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
|
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
PIY PIY '2-phenyl-1H-imidazole ' non-polymer 19 11 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PIY
#
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
PIY HN1 H H 0.000 0.058 0.038 0.003
PIY N1 N NR15 0.000 -0.824 -0.513 0.007
PIY C4 C CR15 0.000 -0.930 -1.878 0.020
PIY H4 H H 0.000 -0.112 -2.588 0.028
PIY C5 C CR15 0.000 -2.247 -2.171 0.020
PIY H5 H H 0.000 -2.675 -3.166 0.030
PIY N3 N NRD5 0.000 -2.934 -1.023 0.007
PIY C2 C CR5 0.000 -2.092 -0.014 -0.001
PIY C6 C CR6 0.000 -2.459 1.419 -0.015
PIY C11 C CR16 0.000 -1.463 2.397 -0.017
PIY H11 H H 0.000 -0.419 2.108 -0.003
PIY C10 C CR16 0.000 -1.812 3.732 -0.036
PIY H10 H H 0.000 -1.040 4.492 -0.046
PIY C9 C CR16 0.000 -3.145 4.102 -0.041
PIY H9 H H 0.000 -3.413 5.151 -0.051
PIY C8 C CR16 0.000 -4.136 3.137 -0.034
PIY H8 H H 0.000 -5.178 3.433 -0.038
PIY C7 C CR16 0.000 -3.802 1.799 -0.021
PIY H7 H H 0.000 -4.579 1.045 -0.015
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
PIY HN1 n/a N1 START
PIY N1 HN1 C4 .
PIY C4 N1 C5 .
PIY H4 C4 . .
PIY C5 C4 N3 .
PIY H5 C5 . .
PIY N3 C5 C2 .
PIY C2 N3 C6 .
PIY C6 C2 C11 .
PIY C11 C6 C10 .
PIY H11 C11 . .
PIY C10 C11 C9 .
PIY H10 C10 . .
PIY C9 C10 C8 .
PIY H9 C9 . .
PIY C8 C9 C7 .
PIY H8 C8 . .
PIY C7 C8 H7 .
PIY H7 C7 . END
PIY N1 C2 . ADD
PIY C6 C7 . 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
PIY N1 C2 single 1.340 0.020
PIY C4 N1 single 1.350 0.020
PIY C6 C2 single 1.490 0.020
PIY C2 N3 double 1.350 0.020
PIY N3 C5 single 1.350 0.020
PIY C5 C4 double 1.380 0.020
PIY H4 C4 single 1.083 0.020
PIY H5 C5 single 1.083 0.020
PIY C6 C7 double 1.390 0.020
PIY C11 C6 single 1.390 0.020
PIY C7 C8 single 1.390 0.020
PIY H7 C7 single 1.083 0.020
PIY C8 C9 double 1.390 0.020
PIY H8 C8 single 1.083 0.020
PIY C9 C10 single 1.390 0.020
PIY H9 C9 single 1.083 0.020
PIY C10 C11 double 1.390 0.020
PIY H10 C10 single 1.083 0.020
PIY H11 C11 single 1.083 0.020
PIY N1 HN1 single 1.040 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
PIY HN1 N1 C4 126.000 3.000
PIY HN1 N1 C2 126.000 3.000
PIY C4 N1 C2 108.000 3.000
PIY N1 C4 H4 126.000 3.000
PIY N1 C4 C5 108.000 3.000
PIY H4 C4 C5 126.000 3.000
PIY C4 C5 H5 126.000 3.000
PIY C4 C5 N3 108.000 3.000
PIY H5 C5 N3 126.000 3.000
PIY C5 N3 C2 108.000 3.000
PIY N3 C2 C6 126.000 3.000
PIY N3 C2 N1 108.000 3.000
PIY C6 C2 N1 108.000 3.000
PIY C2 C6 C11 120.000 3.000
PIY C2 C6 C7 120.000 3.000
PIY C11 C6 C7 120.000 3.000
PIY C6 C11 H11 120.000 3.000
PIY C6 C11 C10 120.000 3.000
PIY H11 C11 C10 120.000 3.000
PIY C11 C10 H10 120.000 3.000
PIY C11 C10 C9 120.000 3.000
PIY H10 C10 C9 120.000 3.000
PIY C10 C9 H9 120.000 3.000
PIY C10 C9 C8 120.000 3.000
PIY H9 C9 C8 120.000 3.000
PIY C9 C8 H8 120.000 3.000
PIY C9 C8 C7 120.000 3.000
PIY H8 C8 C7 120.000 3.000
PIY C8 C7 H7 120.000 3.000
PIY C8 C7 C6 120.000 3.000
PIY H7 C7 C6 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
PIY CONST_1 HN1 N1 C2 N3 180.000 0.000 0
PIY CONST_2 HN1 N1 C4 C5 180.000 0.000 0
PIY CONST_3 N1 C4 C5 N3 0.000 0.000 0
PIY CONST_4 C4 C5 N3 C2 0.000 0.000 0
PIY CONST_5 C5 N3 C2 C6 180.000 0.000 0
PIY var_1 N3 C2 C6 C11 179.709 20.000 1
PIY CONST_6 C2 C6 C7 C8 180.000 0.000 0
PIY CONST_7 C2 C6 C11 C10 180.000 0.000 0
PIY CONST_8 C6 C11 C10 C9 0.000 0.000 0
PIY CONST_9 C11 C10 C9 C8 0.000 0.000 0
PIY CONST_10 C10 C9 C8 C7 0.000 0.000 0
PIY CONST_11 C9 C8 C7 C6 0.000 0.000 0
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
PIY plan-1 N1 0.020
PIY plan-1 C2 0.020
PIY plan-1 C4 0.020
PIY plan-1 HN1 0.020
PIY plan-1 N3 0.020
PIY plan-1 C5 0.020
PIY plan-1 C6 0.020
PIY plan-1 H4 0.020
PIY plan-1 H5 0.020
PIY plan-2 C6 0.020
PIY plan-2 C2 0.020
PIY plan-2 C7 0.020
PIY plan-2 C11 0.020
PIY plan-2 C8 0.020
PIY plan-2 C9 0.020
PIY plan-2 C10 0.020
PIY plan-2 H7 0.020
PIY plan-2 H8 0.020
PIY plan-2 H9 0.020
PIY plan-2 H10 0.020
PIY plan-2 H11 0.020
# ------------------------------------------------------
|
