An experimental and theoretical study of the molecular structure of an organic arsenate templated by 4-aminopyridine, with the general formula (C5H7N2)(C5H8N2)[AsO4]·H2O ((4-APH)(4-APH2)[AsO4]·H2O), is presented. The optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound calculated using DFT methods are in agreement with the experimental values. The theoretical calculations were performed using density functional theory (DFT) method at B3LYP/6-311 + + G(d,p) basis set levels. A detailed interpretation of the IR and Raman spectra were reported. The thermodynamic functions (heat capacity, entropy, and enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. The molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO-LUMO energy gap, Molecular electrostatic potential (MEP), NLO characteristic and Hirshfeld surface analysis were performed with the same DFT level. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were investigated based on the natural bond orbital (NBO) analysis. The molecular docking simulation results showed an excellent agreement with the experimental findings and satisfactory support the antiviral effects, the druggability and pharmacokinetic properties of the compound.