You could examine the interactions between the receptor and the docked ligand in AutoDockTools:
Part 1 Setup: Analyze->Dockings->Open -in the 'Docking Log File' widget which opens select your docking log file + click Open
Analyze->Macromolecule->Open (this will load your receptor.pdbqt) Analyze->Clustering->Show -Click on the lowest energy bar to put the ligand in the best docked pose in this dlg file.
Part 2 Analyze Visualized Interactions: Analyze->Dockings->Show Interactions Now ADT shows: --hydrogen bonds between the ligand + receptor (green spheres) --close-contacts between atoms ligand and specific atoms in receptor (wire-frame spheres, colored by atom type for the receptor atoms (receptor residues are labelled); patches of color on the molecular surface of the ligand) --opens the "Binding Site Interactions display options" widget.
This widget can be used to adjust the displayed features AND to output various lists of contacts. These include ligand contacts, receptor contacts' and hydrogen bonds. Clicking on one of these in the drop-down menu results in printing the corresponding list in the python shell of ADT (which is opened by clicking on the button with >>> in a white-box). eg ligand contacts: 'residues in 'ligand'-> 'receptor' residues in close contact 1 I:IND201-> B:ASP25, A:ASP25, B:ARG8, B:VAL32, B:VAL82, B:ASP30, B:PRO81, A:ARG8, B:GLY27, B:ILE84, A:LEU23, B:ALA28, B:ASP29, A:VAL82,
receptor contacts: 'residues in 'receptor'-> 'ligand' residues in close contact 1 B:ASP25-> I:IND201, 2 A:ASP25-> I:IND201, 3 B:ARG8-> I:IND201, 4 B:VAL32-> I:IND201, 5 B:VAL82-> I:IND201, 6 B:ASP30-> I:IND201, 7 B:PRO81-> I:IND201, 8 A:ARG8-> I:IND201, 9 B:GLY27-> I:IND201, 10 B:ILE84-> I:IND201, 11 A:LEU23-> I:IND201, 12 B:ALA28-> I:IND201, 13 B:ASP29-> I:IND201, 14 A:VAL82-> I:IND201
hydrogen bonds: 'hydrogen bonds (donor residue->acceptor residue(s)) 1 ind:I:IND201-> hsg1:B:GLY27, hsg1:B:ASP25, 2 hsg1:B:ASP29-> ind:I:IND201, 3 hsg1:B:ARG8-> ind:I:IND201'
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