Unexpected generated molecule with double cuts MMPDB #27

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opened 2025-10-14 17:01:15 -06:00 by navan · 0 comments

navan commented

2025-10-14 17:01:15 -06:00

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Originally created by @alicecapecchi on 6/5/2023

Hi!
I am getting an unexpected generated molecule when using double cuts. The transformation, which in this case is the linker, is attached the wrong way around (details below). I would really appreciate your help :)

Using the two following molecules to create an MMPDB
c1ccc(cc1)c2ccc3c(c2)c(c(cc3NCc4cn5cc(cnc5n4)F)c6ccccc6)c7ccccc7 test1
c1ccc(cc1)c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7 test2

to then generate new molecules from the molecule to improve
c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7

the following molecule is proposed
Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1

while the expected generated molecule would be
c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7.

Please let me know if any other information is needed to better understand my issue.
Thanks a lot,
Alice

*Originally created by @alicecapecchi on 6/5/2023* Hi! I am getting an unexpected generated molecule when using double cuts. The transformation, which in this case is the linker, is attached the wrong way around (details below). I would really appreciate your help :) Using the two following molecules to create an MMPDB c1ccc(cc1)c2ccc3c(c2)c(c(cc3NCc4cn5cc(cnc5n4)F)c6ccccc6)c7ccccc7 test1 c1ccc(cc1)c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7 test2 to then generate new molecules from the molecule to improve c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7 the following molecule is proposed Fc1cn2cc(CNc3cc(-c4ccccc4)c(-c4ccccc4)c4ccccc34)cnc2n1 while the expected generated molecule would be c2ccc3c(c2)c(c(cc3NCc4[nH]c5c(n4)ccc(c5F)F)c6ccccc6)c7ccccc7. Please let me know if any other information is needed to better understand my issue. Thanks a lot, Alice