By visual inspection, we determined that TanimotoCombo is useful for recognizing cases where geometric differences are caused by particularly flexible moieties, such as single bond rotations in an alkyl chain. These differences can often be attributed to minor differences between force fields leading to flexible bond rotations, not to larger differences in force fields that result in more substantial geometric differences. Thus, here, we find that TanimotoCombo alone does not serve to help us isolate geometry differences that are likely due to substantial force field differences; instead, low TanimotoCombo values can result from simple bond rotations that result from molecules energy minimizing to different local minima that we do not consider particularly interesting by visual inspection. However, TanimotoCombo in conjunction with TFD can be used to identify geometric differences that suggest underlying inconsistencies in parameterization.