Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model

The 3 ns unrestrained MD simulations were carried out on the DNA/duocarmycin complex based on (1) the classic RESP charge model, and (2) the QM-polarized ligand docking (QPLD)-based charge model. The RMSDs of the trajectories and the ΔGbind of the QPLD model perform much better than the RESP model, with the ΔGbind estimation for QPLD model (−16.11 kcal/mol) versus ΔGbind estimation for RESP model (−10.05 kcal/mol).