Menu ▾ ▴

#704 SMILES import makes cis amide and carbamate bonds

v_1.1.0
open
nobody
None
1
2014-02-03
2014-01-31
Anonymous
No

trying to create structures of amides and carbamates via a SMILES import gives back after the create 3D step, compounds which have the amide bonds cis, not trans. The SMILES strings are created in ChemDraw. Pasting back into Chemdraw yields the correct structure. If I instead export out of Chemdraw as a .mol file, then the import and conversion to 3D produced the correct trans isomer.

an example structure I am having issues with is:
O=C(O)C@@HCC(NC(C)(C)C)=O

Discussion

  • Martin Stoermer

    Martin Stoermer - 2014-02-01

    This was my ticket, Martin Stoermer, seem not to have been logged in when I posted it

     

  • Geoff Hutchison

    Geoff Hutchison - 2014-02-03

    This is an ill-formed SMILES. Even if I clean it up a bit:

    O=C(O)[C@@H]CC(NC(C)(C)C)=O

    There still isn't any stereochemistry on that carbon. It has one bond to the hydrogen, two bonds to the carbons, and then the other bond (for a tetrahedral carbon) is left undefined.

    Now, you may have indicated wedges and hashes with ChemDraw, but it'd really help if you had more SMILES that you think cause problems.

    And yes, there is specific code to create trans amide bonds. There may be bugs, but I'm not even sure what the code is supposed to do with that string.