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Fragmentation failures occur when the stereochemistry of a fragment can no not be fixed.

Fragmenter rewrite(OE) failure molecules (cmiles), note that molecule 1 also failed in fragmenter=0.0.7

...

Parent molecule

Fragmenter=0.0.7 molecule

OE

[H:39][c:10]1[c:24]([c:23]([c:13]([c:12]([c:11]1[H:40])[O:45][C:46]([H:47])([H:48])[H:49])[H:41])[N:22]([H:43])[c:1]2[n:21][c:20]3[c:17]([c:15]([n:14]2)[O:16][C:3]([H:26])([H:27])[C:4]4([C:5]([C:6]([C:7]([C:8]([C:9]4([H:37])[H:38])([H:35])[H:36])([H:33])[H:34])([H:31])[H:32])([H:29])[H:30])[H:28])[N:18]=[C:2]([N:19]3[H:42])[H:25])[H:44]

[H:21][c:1]1[c:2]([c:7]([c:4]([c:8]([c:3]1[H:23])[O:19][C:12]([H:26])([H:27])[H:28])[H:24])[N:18]([H:33])[c:11]2[n:15][c:9]3[c:6]([c:10]([n:16]2)[O:20][C:13]([H:29])([H:30])[H:31])[N:14]=[C:5]([N:17]3[H:32])[H:25])[H:22]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:45])[H:44])[N:10]([H:11])[c:12]2[n:13][c:14]3[c:15]([c:16]([n:17]2)[O:18][C:19]([H:20])([H:21])[C:22]4([C:27]([C:26]([C:25]([C:24]([C:23]4([H:36])[H:37])([H:34])[H:35])([H:32])[H:33])([H:30])[H:31])([H:28])[H:29])[H:38])[N:39]=[C:40]([N:41]3[H:42])[H:43])[H:9])[H:8]

[H:17][c:1]1[c:2]([c:4]([c:9]([c:5]([c:3]1[H:19])[H:21])[N:16]([H:25])[c:11]2[n:12][c:6]([c:8]3[c:10]([n:14]2)[N:15]([C:7](=[N:13]3)[H:23])[H:24])[H:22])[H:20])[H:18]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[Cl:43])[H:44])[H:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[I:21])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:23]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[I:43])[H:44])[H:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[I:21])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:23]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:58])[H:57])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[C:43]([H:44])([H:45])[C:46]([H:47])([H:48])[H:49])[H:50])[H:51])[H:52])[N+:53]([H:54])([H:55])[H:56])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[C:15]([H:39])([H:40])[N:18]([H:42])[C:7](=[O:20])[C@@:12]2([C:10]([C:9]([C:11]([N:17]2[C:8](=[O:21])[C@@:16]([H:41])([C:14]([H:36])([H:37])[H:38])[N+:19]([H:43])([H:44])[H:45])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:25])[C:13]([H:33])([H:34])[H:35])[H:23]

OE+AT_RDKIT

Image RemovedImage Added

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[F:43])[H:44])[H:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[F:21])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:23]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[Cl:42])[H:43])[H:44])[Cl:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:6]([c:4]([c:3]([c:5]1[Cl:19])[H:23])[C:14]([H:34])([H:35])[N:16]([H:36])[C:7](=[O:17])[C@@:12]2([C:10]([C:9]([C:11]([N:15]2[C:8](=[O:18])[C:13]([H:31])([H:32])[H:33])([H:28])[H:29])([H:24])[H:25])([H:26])[H:27])[H:30])[Cl:20])[H:22]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:58])[H:57])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[C:42]([H:43])([H:44])[H:45])[H:46])[H:47])[C:48]([H:49])([H:50])[H:51])[H:52])[N+:53]([H:54])([H:55])[H:56])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:23])[H:25])[C:14]([H:36])([H:37])[C@:15]([H:38])([C:8](=[O:20])[N:16]2[C@:12]([C:10]([C:9]([C:11]2([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])([H:32])[C:7](=[O:19])[N:17]([H:39])[C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])[H:24])[H:22]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:55])[H:54])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[C:43]([H:44])([H:45])[H:46])[H:47])[H:48])[H:49])[N+:50]([H:51])([H:52])[H:53])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:23])[H:25])[C:14]([H:36])([H:37])[C@:15]([H:38])([C:8](=[O:20])[N:16]2[C@:12]([C:10]([C:9]([C:11]2([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])([H:32])[C:7](=[O:19])[N:17]([H:39])[C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])[H:24])[H:22]

OE

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:41]([c:40]([c:39]([c:38]([c:37]3[H:46])[H:45])[H:44])[H:43])[H:42])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:23])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:24])[H:22]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:55])[H:54])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[C:42]([H:43])([H:44])[H:45])[H:46])[H:47])[Cl:48])[H:49])[N+:50]([H:51])([H:52])[H:53])[H:9])[H:8]

[H:21][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:23])[H:25])[C:14]([H:36])([H:37])[C@:15]([H:38])([C:8](=[O:20])[N:16]2[C@:12]([C:10]([C:9]([C:11]2([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])([H:32])[C:7](=[O:19])[N:17]([H:39])[C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])[H:24])[H:22]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[F:42])[H:43])[H:44])[Cl:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:23][c:1]1[c:2]([c:6]([c:3]([c:4]([c:5]1[F:21])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:25])[Cl:22])[H:24]

OE+AT_RDKIT

[H:1][c:2]1[c:7]([c:6]([c:5]([c:4]([c:3]1[H:52])[H:51])[C:10]([H:11])([H:12])[C@:13]([H:14])([C:15](=[O:16])[N:17]2[C@:18]([C:19]([C:20]([C:21]2([H:22])[H:23])([H:24])[H:25])([H:26])[H:27])([H:28])[C:29](=[O:30])[N:31]([H:32])[C:33]([H:34])([H:35])[c:36]3[c:37]([c:38]([c:39]([c:40]([c:41]3[H:42])[Br:43])[H:44])[H:45])[H:46])[N+:47]([H:48])([H:49])[H:50])[H:9])[H:8]

[H:22][c:1]1[c:2]([c:5]([c:4]([c:6]([c:3]1[H:24])[Br:21])[H:25])[C:14]([H:36])([H:37])[N:17]([H:39])[C:7](=[O:19])[C@@:12]2([C:10]([C:9]([C:11]([N:16]2[C:8](=[O:20])[C@@:15]([H:38])([C:13]([H:33])([H:34])[H:35])[N+:18]([H:40])([H:41])[H:42])([H:30])[H:31])([H:26])[H:27])([H:28])[H:29])[H:32])[H:23]

OE

[H:1][c:2]1[c:3]([c:4]([c:5]([c:6]([c:7]1[O:8][C:9]2=[C:10]([c:11]3[c:12]([n:13][c:14]([n:15][c:16]3[N:17]([C:18]2=[O:19])[C:20]([H:21])([H:22])[H:23])[N:24]([H:25])[C:26]([C:27]([H:28])([H:29])[H:30])([C:31]([H:32])([H:33])[H:34])[C:35]([H:36])([H:37])[O:38][H:39])[H:40])[H:41])[F:42])[H:43])[F:44])[H:45]

[H:19][c:1]1[c:2]2[c:3]([n:14][c:4]([n:13]1)[N:16]([H:33])[C:12]([C:8]([H:22])([H:23])[H:24])([C:9]([H:25])([H:26])[H:27])[C:11]([H:31])([H:32])[O:18][H:34])[N:15]([C:7](=[O:17])[C:6](=[C:5]2[H:20])[H:21])[C:10]([H:28])([H:29])[H:30]

AT_RDKIT

[H:32][c:12]1[c:11]([c:10]([c:23]([c:14]([c:13]1[H:33])[N:15]([H:34])[C:16]2([C:17]([C:18]([C:19]([C:20]([C:21]([C:22]2([H:46])[H:47])([H:44])[H:45])([H:42])[H:43])([H:40])[H:41])([H:38])[H:39])([H:36])[H:37])[H:35])[H:48])[C:9]3=[C:7]([C:6](=[C:25]([S:24]3)[C:26](=[O:27])[O-:28])[O:5][C:4]([H:29])([H:30])[C:2](=[O:1])[O-:3])[Br:8])[H:31]

[H:15][c:1]1[c:2]([c:4]([c:6]([c:5]([c:3]1[H:17])[H:19])[N:14]([H:33])[C:13]2([C:11]([C:9]([C:7]([C:8]([C:10]([C:12]2([H:30])[H:31])([H:26])[H:27])([H:22])[H:23])([H:20])[H:21])([H:24])[H:25])([H:28])[H:29])[H:32])[H:18])[H:16]

AT_RDKIT

Image RemovedImage Added

[H:45][c:39]1[c:40]([c:41]([c:42]([c:43]([c:44]1[H:49])[H:48])[O:38][c:18]2[c:19]([c:20]([c:21]([c:16]([c:17]2[H:32])[O:15][C:14]([H:30])([H:31])[C:13]([H:28])([H:29])[C:12]([H:26])([H:27])[C:11]3=[C:4]([N:34]([c:5]4[c:10]3[c:9]([c:8]([c:7]([c:6]4[H:22])[H:23])[H:24])[H:25])[H:35])[C:2](=[O:1])[O-:3])[H:33])[H:36])[H:37])[H:47])[H:46]

[H:15][c:2]1[c:1]([c:3]([c:6]([c:4]([c:5]1[H:16])[H:11])[O:9][C:8]([H:12])([H:13])[C:7]([H:17])([H:18])[H:19])[H:10])[H:14]

AT_RDKIT (2021.03.1)

Using rdkit=2020.09.3 resolves this issue, so there must be a difference in the conformer generation which is causing the difference in fragments for this tyk2 series.

Image RemovedImage Added

[H:23][c:1]1[c:2]([c:3]([c:4]([c:5]([c:6]1[H:25])[Cl:7])[C:8](=[O:9])[N:10]([H:26])[c:11]2[c:12]([c:13]([n:14][c:15]([c:16]2[H:29])[N:17]([H:30])[C:18](=[O:19])[C:20]([H:22])([H:31])[O:33][H:32])[H:28])[H:27])[Cl:21])[H:24]

[H:15][c:4]1[c:1]([c:3]([n:8][c:5]([c:2]1[H:11])[N:9]([H:12])[C:6](=[O:10])[C:7]([H:16])([H:17])[H:18])[H:14])[H:13]

AT_RDKIT

[H:21][c:1]1[c:2]([c:3]([c:4]([c:5]([c:6]1[H:23])[Cl:7])[C:8](=[O:9])[N:10]([H:24])[c:11]2[c:12]([c:13]([n:14][c:15]([c:16]2[H:27])[N:17]([H:28])[C:18](=[O:19])[C:30]3([C:31]([C:32]([C:33]([C:34]3([H:41])[H:42])([H:39])[H:40])([H:37])[H:38])([H:35])[H:36])[H:29])[H:26])[H:25])[Cl:20])[H:22]

[H:19][c:4]1[c:1]([c:3]([n:12][c:5]([c:2]1[H:15])[N:13]([H:16])[C:6](=[O:14])[C:11]2([C:9]([C:7]([C:8]([C:10]2([H:26])[H:27])([H:22])[H:23])([H:20])[H:21])([H:24])[H:25])[H:28])[H:18])[H:17]

AT_RDKIT

[H:44][c:38]1[c:39]([c:40]([c:41]([c:42]([c:43]1[H:48])[H:47])[c:19]2[c:20]([c:21]([c:16]([c:17]([c:18]2[H:37])[H:32])[O:15][C:14]([H:30])([H:31])[C:13]([H:28])([H:29])[C:12]([H:26])([H:27])[C:11]3=[C:4]([N:34]([c:5]4[c:10]3[c:9]([c:8]([c:7]([c:6]4[H:22])[H:23])[H:24])[H:25])[H:35])[C:2](=[O:1])[O-:3])[H:33])[H:36])[H:46])[H:45]

[H:16][c:5]1[c:1]([c:3]([c:6]([c:4]([c:2]1[H:15])[H:11])[O:9][C:8]([H:12])([H:13])[C:7]([H:17])([H:18])[H:19])[H:10])[H:14]

AT_RDKIT

[H:27][c:1]1[c:2]([c:3]([c:4]([c:5]([c:6]1[H:29])[Cl:7])[C:8](=[O:9])[N:10]([H:30])[c:11]2[c:12]([c:13]([n:14][c:15]([c:16]2[H:33])[N:17]([H:34])[C:18](=[O:19])[C:20]3([C:22]([C:21]3([H:35])[H:36])([H:23])[H:26])[H:25])[H:32])[H:31])[Cl:24])[H:28]

[H:17][c:4]1[c:1]([c:3]([n:10][c:5]([c:2]1[H:13])[N:11]([H:14])[C:6](=[O:12])[C:9]2([C:7]([C:8]2([H:20])[H:21])([H:18])[H:19])[H:22])[H:16])[H:15]

AT_RDKIT

[H:23][c:1]1[c:2]([c:3]([c:4]([c:5]([c:6]1[H:25])[Cl:7])[C:8](=[O:9])[N:10]([H:26])[c:11]2[c:12]([c:13]([n:14][c:15]([c:16]2[H:29])[N:17]([H:30])[C:18](=[O:19])[C:20]([H:22])([H:31])[C:33]3([C:34]([C:35]3([H:38])[H:39])([H:36])[H:37])[H:32])[H:28])[H:27])[Cl:21])[H:24]

[H:21][c:4]1[c:1]([c:3]([n:11][c:5]([c:2]1[H:19])[N:12]([H:17])[C:6](=[O:13])[C:10]([H:15])([H:16])[C:9]2([C:7]([C:8]2([H:24])[H:25])([H:22])[H:23])[H:14])[H:20])[H:18]

AT_RDKIT

[H:25][c:9]1[c:8]([c:7]([c:1]([c:3]([c:13]1[O:16][C:12]2=[C:6]([c:5]3[c:11]([n:17][c:4]([n:20][c:10]3[N:19]([C:2]2=[O:18])[C:14]([H:27])([H:28])[H:29])[N:21]([H:30])[C:34]4([C:33]([C:32]([N:37]([C:36]([C:35]4([H:43])[H:44])([H:45])[H:46])[C:47](=[O:48])[C:49]([H:50])([H:51])[H:52])([H:38])[H:39])([H:40])[H:41])[H:42])[H:26])[H:23])[F:15])[H:22])[F:31])[H:24]

[H:25][c:1]1[c:2]2[c:3]([n:17][c:4]([n:16]1)[N:20]([H:24])[C:13]3([C:9]([C:11]([N:19]([C:12]([C:10]3([H:30])[H:31])([H:34])[H:35])[C:8](=[O:22])[C:14]([H:36])([H:37])[H:38])([H:32])[H:33])([H:28])[H:29])[H:23])[N:18]([C:7](=[O:21])[C:6](=[C:5]2[H:26])[H:27])[C:15]([H:39])([H:40])[H:41]

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