MOL to InChI Converter

In short: Convert MOL or SDF structure blocks into standard InChI identifiers for chemistry data workflows. It is free, works in your web browser and needs no download.

Paste a MOL or SDF block and convert it into a standard InChI identifier.

File Format Explained

MOL stores a molecule as atom and bond tables, often with 2D or 3D coordinates. It is useful for editable structure exchange.

InChI is a standardized text identifier generated from the structure. It is useful for search, indexing, registration, and comparing chemical records across databases.

Conversion quality depends on the MOL file having clear atoms, bonds, charges, and stereochemistry. Review the generated InChI for salts, tautomers, and stereochemical layers.

About MOL files

A MOL file (MDL Molfile) stores a single structure as a connection table: a header, a counts line, an atom block with x, y, z coordinates and element symbols, and a bond block listing which atoms are connected and with what bond order. Most chemistry software can export MOL, which makes it a common exchange format. Two versions exist: V2000, the classic fixed-column format, and V3000, which supports larger molecules and more features.

Why convert to InChI

InChI gives a standard identifier that does not depend on atom order or drawing coordinates. Two MOL files of the same molecule drawn differently produce the same standard InChI, which makes it easy to check for duplicates or search databases.

How to use it

1. Open the .mol file in a text editor and copy everything, including the header lines and the final M END line.
2. Paste it into the input box and convert.
3. Copy the InChI, or shorten it further with InChI to InChIKey.

Troubleshooting: MOL files are column-sensitive, so a file reformatted by a word processor may fail. Copy from a plain-text editor.