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You can visualize your results below. You can also download them for offline analysis.

Grid center: Ligand Center
Center coordinates (Å):(4.84, -1.5, 13.38)
Grid dimensions (Grid points): (69, 69, 61)
Grid dimensions (Å):(25.875, 25.875, 22.875)

Total runtime: 00:25:42

For each ligand conformation, the AutoDock score is reported in kcal/mol, and the all-atom RMSD to the original pdb conformation is reported in Å.

To move the protein-ligand complex: Use 'Shift' + 'double-click' and then drag the complex to your preferred placement.

To rotate around the Z axis: Hold 'Shift' and then drag horizontally.

For more things you can do within JSmol, Click here.

RMSD values are calculated by comparing the original conformation with each fragment conformation, considering all heavy atoms.

The Energy versus RMSD plots show the RMSD values of each computed fragment conformation in comparison to its energy. In the case of a redocking job, the reference conformation for RMSD calculation is the original pdb. For other kinds of jobs, the reference conformation is the ligand's lowest-energy conformation produced by DINC. By default, RMSD calculations involve all the heavy atoms of the ligand. If the ligand is a peptide, you can also visualize plots produced by calculating RMSD values with backbone atoms only, or alpha carbons only.