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
195
196
197
198
199
200
201
202
203
204
205
206
207
|
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
DNG DNG 'N-FORMYL-D-NORLEUCINE ' non-polymer 23 11 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_DNG
#
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
DNG OXT O OC -0.500 0.000 0.000 0.000
DNG C C C 0.000 -0.531 -0.327 -1.085
DNG O O OC -0.500 -0.190 -1.347 -1.725
DNG CA C CH1 0.000 -1.641 0.622 -1.493
DNG HA H H 0.000 -2.043 1.118 -0.599
DNG N N NH1 0.000 -2.665 -0.204 -2.085
DNG H H H 0.000 -2.650 -0.341 -3.085
DNG C1 C C1 0.000 -3.663 -0.814 -1.357
DNG H1 H H 0.000 -4.366 -1.403 -1.920
DNG O1 O O 0.000 -3.847 -0.767 -0.147
DNG CB C CH2 0.000 -1.154 1.677 -2.484
DNG HB2 H H 0.000 -0.750 1.157 -3.355
DNG HB3 H H 0.000 -0.358 2.248 -2.001
DNG CG C CH2 0.000 -2.268 2.629 -2.928
DNG HG2 H H 0.000 -2.652 3.148 -2.048
DNG HG3 H H 0.000 -3.069 2.039 -3.379
DNG CD C CH2 0.000 -1.754 3.652 -3.941
DNG HD2 H H 0.000 -1.389 3.115 -4.819
DNG HD3 H H 0.000 -0.929 4.204 -3.485
DNG CE C CH3 0.000 -2.847 4.623 -4.358
DNG HE3 H H 0.000 -3.204 5.141 -3.505
DNG HE2 H H 0.000 -2.456 5.320 -5.054
DNG HE1 H H 0.000 -3.645 4.088 -4.805
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
DNG OXT n/a C START
DNG C OXT CA .
DNG O C . .
DNG CA C CB .
DNG HA CA . .
DNG N CA C1 .
DNG H N . .
DNG C1 N O1 .
DNG H1 C1 . .
DNG O1 C1 . .
DNG CB CA CG .
DNG HB2 CB . .
DNG HB3 CB . .
DNG CG CB CD .
DNG HG2 CG . .
DNG HG3 CG . .
DNG CD CG CE .
DNG HD2 CD . .
DNG HD3 CD . .
DNG CE CD HE1 .
DNG HE3 CE . .
DNG HE2 CE . .
DNG HE1 CE . END
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
DNG O1 C1 double 1.220 0.020
DNG C1 N single 1.330 0.020
DNG H1 C1 single 1.077 0.020
DNG N CA single 1.450 0.020
DNG H N single 1.010 0.020
DNG CA C single 1.500 0.020
DNG CB CA single 1.524 0.020
DNG HA CA single 1.099 0.020
DNG O C deloc 1.250 0.020
DNG C OXT deloc 1.250 0.020
DNG CG CB single 1.524 0.020
DNG HB2 CB single 1.092 0.020
DNG HB3 CB single 1.092 0.020
DNG CD CG single 1.524 0.020
DNG HG2 CG single 1.092 0.020
DNG HG3 CG single 1.092 0.020
DNG CE CD single 1.513 0.020
DNG HD2 CD single 1.092 0.020
DNG HD3 CD single 1.092 0.020
DNG HE1 CE single 1.059 0.020
DNG HE2 CE single 1.059 0.020
DNG HE3 CE 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
DNG OXT C O 123.000 3.000
DNG OXT C CA 118.500 3.000
DNG O C CA 118.500 3.000
DNG C CA HA 108.810 3.000
DNG C CA N 111.600 3.000
DNG C CA CB 109.470 3.000
DNG HA CA N 108.550 3.000
DNG HA CA CB 108.340 3.000
DNG N CA CB 110.000 3.000
DNG CA N H 118.500 3.000
DNG CA N C1 120.000 3.000
DNG H N C1 120.000 3.000
DNG N C1 H1 120.000 3.000
DNG N C1 O1 120.000 3.000
DNG H1 C1 O1 123.000 3.000
DNG CA CB HB2 109.470 3.000
DNG CA CB HB3 109.470 3.000
DNG CA CB CG 111.000 3.000
DNG HB2 CB HB3 107.900 3.000
DNG HB2 CB CG 109.470 3.000
DNG HB3 CB CG 109.470 3.000
DNG CB CG HG2 109.470 3.000
DNG CB CG HG3 109.470 3.000
DNG CB CG CD 111.000 3.000
DNG HG2 CG HG3 107.900 3.000
DNG HG2 CG CD 109.470 3.000
DNG HG3 CG CD 109.470 3.000
DNG CG CD HD2 109.470 3.000
DNG CG CD HD3 109.470 3.000
DNG CG CD CE 111.000 3.000
DNG HD2 CD HD3 107.900 3.000
DNG HD2 CD CE 109.470 3.000
DNG HD3 CD CE 109.470 3.000
DNG CD CE HE3 109.470 3.000
DNG CD CE HE2 109.470 3.000
DNG CD CE HE1 109.470 3.000
DNG HE3 CE HE2 109.470 3.000
DNG HE3 CE HE1 109.470 3.000
DNG HE2 CE HE1 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
DNG var_1 OXT C CA CB 97.015 20.000 3
DNG var_2 C CA N C1 87.219 20.000 3
DNG var_3 CA N C1 O1 -0.029 20.000 1
DNG var_4 C CA CB CG 178.921 20.000 3
DNG var_5 CA CB CG CD -178.791 20.000 3
DNG var_6 CB CG CD CE -178.476 20.000 3
DNG var_7 CG CD CE HE1 -60.300 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
DNG chir_01 CA N C CB negativ
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
DNG plan-1 C1 0.020
DNG plan-1 O1 0.020
DNG plan-1 N 0.020
DNG plan-1 H1 0.020
DNG plan-1 H 0.020
DNG plan-2 N 0.020
DNG plan-2 C1 0.020
DNG plan-2 CA 0.020
DNG plan-2 H 0.020
DNG plan-2 H1 0.020
DNG plan-3 C 0.020
DNG plan-3 CA 0.020
DNG plan-3 O 0.020
DNG plan-3 OXT 0.020
# ------------------------------------------------------
|
