Ligand fixer

Use this when a ligand file fails RDKit, Meeko, or AutoDock-style preparation and needs safe cleanup before docking.

Job name

Ligand(s)

Configure input settings on the left, then click "Submit"

Related tools

Filter DNA

Clean and filter DNA sequences by removing or replacing non-standard nucleotide characters. Supports multiple filter modes including standard 4 bases, IUPAC ambiguity codes, and custom character sets.

FASTA splitter

Split large FASTA files into smaller chunks. Divide by sequence count or create individual files for each sequence.

Filter protein

Clean and filter protein sequences by removing or replacing non-standard amino acid characters. Supports multiple filter modes including standard 20 amino acids, IUPAC codes, and custom character sets.

PDB2PQR

PDB2PQR prepares protein structures for electrostatics calculations by adding missing atoms, predicting protonation states using PROPKA, and assigning atomic charges and radii from standard force fields.

InChI to SMILES

Convert InChI strings into SMILES with batch support and downloadable outputs.

MOL2 to SMILES

Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.

SDF to SMILES

Convert SDF ligand files, including multi-record batches, into SMILES strings.

SMILES to InChI

Convert SMILES strings into InChI strings with batch support and downloadable outputs.

SMILES to MOL2

Convert SMILES strings into 3D MOL2 files for docking and molecular modeling workflows.

SMILES to PDB

Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.

What is Ligand fixer?

Ligand fixer is meant for ligand files that already exist but fail during RDKit, Meeko, or docking preparation. If AutoDock Vina, DiffDock, or another RDKit-based workflow rejects an SDF, MOL, or MOL2 ligand, this tool applies safe cleanup steps and re-exports a repaired SDF.

It is not the general "start from SMILES" path. If you have a trusted SMILES string and want to generate a fresh structure file, use SMILES to SDF instead.

Ligand fixer is designed for common failure modes such as:

invalid or inconsistent valence that breaks RDKit sanitization
extra salt or counterion fragments that confuse docking prep
missing explicit hydrogens
2D or missing coordinates
multi-record SDF uploads that need to be split into separate ligands

How to use Ligand fixer online

Upload one or more ligand structure files, or paste one ligand block into the text area. Supported structure formats are:

Format	Extensions
SDF / MDL Molfile	`.sdf`, `.sd`, `.mol`
Tripos MOL2	`.mol2`

You can upload up to 10 public inputs per job. Multi-record SDF files are automatically split into separate entries and processed one by one.

Repair settings

Setting	Description
`Sanitize and normalize`	Runs RDKit cleanup and sanitization, plus targeted safe chemistry repairs where supported.
`Keep largest fragment`	Removes salts and counterions by keeping only the largest fragment.
`Add hydrogens`	Adds explicit hydrogens before export.
`Generate 3D coordinates`	Generates a 3D conformer when the ligand has no usable 3D coordinates.
`Run docking preflight`	Reports whether the repaired ligand appears ready for RDKit-based docking preparation.
`Merge outputs into one SDF`	Returns one combined `fixed_batch.sdf` instead of separate repaired files.

What Ligand fixer currently repairs

The tool is intentionally conservative. It focuses on repairs that are high-confidence enough to automate without silently inventing chemistry.

Current repair and normalization behavior includes:

preserving uploaded ligand files and splitting multi-record SDF input into separate entries
fragment cleanup by keeping the largest fragment
adding explicit hydrogens
generating 3D coordinates when needed
targeted charge repair for common RDKit failure cases such as neutral tetravalent nitrogen that should be represented as N+

When a ligand still cannot be sanitized safely, the tool does not force a guess. That entry fails, and the JSON report explains which ligand failed and why.

Output files

By default, each successful ligand is returned as its own repaired file with _fixed added to the original name, for example:

Ligand (3).sdf -> Ligand (3)_fixed.sdf
pose.mol2 -> pose_fixed.sdf

If Merge outputs into one SDF is enabled, the tool returns a single fixed_batch.sdf instead of individual repaired SDF files.

Every job also includes:

ligand_fixer_report.json with per-entry success, failure, warnings, and preflight status

Limitations

This tool does not accept SMILES as an input workflow. Use SMILES to SDF for that.
Severe aromaticity or bond-order problems can still fail with errors such as Can't kekulize mol.
Protonation-state selection, tautomer enumeration, and full medicinal-chemistry normalization are out of scope.
The generated 3D conformer is a practical docking-prep geometry, not an exhaustive conformer search.