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Figure 1. Schematic illustration of a protein-ligand-solvent system. It is shown that the ratio between solvent volume and protein-ligand volume in a spherical shell of thickness Ar close to the ligand is smaller than that in a spherical shell with thickness Ar2. It is also smaller than that in the reference sphere with radius R. The differences in these volume ratios directly affect pij (r) and p 'W in Equation 2, since these number densities are calculated depending on the available protein volumes.

Figure 1. Schematic illustration of a protein-ligand-solvent system. It is shown that the ratio between solvent volume and protein-ligand volume in a spherical shell of thickness Ar close to the ligand is smaller than that in a spherical shell with thickness Ar2. It is also smaller than that in the reference sphere with radius R. The differences in these volume ratios directly affect pij (r) and p 'W in Equation 2, since these number densities are calculated depending on the available protein volumes.

Reference state 2

Independent of the protein-ligand complexes used to derive the PMF, a more general reference state can be defined as

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