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How do I flip the chiral center for a bicyclic system?

A nice way to do this is to use LigPrep. If your input molecule does not have R/S designation, you can first run a LigPrep job that determines the chirality from 3D structure just in order to add this property to the molecule. You can then change the property for the desired chiral center (say from R to S) in the property column, then run a second LigPrep job that retains the chiral center information in order to flip the center.

Keywords: bicyclic system, flip , chirality, Maestro

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