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This study examines several drugs employed in treating Cytomegalovirus (CMV) infections, including Cidofovir, Foscarnet, Ganciclovir, Maribavir, and Valganciclovir. The investigation involves the calculation of degree-based topological indices for these drugs. A quantitative structure–property relationship model is established using linear regression analysis, connecting the drug’s topological indices to eleven physicochemical properties to assess their efficacy. The findings indicate that the third Zagreb index is the most reliable predictor for boiling point, enthalpy of vaporization, and flashpoint. In contrast, the first Zagreb index is the optimal predictor for molar refractivity, polarizability, and surface tension. The forgotten index proves effective in predicting molar volume, and the Randić index is identified as a useful predictor for density.