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Three-dimensional force spectroscopy measurements on 3,4,9,10-perylene-tetra-carboxylic dianhydride adsorbed on Ag(111) are combined with first-principles calculations to characterize the dissipative tip-molecule interactions with submolecular resolution. The experiments reveal systematic differences between the energy dissipation at the end groups and the center of the molecules that change with the tip-sample distance. Guided by the strength of the experimental conservative forces, an Ag-contaminated Si tip is identified as the likely tip termination in the experiments. Based on this tip configuration, the energy dissipation in the tip-sample contact is determined from the approach and retraction force curves calculated as a function of distance for different molecule sites. These calculations provide an explanation for the experimental trends in terms of the competition between localized dissipation mechanisms involving the quite mobile oxygen atoms on the sides of the molecule, and global molecular deformations involving the more rigid perylene core. The results confirm that the observed dissipation can be explained in terms of adhesion hysteresis and show the power of combined experimental-theoretical spectroscopy studies in the characterization of the underlying microscopic mechanisms., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)