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
208
209
210
211
212
213
214
215
216
217
218
|
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
CFD CFD '(2R,3E,5R)-5-amino-2,4-dimethylhex-3' non-polymer 25 10 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CFD
#
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
CFD O O O 0.000 0.000 0.000 0.000
CFD C C C1 0.000 -0.939 0.456 0.609
CFD H H H 0.000 -0.848 0.665 1.661
CFD CD C CH1 0.000 -2.237 0.731 -0.106
CFD HD H H 0.000 -2.137 0.457 -1.166
CFD CE C CH3 0.000 -2.574 2.220 0.006
CFD HEB H H 0.000 -2.670 2.485 1.028
CFD HEA H H 0.000 -1.800 2.793 -0.435
CFD HE H H 0.000 -3.487 2.415 -0.495
CFD CG1 C C1 0.000 -3.338 -0.083 0.522
CFD H1G1 H H 0.000 -3.646 0.119 1.534
CFD CB1 C C 0.000 -3.921 -1.035 -0.163
CFD CG2 C CH3 0.000 -3.409 -1.400 -1.533
CFD HG2B H H 0.000 -2.354 -1.298 -1.555
CFD HG2A H H 0.000 -3.671 -2.402 -1.754
CFD HG2 H H 0.000 -3.840 -0.756 -2.256
CFD CA C CH1 0.000 -5.105 -1.765 0.418
CFD HA H H 0.000 -5.275 -1.426 1.450
CFD CB2 C CH3 0.000 -6.348 -1.475 -0.426
CFD HB2B H H 0.000 -6.541 -0.433 -0.424
CFD HB2A H H 0.000 -6.185 -1.801 -1.420
CFD HB2 H H 0.000 -7.180 -1.988 -0.018
CFD N N NH2 0.000 -4.838 -3.210 0.415
CFD HNA H H 0.000 -3.987 -3.572 0.000
CFD HN H H 0.000 -5.503 -3.855 0.826
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
CFD O n/a C START
CFD C O CD .
CFD H C . .
CFD CD C CG1 .
CFD HD CD . .
CFD CE CD HE .
CFD HEB CE . .
CFD HEA CE . .
CFD HE CE . .
CFD CG1 CD CB1 .
CFD H1G1 CG1 . .
CFD CB1 CG1 CA .
CFD CG2 CB1 HG2 .
CFD HG2B CG2 . .
CFD HG2A CG2 . .
CFD HG2 CG2 . .
CFD CA CB1 N .
CFD HA CA . .
CFD CB2 CA HB2 .
CFD HB2B CB2 . .
CFD HB2A CB2 . .
CFD HB2 CB2 . .
CFD N CA HN .
CFD HNA N . .
CFD HN N . 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
CFD N CA single 1.450 0.020
CFD HN N single 1.010 0.020
CFD HNA N single 1.010 0.020
CFD HA CA single 1.099 0.020
CFD CB2 CA single 1.524 0.020
CFD CA CB1 single 1.500 0.020
CFD CD C single 1.510 0.020
CFD C O double 1.220 0.020
CFD H C single 1.077 0.020
CFD HB2 CB2 single 1.059 0.020
CFD HB2A CB2 single 1.059 0.020
CFD HB2B CB2 single 1.059 0.020
CFD CB1 CG1 double 1.340 0.020
CFD CG2 CB1 single 1.500 0.020
CFD H1G1 CG1 single 1.077 0.020
CFD CG1 CD single 1.510 0.020
CFD HG2 CG2 single 1.059 0.020
CFD HG2A CG2 single 1.059 0.020
CFD HG2B CG2 single 1.059 0.020
CFD CE CD single 1.524 0.020
CFD HD CD single 1.099 0.020
CFD HE CE single 1.059 0.020
CFD HEA CE single 1.059 0.020
CFD HEB 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
CFD O C H 123.000 3.000
CFD O C CD 120.500 3.000
CFD H C CD 120.000 3.000
CFD C CD HD 108.810 3.000
CFD C CD CE 109.470 3.000
CFD C CD CG1 109.500 3.000
CFD HD CD CE 108.340 3.000
CFD HD CD CG1 108.810 3.000
CFD CE CD CG1 109.470 3.000
CFD CD CE HEB 109.470 3.000
CFD CD CE HEA 109.470 3.000
CFD CD CE HE 109.470 3.000
CFD HEB CE HEA 109.470 3.000
CFD HEB CE HE 109.470 3.000
CFD HEA CE HE 109.470 3.000
CFD CD CG1 H1G1 120.000 3.000
CFD CD CG1 CB1 120.500 3.000
CFD H1G1 CG1 CB1 120.000 3.000
CFD CG1 CB1 CG2 120.000 3.000
CFD CG1 CB1 CA 120.000 3.000
CFD CG2 CB1 CA 120.000 3.000
CFD CB1 CG2 HG2B 109.470 3.000
CFD CB1 CG2 HG2A 109.470 3.000
CFD CB1 CG2 HG2 109.470 3.000
CFD HG2B CG2 HG2A 109.470 3.000
CFD HG2B CG2 HG2 109.470 3.000
CFD HG2A CG2 HG2 109.470 3.000
CFD CB1 CA HA 108.810 3.000
CFD CB1 CA CB2 109.470 3.000
CFD CB1 CA N 109.470 3.000
CFD HA CA CB2 108.340 3.000
CFD HA CA N 109.470 3.000
CFD CB2 CA N 109.470 3.000
CFD CA CB2 HB2B 109.470 3.000
CFD CA CB2 HB2A 109.470 3.000
CFD CA CB2 HB2 109.470 3.000
CFD HB2B CB2 HB2A 109.470 3.000
CFD HB2B CB2 HB2 109.470 3.000
CFD HB2A CB2 HB2 109.470 3.000
CFD CA N HNA 120.000 3.000
CFD CA N HN 120.000 3.000
CFD HNA N HN 120.000 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
CFD var_1 O C CD CG1 119.956 20.000 1
CFD var_2 C CD CE HE -179.973 20.000 3
CFD var_3 C CD CG1 CB1 -113.980 20.000 1
CFD CONST_1 CD CG1 CB1 CA -174.443 0.000 0
CFD var_4 CG1 CB1 CG2 HG2 -84.994 20.000 1
CFD var_5 CG1 CB1 CA N -125.034 20.000 3
CFD var_6 CB1 CA CB2 HB2 179.979 20.000 3
CFD var_7 CB1 CA N HN 176.013 20.000 1
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
CFD chir_01 CA N CB2 CB1 positiv
CFD chir_02 CD C CG1 CE 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
CFD plan-1 N 0.020
CFD plan-1 CA 0.020
CFD plan-1 HN 0.020
CFD plan-1 HNA 0.020
CFD plan-2 C 0.020
CFD plan-2 O 0.020
CFD plan-2 CD 0.020
CFD plan-2 H 0.020
CFD plan-3 CB1 0.020
CFD plan-3 CA 0.020
CFD plan-3 CG1 0.020
CFD plan-3 CG2 0.020
CFD plan-3 CD 0.020
CFD plan-3 H1G1 0.020
# ------------------------------------------------------
|
