A study of the relationships between electronic structure and dopamine D3 receptor binding affinity was carried out for a series of [4-(4-carboxamidobutyl)]-1-arylpiperazines. Local atomic reactivity indices were obtained at the B3LYP/6-31G(d,p) level after full geometry optimization. A statistically significant equation relating structure with activity was obtained allowing suggesting at least two atoms as targets for substitution. Also we carried out a docking analysis of these molecules to a D3 receptor structure obtained from the Protein Data Bank. We analyzed the possibility of finding equivalences between some elements appearing in the QSAR equation and others from the docking results. We concluded that docking studies, as carried out here, are not equivalent to the QSAR ones. It is suggested that QSAR and docking study of series of molecules with low or very low conformational freedom can begin to solve these discrepancies.