4 N3 0.000 0.000 0
CFZ CONST_5 C5 C4 N4 HN4 -179.968 0.000 0
CFZ CONST_6 C5 C4 N3 C2 0.000 0.000 0
CFZ 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
CFZ chir_01 "C1'" N1 "C2'" "O4'" negativ
CFZ chir_02 "C2'" "C1'" "F2'" "C3'" positiv
CFZ chir_03 "C3'" "C2'" "O3'" "C4'" positiv
CFZ 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
CFZ plan-1 N1 0.020
CFZ plan-1 C2 0.020
CFZ plan-1 C6 0.020
CFZ plan-1 "C1'" 0.020
CFZ plan-1 N3 0.020
CFZ plan-1 C4 0.020
CFZ plan-1 C5 0.020
CFZ plan-1 O2 0.020
CFZ plan-1 N4 0.020
CFZ plan-1 H5 0.020
CFZ plan-1 H6 0.020
CFZ plan-1 HN4A 0.020
CFZ plan-1 HN4 0.020
CFZ plan-2 N4 0.020
CFZ plan-2 C4 0.020
CFZ plan-2 HN4 0.020
CFZ plan-2 HN4A 0.020
# ------------------------------------------------------
|
