Open Babel

(1.0.0)

Run Open Babel online with molecular format conversion, coordinate generation, and hydrogen options.

Run

Molecule or structure

Configuration

Formats

Input format

Output format

Conversion options

Generate coordinates

Hydrogens

pH correction

Partial charges

Force field minimization

Output

Configure inputs to begin

Set options on the left, then click “Convert”.

What is Open Babel?

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.

How to use Open Babel online

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.

Inputs

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.

Settings

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.

Results

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.

How Open Babel conversion works

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:

Information loss: Not every format stores the same fields. SMILES lacks 3D coordinates. PDB often omits bond orders. SDF can store molecule properties that simpler formats may drop.
Perceived chemistry: When an input format does not define bonds or bond orders explicitly, Open Babel may infer connectivity, aromaticity, atom types, or valence from the available structure.
Coordinates: Open Babel does not generate coordinates unless coordinate generation is requested. A SMILES to SDF conversion without Generate coordinates can produce an SDF record without useful coordinates.
Hydrogens, charges, and pH: Hydrogen addition, deletion, Gasteiger partial charges, and pH correction can change formulas and charges. They should be treated as chemical preparation steps, not purely cosmetic formatting.
Force fields: Minimization needs meaningful coordinates. For SMILES or InChI input, generate 3D coordinates before running MMFF94, MMFF94s, UFF, GAFF, or Ghemical minimization.
Format-specific behavior: Some formats have special read or write options in the full Open Babel command line tool. ProteinIQ includes the common conversion controls available in the browser runtime, not every advanced CLI option.

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.

When to use Open Babel vs focused conversion tools

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.

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