ICM Dock
Molsoft ICM 3.8-7b
standard
Standard ICM conversion procedure was used to add hydrogens, assign atom types and charges.
All water molecules were removed, except if it is within hydrogen bond distance with the NH of residue Thr232 and Asn233.
Role of this water molecule in stabilization of the complex was deduced from PDB complexes of related ligand such as 4GMI
The 12 pdbs that contain that single water molecule are for compounds: 1,3,6,7,9,11,13,15,17,18,19,20
All compounds were docked to their corresponding pdb
For each PDB, two alternative protonation states were generated in which either Asp 32 or Asp 228 was protonated.
Monte Carlo search 'effort' parameter was set to 10.
Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Five independent docking runs were performed and resulting poses combined.
The top 5 poses according to the ICM VLS score were submitted.
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