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
|
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
25R 25R '2,5-dimethylpyrazine ' non-polymer 16 8 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_25R
#
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
25R C8 C CH3 0.000 0.000 0.000 0.000
25R H8 H H 0.000 0.354 0.002 -0.998
25R H8A H H 0.000 0.345 0.869 0.499
25R H8B H H 0.000 0.361 -0.861 0.500
25R C5 C CR6 0.000 -1.507 -0.014 -0.001
25R C6 C CR16 0.000 -2.210 1.177 0.001
25R H6 H H 0.000 -1.678 2.120 0.003
25R N1 N NRD6 0.000 -3.531 1.165 0.000
25R N4 N NRD6 0.000 -2.157 -1.165 0.000
25R C3 C CR16 0.000 -3.478 -1.177 0.000
25R H3 H H 0.000 -4.010 -2.120 0.000
25R C2 C CR6 0.000 -4.181 0.014 0.000
25R C7 C CH3 0.000 -5.688 0.001 0.000
25R H7B H H 0.000 -6.034 -0.867 0.500
25R H7A H H 0.000 -6.049 0.862 0.498
25R H7 H H 0.000 -6.041 -0.003 -0.998
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
25R C8 n/a C5 START
25R H8 C8 . .
25R H8A C8 . .
25R H8B C8 . .
25R C5 C8 N4 .
25R C6 C5 N1 .
25R H6 C6 . .
25R N1 C6 . .
25R N4 C5 C3 .
25R C3 N4 C2 .
25R H3 C3 . .
25R C2 C3 C7 .
25R C7 C2 H7 .
25R H7B C7 . .
25R H7A C7 . .
25R H7 C7 . END
25R N1 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
25R N1 C2 double 1.350 0.020
25R N1 C6 single 1.337 0.020
25R C2 C3 single 1.390 0.020
25R C7 C2 single 1.506 0.020
25R C3 N4 double 1.337 0.020
25R N4 C5 single 1.350 0.020
25R C6 C5 double 1.390 0.020
25R C5 C8 single 1.506 0.020
25R H3 C3 single 1.083 0.020
25R H6 C6 single 1.083 0.020
25R H7 C7 single 1.059 0.020
25R H7A C7 single 1.059 0.020
25R H7B C7 single 1.059 0.020
25R H8 C8 single 1.059 0.020
25R H8A C8 single 1.059 0.020
25R H8B C8 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
25R H8 C8 H8A 109.470 3.000
25R H8 C8 H8B 109.470 3.000
25R H8A C8 H8B 109.470 3.000
25R H8 C8 C5 109.470 3.000
25R H8A C8 C5 109.470 3.000
25R H8B C8 C5 109.470 3.000
25R C8 C5 C6 120.000 3.000
25R C8 C5 N4 120.000 3.000
25R C6 C5 N4 120.000 3.000
25R C5 C6 H6 120.000 3.000
25R C5 C6 N1 120.000 3.000
25R H6 C6 N1 120.000 3.000
25R C6 N1 C2 120.000 3.000
25R C5 N4 C3 120.000 3.000
25R N4 C3 H3 120.000 3.000
25R N4 C3 C2 120.000 3.000
25R H3 C3 C2 120.000 3.000
25R C3 C2 C7 120.000 3.000
25R C3 C2 N1 120.000 3.000
25R C7 C2 N1 120.000 3.000
25R C2 C7 H7B 109.470 3.000
25R C2 C7 H7A 109.470 3.000
25R C2 C7 H7 109.470 3.000
25R H7B C7 H7A 109.470 3.000
25R H7B C7 H7 109.470 3.000
25R H7A C7 H7 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
25R var_1 H8B C8 C5 N4 -29.988 20.000 1
25R CONST_1 C8 C5 C6 N1 180.000 0.000 0
25R CONST_2 C5 C6 N1 C2 0.000 0.000 0
25R CONST_3 C6 N1 C2 C3 0.000 0.000 0
25R CONST_4 C8 C5 N4 C3 180.000 0.000 0
25R CONST_5 C5 N4 C3 C2 0.000 0.000 0
25R CONST_6 N4 C3 C2 C7 180.000 0.000 0
25R var_2 C3 C2 C7 H7 -89.952 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
25R plan-1 N1 0.020
25R plan-1 C2 0.020
25R plan-1 C6 0.020
25R plan-1 C3 0.020
25R plan-1 N4 0.020
25R plan-1 C5 0.020
25R plan-1 C7 0.020
25R plan-1 H3 0.020
25R plan-1 C8 0.020
25R plan-1 H6 0.020
# ------------------------------------------------------
|
