Below we provide an example of Molecular Dynamics of HIV-integrase monomer with 1- (5- CHLOROINDOL-3- YL)-3 -HYDROXY-3 -(2H- TETRAZOL- 5- YL)-PROPENONE (pdb code 1qs4).
The protein structure is taken from the original 1qs4 pdb data and combined with the missing loop data from 2itg structure. The complete calculation yuilds -27kJ/mol binding energy, close to the experimentally observed value.
The inhibitor molecule is shown in red licorice. The Mg++ ion is shown as a megenta sphere.
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