Research Article
Combined Docking with Classical Force Field and Quantum Chemical Semiempirical Method PM7
Table 1
IN/INN indexes for minima sets: MMFF94 + PCM, PM7 + COSMO (1SCF), and PM7 + COSMO. Complex ID identifies the respective protein-ligand structure in the Protein Data Bank [32]. MMFF94 + PCM designates the low energy minima set found in works [1, 2] for the target energy function calculated in MMFF94 force field with the implicit PCM solvent model (8192 low energy minima). Energies of all 8192 minima of the MMFF94 + PCM set are recalculated without geometry optimization using the PM7 method with the COSMO solvent model, and this minima set is designated as PM7 + COSMO (1SCF). The low energy minima set designated as PM7 + COSMO is obtained by the local optimization of the energy of the protein-ligand complex from the initial configurations corresponding to each minimum of the minima set MMFF94 + PCM using the PM7 method in vacuum with variations of all ligand atoms Cartesian coordinates and subsequent recalculation of minima energies taking into account the COSMO solvent model.
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