Overall, we found that SepTop performed well on pharmaceutically relevant test systems which had been previously studied, and then we applied it to a larger number of compounds two different targets (MALT1 and BACE1) involving both transformations which are possible for typical RBFE calculations, and those which are challenging or impractical. Some of these challenging transformations involved scaffoldhopping transformations. These tests also involved larger numbers of ligands. We found that SepTop performed as well as standard RBFE calculations for transformations within a given congeneric series, but avoided complexities of atom mapping and required minimal human intervention to set up the calculations. For scaffold-hopping transformations, accuracy was predictably somewhat lower, likely because these transformations are dramatically more difficult to sample, but these preliminary results are nevertheless encouraging. Overall, this suggests that SepTop may be a general and broadly useful approach for relative binding free energy calculations that expands their domain of applicability.