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
276
277
278
279
280
281
282
283
284
|
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
KHO KHO '4-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TET' non-polymer 37 19 .
# ------------------------------------------------------
# ------------------------------------------------------
#
# --- DESCRIPTION OF MONOMERS ---
#
data_comp_KHO
#
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
KHO O6 O OH1 0.000 0.000 0.000 0.000
KHO HO6 H H 0.000 0.912 -0.244 -0.207
KHO C4 C CH1 0.000 -0.798 -0.102 -1.180
KHO H4 H H 0.000 -0.769 -1.134 -1.556
KHO C5 C CH2 0.000 -0.257 0.848 -2.251
KHO H51 H H 0.000 0.783 0.593 -2.467
KHO H52 H H 0.000 -0.309 1.875 -1.881
KHO O5 O O2 0.000 -1.035 0.729 -3.441
KHO C1 C CH1 0.000 -2.335 1.239 -3.157
KHO H1 H H 0.000 -2.246 2.247 -2.729
KHO O4 O OH1 0.000 -3.094 1.304 -4.367
KHO HO4 H H 0.000 -2.647 1.887 -4.996
KHO C3 C CH1 0.000 -2.246 0.285 -0.855
KHO H3 H H 0.000 -2.265 1.275 -0.380
KHO C2 C CH1 0.000 -3.049 0.325 -2.159
KHO H2 H H 0.000 -3.121 -0.689 -2.577
KHO O2 O OH1 0.000 -4.362 0.829 -1.903
KHO HO2 H H 0.000 -4.863 0.857 -2.730
KHO "O1'" O O2 0.000 -2.813 -0.683 0.029
KHO "C1'" C CH1 0.000 -3.641 0.032 0.947
KHO "H1'" H H 0.000 -4.320 0.698 0.396
KHO "O4'" O O2 0.000 -2.826 0.800 1.840
KHO "C4'" C CH1 0.000 -3.024 0.355 3.190
KHO "H4'" H H 0.000 -2.260 -0.387 3.463
KHO "C5'" C CH2 0.000 -2.979 1.544 4.153
KHO "H5'1" H H 0.000 -3.181 1.197 5.169
KHO "H5'2" H H 0.000 -3.735 2.276 3.863
KHO "O5'" O OH1 0.000 -1.684 2.148 4.103
KHO "H5'" H H 0.000 -1.655 2.898 4.712
KHO "C3'" C CH1 0.000 -4.431 -0.292 3.203
KHO "H3'" H H 0.000 -5.217 0.472 3.293
KHO "O3'" O OH1 0.000 -4.543 -1.269 4.241
KHO H6 H H 0.000 -5.387 -1.732 4.156
KHO "C2'" C CH1 0.000 -4.459 -0.960 1.800
KHO "H2'" H H 0.000 -3.973 -1.945 1.828
KHO "O2'" O OH1 0.000 -5.797 -1.069 1.311
KHO H5 H H 0.000 -5.782 -1.405 0.405
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
KHO O6 n/a C4 START
KHO HO6 O6 . .
KHO C4 O6 C3 .
KHO H4 C4 . .
KHO C5 C4 O5 .
KHO H51 C5 . .
KHO H52 C5 . .
KHO O5 C5 C1 .
KHO C1 O5 O4 .
KHO H1 C1 . .
KHO O4 C1 HO4 .
KHO HO4 O4 . .
KHO C3 C4 "O1'" .
KHO H3 C3 . .
KHO C2 C3 O2 .
KHO H2 C2 . .
KHO O2 C2 HO2 .
KHO HO2 O2 . .
KHO "O1'" C3 "C1'" .
KHO "C1'" "O1'" "O4'" .
KHO "H1'" "C1'" . .
KHO "O4'" "C1'" "C4'" .
KHO "C4'" "O4'" "C3'" .
KHO "H4'" "C4'" . .
KHO "C5'" "C4'" "O5'" .
KHO "H5'1" "C5'" . .
KHO "H5'2" "C5'" . .
KHO "O5'" "C5'" "H5'" .
KHO "H5'" "O5'" . .
KHO "C3'" "C4'" "C2'" .
KHO "H3'" "C3'" . .
KHO "O3'" "C3'" H6 .
KHO H6 "O3'" . .
KHO "C2'" "C3'" "O2'" .
KHO "H2'" "C2'" . .
KHO "O2'" "C2'" H5 .
KHO H5 "O2'" . END
KHO C1 C2 . ADD
KHO "C1'" "C2'" . 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
KHO O4 C1 single 1.432 0.020
KHO C1 C2 single 1.524 0.020
KHO C1 O5 single 1.426 0.020
KHO H1 C1 single 1.099 0.020
KHO HO4 O4 single 0.967 0.020
KHO O2 C2 single 1.432 0.020
KHO C2 C3 single 1.524 0.020
KHO H2 C2 single 1.099 0.020
KHO HO2 O2 single 0.967 0.020
KHO "O1'" C3 single 1.426 0.020
KHO C3 C4 single 1.524 0.020
KHO H3 C3 single 1.099 0.020
KHO "C1'" "O1'" single 1.426 0.020
KHO "C1'" "C2'" single 1.524 0.020
KHO "O4'" "C1'" single 1.426 0.020
KHO "H1'" "C1'" single 1.099 0.020
KHO "C2'" "C3'" single 1.524 0.020
KHO "O2'" "C2'" single 1.432 0.020
KHO "H2'" "C2'" single 1.099 0.020
KHO "O3'" "C3'" single 1.432 0.020
KHO "C3'" "C4'" single 1.524 0.020
KHO "H3'" "C3'" single 1.099 0.020
KHO H6 "O3'" single 0.967 0.020
KHO H5 "O2'" single 0.967 0.020
KHO "C4'" "O4'" single 1.426 0.020
KHO "C5'" "C4'" single 1.524 0.020
KHO "H4'" "C4'" single 1.099 0.020
KHO "O5'" "C5'" single 1.432 0.020
KHO "H5'1" "C5'" single 1.092 0.020
KHO "H5'2" "C5'" single 1.092 0.020
KHO "H5'" "O5'" single 0.967 0.020
KHO C4 O6 single 1.432 0.020
KHO C5 C4 single 1.524 0.020
KHO H4 C4 single 1.099 0.020
KHO HO6 O6 single 0.967 0.020
KHO O5 C5 single 1.426 0.020
KHO H51 C5 single 1.092 0.020
KHO H52 C5 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
KHO HO6 O6 C4 109.470 3.000
KHO O6 C4 H4 109.470 3.000
KHO O6 C4 C5 109.470 3.000
KHO O6 C4 C3 109.470 3.000
KHO H4 C4 C5 108.340 3.000
KHO H4 C4 C3 108.340 3.000
KHO C5 C4 C3 111.000 3.000
KHO C4 C5 H51 109.470 3.000
KHO C4 C5 H52 109.470 3.000
KHO C4 C5 O5 109.470 3.000
KHO H51 C5 H52 107.900 3.000
KHO H51 C5 O5 109.470 3.000
KHO H52 C5 O5 109.470 3.000
KHO C5 O5 C1 111.800 3.000
KHO O5 C1 H1 109.470 3.000
KHO O5 C1 O4 109.470 3.000
KHO O5 C1 C2 109.470 3.000
KHO H1 C1 O4 109.470 3.000
KHO H1 C1 C2 108.340 3.000
KHO O4 C1 C2 109.470 3.000
KHO C1 O4 HO4 109.470 3.000
KHO C4 C3 H3 108.340 3.000
KHO C4 C3 C2 111.000 3.000
KHO C4 C3 "O1'" 109.470 3.000
KHO H3 C3 C2 108.340 3.000
KHO H3 C3 "O1'" 109.470 3.000
KHO C2 C3 "O1'" 109.470 3.000
KHO C3 C2 H2 108.340 3.000
KHO C3 C2 O2 109.470 3.000
KHO C3 C2 C1 111.000 3.000
KHO H2 C2 O2 109.470 3.000
KHO H2 C2 C1 108.340 3.000
KHO O2 C2 C1 109.470 3.000
KHO C2 O2 HO2 109.470 3.000
KHO C3 "O1'" "C1'" 111.800 3.000
KHO "O1'" "C1'" "H1'" 109.470 3.000
KHO "O1'" "C1'" "O4'" 109.470 3.000
KHO "O1'" "C1'" "C2'" 109.470 3.000
KHO "H1'" "C1'" "O4'" 109.470 3.000
KHO "H1'" "C1'" "C2'" 108.340 3.000
KHO "O4'" "C1'" "C2'" 109.470 3.000
KHO "C1'" "O4'" "C4'" 111.800 3.000
KHO "O4'" "C4'" "H4'" 109.470 3.000
KHO "O4'" "C4'" "C5'" 109.470 3.000
KHO "O4'" "C4'" "C3'" 109.470 3.000
KHO "H4'" "C4'" "C5'" 108.340 3.000
KHO "H4'" "C4'" "C3'" 108.340 3.000
KHO "C5'" "C4'" "C3'" 111.000 3.000
KHO "C4'" "C5'" "H5'1" 109.470 3.000
KHO "C4'" "C5'" "H5'2" 109.470 3.000
KHO "C4'" "C5'" "O5'" 109.470 3.000
KHO "H5'1" "C5'" "H5'2" 107.900 3.000
KHO "H5'1" "C5'" "O5'" 109.470 3.000
KHO "H5'2" "C5'" "O5'" 109.470 3.000
KHO "C5'" "O5'" "H5'" 109.470 3.000
KHO "C4'" "C3'" "H3'" 108.340 3.000
KHO "C4'" "C3'" "O3'" 109.470 3.000
KHO "C4'" "C3'" "C2'" 111.000 3.000
KHO "H3'" "C3'" "O3'" 109.470 3.000
KHO "H3'" "C3'" "C2'" 108.340 3.000
KHO "O3'" "C3'" "C2'" 109.470 3.000
KHO "C3'" "O3'" H6 109.470 3.000
KHO "C3'" "C2'" "H2'" 108.340 3.000
KHO "C3'" "C2'" "O2'" 109.470 3.000
KHO "C3'" "C2'" "C1'" 111.000 3.000
KHO "H2'" "C2'" "O2'" 109.470 3.000
KHO "H2'" "C2'" "C1'" 108.340 3.000
KHO "O2'" "C2'" "C1'" 109.470 3.000
KHO "C2'" "O2'" H5 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
KHO var_1 HO6 O6 C4 C3 -179.960 20.000 1
KHO var_2 O6 C4 C5 O5 180.000 20.000 3
KHO var_3 C4 C5 O5 C1 60.000 20.000 1
KHO var_4 C5 O5 C1 O4 180.000 20.000 1
KHO var_5 O5 C1 C2 C3 60.000 20.000 3
KHO var_6 O5 C1 O4 HO4 -59.938 20.000 1
KHO var_7 O6 C4 C3 "O1'" -60.000 20.000 3
KHO var_8 C4 C3 C2 O2 180.000 20.000 3
KHO var_9 C3 C2 O2 HO2 179.689 20.000 1
KHO var_10 C4 C3 "O1'" "C1'" 142.231 20.000 1
KHO var_11 C3 "O1'" "C1'" "O4'" -70.434 20.000 1
KHO var_12 "O1'" "C1'" "C2'" "C3'" 150.000 20.000 3
KHO var_13 "O1'" "C1'" "O4'" "C4'" -120.000 20.000 1
KHO var_14 "C1'" "O4'" "C4'" "C3'" -30.000 20.000 1
KHO var_15 "O4'" "C4'" "C5'" "O5'" -62.804 20.000 3
KHO var_16 "C4'" "C5'" "O5'" "H5'" -179.993 20.000 1
KHO var_17 "O4'" "C4'" "C3'" "C2'" 30.000 20.000 3
KHO var_18 "C4'" "C3'" "O3'" H6 -172.991 20.000 1
KHO var_19 "C4'" "C3'" "C2'" "O2'" -150.000 20.000 3
KHO var_20 "C3'" "C2'" "O2'" H5 174.419 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
KHO chir_01 C1 O4 C2 O5 negativ
KHO chir_02 C2 C1 O2 C3 positiv
KHO chir_03 C3 C2 "O1'" C4 negativ
KHO chir_04 "C1'" "O1'" "C2'" "O4'" negativ
KHO chir_05 "C2'" "C1'" "C3'" "O2'" negativ
KHO chir_06 "C3'" "C2'" "O3'" "C4'" negativ
KHO chir_07 "C4'" "C3'" "O4'" "C5'" negativ
KHO chir_08 C4 C3 O6 C5 positiv
# ------------------------------------------------------
|
