The CSD has a fair number of structures with a big charged aromatic moiety and a counter-ion, things like the attached TUDTES.mol2
Using SVN 4747, I'm not seeing charges when I convert to SMILES - I get OCCn1c(=O)n(C)c2c(c1=O)n(C)cn2C.I out of obprop, where I would expect OCCn1c(=O)n(C)c2c(c1=O)[n+](C)cn2C.[I-] And I'm also losing charges on conversion to PDB, I would expect ATOM 1 I1 RES A 1 4.943 9.201 1.691 1.00 0.00 I1- ATOM 6 N1 RES A 2 0.313 6.282 9.632 1.00 0.00 N1+ rather than ATOM 1 I1 RES A 1 4.943 9.201 1.691 1.00 0.00 I ATOM 6 N1 RES A 2 0.313 6.282 9.632 1.00 0.00 N
TUDTES.mol2
Description: Binary data
When I run obgen on OCCn1c(=O)n(C)c2c(c1=O)n(C)cn2C, I get two extra hydrogens added even though the aromatic section is described with aromatic atom types, and the result has canonical SMILES OCCN1C(=O)[C@@H]2N(C)CN([C@H]2N(C1=O)C)C so the aromaticity has been lost. OCCn1c(=O)n(C)c2c(c1=O)[n+](C)cn2C round-trips happily through obgen. Tom
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