Well-ordered metal-organic nanostructures of Fe-PTCDA (Perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride) chains and networks are grown on a Au(111) surface. These structures are investigated by high resolution scanning tunneling microscopy (STM). Digitized frontier orbital shifts are followed in scanning tunneling spectroscopy (STS). By comparing the frontier energies with the molecular coordination environments, we conclude that the specific coordination affects the magnitude of charge transfer onto each PTCDA in the Fe-PTCDA hybridization system. A basic model is derived, which captures the essential underlying physics and correlates the observed energetic shift of the frontier orbital with the charge transfer. Keywords: scanning tunneling microscopy, scanning tunneling spectroscopy, metal-organic coordination, self-assembled nanostructure, charge transfer.