Open Babel
Run Open Babel online with molecular format conversion, coordinate generation, and hydrogen options.
Input
Output
Configure input settings on the left, then click "Convert"
Run Open Babel online with molecular format conversion, coordinate generation, and hydrogen options.
Convert SDF ligand files, including multi-record batches, into SMILES strings.
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.
Convert Protein Data Bank files to Structure Data Format
Convert Structure Data Format files to Protein Data Bank format
Open Babel converts molecular and structure files across the Open Babel format catalog directly in the browser. It is most useful when a workflow needs to move between compact identifiers such as SMILES or InChI, structure files such as MOL, SDF, MOL2, PDB, PDBQT, CIF, and XYZ, or file types used by docking and computational chemistry programs.
Open Babel handles format translation, not experimental validation. A successful conversion means the input could be parsed and written in the selected output format; it does not guarantee that all chemistry was preserved perfectly. Bond orders, aromaticity, atom typing, charges, hydrogens, residue annotations, and coordinates depend on what the input format contains and what the output format can store.
Open Babel can be run online in ProteinIQ by pasting molecular text or uploading a supported file, selecting the input and output formats, and choosing optional coordinate, hydrogen, charge, pH, and force-field settings. The result is a downloadable converted file with a conversion log that records the formats and Open Babel arguments used.
| Input | Description |
|---|---|
Molecule or structure | Pasted text or one uploaded text file. Common inputs include SMILES, InChI, MOL, SDF, MOL2, PDB, PDBQT, CIF, mmCIF, XYZ, CML, FASTA, and computational chemistry files. |
Input format | Auto-detect by default. Detection checks the uploaded filename extension first, then common content signatures, then SMILES as a fallback. Selecting a format overrides detection. |
Output format | Format Open Babel writes. The default is mol. The searchable selector includes the local Open Babel catalog. |
| Setting | Default | Description |
|---|---|---|
Generate coordinates | No change | Optionally generates 2D or 3D coordinates before writing the output. Coordinate generation is useful when converting line notations such as SMILES into MOL or SDF. |
Hydrogens | No change | Adds all hydrogens, adds only polar hydrogens, adds only non-polar hydrogens, deletes all hydrogens, deletes non-polar hydrogens, or leaves hydrogen representation unchanged. |
pH correction | Empty | Optional numeric pH for Open Babel protonation correction. This changes protonation on an atom by atom basis, so molecules with multiple ionizable centers can be fully ionized at the requested pH. |
Partial charges | No change | Optionally assigns Gasteiger partial charges before writing the output. Whether charges appear in the file depends on the selected output format. |
Force field minimization | No minimization | Optionally minimizes geometry with MMFF94, MMFF94s, UFF, GAFF, or Ghemical. Use a coordinate-bearing input or select Generate 3D before minimization. |
Minimization steps | 250 | Maximum steepest-descent steps used when force-field minimization is enabled. |
| Output | Description |
|---|---|
Preview | Text preview of the converted file when the output is viewable as text. |
Converted file | Primary downloadable output with the selected output format extension. |
Conversion log | Secondary text file containing the detected or selected formats, settings, Open Babel arguments, runtime messages, and timestamp. |
The preview supports common structure formats such as MOL, SDF, MOL2, PDB, PDBQT, CIF, mmCIF, PQR, and XYZ. Other outputs remain downloadable even when the preview is not useful.
Open Babel reads the input into its internal molecular representation, applies requested operations, then writes the molecule through the selected output format. Its official documentation describes the obabel program as a command line tool for interconverting chemical data formats and performing simple molecular manipulation.
Several details affect conversion quality:
Generate coordinates can produce an SDF record without useful coordinates.For one-step conversions with tighter defaults, use SMILES to SDF, SDF to SMILES, PDB to SDF, or SDF to PDB. For electrostatics-ready PQR files with force-field charges and radii, use PDB2PQR.
Open Babel is the right choice when the exact source and destination formats matter, especially for less common formats. It is also useful for quick exploratory conversions before docking, structure cleanup, database import, or computational chemistry setup.
Focused conversion tools are better when the conversion has product-specific validation or domain-specific preparation. For example, SMILES to SDF is a better fit for batch ligand 3D generation with named entries, while PDB2PQR is better for assigning biomolecular charges and radii before electrostatics calculations.
For docking workflows, Open Babel can prepare file formats such as SDF, MOL2, PDB, and PDBQT, but docking quality still depends on receptor preparation, ligand protonation, charge assignment, conformer generation, and the docking method. Use AutoDock Vina or GNINA when the goal is binding pose prediction rather than file conversion.