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
|
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
HCX HCX '(SOUTH) BICYCLO[3.1.0]HEXANE ' non-polymer 25 12 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_HCX
#
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
HCX O1P O O 0.000 0.000 0.000 0.000
HCX P P P 0.000 -0.567 -1.045 -0.924
HCX HP1 H H 0.000 0.019 -0.955 -2.175
HCX O2P O OH1 0.000 -0.383 -2.542 -0.316
HCX H2P H H 0.000 -0.598 -2.722 0.612
HCX "O5'" O O2 0.000 -2.186 -0.939 -1.044
HCX "C5'" C CH2 0.000 -2.889 -2.018 -1.631
HCX "H5'1" H H 0.000 -3.175 -2.739 -0.862
HCX "H5'2" H H 0.000 -2.260 -2.512 -2.375
HCX "C4'" C CH1 0.000 -4.143 -1.468 -2.307
HCX "H4'" H H 0.000 -4.688 -2.280 -2.809
HCX "C3'" C CH1 0.000 -3.785 -0.360 -3.324
HCX H1 H H 0.000 -2.753 -0.479 -3.682
HCX "O3'" O OH1 0.000 -4.702 -0.385 -4.415
HCX "H3'" H H 0.000 -4.457 -1.094 -5.024
HCX "C2'" C CH2 0.000 -3.948 0.971 -2.571
HCX "H2'1" H H 0.000 -4.355 1.748 -3.220
HCX "H2'2" H H 0.000 -2.999 1.309 -2.150
HCX "C1'" C CH1 0.000 -4.918 0.687 -1.458
HCX "H1'" H H 0.000 -4.818 1.287 -0.543
HCX C7 C CH2 0.000 -6.244 0.016 -1.696
HCX H72 H H 0.000 -6.608 -0.333 -2.666
HCX H71 H H 0.000 -7.031 -0.105 -0.949
HCX C4 C CH1 0.000 -5.037 -0.790 -1.292
HCX H4 H H 0.000 -5.017 -1.182 -0.266
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
HCX O1P n/a P START
HCX P O1P "O5'" .
HCX HP1 P . .
HCX O2P P H2P .
HCX H2P O2P . .
HCX "O5'" P "C5'" .
HCX "C5'" "O5'" "C4'" .
HCX "H5'1" "C5'" . .
HCX "H5'2" "C5'" . .
HCX "C4'" "C5'" "C3'" .
HCX "H4'" "C4'" . .
HCX "C3'" "C4'" "C2'" .
HCX H1 "C3'" . .
HCX "O3'" "C3'" "H3'" .
HCX "H3'" "O3'" . .
HCX "C2'" "C3'" "C1'" .
HCX "H2'1" "C2'" . .
HCX "H2'2" "C2'" . .
HCX "C1'" "C2'" C4 .
HCX "H1'" "C1'" . .
HCX C7 "C1'" H71 .
HCX H72 C7 . .
HCX H71 C7 . .
HCX C4 "C1'" H4 .
HCX H4 C4 . END
HCX C4 C7 . ADD
HCX C4 "C4'" . 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
HCX P O1P double 1.480 0.020
HCX O2P P single 1.610 0.020
HCX "O5'" P single 1.610 0.020
HCX H2P O2P single 0.967 0.020
HCX "C5'" "O5'" single 1.426 0.020
HCX C4 C7 single 1.524 0.020
HCX C4 "C4'" single 1.524 0.020
HCX C4 "C1'" single 1.524 0.020
HCX H4 C4 single 1.099 0.020
HCX C7 "C1'" single 1.524 0.020
HCX H71 C7 single 1.092 0.020
HCX H72 C7 single 1.092 0.020
HCX "C1'" "C2'" single 1.524 0.020
HCX "C2'" "C3'" single 1.524 0.020
HCX "H2'1" "C2'" single 1.092 0.020
HCX "H2'2" "C2'" single 1.092 0.020
HCX "C4'" "C5'" single 1.524 0.020
HCX "H5'1" "C5'" single 1.092 0.020
HCX "H5'2" "C5'" single 1.092 0.020
HCX "C3'" "C4'" single 1.524 0.020
HCX "H4'" "C4'" single 1.099 0.020
HCX "H1'" "C1'" single 1.099 0.020
HCX "O3'" "C3'" single 1.432 0.020
HCX H1 "C3'" single 1.099 0.020
HCX "H3'" "O3'" single 0.967 0.020
HCX HP1 P single 1.383 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
HCX O1P P HP1 109.500 3.000
HCX O1P P O2P 109.500 3.000
HCX O1P P "O5'" 109.500 3.000
HCX HP1 P O2P 109.500 3.000
HCX HP1 P "O5'" 109.500 3.000
HCX O2P P "O5'" 109.500 3.000
HCX P O2P H2P 120.000 3.000
HCX P "O5'" "C5'" 120.500 3.000
HCX "O5'" "C5'" "H5'1" 109.470 3.000
HCX "O5'" "C5'" "H5'2" 109.470 3.000
HCX "O5'" "C5'" "C4'" 109.470 3.000
HCX "H5'1" "C5'" "H5'2" 107.900 3.000
HCX "H5'1" "C5'" "C4'" 109.470 3.000
HCX "H5'2" "C5'" "C4'" 109.470 3.000
HCX "C5'" "C4'" "H4'" 108.340 3.000
HCX "C5'" "C4'" "C3'" 111.000 3.000
HCX "C5'" "C4'" C4 111.000 3.000
HCX "H4'" "C4'" "C3'" 108.340 3.000
HCX "H4'" "C4'" C4 108.340 3.000
HCX "C3'" "C4'" C4 111.000 3.000
HCX "C4'" "C3'" H1 108.340 3.000
HCX "C4'" "C3'" "O3'" 109.470 3.000
HCX "C4'" "C3'" "C2'" 111.000 3.000
HCX H1 "C3'" "O3'" 109.470 3.000
HCX H1 "C3'" "C2'" 108.340 3.000
HCX "O3'" "C3'" "C2'" 109.470 3.000
HCX "C3'" "O3'" "H3'" 109.470 3.000
HCX "C3'" "C2'" "H2'1" 109.470 3.000
HCX "C3'" "C2'" "H2'2" 109.470 3.000
HCX "C3'" "C2'" "C1'" 111.000 3.000
HCX "H2'1" "C2'" "H2'2" 107.900 3.000
HCX "H2'1" "C2'" "C1'" 109.470 3.000
HCX "H2'2" "C2'" "C1'" 109.470 3.000
HCX "C2'" "C1'" "H1'" 108.340 3.000
HCX "C2'" "C1'" C7 109.470 3.000
HCX "C2'" "C1'" C4 111.000 3.000
HCX "H1'" "C1'" C7 108.340 3.000
HCX "H1'" "C1'" C4 108.340 3.000
HCX C7 "C1'" C4 60.000 3.000
HCX "C1'" C7 H72 109.470 3.000
HCX "C1'" C7 H71 109.470 3.000
HCX "C1'" C7 C4 60.000 3.000
HCX H72 C7 H71 107.900 3.000
HCX H72 C7 C4 109.470 3.000
HCX H71 C7 C4 109.470 3.000
HCX "C1'" C4 H4 108.340 3.000
HCX "C1'" C4 C7 60.000 3.000
HCX "C1'" C4 "C4'" 111.000 3.000
HCX C7 C4 "C4'" 111.000 3.000
HCX H4 C4 C7 108.340 3.000
HCX H4 C4 "C4'" 108.340 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
HCX var_1 O1P P O2P H2P 45.823 20.000 1
HCX var_2 O1P P "O5'" "C5'" -166.304 20.000 1
HCX var_3 P "O5'" "C5'" "C4'" -149.995 20.000 1
HCX var_4 "O5'" "C5'" "C4'" "C3'" 55.398 20.000 3
HCX var_5 "C5'" "C4'" "C3'" "C2'" -90.000 20.000 3
HCX var_6 "C4'" "C3'" "O3'" "H3'" -79.209 20.000 1
HCX var_7 "C4'" "C3'" "C2'" "C1'" -30.000 20.000 3
HCX var_8 "C3'" "C2'" "C1'" C4 30.000 20.000 3
HCX var_9 "C2'" "C1'" C7 C4 90.000 20.000 3
HCX var_10 "C2'" "C1'" C4 C7 -117.248 20.000 3
HCX var_11 "C1'" C4 "C4'" "C5'" 90.000 20.000 3
HCX var_1 "C4'" C4 C7 "C1'" 0.000 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
HCX chir_01 C4 C7 "C4'" "C1'" negativ
HCX chir_02 "C4'" C4 "C5'" "C3'" positiv
HCX chir_03 "C1'" C4 C7 "C2'" positiv
HCX chir_04 "C3'" "C2'" "C4'" "O3'" negativ
# ------------------------------------------------------
|
