The development of sequence-specific minor groove binding ligands is a modern and rapidly growing field of research because of their extraordinary importance as transcription-controlling drugs. We performed three molecular dynamics simulations in order to clarify the influence of minor groove binding of two ImHpPyPy-beta -Dp polyamides to the d(CCAGTACTGG)(2) decamer in the B-form. This decamer contains the recognition sequence for the trp repressor (5 ' -GTACT-3 '), and it was investigated recently by X-ray crystallography. On one hand we are able to reproduce X-ray-determined DNA-drug contacts, and on the other hand we provide new contact information which is important for the development of potential ligands. The new insights show how the P-tail of the polyamide ligands contributes to binding. Our simulations also indicate that complexation freezes the DNA backbone in a specific B-I or B-II substate conformation and thus optimizes nonbonded contacts. The existence of this distinct B-I/B-II substate pattern also allows the formation of water-mediated contacts. Thus. we suggest the B-I reversible arrow B-II substate behavior to be an important part of the indirect readout of DNA.