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
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
|
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
0AY 0AY 'diethyl [(1R)-1,5-diaminopentyl]boro' non-polymer 37 14 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_0AY
#
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
0AY NZ N NH2 0.000 0.000 0.000 0.000
0AY H1NZ H H 0.000 0.488 0.887 0.053
0AY H2NZ H H 0.000 0.442 -0.783 -0.467
0AY CE C CH2 0.000 -1.335 -0.148 0.594
0AY H1E H H 0.000 -1.667 0.816 0.986
0AY H2E H H 0.000 -1.292 -0.875 1.408
0AY CD C CH2 0.000 -2.318 -0.633 -0.474
0AY H1D H H 0.000 -1.983 -1.596 -0.866
0AY H2D H H 0.000 -2.359 0.095 -1.287
0AY CG C CH2 0.000 -3.708 -0.788 0.145
0AY H1G H H 0.000 -4.041 0.176 0.537
0AY H2G H H 0.000 -3.665 -1.515 0.958
0AY CB C CH2 0.000 -4.691 -1.271 -0.924
0AY H1B H H 0.000 -4.357 -2.234 -1.316
0AY H2B H H 0.000 -4.732 -0.543 -1.736
0AY CA C CH1 0.000 -6.081 -1.426 -0.305
0AY HA H H 0.000 -6.039 -2.159 0.513
0AY N N NH2 0.000 -7.025 -1.891 -1.330
0AY H2N H H 0.000 -7.516 -2.770 -1.213
0AY H1N H H 0.000 -7.191 -1.337 -2.162
0AY B B B 0.000 -6.561 -0.041 0.258
0AY O O O2 0.000 -5.725 1.101 0.140
0AY C3 C CH2 0.000 -6.257 2.127 -0.700
0AY H13 H H 0.000 -7.253 2.405 -0.349
0AY H23 H H 0.000 -6.324 1.758 -1.726
0AY C5 C CH3 0.000 -5.339 3.350 -0.655
0AY H35 H H 0.000 -4.372 3.083 -0.996
0AY H25 H H 0.000 -5.731 4.113 -1.277
0AY H15 H H 0.000 -5.273 3.709 0.340
0AY OXT O O2 0.000 -7.831 0.070 0.884
0AY C1 C CH2 0.000 -7.790 -0.052 2.307
0AY H11 H H 0.000 -7.229 0.786 2.727
0AY H21 H H 0.000 -7.300 -0.989 2.578
0AY C2 C CH3 0.000 -9.216 -0.042 2.861
0AY H32 H H 0.000 -9.190 -0.133 3.917
0AY H22 H H 0.000 -9.695 0.868 2.600
0AY H12 H H 0.000 -9.763 -0.854 2.454
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
0AY NZ n/a CE START
0AY H1NZ NZ . .
0AY H2NZ NZ . .
0AY CE NZ CD .
0AY H1E CE . .
0AY H2E CE . .
0AY CD CE CG .
0AY H1D CD . .
0AY H2D CD . .
0AY CG CD CB .
0AY H1G CG . .
0AY H2G CG . .
0AY CB CG CA .
0AY H1B CB . .
0AY H2B CB . .
0AY CA CB B .
0AY HA CA . .
0AY N CA H1N .
0AY H2N N . .
0AY H1N N . .
0AY B CA OXT .
0AY O B C3 .
0AY C3 O C5 .
0AY H13 C3 . .
0AY H23 C3 . .
0AY C5 C3 H15 .
0AY H35 C5 . .
0AY H25 C5 . .
0AY H15 C5 . .
0AY OXT B C1 .
0AY C1 OXT C2 .
0AY H11 C1 . .
0AY H21 C1 . .
0AY C2 C1 H12 .
0AY H32 C2 . .
0AY H22 C2 . .
0AY H12 C2 . 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
0AY N CA single 1.450 0.020
0AY H1N N single 1.010 0.020
0AY H2N N single 1.010 0.020
0AY B CA single 1.600 0.020
0AY HA CA single 1.099 0.020
0AY CA CB single 1.524 0.020
0AY H1B CB single 1.092 0.020
0AY H2B CB single 1.092 0.020
0AY CB CG single 1.524 0.020
0AY H1G CG single 1.092 0.020
0AY H2G CG single 1.092 0.020
0AY CG CD single 1.524 0.020
0AY H1D CD single 1.092 0.020
0AY H2D CD single 1.092 0.020
0AY CD CE single 1.524 0.020
0AY H1E CE single 1.092 0.020
0AY H2E CE single 1.092 0.020
0AY CE NZ single 1.450 0.020
0AY H1NZ NZ single 1.010 0.020
0AY H2NZ NZ single 1.010 0.020
0AY O B single 1.434 0.020
0AY OXT B single 1.434 0.020
0AY C1 OXT single 1.426 0.020
0AY C2 C1 single 1.513 0.020
0AY H11 C1 single 1.092 0.020
0AY H21 C1 single 1.092 0.020
0AY H12 C2 single 1.059 0.020
0AY H22 C2 single 1.059 0.020
0AY H32 C2 single 1.059 0.020
0AY C3 O single 1.426 0.020
0AY H13 C3 single 1.092 0.020
0AY H23 C3 single 1.092 0.020
0AY C5 C3 single 1.513 0.020
0AY H15 C5 single 1.059 0.020
0AY H25 C5 single 1.059 0.020
0AY H35 C5 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
0AY H1NZ NZ H2NZ 120.000 3.000
0AY H1NZ NZ CE 120.000 3.000
0AY H2NZ NZ CE 120.000 3.000
0AY NZ CE H1E 109.470 3.000
0AY NZ CE H2E 109.470 3.000
0AY NZ CE CD 109.470 3.000
0AY H1E CE H2E 107.900 3.000
0AY H1E CE CD 109.470 3.000
0AY H2E CE CD 109.470 3.000
0AY CE CD H1D 109.470 3.000
0AY CE CD H2D 109.470 3.000
0AY CE CD CG 111.000 3.000
0AY H1D CD H2D 107.900 3.000
0AY H1D CD CG 109.470 3.000
0AY H2D CD CG 109.470 3.000
0AY CD CG H1G 109.470 3.000
0AY CD CG H2G 109.470 3.000
0AY CD CG CB 111.000 3.000
0AY H1G CG H2G 107.900 3.000
0AY H1G CG CB 109.470 3.000
0AY H2G CG CB 109.470 3.000
0AY CG CB H1B 109.470 3.000
0AY CG CB H2B 109.470 3.000
0AY CG CB CA 111.000 3.000
0AY H1B CB H2B 107.900 3.000
0AY H1B CB CA 109.470 3.000
0AY H2B CB CA 109.470 3.000
0AY CB CA HA 108.340 3.000
0AY CB CA N 109.470 3.000
0AY CB CA B 109.470 3.000
0AY HA CA N 109.470 3.000
0AY HA CA B 109.470 3.000
0AY N CA B 109.500 3.000
0AY CA N H2N 120.000 3.000
0AY CA N H1N 120.000 3.000
0AY H2N N H1N 120.000 3.000
0AY CA B O 120.000 3.000
0AY CA B OXT 120.000 3.000
0AY O B OXT 120.000 3.000
0AY B O C3 120.000 3.000
0AY O C3 H13 109.470 3.000
0AY O C3 H23 109.470 3.000
0AY O C3 C5 109.470 3.000
0AY H13 C3 H23 107.900 3.000
0AY H13 C3 C5 109.470 3.000
0AY H23 C3 C5 109.470 3.000
0AY C3 C5 H35 109.470 3.000
0AY C3 C5 H25 109.470 3.000
0AY C3 C5 H15 109.470 3.000
0AY H35 C5 H25 109.470 3.000
0AY H35 C5 H15 109.470 3.000
0AY H25 C5 H15 109.470 3.000
0AY B OXT C1 120.000 3.000
0AY OXT C1 H11 109.470 3.000
0AY OXT C1 H21 109.470 3.000
0AY OXT C1 C2 109.470 3.000
0AY H11 C1 H21 107.900 3.000
0AY H11 C1 C2 109.470 3.000
0AY H21 C1 C2 109.470 3.000
0AY C1 C2 H32 109.470 3.000
0AY C1 C2 H22 109.470 3.000
0AY C1 C2 H12 109.470 3.000
0AY H32 C2 H22 109.470 3.000
0AY H32 C2 H12 109.470 3.000
0AY H22 C2 H12 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
0AY var_1 H2NZ NZ CE CD -56.069 20.000 1
0AY var_2 NZ CE CD CG 179.973 20.000 3
0AY var_3 CE CD CG CB 179.963 20.000 3
0AY var_4 CD CG CB CA 180.000 20.000 3
0AY var_5 CG CB CA B 60.025 20.000 3
0AY var_6 CB CA N H1N -59.981 20.000 1
0AY var_7 CB CA B OXT 179.975 20.000 1
0AY var_8 CA B O C3 114.870 20.000 1
0AY var_9 B O C3 C5 175.000 20.000 1
0AY var_10 O C3 C5 H15 -59.988 20.000 3
0AY var_11 CA B OXT C1 95.066 20.000 1
0AY var_12 B OXT C1 C2 -175.009 20.000 1
0AY var_13 OXT C1 C2 H12 59.950 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
0AY chir_01 CA N CB B 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
0AY plan-1 N 0.020
0AY plan-1 CA 0.020
0AY plan-1 H1N 0.020
0AY plan-1 H2N 0.020
0AY plan-2 NZ 0.020
0AY plan-2 CE 0.020
0AY plan-2 H1NZ 0.020
0AY plan-2 H2NZ 0.020
# ------------------------------------------------------
|
