SMARTS for cis amide

Question

Is there a SMARTS pattern for cis (and trans) amide bonds?

This seems to be the SMARTS for any amide:

[NX3][CX3](=[OX1])[#6]

But I am not sure whether or not the SMARTS format has cis/trans definitions for “single” bonds such as amides.

Answer 1

No, not really.

For a double bond, you'd use the same '\' and '/' characters to indicate cis- and trans- stereochemistry that you use in SMILES. But as you indicate, there isn't a double bond for such stereochemistry.

My personal preference in scripts, code, etc. is to match the double bond, and then use my own code to check the relative positions of substituents around the central double bond. In this case, you could look at a dihedral angle around the C-C-N plane.

For future reference, an excellent resource for testing SMARTS patterns is SMARTSView.