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
|
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
AOL AOL '(1R,2R,3S,4S,5R)-5-AMINOCYCLOPENTANE' non-polymer 21 10 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_AOL
#
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
AOL O1 O OH1 0.000 0.000 0.000 0.000
AOL HO1 H H 0.000 0.056 0.298 0.918
AOL C1 C CH1 0.000 -0.939 0.811 -0.707
AOL H1 H H 0.000 -0.615 1.862 -0.709
AOL C2 C CH1 0.000 -2.351 0.680 -0.080
AOL H2 H H 0.000 -2.988 1.525 -0.377
AOL O2 O OH1 0.000 -2.269 0.585 1.343
AOL HO2 H H 0.000 -3.151 0.423 1.705
AOL C3 C CH1 0.000 -2.875 -0.643 -0.691
AOL H3 H H 0.000 -3.974 -0.662 -0.681
AOL O3 O OH1 0.000 -2.349 -1.767 0.018
AOL HO3 H H 0.000 -2.688 -1.763 0.923
AOL C5 C CH1 0.000 -1.120 0.299 -2.152
AOL H5 H H 0.000 -1.290 1.145 -2.833
AOL N5 N NH2 0.000 0.071 -0.452 -2.570
AOL HN52 H H 0.000 -0.002 -1.434 -2.810
AOL HN51 H H 0.000 0.973 0.006 -2.621
AOL C4 C CH1 0.000 -2.349 -0.625 -2.140
AOL H4 H H 0.000 -3.122 -0.231 -2.816
AOL O4 O OH1 0.000 -1.975 -1.944 -2.542
AOL HO4 H H 0.000 -2.754 -2.516 -2.533
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
AOL O1 n/a C1 START
AOL HO1 O1 . .
AOL C1 O1 C5 .
AOL H1 C1 . .
AOL C2 C1 C3 .
AOL H2 C2 . .
AOL O2 C2 HO2 .
AOL HO2 O2 . .
AOL C3 C2 O3 .
AOL H3 C3 . .
AOL O3 C3 HO3 .
AOL HO3 O3 . .
AOL C5 C1 C4 .
AOL H5 C5 . .
AOL N5 C5 HN51 .
AOL HN52 N5 . .
AOL HN51 N5 . .
AOL C4 C5 O4 .
AOL H4 C4 . .
AOL O4 C4 HO4 .
AOL HO4 O4 . END
AOL C4 C3 . 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
AOL O4 C4 single 1.432 0.020
AOL HO4 O4 single 0.967 0.020
AOL C4 C3 single 1.524 0.020
AOL C4 C5 single 1.524 0.020
AOL H4 C4 single 1.099 0.020
AOL O3 C3 single 1.432 0.020
AOL C3 C2 single 1.524 0.020
AOL H3 C3 single 1.099 0.020
AOL HO3 O3 single 0.967 0.020
AOL O2 C2 single 1.432 0.020
AOL C2 C1 single 1.524 0.020
AOL H2 C2 single 1.099 0.020
AOL HO2 O2 single 0.967 0.020
AOL C1 O1 single 1.432 0.020
AOL C5 C1 single 1.524 0.020
AOL H1 C1 single 1.099 0.020
AOL HO1 O1 single 0.967 0.020
AOL N5 C5 single 1.450 0.020
AOL H5 C5 single 1.099 0.020
AOL HN51 N5 single 1.010 0.020
AOL HN52 N5 single 1.010 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
AOL HO1 O1 C1 109.470 3.000
AOL O1 C1 H1 109.470 3.000
AOL O1 C1 C2 109.470 3.000
AOL O1 C1 C5 109.470 3.000
AOL H1 C1 C2 108.340 3.000
AOL H1 C1 C5 108.340 3.000
AOL C2 C1 C5 111.000 3.000
AOL C1 C2 H2 108.340 3.000
AOL C1 C2 O2 109.470 3.000
AOL C1 C2 C3 111.000 3.000
AOL H2 C2 O2 109.470 3.000
AOL H2 C2 C3 108.340 3.000
AOL O2 C2 C3 109.470 3.000
AOL C2 O2 HO2 109.470 3.000
AOL C2 C3 H3 108.340 3.000
AOL C2 C3 O3 109.470 3.000
AOL C2 C3 C4 111.000 3.000
AOL H3 C3 O3 109.470 3.000
AOL H3 C3 C4 108.340 3.000
AOL O3 C3 C4 109.470 3.000
AOL C3 O3 HO3 109.470 3.000
AOL C1 C5 H5 108.340 3.000
AOL C1 C5 N5 109.470 3.000
AOL C1 C5 C4 111.000 3.000
AOL H5 C5 N5 109.470 3.000
AOL H5 C5 C4 108.340 3.000
AOL N5 C5 C4 109.470 3.000
AOL C5 N5 HN52 120.000 3.000
AOL C5 N5 HN51 120.000 3.000
AOL HN52 N5 HN51 120.000 3.000
AOL C5 C4 H4 108.340 3.000
AOL C5 C4 O4 109.470 3.000
AOL C5 C4 C3 111.000 3.000
AOL H4 C4 O4 109.470 3.000
AOL H4 C4 C3 108.340 3.000
AOL O4 C4 C3 109.470 3.000
AOL C4 O4 HO4 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
AOL var_1 HO1 O1 C1 C5 -176.213 20.000 1
AOL var_2 O1 C1 C2 C3 -90.000 20.000 3
AOL var_3 C1 C2 O2 HO2 -174.869 20.000 1
AOL var_4 C1 C2 C3 O3 90.000 20.000 3
AOL var_5 C2 C3 O3 HO3 65.164 20.000 1
AOL var_6 O1 C1 C5 C4 90.000 20.000 3
AOL var_7 C1 C5 N5 HN51 -62.129 20.000 1
AOL var_8 C1 C5 C4 O4 -120.000 20.000 3
AOL var_9 C5 C4 C3 C2 30.000 20.000 3
AOL var_10 C5 C4 O4 HO4 -179.926 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
AOL chir_01 C4 O4 C3 C5 negativ
AOL chir_02 C3 C4 O3 C2 negativ
AOL chir_03 C2 C3 O2 C1 negativ
AOL chir_04 C1 C2 O1 C5 negativ
AOL chir_05 C5 C4 C1 N5 negativ
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
AOL plan-1 N5 0.020
AOL plan-1 C5 0.000
AOL plan-1 HN51 0.000
AOL plan-1 HN52 0.000
# ------------------------------------------------------
|
