A novel complex silver nitrate of 5-iodindole molecule has been synthesized and characterized by single-crystal X-ray diffraction, infrared and Raman spectroscopy, and 1H NMR analysis. DFT calculations were performed using the B3LYP with 6-311++G(d,p) basis set for light atoms (C,H, N, and O) and the DGDZVP basis set for heavy atoms (Ag and I). Theoretical and experimental bond lengths and bond angles have been compared and determined to be in good agreement with each other. By using 1H NMR analysis, the chemical shift values of H atoms in this new structure were determined and compared with the theoretically calculated values. Also, experimental FT-IR and FT-Raman modes of the complex structure assigned that depending on total energy distribution (TED) values have been compared with theoretical wavenumbers. The HOMO-LUMO energy gap, the frontier molecular orbital, the molecular electrostatic potential map, and atomic charge analysis have been carried out to reveal the electronic properties of the structure. The non-linear optical properties of the title molecule and its thermodynamic properties such as entropy, heat capacity, enthalpy change, and Gibbs free energy at different temperatures were investigated. Finally, the antibacterial activity of this new structure obtained from the synthesis of 5-iodoindole with silver nitrate has been evaluated.