The prepared protein and ligand structures were parameterized using the corresponding force field parameters (see below). The remainder of the preparation and the simulation protocol followed the non-equilibrium TI protocol from the study of Gapsys et al. and is summarized in the following. For each perturbation, hybrid coordinates and topologies were generated from the physical end state ligand coordinates and topologies using pmx. A mapping between the atoms of two molecules was established following a predefined set of rules to ensure minimal perturbation and system stability during the simulations. The pmx method follows a sequential, dual mapping approach. In the first step, pmx identifies the maximum common substructure between the two molecules and proposes this as a basis for mapping. In the second step, pmx superimposes the molecules and suggests a mapping based on the inter-atomic distances. Finally, the mapping with more atoms identified for direct morphing between the ligands is selected. Additionally, pmx incorporates a number of empirical rules to ensure simulation stability, e.g. avoiding ring and bond breaking, preventing mappings that result in disconnected fragments, disallowing mapping heavy atoms to hydrogens. The obtained mapping is used to create hybrid structures and topologies following a single topology approach.