Tagging these molecule pairs as 'different' would be unhelpful because the differences are not due to substantial changes in force field parameters. Most molecule pairs in this category displayed cases of what might be called "conformer chirality"where an achiral molecule was minimized to two similar but non-superimposable structures -essentially, collapsing down to two minima which are equivalent to the force field but not geometrically identical. A number of molecule pairs, most with small flexible ring systems, yielded TFD values greater than 1 (which should not be possible). While this behavior was unexpected, we continued to use RDKit's implementation without modifications. Considering these results, we removed molecule pairs with a TFD greater than 0.60 or a TanimotoCombo less than 0.25.