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
233
234
235
236
237
238
239
240
241
242
243
244
245
|
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
KYQ KYQ '(E)-N~6~-(1-carboxy-2-hydroxyethylid' peptide 30 16 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_KYQ
#
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
KYQ N N NH2 0.000 0.000 0.000 0.000
KYQ HN1 H H 0.000 0.901 0.299 -0.355
KYQ HN2 H H 0.000 -0.253 0.216 0.957
KYQ CA C CH1 0.000 -0.931 -0.740 -0.864
KYQ HA H H 0.000 -1.071 -1.755 -0.467
KYQ CB C CH2 0.000 -2.278 -0.015 -0.900
KYQ HB H H 0.000 -2.940 -0.514 -1.611
KYQ HBA H H 0.000 -2.126 1.020 -1.211
KYQ CG C CH2 0.000 -2.910 -0.043 0.494
KYQ HG H H 0.000 -2.246 0.455 1.203
KYQ HGA H H 0.000 -3.060 -1.079 0.804
KYQ CD C CH2 0.000 -4.257 0.681 0.458
KYQ HD H H 0.000 -4.919 0.182 -0.253
KYQ HDA H H 0.000 -4.104 1.717 0.146
KYQ CE C CH2 0.000 -4.888 0.653 1.851
KYQ HE H H 0.000 -4.224 1.152 2.561
KYQ HEA H H 0.000 -5.038 -0.383 2.161
KYQ NZ N N 0.000 -6.178 1.347 1.817
KYQ C11 C C 0.000 -7.261 0.697 2.028
KYQ C12 C C 0.000 -8.572 1.374 1.888
KYQ O15 O OC -0.500 -9.629 0.739 2.095
KYQ O16 O OC -0.500 -8.621 2.581 1.562
KYQ C13 C CH2 0.000 -7.202 -0.757 2.420
KYQ H13 H H 0.000 -6.730 -0.850 3.400
KYQ H13A H H 0.000 -6.617 -1.309 1.682
KYQ O14 O OH1 0.000 -8.527 -1.290 2.475
KYQ HO14 H H 0.000 -8.488 -2.222 2.727
KYQ C C C 0.000 -0.367 -0.819 -2.259
KYQ O O OC -0.500 0.516 -0.011 -2.623
KYQ OXT O OC -0.500 -0.780 -1.694 -3.051
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
KYQ N n/a CA START
KYQ HN1 N . .
KYQ HN2 N . .
KYQ CA N C .
KYQ HA CA . .
KYQ CB CA CG .
KYQ HB CB . .
KYQ HBA CB . .
KYQ CG CB CD .
KYQ HG CG . .
KYQ HGA CG . .
KYQ CD CG CE .
KYQ HD CD . .
KYQ HDA CD . .
KYQ CE CD NZ .
KYQ HE CE . .
KYQ HEA CE . .
KYQ NZ CE C11 .
KYQ C11 NZ C13 .
KYQ C12 C11 O16 .
KYQ O15 C12 . .
KYQ O16 C12 . .
KYQ C13 C11 O14 .
KYQ H13 C13 . .
KYQ H13A C13 . .
KYQ O14 C13 HO14 .
KYQ HO14 O14 . .
KYQ C CA . END
KYQ O C . .
KYQ OXT C . .
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
KYQ CA N single 1.450 0.020
KYQ CB CA single 1.524 0.020
KYQ C CA single 1.500 0.020
KYQ HA CA single 1.099 0.020
KYQ CG CB single 1.524 0.020
KYQ HB CB single 1.092 0.020
KYQ HBA CB single 1.092 0.020
KYQ CD CG single 1.524 0.020
KYQ HG CG single 1.092 0.020
KYQ HGA CG single 1.092 0.020
KYQ CE CD single 1.524 0.020
KYQ HD CD single 1.092 0.020
KYQ HDA CD single 1.092 0.020
KYQ NZ CE single 1.455 0.020
KYQ HE CE single 1.092 0.020
KYQ HEA CE single 1.092 0.020
KYQ C11 NZ double 1.260 0.020
KYQ C12 C11 single 1.460 0.020
KYQ C13 C11 single 1.510 0.020
KYQ O15 C12 deloc 1.250 0.020
KYQ O16 C12 deloc 1.250 0.020
KYQ O14 C13 single 1.432 0.020
KYQ H13 C13 single 1.092 0.020
KYQ H13A C13 single 1.092 0.020
KYQ HO14 O14 single 0.967 0.020
KYQ O C deloc 1.250 0.020
KYQ OXT C deloc 1.250 0.020
KYQ HN1 N single 1.010 0.020
KYQ HN2 N single 1.010 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
KYQ HN1 N HN2 120.000 3.000
KYQ HN1 N CA 120.000 3.000
KYQ HN2 N CA 120.000 3.000
KYQ N CA HA 109.470 3.000
KYQ N CA CB 109.470 3.000
KYQ N CA C 109.470 3.000
KYQ HA CA CB 108.340 3.000
KYQ HA CA C 108.810 3.000
KYQ CB CA C 109.470 3.000
KYQ CA CB HB 109.470 3.000
KYQ CA CB HBA 109.470 3.000
KYQ CA CB CG 111.000 3.000
KYQ HB CB HBA 107.900 3.000
KYQ HB CB CG 109.470 3.000
KYQ HBA CB CG 109.470 3.000
KYQ CB CG HG 109.470 3.000
KYQ CB CG HGA 109.470 3.000
KYQ CB CG CD 111.000 3.000
KYQ HG CG HGA 107.900 3.000
KYQ HG CG CD 109.470 3.000
KYQ HGA CG CD 109.470 3.000
KYQ CG CD HD 109.470 3.000
KYQ CG CD HDA 109.470 3.000
KYQ CG CD CE 111.000 3.000
KYQ HD CD HDA 107.900 3.000
KYQ HD CD CE 109.470 3.000
KYQ HDA CD CE 109.470 3.000
KYQ CD CE HE 109.470 3.000
KYQ CD CE HEA 109.470 3.000
KYQ CD CE NZ 105.000 3.000
KYQ HE CE HEA 107.900 3.000
KYQ HE CE NZ 109.470 3.000
KYQ HEA CE NZ 109.470 3.000
KYQ CE NZ C11 127.000 3.000
KYQ NZ C11 C12 116.500 3.000
KYQ NZ C11 C13 116.500 3.000
KYQ C12 C11 C13 120.000 3.000
KYQ C11 C12 O15 120.000 3.000
KYQ C11 C12 O16 120.000 3.000
KYQ O15 C12 O16 123.000 3.000
KYQ C11 C13 H13 109.470 3.000
KYQ C11 C13 H13A 109.470 3.000
KYQ C11 C13 O14 109.500 3.000
KYQ H13 C13 H13A 107.900 3.000
KYQ H13 C13 O14 109.470 3.000
KYQ H13A C13 O14 109.470 3.000
KYQ C13 O14 HO14 109.470 3.000
KYQ CA C O 118.500 3.000
KYQ CA C OXT 118.500 3.000
KYQ O C OXT 123.000 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
KYQ var_1 HN2 N CA C 175.000 20.000 1
KYQ var_2 N CA CB CG -64.970 20.000 3
KYQ var_3 CA CB CG CD 179.993 20.000 3
KYQ var_4 CB CG CD CE 180.000 20.000 3
KYQ var_5 CG CD CE NZ -179.983 20.000 3
KYQ var_6 CD CE NZ C11 114.762 20.000 1
KYQ CONST_1 CE NZ C11 C13 0.000 0.000 0
KYQ var_7 NZ C11 C12 O16 0.018 20.000 1
KYQ var_8 NZ C11 C13 O14 -174.529 20.000 3
KYQ var_9 C11 C13 O14 HO14 -179.986 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
KYQ chir_01 CA N CB C 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
KYQ plan-1 N 0.020
KYQ plan-1 CA 0.020
KYQ plan-1 HN1 0.020
KYQ plan-1 HN2 0.020
KYQ plan-2 NZ 0.020
KYQ plan-2 CE 0.020
KYQ plan-2 C11 0.020
KYQ plan-2 C12 0.020
KYQ plan-2 C13 0.020
KYQ plan-3 C12 0.020
KYQ plan-3 C11 0.020
KYQ plan-3 O16 0.020
KYQ plan-3 O15 0.020
KYQ plan-4 C 0.020
KYQ plan-4 CA 0.020
KYQ plan-4 O 0.020
KYQ plan-4 OXT 0.020
# ------------------------------------------------------
|
