We identified molecule pairs displaying parameterization differences which led to different geometries using TFD and Tanimo-toCombo. TFD is sensitive to ring deformations, torsional differences, and atom planarity changes, which makes it useful for recognizing differences in parameterization. TanimotoCombo, with greater sensitivity to coordinate differences caused by conformational flexibility in a molecule, is more useful for removing cases that are less likely to be caused by parameterization differences, or which may simply be due to minor differences in which rotamer a molecule minimizes to.