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
|
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
PYC PYC 'PYRROLE-2-CARBOXYLATE ' non-polymer 12 8 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_PYC
#
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
PYC O8 O OC -0.500 0.000 0.000 0.000
PYC C1 C C 0.000 -0.963 -0.799 0.004
PYC O7 O OC -0.500 -0.751 -2.032 0.006
PYC C2 C CR5 0.000 -2.334 -0.292 0.001
PYC N6 N NR15 0.000 -3.484 -1.051 -0.001
PYC HN6 H H 0.000 -3.524 -2.090 0.000
PYC C5 C CR15 0.000 -4.549 -0.223 -0.003
PYC H61 H H 0.000 -5.586 -0.533 -0.005
PYC C4 C CR15 0.000 -4.111 1.060 -0.004
PYC H41 H H 0.000 -4.734 1.946 -0.009
PYC C3 C CR15 0.000 -2.714 1.037 0.005
PYC H31 H H 0.000 -2.055 1.896 0.013
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
PYC O8 n/a C1 START
PYC C1 O8 C2 .
PYC O7 C1 . .
PYC C2 C1 N6 .
PYC N6 C2 C5 .
PYC HN6 N6 . .
PYC C5 N6 C4 .
PYC H61 C5 . .
PYC C4 C5 C3 .
PYC H41 C4 . .
PYC C3 C4 H31 .
PYC H31 C3 . END
PYC 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
PYC O7 C1 deloc 1.250 0.020
PYC C1 O8 deloc 1.250 0.020
PYC C2 C1 single 1.490 0.020
PYC C2 C3 double 1.387 0.020
PYC N6 C2 single 1.340 0.020
PYC C3 C4 single 1.380 0.020
PYC H31 C3 single 1.083 0.020
PYC C4 C5 double 1.380 0.020
PYC H41 C4 single 1.083 0.020
PYC C5 N6 single 1.350 0.020
PYC H61 C5 single 1.083 0.020
PYC HN6 N6 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
PYC O8 C1 O7 123.000 3.000
PYC O8 C1 C2 120.000 3.000
PYC O7 C1 C2 120.000 3.000
PYC C1 C2 N6 126.000 3.000
PYC C1 C2 C3 126.000 3.000
PYC N6 C2 C3 108.000 3.000
PYC C2 N6 HN6 126.000 3.000
PYC C2 N6 C5 108.000 3.000
PYC HN6 N6 C5 126.000 3.000
PYC N6 C5 H61 126.000 3.000
PYC N6 C5 C4 108.000 3.000
PYC H61 C5 C4 126.000 3.000
PYC C5 C4 H41 126.000 3.000
PYC C5 C4 C3 108.000 3.000
PYC H41 C4 C3 126.000 3.000
PYC C4 C3 H31 126.000 3.000
PYC C4 C3 C2 108.000 3.000
PYC H31 C3 C2 126.000 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
PYC var_1 O8 C1 C2 N6 179.695 20.000 1
PYC CONST_1 C1 C2 C3 C4 180.000 0.000 0
PYC CONST_2 C1 C2 N6 C5 180.000 0.000 0
PYC CONST_3 C2 N6 C5 C4 0.000 0.000 0
PYC CONST_4 N6 C5 C4 C3 0.000 0.000 0
PYC CONST_5 C5 C4 C3 C2 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
PYC plan-1 C1 0.020
PYC plan-1 O7 0.020
PYC plan-1 O8 0.020
PYC plan-1 C2 0.020
PYC plan-2 C2 0.020
PYC plan-2 C1 0.020
PYC plan-2 C3 0.020
PYC plan-2 N6 0.020
PYC plan-2 C4 0.020
PYC plan-2 C5 0.020
PYC plan-2 H31 0.020
PYC plan-2 H41 0.020
PYC plan-2 H61 0.020
PYC plan-2 HN6 0.020
# ------------------------------------------------------
|
