I am using the ETKDG method for producing conformations for ureas and thioureas.
The outputted conformers are planar for the substituted N but for the terminal
unsubstituted N, the conformation is wrong as the NH2 is not planar to the C=O.
The code I am using is as follows:
urea = Chem.MolFromSmiles("NC(=O)NC1=CC=CC=C1")
h_urea = Chem.AddHs(urea)
AllChem.EmbedMultipleConfs(h_urea,numConfs=20,randomSeed=0xf00d,useExpTorsionAnglePrefs=True,\
useBasicKnowledge=True)
AllChem.AlignMolConformers(h_urea,h_urea.GetSubstructMatch(Chem.MolFromSmiles('C(=O)N')))
p = py3Dmol.view(width=400,height=400)
interact(drawit,
m=fixed(h_urea),p=fixed(p),confId=(0,h_urea.GetNumConformers()-1))
Many thanks,
Susan
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