Free Online MOL2 Viewer (No Signup)
Also opens DWG, DXF, STEP, IGES, IFC, SKP, STL, OBJ, GLB, FBX, 3DM and other 3D/CAD files. Drop any file on the viewer.
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Describe a compound, a protein or a crystal. The AI finds it in PubChem or the Protein Data Bank, or builds it, and opens it here.
Create a model with AI
Describe what you need, or add a photo, and AI builds it at real size in the viewer. Ask for changes in the chat, then export it. Free, with your own Anthropic or OpenAI key.
Open the AI GeneratorWhat Is an MOL2 File?
A .mol2 file is plain text in sections that start with a @<TRIPOS> tag. @<TRIPOS>MOLECULE names the molecule and gives its counts, @<TRIPOS>ATOM lists each atom with its name, coordinates, SYBYL atom type (such as C.ar for an aromatic carbon or N.am for an amide nitrogen), residue and partial charge, and @<TRIPOS>BOND lists each bond with its type (1, 2, 3, ar, am).
A file can hold many molecules one after another, which is how docking libraries and virtual-screening sets are often shipped. UCSF Chimera and ChimeraX, Open Babel, AutoDock Tools, DOCK, GOLD and SYBYL all read and write it.
For the MDL formats, see the SDF and MOL viewer; for proteins, the PDB viewer; for every molecular format on one page, the molecule viewer.
Who Uses MOL2 Files?
Computational chemists and drug-discovery teams preparing ligands and receptors for docking, researchers working with virtual-screening libraries, students in molecular-modelling courses, and anyone sent a .mol2 file without Chimera or SYBYL on hand.
Common Use Cases
- Check a ligand prepared for docking before a run
- Look through the molecules of a screening library, one layer per molecule
- Compare docked poses or conformers saved together in one file
- Share a docking ligand with a colleague as a link that opens in any browser
- Export a molecule as GLB, OBJ or STL for a render, a slide or a 3D print
Features
Opens .mol2 Files
Tripos MOL2 files with one or many molecules.
SYBYL Types Read
Elements from the SYBYL atom types and bond orders from the bond types, aromatic bonds included.
Ball and Stick
Atoms coloured by element, with double, triple and aromatic bonds drawn as parallel cylinders.
Space Filling
A layer with every atom at its van der Waals radius.
One Layer per Molecule
A file with many molecules opens with each one on its own layer, named from the file.
Export to GLB, STL or USDZ
Save the structure as GLB, glTF, OBJ, STL, 3MF, PLY, FBX or USDZ for a render, a 3D print or AR, or the view as a PNG.
Measure in Ångströms
Click two atoms to measure the distance between them, in Å.
View in VR
On a headset browser the molecule stands on a table in front of you.
Nothing Is Uploaded
The file is read entirely in your browser. No account, no upload, no copy on a server.
Share and Embed
Send a link that opens the molecule in any browser, or drop the viewer into your own page with one iframe.
Compatibility & Format Notes
The MOLECULE, ATOM and BOND sections are read. The element comes from the SYBYL atom type, and bond types become single, double, triple and aromatic bonds; amide bonds are drawn as single bonds. A file with many molecules opens with one layer per molecule, named from its MOLECULE section, for the first 200 molecules; the status line counts the rest.
Molecules open as ball and stick, coloured by element in the Jmol colours, with double and triple bonds drawn as parallel cylinders and a Space filling layer beside them.
Coordinates are read in ångströms (Å) and kept at that scale, so the measuring tool reads distances in Å. Bonds are taken from the file where it lists them and worked out from covalent radii for the rest. Very large structures, such as a whole virus capsid with millions of atoms, open with the cartoon and with their atoms drawn as points so the browser keeps up.
Embed on Your Website
Add this viewer to your own site with a single line of HTML. Click Embed in the toolbar to generate an embed code, or use the snippet below with your own file URL.
Your Files Stay on Your Computer
Your MOL2 files are parsed entirely in your browser. Nothing is uploaded, stored, or shared unless you explicitly click the Share button. Shared files are hosted for 90 days then deleted.
Frequently Asked Questions
▶Does a MOL2 file with many molecules open?
Yes. Each molecule is its own layer, named from its MOLECULE section, so you can show one, several or all of them.
▶Are SYBYL atom types and bond types used?
Yes. The element of each atom comes from its SYBYL type (C.3, C.ar, N.pl3 and so on), and bond types 1, 2, 3 and ar are drawn as single, double, triple and aromatic bonds.
▶Are partial charges shown?
No. Atoms are coloured by element; the charge column is read past.
▶How many molecules of a library are drawn?
The first 200 molecules of a file, each on its own layer. The status line says how many the file holds, so you know when to split a large library into smaller files.
▶Do I need Chimera, SYBYL or Open Babel?
No. The file is read and drawn in your browser, on any computer, tablet or phone.
▶Can I 3D print the molecule?
Yes. Export STL or 3MF and open it in your slicer. Thin cartoon ribbons and sticks are fragile at small sizes, so for a sturdy print switch on Space filling (or ball and stick for a small molecule) before exporting, and scale the model up in the slicer: one ångström in the file is one unit in the export.
▶Is this MOL2 viewer really free?
Yes, completely free. No signup, no watermarks, no file size limits on the viewer (the optional share-link feature has a 100 MB upload cap). Built by Innerscene as a tool for architects, engineers, and designers.
▶Are my files uploaded to a server?
No. All parsing, rendering, and conversion runs in your browser: nothing is uploaded, stored, or transmitted by default. The Share button is the only feature that uploads a file, and only when you explicitly click it.
▶Can I convert to another format?
Yes. Click Export in the toolbar to save the structure as GLB, glTF, OBJ, STL, 3MF, PLY, FBX or USDZ, or the view as a PNG picture. The export carries the layers you have switched on, so turn on Space filling or Polymer atoms first if you want them in the file. There is no PDB or SDF writer: the exports are 3D models of the picture you see.
▶Can I embed this viewer on my own site?
Yes. Click Embed in the toolbar to generate a one-line <iframe> snippet you can paste into any HTML page. You can choose whether the embed shows the viewer’s toolbar.