Dear RDKit lovers,
Very recently I tested the new option added in the RDKit Add Conformers node called “use experimental torsion angle terms”. As highlighted in this thread, this option decreases the likelihood to obtain a structure with cis amide groups. This new option works very well and it avoids the generation of such problematic structures (at least in one of my test sets). In my opinion this makes RDKit the best option for 3D structure generation in KNIME, so thanks a lot to all the developers for this great improvement!
Nevertheless I think there is a couple of more issues in the generation of 3D structures that need to be addressed and for which I would like to have your opinion:
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The first is related to the planarity of amide groups. In several cases I obtain molecules with non-planar amides. The dihedral of such groups can reach values up to around 20º for secondary amides and up to around 40º for tertiary amides. Can the generation of such structures be avoided? It would be great if the planarity of amides could somehow be promoted in future RDKit releases.
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The 3D coordinates generator produces non planar sulfonamide nitrogens, even in case of primary sulfonamides. Shouldn't these groups be planar?
I will appreciate any comment regarding these issues.
Gio