Some of the benzopyrene (BP)-DNA adduct are known to build intercalated motif between flanking base pairs in damaged DNA depending on the structural condition. The size of benzopyrene itself is definitely not comparable with any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular dynamics simulation based on the theory of molecular mechanics. The specific consequences about the structural properties of the intercalated structures and benzopyrene motif in minor groove of the double helix are deduced after 5 ns simulation time.