SMILES to PDBQT Converter

Convert SMILES to PDBQT in two steps: generate a 3D PDB from SMILES, then transform the structure into PDBQT text for docking-ready workflows.

Technical Workflow

• Step 1: the tool requests 3D PDB coordinates from a public SMILES conversion endpoint.
• Step 2: PDB atom lines are rewritten into PDBQT-style records with atom type and charge columns.
• Use this quick converter for drafts; fine-tune protonation and torsion settings in docking software when needed.

File Format Explained

SMILES is a compact connectivity string. It is good for describing a ligand quickly, but it does not contain docking atom types, charges, torsions, or 3D coordinates.

PDBQT is an AutoDock-style docking format. It stores PDB-like coordinates plus partial charge and AutoDock atom type fields, and ligand files may include torsion tree records such as ROOT, BRANCH, ENDBRANCH, and TORSDOF.

This converter creates a browser-side PDBQT draft. For production AutoDock Vina docking, review hydrogens, protonation, charge model, atom typing, and rotatable bonds.