In order to determine the possible mechanisms of interactions of monoclonal antibody B2 with haptens and early synthesized peptide-mimotope of benzo[a]pyrene using the phage display method, amino acid sequences of variable fragments of heavy and light chains are determined and a model of Fab-fragment is constructed. The structure of the antibody active center is determined using molecular docking with polycyclic aromatic hydrocarbons. It is identified that the active center of monoclonal antibody B2 brings the two pockets of binding. The correlation between preliminarily obtained experimental data on the cross-reactivity of monoclonal antibody B2 with some ligands and calculated bond energy is found. It is shown that synthetic peptide-mimotope of benzo[a]pyrene is weak competing with the conjugate of benzo[a]pyrene for binding with monoclonal antibody B2. The immunization of mice with the conjugate of peptide and bovine serum albumin results in creation of antibodies to benzo[a]anthracene and anthracene but not to benzo[a]pyrene. The model of peptide-mimotope of benzo[a]pyrene from pIII protein of bacteriophage is built. It is determined that tryptophan included into peptide composition can be exposed on the surface and be available for antibody. The data of modeling obtained in this study can be applicable for further optimization as both the structure of peptide-mimotope of benzo[a]pyrene and for active center of monoclonal antibody B2.