Knowledge Based Docking Score

We can find the bond distances between residues of proteins and ligands using PLIF.

For calculating interaction energy vectors, van der Waals, Coulomb, and hydrogen bonding (hbond) energy terms are used. The van der Waals energy is calculated with the 12–6 Lennard-Jones potential

where ϵ and σ are the parameters, and r is the distance between two atoms. The Coulomb energy is calculated with the Coulomb potential

where ϵ0 is a constant, and Q and Q′ are the charges of the two given atoms. The hydrogen bonding energy is calculated with the following formula

where Chbond is a constant parameter, and g and h are functions that output a value of 1.00 for distances or angles within the preferred range and values of 0.00–1.00 for distances or angles that lie outside those limits. According to Friesner et al., the value of g(Δr) is 1.00 if the H···X hydrogen bond distance is 0.25–1.85 Å and decreases to zero in a linear fashion for distances in 2.10–2.50 Å. Similarly, the value of h(Δα) is 1.00 if the Z–H···X angle is 210°–150° and decreases to zero in the ranges of 150°–120° and 210°–240°.

Knowing the donor atom and the acceptor atom you could figure out the charge.

This is the basic idea behind knowledge based scoring algorithms.