A procedure was developed for quantitative estimation of the ligand affinity for the DNA minor groove with allowance for ligand hydration, whereby the binding energy was calculated as the difference in the energies of ligand-DNA and ligand-water interactions. Adequacy of the procedure was demonstrated with the structural motifs (pyrrolecarboxamide, benzimidazole, furancarboxamide, and phthalimide) of well-known ligands for the case of a d(GCA₁₀CG)·d(CGT₁₀GC) duplex. On the strength of the results obtained, an indole-based motif was proposed as the basis for a highly affined minor groove binder.