Metal-organic complexes were formed by means of inelastic excitations in a scanning tunneling microscope (STM). The electronic structure of the complex was characterized using STM imaging and spectroscopy. By exploiting the symmetry of the complex, its electronic structure can be rationalized from linear combinations of molecular orbitals. The actual bonding geometry, which cannot be inferred from STM alone, was determined from atomic force microscopy images with atomic resolution. Our study demonstrates that the combination of these techniques enables a direct quantification of the interplay of geometry and electronic coupling in metal-organic complexes in real space.