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
|
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
275 275 '5-amino-1,2-dimethylpyridinium ' non-polymer 20 9 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_275
#
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
275 N6 N NH2 0.000 0.000 0.000 0.000
275 H61 H H 0.000 0.561 0.849 0.003
275 H62 H H 0.000 0.479 -0.898 -0.002
275 C5 C CR6 0.000 -1.396 0.066 -0.001
275 C4 C CR16 0.000 -2.046 1.297 0.002
275 H4 H H 0.000 -1.482 2.221 0.005
275 C3 C CR16 0.000 -3.431 1.310 0.001
275 H3 H H 0.000 -3.970 2.250 0.003
275 C7 C CR16 0.000 -2.156 -1.098 -0.004
275 H7 H H 0.000 -1.662 -2.062 -0.011
275 N8 N NR6 1.000 -3.473 -1.039 0.001
275 C9 C CH3 0.000 -4.241 -2.287 0.003
275 H93 H H 0.000 -3.650 -3.066 0.410
275 H92 H H 0.000 -5.114 -2.164 0.590
275 H91 H H 0.000 -4.516 -2.535 -0.990
275 C2 C CR6 0.000 -4.118 0.110 -0.002
275 C1 C CH3 0.000 -5.625 0.117 -0.002
275 H13 H H 0.000 -5.982 -0.690 0.582
275 H12 H H 0.000 -5.974 1.030 0.407
275 H11 H H 0.000 -5.979 0.018 -0.995
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
275 N6 n/a C5 START
275 H61 N6 . .
275 H62 N6 . .
275 C5 N6 C7 .
275 C4 C5 C3 .
275 H4 C4 . .
275 C3 C4 H3 .
275 H3 C3 . .
275 C7 C5 N8 .
275 H7 C7 . .
275 N8 C7 C2 .
275 C9 N8 H91 .
275 H93 C9 . .
275 H92 C9 . .
275 H91 C9 . .
275 C2 N8 C1 .
275 C1 C2 H11 .
275 H13 C1 . .
275 H12 C1 . .
275 H11 C1 . END
275 C2 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
275 C1 C2 single 1.506 0.020
275 C2 C3 double 1.390 0.020
275 C2 N8 single 1.410 0.020
275 C3 C4 single 1.390 0.020
275 C4 C5 double 1.390 0.020
275 C5 N6 single 1.355 0.020
275 C7 C5 single 1.390 0.020
275 N8 C7 double 1.337 0.020
275 C9 N8 single 1.465 0.020
275 H11 C1 single 1.059 0.020
275 H12 C1 single 1.059 0.020
275 H13 C1 single 1.059 0.020
275 H3 C3 single 1.083 0.020
275 H4 C4 single 1.083 0.020
275 H61 N6 single 1.010 0.020
275 H62 N6 single 1.010 0.020
275 H7 C7 single 1.083 0.020
275 H91 C9 single 1.059 0.020
275 H92 C9 single 1.059 0.020
275 H93 C9 single 1.059 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
275 H61 N6 H62 120.000 3.000
275 H61 N6 C5 120.000 3.000
275 H62 N6 C5 120.000 3.000
275 N6 C5 C4 120.000 3.000
275 N6 C5 C7 120.000 3.000
275 C4 C5 C7 120.000 3.000
275 C5 C4 H4 120.000 3.000
275 C5 C4 C3 120.000 3.000
275 H4 C4 C3 120.000 3.000
275 C4 C3 H3 120.000 3.000
275 C4 C3 C2 120.000 3.000
275 H3 C3 C2 120.000 3.000
275 C5 C7 H7 120.000 3.000
275 C5 C7 N8 120.000 3.000
275 H7 C7 N8 120.000 3.000
275 C7 N8 C9 120.000 3.000
275 C7 N8 C2 120.000 3.000
275 C9 N8 C2 120.000 3.000
275 N8 C9 H93 109.470 3.000
275 N8 C9 H92 109.470 3.000
275 N8 C9 H91 109.470 3.000
275 H93 C9 H92 109.470 3.000
275 H93 C9 H91 109.470 3.000
275 H92 C9 H91 109.470 3.000
275 N8 C2 C1 120.000 3.000
275 N8 C2 C3 120.000 3.000
275 C1 C2 C3 120.000 3.000
275 C2 C1 H13 109.470 3.000
275 C2 C1 H12 109.470 3.000
275 C2 C1 H11 109.470 3.000
275 H13 C1 H12 109.470 3.000
275 H13 C1 H11 109.470 3.000
275 H12 C1 H11 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
275 CONST_1 H62 N6 C5 C7 0.041 0.000 0
275 CONST_2 N6 C5 C4 C3 180.000 0.000 0
275 CONST_3 C5 C4 C3 C2 0.000 0.000 0
275 CONST_4 N6 C5 C7 N8 180.000 0.000 0
275 CONST_5 C5 C7 N8 C2 0.000 0.000 0
275 var_1 C7 N8 C9 H91 -95.762 20.000 1
275 CONST_6 C7 N8 C2 C1 180.000 0.000 0
275 CONST_7 N8 C2 C3 C4 0.000 0.000 0
275 var_2 N8 C2 C1 H11 -84.327 20.000 1
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
275 plan-1 C2 0.020
275 plan-1 C1 0.020
275 plan-1 C3 0.020
275 plan-1 N8 0.020
275 plan-1 C4 0.020
275 plan-1 C5 0.020
275 plan-1 C7 0.020
275 plan-1 H3 0.020
275 plan-1 H4 0.020
275 plan-1 N6 0.020
275 plan-1 H7 0.020
275 plan-1 C9 0.020
275 plan-1 H61 0.020
275 plan-1 H62 0.020
275 plan-2 N6 0.020
275 plan-2 C5 0.020
275 plan-2 H61 0.020
275 plan-2 H62 0.020
# ------------------------------------------------------
|
