SeqChem

Free online chemistry & sequence tools

SDF to MOL Converter

An SDF is just a sequence of MOL records with data fields attached. Converting to MOL strips the metadata and gives you individual structures.


Why strip the SDF wrapper?

Many legacy tools and scripts accept only a single-molecule MOL file and choke on the $$$$ separator and data fields. Converting each record to a plain MOL block makes the library compatible with those tools.

What you lose

All SDF data fields — compound names, IDs, custom properties — disappear. If those matter, keep the original SDF as the system of record and use the MOL files only for the tool that needs them.

Record order

Records are written in the same order as they appear in the source file, one block per molecule.

More converters