The role of the organic group orientation on the geometrical and optical properties in a neutral Au-25 nanocluster has been analyzed through density functional theory (DFT) and time-dependent density functional theory (TDDFT) simulations. Starting from two different X-ray diffraction (XRD) resolved structures which differ in the ligand orientation, we optimized the methyl substituted neutral nanoclusters at the B3LYP//6-31G(d,p)/LANL2DZ level, finding remarkable differences on the bond length and the symmetry of the gold kernels. Despite these differences, the TDDFT estimated absorption features of the two clusters are quite similar, showing that ligand orientation brings minor effects on the optical properties of the nanoclusters. All obtained results are in good agreement with available experimental data.