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
|
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
DPR DPR 'D-PROLINE ' P-peptide 16 8 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DPR
#
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
DPR OXT O OC -0.500 0.000 0.000 0.000
DPR C C C 0.000 -0.357 0.127 -1.192
DPR O O OC -0.500 -0.992 -0.739 -1.834
DPR CA C CH1 0.000 0.077 1.448 -1.734
DPR HA H H 0.000 -0.372 2.267 -1.155
DPR CB C CH2 0.000 1.595 1.590 -1.770
DPR HB2 H H 0.000 2.093 0.723 -1.332
DPR HB3 H H 0.000 1.930 2.496 -1.261
DPR CG C CH2 0.000 1.937 1.680 -3.249
DPR HG2 H H 0.000 2.177 0.707 -3.682
DPR HG3 H H 0.000 2.755 2.377 -3.446
DPR CD C CH2 0.000 0.661 2.209 -3.869
DPR HD2 H H 0.000 0.577 1.970 -4.931
DPR HD3 H H 0.000 0.537 3.285 -3.729
DPR N N NH1 0.000 -0.373 1.498 -3.125
DPR H H H 0.000 -1.231 1.115 -3.498
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
DPR OXT n/a C START
DPR C OXT CA .
DPR O C . .
DPR CA C CB .
DPR HA CA . .
DPR CB CA CG .
DPR HB2 CB . .
DPR HB3 CB . .
DPR CG CB CD .
DPR HG2 CG . .
DPR HG3 CG . .
DPR CD CG N .
DPR HD2 CD . .
DPR HD3 CD . .
DPR N CD H .
DPR H N . END
DPR N CA . 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
DPR N CA single 1.450 0.020
DPR N CD single 1.450 0.020
DPR H N single 1.010 0.020
DPR CB CA single 1.524 0.020
DPR CA C single 1.500 0.020
DPR HA CA single 1.099 0.020
DPR CG CB single 1.524 0.020
DPR HB2 CB single 1.092 0.020
DPR HB3 CB single 1.092 0.020
DPR CD CG single 1.524 0.020
DPR HG2 CG single 1.092 0.020
DPR HG3 CG single 1.092 0.020
DPR HD2 CD single 1.092 0.020
DPR HD3 CD single 1.092 0.020
DPR O C deloc 1.250 0.020
DPR C OXT deloc 1.250 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
DPR OXT C O 123.000 3.000
DPR OXT C CA 118.500 3.000
DPR O C CA 118.500 3.000
DPR C CA HA 108.810 3.000
DPR C CA CB 109.470 3.000
DPR C CA N 111.600 3.000
DPR HA CA CB 108.340 3.000
DPR HA CA N 108.550 3.000
DPR CB CA N 110.000 3.000
DPR CA CB HB2 109.470 3.000
DPR CA CB HB3 109.470 3.000
DPR CA CB CG 111.000 3.000
DPR HB2 CB HB3 107.900 3.000
DPR HB2 CB CG 109.470 3.000
DPR HB3 CB CG 109.470 3.000
DPR CB CG HG2 109.470 3.000
DPR CB CG HG3 109.470 3.000
DPR CB CG CD 111.000 3.000
DPR HG2 CG HG3 107.900 3.000
DPR HG2 CG CD 109.470 3.000
DPR HG3 CG CD 109.470 3.000
DPR CG CD HD2 109.470 3.000
DPR CG CD HD3 109.470 3.000
DPR CG CD N 112.000 3.000
DPR HD2 CD HD3 107.900 3.000
DPR HD2 CD N 109.470 3.000
DPR HD3 CD N 109.470 3.000
DPR CD N H 118.500 3.000
DPR CD N CA 120.000 3.000
DPR H N CA 118.500 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
DPR var_1 OXT C CA CB 63.508 20.000 3
DPR var_2 C CA CB CG 120.000 20.000 3
DPR var_3 CA CB CG CD 30.000 20.000 3
DPR var_4 CB CG CD N -30.000 20.000 3
DPR var_5 CG CD N CA 30.000 20.000 3
DPR var_6 CD N CA C -150.000 20.000 3
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
DPR chir_01 CA N CB C positiv
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
DPR plan-1 N 0.020
DPR plan-1 CA 0.020
DPR plan-1 CD 0.020
DPR plan-1 H 0.020
DPR plan-2 C 0.020
DPR plan-2 CA 0.020
DPR plan-2 O 0.020
DPR plan-2 OXT 0.020
# ------------------------------------------------------
|
