SMILES to MOL Converter
In short: Convert SMILES strings into MOL structure files for compatibility workflows. It is free, works in your web browser and needs no download.
Convert SMILES to downloadable MOL format for editor and ELN compatibility.
Input and output formats
| Input: SMILES | Output: MOL file | |
|---|---|---|
| Full name | SMILES (Simplified Molecular Input Line Entry System) | MOL file (MDL Molfile) |
| What it holds | Atoms, bonds, rings, charges and stereo as one line of text. No coordinates. | An atom list with 2D or 3D coordinates and a bond table for one molecule. |
| File or form | .smi or plain text | .mol |
File Format Explained
SMILES is a compact one-line text identifier for a molecule. It is easy to paste into databases, scripts, and web tools, but it does not store a drawn 2D layout.
MOL, also called a molfile, stores atom and bond tables with coordinates. Use MOL when an editor, ELN, or cheminformatics tool needs an editable structure file instead of a text identifier.
After conversion, check stereochemistry, charges, and aromatic rings before using the MOL file in publication, registration, or computational workflows.
What a MOL file contains
SMILES describes which atoms are bonded, but it carries no coordinates. A MOL file adds a 2D layout: each atom gets x and y coordinates, so other programs can display the molecule without recalculating a layout. That makes MOL a safe choice when you move a structure into ChemDraw-compatible software, electronic lab notebooks, or registration systems.
Reading the output
- Lines 1–3: header (name, program, comment).
- Counts line: number of atoms and bonds, plus the version tag V2000.
- Atom block: one line per atom with x, y, z coordinates and element symbol.
- Bond block: pairs of atom numbers and the bond type (1 single, 2 double, 3 triple).
M ENDcloses the record.
How to use it
- Paste a SMILES such as
CCO(ethanol). - Convert and download or copy the MOL text.
- Save it with a .mol extension and open it in your target program.
Need several molecules in one file? Use SMILES to SDF. Need 3D coordinates for modelling? Try SMILES to PDB.
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