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
219
220
221
222
223
224
225
226
227
228
229
230
231
232
|
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
CAK CAK '[(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDRO' non-polymer 29 16 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_CAK
#
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
CAK OAP O OP -0.666 0.000 0.000 0.000
CAK PAM P P 0.000 -0.985 1.074 -0.407
CAK OAN O OP -0.666 -1.204 1.017 -1.903
CAK OAO O OP -0.666 -0.435 2.432 -0.029
CAK OAL O O2 0.000 -2.386 0.833 0.350
CAK CAK C CH2 0.000 -2.909 -0.405 -0.135
CAK HAK1 H H 0.000 -2.204 -1.209 0.086
CAK HAK2 H H 0.000 -3.058 -0.338 -1.214
CAK CAF C CH1 0.000 -4.247 -0.696 0.549
CAK HAF H H 0.000 -4.114 -0.674 1.639
CAK CAE C CH2 0.000 -5.270 0.365 0.138
CAK HAE1 H H 0.000 -5.401 0.344 -0.946
CAK HAE2 H H 0.000 -4.911 1.351 0.441
CAK CAD C CH1 0.000 -6.608 0.075 0.821
CAK HAD H H 0.000 -6.474 0.097 1.912
CAK OAJ O OH1 0.000 -7.564 1.066 0.438
CAK HAJ H H 0.000 -8.409 0.882 0.871
CAK CAC C CH1 0.000 -7.108 -1.307 0.396
CAK HAC H H 0.000 -7.241 -1.329 -0.694
CAK OAI O OH1 0.000 -8.358 -1.579 1.035
CAK HAI H H 0.000 -9.004 -0.908 0.775
CAK CAB C CH1 0.000 -6.085 -2.368 0.807
CAK HAB H H 0.000 -5.952 -2.346 1.897
CAK OAH O OH1 0.000 -6.552 -3.659 0.411
CAK HAH H H 0.000 -7.397 -3.841 0.843
CAK CAA C CH1 0.000 -4.747 -2.078 0.123
CAK HAA H H 0.000 -4.880 -2.100 -0.967
CAK OAG O OH1 0.000 -3.791 -3.068 0.507
CAK HAG H H 0.000 -4.108 -3.941 0.239
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
CAK OAP n/a PAM START
CAK PAM OAP OAL .
CAK OAN PAM . .
CAK OAO PAM . .
CAK OAL PAM CAK .
CAK CAK OAL CAF .
CAK HAK1 CAK . .
CAK HAK2 CAK . .
CAK CAF CAK CAE .
CAK HAF CAF . .
CAK CAE CAF CAD .
CAK HAE1 CAE . .
CAK HAE2 CAE . .
CAK CAD CAE CAC .
CAK HAD CAD . .
CAK OAJ CAD HAJ .
CAK HAJ OAJ . .
CAK CAC CAD CAB .
CAK HAC CAC . .
CAK OAI CAC HAI .
CAK HAI OAI . .
CAK CAB CAC CAA .
CAK HAB CAB . .
CAK OAH CAB HAH .
CAK HAH OAH . .
CAK CAA CAB OAG .
CAK HAA CAA . .
CAK OAG CAA HAG .
CAK HAG OAG . END
CAK CAF CAA . 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
CAK OAN PAM deloc 1.510 0.020
CAK OAO PAM deloc 1.510 0.020
CAK PAM OAP deloc 1.510 0.020
CAK OAL PAM single 1.610 0.020
CAK CAK OAL single 1.426 0.020
CAK CAF CAK single 1.524 0.020
CAK HAK1 CAK single 1.092 0.020
CAK HAK2 CAK single 1.092 0.020
CAK CAF CAA single 1.524 0.020
CAK CAE CAF single 1.524 0.020
CAK HAF CAF single 1.099 0.020
CAK OAG CAA single 1.432 0.020
CAK CAA CAB single 1.524 0.020
CAK HAA CAA single 1.099 0.020
CAK HAG OAG single 0.967 0.020
CAK OAH CAB single 1.432 0.020
CAK CAB CAC single 1.524 0.020
CAK HAB CAB single 1.099 0.020
CAK HAH OAH single 0.967 0.020
CAK OAI CAC single 1.432 0.020
CAK CAC CAD single 1.524 0.020
CAK HAC CAC single 1.099 0.020
CAK HAI OAI single 0.967 0.020
CAK OAJ CAD single 1.432 0.020
CAK CAD CAE single 1.524 0.020
CAK HAD CAD single 1.099 0.020
CAK HAJ OAJ single 0.967 0.020
CAK HAE1 CAE single 1.092 0.020
CAK HAE2 CAE single 1.092 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
CAK OAP PAM OAN 119.900 3.000
CAK OAP PAM OAO 119.900 3.000
CAK OAP PAM OAL 108.200 3.000
CAK OAN PAM OAO 119.900 3.000
CAK OAN PAM OAL 108.200 3.000
CAK OAO PAM OAL 108.200 3.000
CAK PAM OAL CAK 120.500 3.000
CAK OAL CAK HAK1 109.470 3.000
CAK OAL CAK HAK2 109.470 3.000
CAK OAL CAK CAF 109.470 3.000
CAK HAK1 CAK HAK2 107.900 3.000
CAK HAK1 CAK CAF 109.470 3.000
CAK HAK2 CAK CAF 109.470 3.000
CAK CAK CAF HAF 108.340 3.000
CAK CAK CAF CAE 109.470 3.000
CAK CAK CAF CAA 111.000 3.000
CAK HAF CAF CAE 108.340 3.000
CAK HAF CAF CAA 108.340 3.000
CAK CAE CAF CAA 111.000 3.000
CAK CAF CAE HAE1 109.470 3.000
CAK CAF CAE HAE2 109.470 3.000
CAK CAF CAE CAD 111.000 3.000
CAK HAE1 CAE HAE2 107.900 3.000
CAK HAE1 CAE CAD 109.470 3.000
CAK HAE2 CAE CAD 109.470 3.000
CAK CAE CAD HAD 108.340 3.000
CAK CAE CAD OAJ 109.470 3.000
CAK CAE CAD CAC 111.000 3.000
CAK HAD CAD OAJ 109.470 3.000
CAK HAD CAD CAC 108.340 3.000
CAK OAJ CAD CAC 109.470 3.000
CAK CAD OAJ HAJ 109.470 3.000
CAK CAD CAC HAC 108.340 3.000
CAK CAD CAC OAI 109.470 3.000
CAK CAD CAC CAB 111.000 3.000
CAK HAC CAC OAI 109.470 3.000
CAK HAC CAC CAB 108.340 3.000
CAK OAI CAC CAB 109.470 3.000
CAK CAC OAI HAI 109.470 3.000
CAK CAC CAB HAB 108.340 3.000
CAK CAC CAB OAH 109.470 3.000
CAK CAC CAB CAA 111.000 3.000
CAK HAB CAB OAH 109.470 3.000
CAK HAB CAB CAA 108.340 3.000
CAK OAH CAB CAA 109.470 3.000
CAK CAB OAH HAH 109.470 3.000
CAK CAB CAA HAA 108.340 3.000
CAK CAB CAA OAG 109.470 3.000
CAK CAB CAA CAF 111.000 3.000
CAK HAA CAA OAG 109.470 3.000
CAK HAA CAA CAF 108.340 3.000
CAK OAG CAA CAF 109.470 3.000
CAK CAA OAG HAG 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
CAK var_1 OAP PAM OAL CAK -64.993 20.000 1
CAK var_2 PAM OAL CAK CAF 179.966 20.000 1
CAK var_3 OAL CAK CAF CAE 64.987 20.000 3
CAK var_4 CAK CAF CAA CAB 180.000 20.000 3
CAK var_5 CAK CAF CAE CAD 180.000 20.000 3
CAK var_6 CAF CAE CAD CAC -60.000 20.000 3
CAK var_7 CAE CAD OAJ HAJ -179.979 20.000 1
CAK var_8 CAE CAD CAC CAB 60.000 20.000 3
CAK var_9 CAD CAC OAI HAI 59.985 20.000 1
CAK var_10 CAD CAC CAB CAA -60.000 20.000 3
CAK var_11 CAC CAB OAH HAH -60.051 20.000 1
CAK var_12 CAC CAB CAA OAG 180.000 20.000 3
CAK var_13 CAB CAA OAG HAG 59.964 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
CAK chir_01 CAF CAK CAA CAE positiv
CAK chir_02 CAA CAF OAG CAB negativ
CAK chir_03 CAB CAA OAH CAC positiv
CAK chir_04 CAC CAB OAI CAD negativ
CAK chir_05 CAD CAC OAJ CAE positiv
# ------------------------------------------------------
|
