A free energy function can be defined as any mathematical expression that relates macroscopic free energy changes to microscopic or molecular properties. Free energy functions can be used to explain and predict the affinity of a ligand for a protein and to discriminate between native and non-native binding modes. The development of this type of function will have important implications, especially for rational drug discovery and design. However, this is no small task, for there is a natural tension between developing a function fast enough to solve the scoring problem but rigorous enough to explain and predict binding affinities. Here, we present a free energy function that is computationally inexpensive and fast, yet theoretically sound.