SMILES to SDF Converter
In short: Convert SMILES strings into SDF format for screening and dataset workflows. It is free, works in your web browser and needs no download.
Convert SMILES to SDF for dataset and virtual screening pipelines.
Input and output formats
| Input: SMILES | Output: SDF | |
|---|---|---|
| Full name | SMILES (Simplified Molecular Input Line Entry System) | SDF (Structure Data File) |
| What it holds | Atoms, bonds, rings, charges and stereo as one line of text. No coordinates. | One or more MOL records, each with optional data fields, split by $$$$. |
| File or form | .smi or plain text | .sdf |
File Format Explained
SMILES is a compact string representation of molecular connectivity. It is convenient for search and exchange, but it usually does not include rich metadata.
SDF is a structure-data file format that can store one or many molecule records, usually with MOL-style atom/bond blocks plus optional property fields. SDF is common in screening libraries, compound datasets, and cheminformatics pipelines.
Use SDF when you need a file that can carry structure records and compound properties together. Review stereochemistry and generated coordinates before batch use.
Why SDF
SDF (structure-data file) stores one or more structures, each as a MOL connection table followed by optional named data fields and a $$$$ separator. It is the standard way to move compound sets between cheminformatics tools, compound registration systems, and databases, because properties such as IDs, names, or assay results can travel with each structure.
How to use it
- Paste a SMILES, for example paracetamol
CC(=O)NC1=CC=C(C=C1)O. - Convert and download the .sdf file.
- Open it in your chemistry software, or combine several converted files into one library.
Example record layout
- Header lines, then the counts line with atom and bond numbers.
- The atom block (coordinates and elements) and the bond block.
M END, then any data fields such as> <NAME>followed by a value.$$$$to close the record.
FAQ
How is SDF different from MOL? A MOL file holds one structure; an SDF can hold many, with data. Can I go back to identifiers? Yes, with SDF to InChIKey or SDF to InChI.
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