BINANA

Advanced Parameters

Parameters used to identify close contacts.

Closest Contacts Dist1 Cutoff

Ligand/protein atoms that come within this number of angstroms are "closest contacts."

Close Contacts Dist2 Cutoff

Ligand/protein atoms that come within this number of angstroms are "close contacts."

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Parameters used to identify hydrogen and halogen bonds.

Hydrogen Bond Dist Cutoff

A hydrogen bond is identified if the hydrogen-bond donor comes within this number of angstroms of the hydrogen-bond acceptor.

Hydrogen and Halogen Bond Angle Cutoff

A hydrogen or halogen bond is identified if the angle formed between the donor, the hydrogen/halide atom, and the acceptor is no greater than this number of degrees.

Halogen Bond Dist Cutoff

A halogen bond is identified if the halogen-bond donor comes within this number of angstroms of the halogen-bond acceptor.

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Parameters used to identify interactions between aromatic rings. Once an aromatic ring is identified, a plane is defined that passes through three ring atoms. The center of the ring is the average of all ring-atom coordinates, and the radius is the maximum distance between the center and any of those atoms. A ring disk is centered on the ring center point, oriented along the ring plane.

π Padding Dist

The radius of the ring disk is equal to that of the ring plus a small buffer (this number of angstroms).

π-π Interacting Dist Cutoff

A π-π or T-stacking interaction is identified if the centers of two aromatic rings are within this number of angstroms.

π-Stacking Angle Tolerance

A π-π stacking interaction is identified if the angle between the normal vectors of two aromatic rings is less than this number of degrees.

T-Stacking Angle Tolerance

A T-stacking interaction is identified if the angle between the normal vectors of two aromatic rings is within this number of degrees of being perpendicular.

T-Stacking Closest Dist Cutoff

A T-stacking interaction is identified if two aromatic rings are within this number of angstroms at their nearest point (see also -pi_pi_interacting_dist_cutoff parameter above).

Cation-π Dist Cutoff

A Cation-π interaction is identified if a charged functional group comes within this distance of an aromaic-ring center.

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Parameters used to identify other notable interactions.

Salt Bridge Dist Cutoff

Charged functional groups that come within this number of angstroms participate in "electrostatic interactions."

Hydrophobic Dist Cutoff

Ligand/receptor carbon atoms that come within this number of angstroms participate in "hydrophobic contacts."

Metal Coordination Dist Cutoff

Atoms such as nitrogens and oxygens that come within this number of angstroms of a metal cation participate in "metal coordination contacts."

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Input Files

Receptor

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This field is required! Formats: PDB, PDBQT. Consider first (1) adding polar hydrogen atoms if necessary and (2) removing any ligands from the file.

Ligand

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This field is required! Formats: PDB, PDBQT, SDF. Consider first adding polar hydrogen atoms if necessary.

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Missing Receptor and/or Ligand

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BINANA 2.2

Input Files

Molecular Viewer

Missing Receptor and/or Ligand