An extensive study was carried out to find formal relationships between electronic structure and 5-HT2B receptor binding affinity in a family of 44 N-benzylphenethylamines. These molecules were also docked to a structure of the human 5-HT2B receptor. The QSAR results were able to detect several atoms involved in the binding with HT2B receptor but failed at least in one important case. Docking results show that some molecules experience strong intramolecular π-π interactions producing folded structures. A given moiety of the molecules is able to interact with more than one residue of the receptor. Not always a certain moiety interacts with the same residue. The necessity of finding a more exact relationship between quantum-chemical and docking results needs a revision of the common skeleton concept.