VinaDock Viz

Input Files

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Receptor (.pdbqt)

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Vina Ligand Poses (.pdbqt)

Binding Poses

Receptor Display

Style

Color

Opacity

Surface (transparent)

Surface opacity

Ligand Display

Style

Color

Show H-bonds

Show polar contacts

Actions

Best pose

Selected

Other poses

π-π / Cat-π

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Load your receptor (.pdbqt) and ligand poses (.pdbqt) from AutoDock Vina to explore binding interactions in 3D.

Ligand–Receptor Interactions

Cutoff distance

Lig Atom	Residue	Rec Atom	Type	Dist (Å)

H-bond

Hydrophobic

π-π Stack

Salt Bridge

Halogen

Interaction Cutoffs

Hydrogen Bond≤ 3.5 Å

Salt Bridge≤ 4.0 Å

Halogen Bond≤ 3.5 Å

π-π Stacking≤ 5.0 Å

Cation-π≤ 5.0 Å

Hydrophobic≤ 4.0 Å

Van der WaalsrA+rB+0.8 Å

References: Jeffrey (1997) "An Introduction to H-Bonding"; Barlow & Thornton (1983); Cavallo et al. (2016) Chem. Rev. 116, 2478; Hunter & Sanders (1990) JACS 112, 5525; Dougherty (1996) Science 271, 163; Bondi (1964) JPC 68, 441; PLIP (Adasme et al. 2021).

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