Use of scanning tunneling microscopy (STM) to determine the adsorption sites of molecules on a metallic surface with accuracy has become a powerful technique. As an example, we demonstrate, using elastic scattering quantum chemistry calculations, that STM images of benzene molecules adsorbed on a palladium-(110) surface exhibit strong internal structures. We demonstrate that each possible high-symmetry adsorption site as well as the molecular orientation with respect to the surface plane can be resolved using STM imaging.