SMILES to MOL2

Generate MOL2 files from SMILES strings for docking, scoring, and modeling workflows.

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Input

SMILES

Add hydrogens

Optimize geometry

10 credits

Output

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

What is SMILES to MOL2?

SMILES to MOL2 converts SMILES strings into three-dimensional MOL2 (Tripos MOL2) files using RDKit. MOL2 is the standard ligand format for many molecular docking programs — AutoDock, DOCK6, GOLD, and Glide all accept it. While SMILES encodes only 2D connectivity, MOL2 carries Tripos atom types, partial charges, and 3D coordinates required by these tools.

How to use SMILES to MOL2 online

ProteinIQ generates 3D MOL2 structures server-side, accepting SMILES strings directly from the browser with no RDKit installation needed.

Input

Input type	Format details
SMILES strings	One SMILES per line, or `name<TAB>SMILES` pairs for named compounds
File upload	`.txt`, `.csv`, `.tsv`, `.smi`, `.smiles` files
PubChem fetch	Compound names or CIDs fetched in batch from PubChem
Batch limit	Up to 10 entries per job

Settings

Setting	Description
`Add hydrogens`	Adds explicit hydrogens before 3D embedding (default: on). Required for accurate geometry and most docking pipelines.
`Optimize geometry`	Runs a short UFF force field minimization after embedding (default: on). Improves coordinate quality for strained or flexible structures.

Output

Each input compound produces a separate .mol2 file, downloadable individually and ready to use as ligand input in docking software.

How it works

RDKit's AllChem.EmbedMolecule generates 3D coordinates using distance geometry. When Add hydrogens is on, Chem.AddHs is called first so hydrogen positions are included. When Optimize geometry is on, Universal Force Field (UFF) minimization via AllChem.UFFOptimizeMolecule refines bond lengths, angles, and torsions. The structure is then written in Tripos MOL2 format.

Limitations

A single conformer is generated per molecule. For ensemble docking or conformer sampling, generate multiple conformers separately.
Very large or highly flexible macrocycles can fail distance geometry embedding.
Tautomer and protonation state are taken as given from the input SMILES. Adjust ionization state before conversion if target pH matters.

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Open Babel

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PDB to SDF Converter

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SDF to PDB Converter

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What is SMILES to MOL2?

How to use SMILES to MOL2 online

ProteinIQ generates 3D MOL2 structures server-side, accepting SMILES strings directly from the browser with no RDKit installation needed.

Input

Input type	Format details
SMILES strings	One SMILES per line, or `name<TAB>SMILES` pairs for named compounds
File upload	`.txt`, `.csv`, `.tsv`, `.smi`, `.smiles` files
PubChem fetch	Compound names or CIDs fetched in batch from PubChem
Batch limit	Up to 10 entries per job

Settings

Setting	Description
`Add hydrogens`	Adds explicit hydrogens before 3D embedding (default: on). Required for accurate geometry and most docking pipelines.
`Optimize geometry`	Runs a short UFF force field minimization after embedding (default: on). Improves coordinate quality for strained or flexible structures.

Output

Each input compound produces a separate .mol2 file, downloadable individually and ready to use as ligand input in docking software.

How it works

Limitations

A single conformer is generated per molecule. For ensemble docking or conformer sampling, generate multiple conformers separately.

Very large or highly flexible macrocycles can fail distance geometry embedding.

Tautomer and protonation state are taken as given from the input SMILES. Adjust ionization state before conversion if target pH matters.