DNA and RNA base-pairs are the most important systems containing multiple hydrogen bonds. Characterizing the energy of individual intermolecular interactions in such systems is vital and still an open problem that has been tackled here within the framework of the natural bond orbital (NBO) and the quantum theory of atoms in molecules (QTAIM) theories. In the NBO language, energy of an individual H-bond depends on the interaction of the n _Y, σ*_XH, and σ_XH orbitals directly involved in H-bonding. A partial charge transfer between donor (n _Y) and acceptor (σ*_XH) orbitals provides a substantial bonding contribution to the energies of the H-bonds, and in the end, the H-bonded complexes. It is accompanied with a repulsive contribution due to the proximity of the n _Y and σ_XH orbitals. Energies of the individual H-bonds, resulting from addition of the both terms, were correlated with several parameters, provided by the QTAIM analysis which has also been extensively used to characterize the hydrogen bond. The calculations were performed for the G–C and A–T Watson–Crick base pairs, their substituted derivatives (by one of two substituents, NH₃ ⁺ or OH₂ ⁺), A–U occurring in RNA and a wobble pair G–U. The best correlations were found for the NBO energy with the electron density and the potential energy density at H-bond critical points. The correlations held for the heterogeneous samples of HBs of different types, i.e. N–H···O, N–H···N, and C–H···O, occurring simultaneously in DNA base pairs.