MolDraw › Chemistry tools › MOL to SDF Converter

MOL to SDF Converter (combine MOL files)

In short: Open one or several MOL files, V2000 or V3000, and get a single SD file. Optionally add data fields for name, formula, molecular weight and SMILES. It is free, runs in your web browser and needs no download.

Coordinates and bonds are copied as they are. Nothing is uploaded: the files are read on your device.

Quick answer: Press Load 3 example MOL files. Aspirin, caffeine and a V3000 paracetamol file are joined into one SDF with 3 records. Each record gets the data fields Name, Formula, MW and SMILES, for example > <MW> 180.159 for aspirin.

Paste MOL blocks (optional; you can also open files)

Open .mol files (several allowed)

Add SD data fields

Ready.

SDF output

How to convert MOL files to SDF

Press Open .mol files and select one or more files, or paste MOL blocks into the box.
Tick the data fields to add: Name, Formula, MW, SMILES.
Tick Write V3000 files as V2000 if your program only reads V2000.
Press Make SDF. The table lists each record, its atom count and formula.
Press Download .sdf or Copy.

MOL file versus SD file

A MOL file (MDL molfile) holds one structure: a title line, a program line, a comment line, a counts line, then the atom block (x, y, z, element, charge) and the bond block, ending with M END. An SD file is a list of such MOL blocks. After each one it may hold data items and then the separator $$$$:

aspirin
…MOL block…
M END
> <Formula>
C9H8O4

> <MW>
180.159

$$$$

Formula and MW are calculated from the structure (implicit hydrogens included). SMILES is canonical and keeps stereochemistry.

Limitations

The structure is not changed or cleaned; errors in the input MOL file are copied into the SDF.
V3000 to V2000 conversion is not possible above 999 atoms or bonds, and V3000-only features (enhanced stereo groups, some Sgroups) may be simplified.
Query and R-group MOL files can be read but their SMILES field may not be meaningful.

Need a MOL file? Draw the structure in MolDraw, a free online chemical structure editor, and export it as MOL.

Open MolDraw editor

Frequently asked questions

How do I convert a MOL file to SDF?

Open the .mol file (or paste its text) and press Make SDF, then Download .sdf. An SDF record is the MOL block followed by optional data fields and a line with $$$$, so the structure and coordinates are kept exactly as they are.

Can I combine several MOL files into one SDF?

Yes. Select several .mol files at once in the file dialog, or paste several MOL blocks one after another. Each becomes one record of the same SD file, in the order given. Files that cannot be read are listed and skipped.

Are V3000 MOL files supported?

Yes. V3000 records are kept as V3000 in the SDF by default. Tick Write V3000 files as V2000 if your program only reads V2000; this works for structures with up to 999 atoms and bonds.

What data fields can be added?

Name (the title line, or the file name when the title is empty), molecular formula, molecular weight in g/mol and canonical isomeric SMILES. Fields already present in an input SDF are kept unless you untick Keep existing fields.

Last updated: October 30, 2026