MOL2 File

What are MOL2 files and how to open them

Are you having problems opening a MOL2 file or are you simply curious about its contents? We're here to explain the properties of these files and provide you with software that can open or handle your MOL2 files.

What is a MOL2 file?

A .MOL2 file is a Tripos Mol2 file.

A Tripos MOL2 file (extension .mol2) is a plain-text representation of a molecule created originally for the SYBYL suite from Tripos Inc. It stores everything needed to fully reconstruct a molecule: atom coordinates in three dimensions, bond connectivity and types, partial atomic charges, substructure/residue information, and optional metadata. Researchers and computational chemistry tools use it for molecular docking, force field modeling, and drug design.

Mol2 files are typically produced by molecular modeling, cheminformatics or molecular docking software, especially SYBYL and its successors. They are read by visualization, simulation or docking programs to render molecule structures, compute interactions, convert to other chemistry file formats or perform structural analysis.

Internally a Mol2 file is ASCII text divided into sections marked by lines like @<TRIPOS>MOLECULE, @<TRIPOS>ATOM, @<TRIPOS>BOND and optionally others such as SUBSTRUCTURE or SET. In the ATOM section each line provides an atom's ID, name, 3D coordinates, SYBYL-style atom type, which substructure it belongs to, and its partial charge. In the BOND section each line lists the bond's ID, the two atoms it connects and its bond type (e.g. single, double, aromatic, amide).

Mol2 files can be identified by starting with a "#" character, containing strings like "MOLECULE", "ATOM", "BOND", "TRIPOS" and "_CHARGES" and by having "0.000" formatted numeric fields (e.g. in coordinates or charges).

How to open MOL2 files

We have identified one MOL2 opener that is compatible with this specific type of MOL2 file.

Programs that open Tripos Mol2 files

Last updated: August 10, 2026

Various apps that use files with this extension

These apps are known to open certain types of MOL2 files. Remember, different programs may use MOL2 files for different purposes, so you may need to try out a few of them to be able to open your specific file.

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