Copy as smiles removes some stereochemistry

"Copy as smiles" on provided molecule discards sterechemisty. Saving molecule in SMILES format also discards sterechemisty information.

Correct SMILES should be C[C@@H]1CC/C(/CC1)=C1/CC[C@H](C)CC/1 or equivalent.

I used MarvinSketch 5.3.8

Thank you for the report.

You are right the exported smiles is not correct. We are working on the bug fix.

Actually the fix is still not read so we cannot include it in Marvin 5.4 release.

Sorry for the inconvenience.

Andras

And I found that Marvin doesn't support stereocenters with lone pairs when converting them into SMILES. For example I can paste [N@H0](O)(C)N into MarvinSketch but after that copying as smiles discards stereoinformation.

Molecule [N@H0](O)(C)N becomes CN(N)O

Is it possible to add support for such types of stereocenters?

 

And I found that Marvin doesn't support

stereocenters with lone pairs when converting them into SMILES. For

example I can paste [N@H0](O)(C)N into MarvinSketch but after that

copying as smiles discards stereoinformation.

The reason is the following:

Nitrogen is under normal circumstances not a stereocenter since it is flexible enough to invert but if the atom itself is in ring and all its' ligands are also in ring smaller than size 12 this flexibility vanish. 

Moreover bridgehead N and N in 3 membered ring can be stereocenter.

Thanks!