File: TestRNA2_fixed2.mol

package info (click to toggle)
rdkit 202503.6-3
  • links: PTS, VCS
  • area: main
  • in suites: sid
  • size: 222,000 kB
  • sloc: cpp: 411,111; python: 78,482; ansic: 26,181; java: 8,285; javascript: 4,404; sql: 2,393; yacc: 1,626; lex: 1,267; cs: 1,090; makefile: 581; xml: 229; fortran: 183; sh: 121
file content (232 lines) | stat: -rw-r--r-- 7,573 bytes parent folder | download | duplicates (2)
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

  -INDIGO-01132508492D

  0  0  0  0  0  0  0  0  0  0  0 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 15 14 0 0 0
M  V30 BEGIN ATOM
M  V30 1 A 1.25 -2.75 0.0 0 CLASS=BASE SEQID=1 ATTCHORD=(2 2 Al)
M  V30 2 R 1.25 -1.25 0.0 0 CLASS=SUGAR SEQID=1 ATTCHORD=(4 1 Cx 15 Br)
M  V30 3 U 4.25 -2.75 0.0 0 CLASS=BASE SEQID=2 ATTCHORD=(2 4 Al)
M  V30 4 R 4.25 -1.25 0.0 0 CLASS=SUGAR SEQID=2 ATTCHORD=(6 3 Cx 5 Br 15 Al)
M  V30 5 P 5.75 -1.25 0.0 0 CLASS=PHOSPHATE SEQID=2 ATTCHORD=(4 4 Al 7 Br)
M  V30 6 C 7.25 -2.75 0.0 0 CLASS=BASE SEQID=3 ATTCHORD=(2 7 Al)
M  V30 7 R 7.25 -1.25 0.0 0 CLASS=SUGAR SEQID=3 ATTCHORD=(6 6 Cx 8 Br 5 Al)
M  V30 8 P 8.75 -1.25 0.0 0 CLASS=PHOSPHATE SEQID=3 ATTCHORD=(4 7 Al 10 Br)
M  V30 9 A 10.25 -2.75 0.0 0 CLASS=BASE SEQID=4 ATTCHORD=(2 10 Al)
M  V30 10 R 10.25 -1.25 0.0 0 CLASS=SUGAR SEQID=4 ATTCHORD=(6 9 Cx 11 Br 8 Al-
M  V30 )
M  V30 11 P 11.75 -1.25 0.0 0 CLASS=PHOSPHATE SEQID=4 ATTCHORD=(4 10 Al 13 Br-
M  V30 )
M  V30 12 U 13.25 -2.75 0.0 0 CLASS=BASE SEQID=5 ATTCHORD=(2 13 Al)
M  V30 13 R 13.25 -1.25 0.0 0 CLASS=SUGAR SEQID=5 ATTCHORD=(6 12 Cx 14 Br 11 -
M  V30 Al)
M  V30 14 P 14.75 -1.25 0.0 0 CLASS=PHOSPHATE SEQID=5 ATTCHORD=(2 13 Al)
M  V30 15 P 2.75 -1.25 0.0 0 CLASS=PHOSPHATE SEQID=1 ATTCHORD=(4 2 Al 4 Br)
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 3 4
M  V30 3 1 4 5
M  V30 4 1 6 7
M  V30 5 1 7 8
M  V30 6 1 5 7
M  V30 7 1 9 10
M  V30 8 1 10 11
M  V30 9 1 8 10
M  V30 10 1 12 13
M  V30 11 1 13 14
M  V30 12 1 11 13
M  V30 13 1 2 15
M  V30 14 1 15 4
M  V30 END BOND
M  V30 END CTAB
M  V30 BEGIN TEMPLATE
M  V30 TEMPLATE 1 BASE/Ade/A NATREPLACE=BASE/A
M  V30 BEGIN CTAB
M  V30 COUNTS 11 12 2 0 0
M  V30 BEGIN ATOM
M  V30 1 C 1.0354 0.2498 0.0 0
M  V30 2 C -0.0792 -0.754 0.0 0
M  V30 3 C -1.5057 -0.2906 0.0 0
M  V30 4 N -1.8177 1.1766 0.0 0
M  V30 5 C -0.7031 2.1804 0.0 0
M  V30 6 N 0.7235 1.717 0.0 0
M  V30 7 N -2.3871 -1.5034 0.0 0
M  V30 8 C -1.5053 -2.7168 0.0 0
M  V30 9 N -0.0787 -2.2532 0.0 0
M  V30 10 N 2.1768 -0.1209 0.0 0
M  V30 11 H -3.5871 -1.5034 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 10
M  V30 2 2 1 6
M  V30 3 1 1 2
M  V30 4 1 9 2
M  V30 5 2 2 3
M  V30 6 1 7 3
M  V30 7 1 3 4
M  V30 8 2 4 5
M  V30 9 1 5 6
M  V30 10 1 7 8
M  V30 11 1 7 11
M  V30 12 2 8 9
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 SUP 1 ATOMS=(1 11) XBONDS=(1 11) BRKXYZ=(9 0.600000 0.000000 0.00000-
M  V30 0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS-
M  V30 =LGRP
M  V30 2 SUP 2 ATOMS=(10 1 2 3 4 5 6 7 8 9 10) XBONDS=(1 11) BRKXYZ=(9 -0.600-
M  V30 000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.0-
M  V30 00000) LABEL=A CLASS=BASE SAP=(3 7 11 Al) NATREPLACE=BASE/A
M  V30 END SGROUP
M  V30 END CTAB
M  V30 TEMPLATE 2 SUGAR/Rib/R NATREPLACE=SUGAR/R
M  V30 BEGIN CTAB
M  V30 COUNTS 12 12 4 0 0
M  V30 BEGIN ATOM
M  V30 1 O -1.1017 -1.0663 0.0 0
M  V30 2 C -0.5897 0.3436 0.0 0 CFG=1
M  V30 3 C 0.0809 -1.9889 0.0 0 CFG=2
M  V30 4 C 0.9095 0.2924 0.0 0 CFG=2
M  V30 5 C 1.3239 -1.1493 0.0 0 CFG=1
M  V30 6 O 1.8285 1.4755 0.0 0
M  V30 7 O 2.4518 -1.5589 0.0 0
M  V30 8 C -1.431 1.5834 0.0 0
M  V30 9 O 0.0399 -3.1881 0.0 0
M  V30 10 O -2.9279 1.4755 0.0 0
M  V30 11 H -3.6017 2.4684 0.0 0
M  V30 12 H 3.0174 1.3125 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 1 3
M  V30 3 1 2 4
M  V30 4 1 2 8 CFG=3
M  V30 5 1 3 5
M  V30 6 1 3 9 CFG=3
M  V30 7 1 4 5
M  V30 8 1 4 6 CFG=1
M  V30 9 1 5 7 CFG=1
M  V30 10 1 6 12
M  V30 11 1 8 10
M  V30 12 1 10 11
M  V30 END BOND
M  V30 BEGIN COLLECTION
M  V30 MDLV30/STEABS ATOMS=(4 2 3 4 5)
M  V30 END COLLECTION
M  V30 BEGIN SGROUP
M  V30 1 SUP 1 ATOMS=(1 11) XBONDS=(1 12) BRKXYZ=(9 0.336900 -0.496450 0.0000-
M  V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS-
M  V30 S=LGRP
M  V30 2 SUP 2 ATOMS=(1 12) XBONDS=(1 10) BRKXYZ=(9 -0.594450 0.081500 0.0000-
M  V30 00 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLAS-
M  V30 S=LGRP
M  V30 3 SUP 3 ATOMS=(1 9) XBONDS=(1 6) BRKXYZ=(9 0.020500 0.599600 0.000000 -
M  V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS=-
M  V30 LGRP
M  V30 4 SUP 4 ATOMS=(9 1 2 3 4 5 6 7 8 10) XBONDS=(3 6 10 12) BRKXYZ=(9 -0.0-
M  V30 20500 -0.599600 0.000000 0.594450 -0.081500 0.000000 0.000000 0.000000-
M  V30  0.000000) BRKXYZ=(9 -0.336900 0.496450 0.000000 0.000000 0.000000 0.0-
M  V30 00000 0.000000 0.000000 0.000000) LABEL=R CLASS=SUGAR SAP=(3 10 11 Al)-
M  V30  SAP=(3 6 12 Br) SAP=(3 3 9 Cx) NATREPLACE=SUGAR/R
M  V30 END SGROUP
M  V30 END CTAB
M  V30 TEMPLATE 3 BASE/Ura/U NATREPLACE=BASE/U
M  V30 BEGIN CTAB
M  V30 COUNTS 9 9 2 0 0
M  V30 BEGIN ATOM
M  V30 1 C 1.8617 1.3499 0.0 0
M  V30 2 C 1.1117 0.0509 0.0 0
M  V30 3 C -0.3883 0.0509 0.0 0
M  V30 4 N -1.1382 1.35 0.0 0
M  V30 5 C -0.3882 2.649 0.0 0
M  V30 6 N 1.1117 2.6489 0.0 0
M  V30 7 O 3.0618 1.3499 0.0 0
M  V30 8 O -0.9882 3.6882 0.0 0
M  V30 9 H -2.3383 1.35 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 2 1 7
M  V30 2 1 1 6
M  V30 3 1 1 2
M  V30 4 2 2 3
M  V30 5 1 3 4
M  V30 6 1 4 5
M  V30 7 1 4 9
M  V30 8 2 5 8
M  V30 9 1 5 6
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 7) BRKXYZ=(9 0.600050 0.000000 0.000000 -
M  V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=L-
M  V30 GRP
M  V30 2 SUP 2 ATOMS=(8 1 2 3 4 5 6 7 8) XBONDS=(1 7) BRKXYZ=(9 -0.600050 0.0-
M  V30 00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) -
M  V30 LABEL=U CLASS=BASE SAP=(3 4 9 Al) NATREPLACE=BASE/U
M  V30 END SGROUP
M  V30 END CTAB
M  V30 TEMPLATE 4 PHOSPHATE/P/P NATREPLACE=PHOSPHATE/P
M  V30 BEGIN CTAB
M  V30 COUNTS 5 4 3 0 0
M  V30 BEGIN ATOM
M  V30 1 P -0.2399 0.0 0.0 0
M  V30 2 O -1.4399 0.0 0.0 0
M  V30 3 O 0.3598 -1.0394 0.0 0
M  V30 4 O 0.9601 0.0 0.0 0
M  V30 5 O 0.3598 1.0394 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 2 1 3
M  V30 3 1 1 4
M  V30 4 1 1 5
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 SUP 1 ATOMS=(1 2) XBONDS=(1 1) BRKXYZ=(9 0.600000 0.000000 0.000000 -
M  V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS=-
M  V30 LGRP
M  V30 2 SUP 2 ATOMS=(1 4) XBONDS=(1 3) BRKXYZ=(9 -0.600000 0.000000 0.000000-
M  V30  0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=OH CLASS-
M  V30 =LGRP
M  V30 3 SUP 3 ATOMS=(3 1 3 5) XBONDS=(2 1 3) BRKXYZ=(9 -0.600000 0.000000 0.-
M  V30 000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=P -
M  V30 CLASS=PHOSPHATE SAP=(3 1 2 Al) SAP=(3 1 4 Br) NATREPLACE=PHOSPHATE/P
M  V30 END SGROUP
M  V30 END CTAB
M  V30 TEMPLATE 5 BASE/Cyt/C NATREPLACE=BASE/C
M  V30 BEGIN CTAB
M  V30 COUNTS 9 9 2 0 0
M  V30 BEGIN ATOM
M  V30 1 C 1.8617 1.3499 0.0 0
M  V30 2 C 1.1117 2.6489 0.0 0
M  V30 3 C -0.3882 2.649 0.0 0
M  V30 4 N -1.1382 1.35 0.0 0
M  V30 5 C -0.3883 0.0509 0.0 0
M  V30 6 N 1.1117 0.0509 0.0 0
M  V30 7 N 3.0618 1.3499 0.0 0
M  V30 8 O -0.9884 -0.9883 0.0 0
M  V30 9 H -2.3383 1.35 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 2 1 6
M  V30 3 1 1 7
M  V30 4 2 2 3
M  V30 5 1 3 4
M  V30 6 1 4 5
M  V30 7 1 4 9
M  V30 8 1 5 6
M  V30 9 2 5 8
M  V30 END BOND
M  V30 BEGIN SGROUP
M  V30 1 SUP 1 ATOMS=(1 9) XBONDS=(1 7) BRKXYZ=(9 0.600050 0.000000 0.000000 -
M  V30 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) LABEL=H CLASS=L-
M  V30 GRP
M  V30 2 SUP 2 ATOMS=(8 1 2 3 4 5 6 7 8) XBONDS=(1 7) BRKXYZ=(9 -0.600050 0.0-
M  V30 00000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000) -
M  V30 LABEL=C CLASS=BASE SAP=(3 4 9 Al) NATREPLACE=BASE/C
M  V30 END SGROUP
M  V30 END CTAB
M  V30 END TEMPLATE
M  END