To calculate relative free energy differences, firstly, every system was simulated at equilibrium in its physical state, e.g. ligand X representing state A and ligand Y representing state B. The simulation protocol involved energy minimization, followed by a brief 10 ps NVT equilibration and finally a production run for 6 ns in the NPT ensemble. From the generated trajectories, the first 2.256 ns were discarded and from the rest 80 snapshots were extracted. These configurations were used to perform rapid (50 ps) alchemical transitions between the physical states: from state A to state B when starting from the equilibrium ensemble generated at the state A and vice versa. The whole procedure, starting with energy minimization, ending with the fast alchemical transitions was repeated 3 times. All in all, the simulation time for one leg of the thermodynamic cycle of 3 replicas adds up to 60 ns for each double free energy difference. This is an equivalent simulation time to a classical equilibrium FEP approach using twelve 5 ns lambda windows, and which happens to be the default in the commercial FEP+ software and used in many published studies.