Figure 6.

The calculations we run are the green arrows. (a) We calculate the absolute “binding” free energy for each molecule, green arrows shown in (a), from water to the hypothetical binding site and then get the difference in absolute binding free energies as ΔΔG_ab = ΔG₁ − ΔG₂. Since in this case ΔG₁ + ΔG_b− ΔG₂ − ΔG_w = 0, then ΔΔG_ab = ΔG_w − ΔG_b. (b) We also calculate the relative “binding” free energy, green arrows shown in (b), by changing atoms to dummy atoms (hollow spheres), and get the relative binding free energy difference as ΔΔG_rl = ΔG_w − ΔG_b. Here the bold bond on the right hand side of both panels represents the bond strained by “binding” to our hypothetical receptor (here represented by introducing restraints).