A C60 molecule sandwiched between two Au(111) based tips is used as a model system to analyze the formation of nanogap molecular junctions including charging effects and self-interaction corrections. In our approach, we combine a DFT-LDA calculation of the structural and electronic properties of the system with an analysis of the interface barrier formation based on the charge transfer and the organic Charge Neutrality Level, as described by the Induced Density of Interface States model. This allows us to determine, as a function of the tip/C60 distance, the self-interaction correction to the frontier molecular orbitals levels, the transport energy gap and the metal/organic barrier height. Our approach offers a fully consistent technique for analyzing a metal/organic interface at the molecular level.