[Method for conformational calculations of large fragments of nucleic acids. III. Long range interactions]

The interactions between atoms which are far away in the polynucleotide chain were analysed. The energy of these atom-atom interactions are turned into energy of group-group interactions (these groups of the nucleotide unit are phosphate, ribose and nucleic base). The analytical expressions for the van der Waals and electrostatic group-group interactions as functions of the mutual distances and orientations are proposed. The calculation of the internucleotide energy interactions as an effective group-group interactions permits to decrease the number of interacting centers and necessary computer operations by 30-100 fold with respect to the method of atom-atom potentials.