Article ID: 164 - Last Modified: May 4, 2011
I am converting smiles strings or 2D structures to 3D structures with LigPrep. How does LigPrep treat 1,4-disubstituted cyclohexanes ?
LigPrep does not have a dedicated algorithm to intelligently choose between the eq/eq, eq/ax, ax/eq, or ax/ax conformations of 1,4-disubstituted cyclohexanes. LigPrep does respect chirality indications if the input SD or SMILES file contains them. These are bond or chirality designators. If no chirality indications are present in the input, and there is a mirror plane including C1 and C4, then one of the possibilities is generated.
Keywords: LigPrep cyclohexane
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