In molecular junctions, the coupling between the electric contacts and the actual molecule is of great importance. Scanning tunneling microscopy (STM) techniques allow, in addition to their imaging possibilities at a high resolution, the option to mechanically manipulate the bonding properties between molecules and metal surfaces and provide the feasibility to subsequently measure transport effects through the molecule. Based on recent experiments studying the lifting of a single PTCDA molecule from an Ag surface, we present the results of our Density Functional Theory based calculations. We discuss the variation of the energies of the molecular levels and the device substrate coupling during the peeling process and describe its effects on the transport properties through the molecule.