We report a theoretical study of the adsorption of a set of small molecules (C2H2, CO, CO2, O2, H2O, CH3OH, C2H5OH) on the metal centers of the “copper paddle-wheel”—a key structural motif of many MOFs. A systematic comparison between DFT of different rungs, single-reference post-HF methods (MP2, SOS–MP2, MP3, DLPNO–CCSD(T)), and multi-reference approaches (CASSCF, DCD–CAS(2), NEVPT2) is performed in order to find a methodology that correctly describes the complicated electronic structure of paddle-wheel structure together with a reasonable description of non-covalent interactions. Apart from comparison with literature data (experimental values wherever possible), benchmark calculations with DLPNO–MR–CCSD were also performed. Despite tested methods show qualitative agreement in the majority of cases, we showed and discussed reasons for quantitative differences as well as more fundamental problems of specific cases.