This chapter presents basic equations for the quantitative evaluation of drug–receptor binding parameters used in software-based molecular pharmacological analyses. These equations can be used by pharmacologists in their research of drug–receptor interactions. Particularly, this chapter covers equations for calculating the potential energy of intermolecular interactions, partitioned to electrostatic (ion–dipole, dipole–dipole, etc.), polarization, exchange repulsion, and dispersion interactions, as well as the equation parameters. Moreover, charge transfer and hydrophobic interactions occurring during the formation of molecular complexes as well as their influence on molecular recognition are described. Details on the protonation of molecules as an important factor for drug–receptor interaction are provided, and experimental data for compounds’ protonation constants are presented. Furthermore, the effects of water environment on the electrostatic interaction energy due to local dielectric screening and hydration of molecules are discussed. Finally, reference experimental data relevant to the analysis of ligand–protein intermolecular interactions are presented, and the relative contribution of various interactions to the total energy of the drug–receptor interaction has been estimated.