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MOL MOL2
File conversion

Convert MOL to MOL2

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Is it possible to convert MOL to MOL2?
Yes - MOL converts to MOL2.

MOL2 (Tripos SYBYL format) is a common target for docking tools. Open Babel converts: obabel input.mol -O output.mol2

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Tested on macOS, Windows & Linux
Last verified Oct 2026

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How to convert MOL to MOL2

Converting a .MOL file to .MOL2 lets you open the content in software that prefers the .MOL2 format, though some details may change compared with the original. We are still putting together the list of programs that handle .MOL files.

A full step-by-step guide for this conversion is on the way; the information above is drawn straight from our database.

About these formats

.MOL MDL Molfile

A MOL file is a plain-text MDL Molfile describing a single chemical molecule - its atoms, bonds, and 2D/3D coordinates. Open it free with Avogadro 2, MolView.org in a browser, or BIOVIA…

Open .MOL details →
.MOL2 Portable Representation Of A SYBYL Molecule

A .MOL2 file is associated with Portable Representation Of A SYBYL Molecule, a misc file.

Open .MOL2 details →