An alternate approach for RBFE, "Separated Topologies", which we will refer to as "SepTop" throughout this paper, has the potential to combine the advantages of ABFE and standard RBFE. This protocol performs two ABFE calculations simultaneously in opposite directions, by (alchemically) inserting one ligand into the binding site, while removing the other ligand at the same time. In contrast to the standard RBFE protocol, the two ligand topologies are completely separate, making atom mapping unnecessary. Consequently, the two ligands can be structurally diverse and do not need to share a fully overlapping binding mode and/or a common scaffold, overcoming limitations of the common RBFE approach mentioned above. This protocol also never needs to sample the apo state of the protein as long as the protein retains its holo structure in the presence of both ligands, since one ligand (or a fraction of both) is always present in the binding site. Therefore, larger protein conformational changes between the bound and unbound state never need to be sampled, giving this approach a benefit in comparison to the absolute protocol. Additionally, if both ligands have the same non-zero charge, the SepTop approach conserves that charge during the transformation in the binding site while in ABFE the net charge in the binding site changes, which can lead to a wide variety of sampling and theoretical problems. The SepTop method was introduced in 2013 in a proof-of-principle study. In that study, the authors compared three RBFE methods, a single topology approach, dual topology, and SepTop, and studied the binding of two ligands to an engineered site in Cytochrome C Peroxidase. In dual topology calculations, a separate set of coordinates is used for each ligand, in contrast to the setup in single or hybrid topology approaches. Separated Topologies can be considered a subcategory of dual topology where ligands are restrained spatially to a specific area. In the study by Rocklin et al., dual topology referred to a different subcategory, the "linked dual topology approach" where the ligands are restrained to each other using e.g. distance restraints. Rocklin et al. found that all three approaches gave comparable results when ligand reorientation was not required, while in the presence of multiple ligand binding modes, SepTop had advantages over the other RBFE approaches. In this latter case, only SepTop gave accurate results by treating individual poses separately using orientational restraints. In the prior SepTop work of Rocklin et al., the RBFE between binding modes was calculated and the contributions of different poses combined to obtain the overall free energy difference. This earlier study seemed to show the approach is viable, but did little to make it practical for applications or to show that it could be useful for pharmaceutically relevant systems. In addition to SepTop, there have been other recent reports of similar approaches to resolve the difficulties of ABFE calculations such as dual topology approaches 30 and the alchemical transfer method. In this paper, we reintroduce SepTop and show that it works on pharmaceutically relevant systems. We develop a prototype Python package to set up SepTop calculations in GRO-MACS and discuss heuristics for picking atoms for orientational restraints. We test the method on several diverse, pharmaceutically relevant systems and report performance and the resulting insights into strengths, weaknesses, and challenges. We first test the approach on systems with small ligand transformations, allowing us to compare SepTop to standard RBFE and validate that it yields correct binding free energies. On more ambitious transformations, we find that SepTop performs well, even when such transformations fall outside the scope of standard RBFE methods.