Hi all, I've generated binding free energy results by using the FEP protocol. From the figure, we can see that the ΔΔG value of -0.936 for the ligand pair compound 1 – compound 2, and the ΔΔG value of -0.67 for the ligand pair compound 2 – compound 3.

However, in Pair 1 (compound 1 – compound 2), the calc ΔG ligand and ΔG complex are -49.71 and -50.65, respectively. I'm not sure the data are normal?

By the way, in Pair 2 (compound 2 – compound 3), the calc ΔG ligand and ΔG complex are 21.16 and 20.49, respectively. So, this is normal too, Thanks!

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