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The free energy of a system of a protein and two water molecules, W1 and W2, can be decomposed into several energy components as shown in the matrix below. As an example, the shaded area has the components from the water molecule itself GW2, along with the water–protein interaction GProtein–W2, and the water–water interaction GW1–W2, and all together, they contribute to the water removal energy for W2.
