Browser-based chemistry conversion

Open Babel Online Converter

Convert chemistry file formats directly in your browser. 100% private. Your molecular data stays on your device.

Choose chemistry data

Engine loads on convert

Drag & drop chemistry files here or click to browse your device PDB, PDBQT, SDF, MOL, MOL2, SMILES, XYZ, CIF · up to 20 files

or paste chemistry text

SMILES / PDB / XYZ / other text

Input format Output format

Conversion options

Add hydrogensAdd explicit hydrogen atoms before writing output. Generate 3D coordinatesBuild and optimize coordinates with MMFF94. Split multi-moleculeCreate one downloadable file per molecule. Keep molecule namePreserve the title stored in the source file.

Converted chemistry data will appear here.

Conversion summary

Detected: —
Output: PDBQT
Atoms: 0
Molecules: 0
Files ready: 0

Supported formats

Runs locally in your browser

Your chemistry files stay on your device throughout conversion.

Batch convert

Process multiple files together and collect every result in one ZIP.

Download instantly

Save a converted chemistry file or a complete batch archive.

Format support

Convert the chemistry formats used in research workflows

Open Babel Online Converter connects common molecular formats in a single browser workflow. Upload a structure, choose the target format, apply conversion options and download the result.

PDB

Protein Data Bank

Move macromolecular coordinates into docking, visualization and modeling workflows.

PDBQT

Docking-ready structures

Prepare text-based structures for AutoDock-compatible ligand and receptor workflows.

SDF / MOL

MDL structure data

Convert single structures or multi-molecule libraries while keeping useful molecule metadata.

MOL2

Sybyl MOL2

Exchange atom types, charges, coordinates and bond information between chemistry tools.

SMILES

Compact line notation

Turn compact molecular strings into coordinate-based files or export structures as SMILES.

XYZ / CIF

Coordinates and crystals

Work with atomic coordinates and crystallographic structure data in familiar text formats.

Simple workflow

How to use the Open Babel online converter

Add your structure

Drop one or more chemistry files into the page, or paste a SMILES string or text-based structure.

Choose conversion settings

Confirm the detected input, select an output format and enable hydrogen, 3D or split-file options.

Convert and download

Inspect the result summary and save a single output file or a ZIP containing the whole batch.

Quick examples

Start with a sample molecule

Load a ready-to-convert structure to explore format detection, molecular preview and download options.

FAQ

Open Babel online conversion questions

Does the converter upload chemistry files?

Conversion runs inside the browser. The selected molecular data is read locally and passed directly to the browser-based chemistry engine.

Which files are supported?

The primary interface supports PDB, PDBQT, SDF, MOL, MOL2, SMILES, XYZ and CIF. These formats cover common structure exchange, docking, molecular library and coordinate workflows.

Can I convert several files together?

Yes. Add up to 20 files, apply one conversion setup and download the completed outputs together as a ZIP archive.

What does Generate 3D Coordinates do?

The option asks Open Babel to build and optimize three-dimensional coordinates using the MMFF94 force field before writing the target file.

Can the converter work offline?

After the application and chemistry runtime are cached, the installable PWA uses cached files whenever the network is unavailable.