Dear all, when I use pybel or openbabel for python to convert "c1ccc2c(c1)n(c(=O)o2)CC(=O)NC[C@@H]3COc4ccccc4O3" into a pdb file, I always get a cis amide, which is not good. However when I use the command "babel -ismi xxx.smi -opdb xxx.pdb --gen3D", I get the correct trans amide. Does someone know the reason and how to get a trans amide with the python module.
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