Molecular File Converter
Convert between chemical file formats with our web-based tool
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Our SDF File Converter accepts Structure-Data File (sdf) records and converts molecular structures and their property fields into various chemical, structural, and depiction file formats. The converter preserves atomic connectivity, coordinates (2D/3D when present), and most property tags. It can add or remove explicit hydrogens, generate simple 3D coordinates when missing, or produce docking-ready output formats. These are intended for downstream workflows such as virtual screening or molecular docking. The list of output formats below covers all supported back-end capabilities.
| Input Format | Data Type | Possible Output Formats |
| SDF | Chemical Structure | PDB, MOL2, SMILES, InChI, PDBQT, XYZ, CML, GAMESS, Gaussian, MOPAC, PNG, SVG |
How to use
- Upload your file: Click Upload File or drag-and-drop your .sdf file into the designated upload area. You may also use the Paste Data option to paste the raw SDF text directly into the input box.
- Select input and output formats: Confirm the input format is sdf (the tool will usually detect this automatically), then choose an output format from the Output Format dropdown (e.g., pdb, mol2, smi, or pdbqt).
- Click the Convert File button: Press Convert File to start the conversion. The converter will parse the SDF records and generate the requested output based on the selected options (hydrogen handling, coordinate generation, property export).
- Download the output file: When the conversion finishes, a download link will appear. Click the link to save the converted file to your device.
The Input: sdf format
An SDF contains one or more MDL molfile records with data fields. Each record ends with $$$$. SDF supports V2000/V3000 and property blocks for each molecule.
Example (short SDF record):
acetone -OEChem-07222109453D 3 2 0 0 0 0 999 V2000 1.2080 -0.0000 0.0000 C 0 0 0 0 0 0 -0.6040 1.0466 0.0000 C 0 0 0 0 0 0 -0.6040 -1.0466 0.0000 O 0 0 0 0 0 0 1 2 1 0 1 3 2 0M END> <Molecular_Weight>58.08$$$$
Common Output Formats
Your choice of output format depends on the software or analysis you plan to use next.
- SDF to SMILES Format: This converts the 3D connection table into a compact, one-dimensional line notation. It is ideal for storing large databases and performing fast substructure searches.
- SDF to PDB Format: Converts chemical structures into the Protein Data Bank format. This is essential for structural biology and viewing molecules in the context of biological systems.
- SDF to MOL2 Format: A comprehensive format from the Sybyl software package that includes detailed atom typing and charge information.
- SDF to PDBQT Format: A specialized version of the PDB format that includes partial charges and atom type information required by AutoDock.
The Core Transformation Process
Regardless of the output you select, the converter performs these fundamental steps:
- Validates the Connection Table: The engine parses the V2000 or V3000 atom and bond blocks to ensure chemical valency and structural integrity.
- Perceives Chemical Properties: The tool automatically detects aromaticity, assigns hybridizations, and calculates missing properties, such as implicit hydrogen counts.
- Translates Coordinate Data: It maps the X, Y, and Z coordinates from the SDF into the specific spatial syntax of the target format, such as the fixed-width columns of a PDB file or the tab-separated structure of a MOL2 file.
Troubleshooting
Below are three common problems encountered when converting from SDF to other formats, why they happen, and how to fix them.
Error: Missing coordinates or “no 3D coordinates found.”
The SDF record contains only 2D coordinates or no coordinate block at all. Some output formats (xyz, many docking formats) require 3D coordinates. You can use the tool option to generate 3D coordinates before conversion (the converter can run a quick geometry builder). Alternatively, prepare 3D structures in a molecular editor or use an external conformer generator and re-export as SDF.
Error: Unrecognized atom or bond types/valence warnings
The SDF uses nonstandard atom labels, unusual valence states, or contains proprietary extensions that the converter cannot map to standard atom types. You can inspect the SDF for nonstandard element symbols or incorrect connectivity. Normalize atom labels (e.g., replace custom labels with standard element symbols) and correct bond orders in a chemical editor, then retry conversion. If the file contains metallorganic complexes with nonstandard coordination, consider using a specialized workflow for metal centers.
Error: Property fields lost, truncated, or mis-encoded
The SDF contains long text fields, non-ASCII characters, or property names that are incompatible with the target format (for example, converting to smiles will lose per-structure property blocks). Some formats impose strict line-length limits (e.g., legacy molfile rules). You can export property blocks separately to csv or json during conversion (choose the “export properties” option). For long text fields or non-ASCII content, normalize or encode the data (UTF-8) before conversion, or use formats that support richer metadata (cml or json).
If your problem isn’t listed here, please report the issue so we can investigate and improve the tool. For assistance or to report a bug, contact us.
Support Our Work
If you rely on our tools for research, teaching, or production work, please consider supporting maintenance and development. Contributions help us maintain an up-to-date format, support, add new output options, and improve conversion accuracy. You can support us through donations, sponsoring feature development, or sharing feedback so we can prioritize fixes and new formats.
Reference
O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33.
Meet the Authors
Mahdi Morshedi Yekta
Founder & Bioinformatics Developer
Mahdi is the founder of ScienceCodons and a Medical Biotechnologist with a deep passion for computational biology. Holding an M.Sc. in Medical Biotechnology, he specializes in transforming complex biological algorithms into accessible, high-performance web tools, bridging the gap between laboratory sciences and software engineering.
Fatemeh Faryadras
Medical Biotechnologist & Researcher
Fatemeh is a Medical Biotechnologist and researcher. With extensive expertise in genetic engineering, molecular cloning, and cancer biology, she combines her rigorous laboratory background with intuitive design principles to create reliable, user-centered scientific calculators and tools.
Dr. Mosayeb Rostamian
Assistant Professor, Infectious Diseases Research Center
Certified Scientific Reviewer
Google ScholarExpert Review Process
To ensure the highest quality and scientific accuracy, this tool's underlying algorithms, formulas, and edge-case handling have been thoroughly reviewed and validated by Dr. Mosayeb Rostamian.
The "Reviewed By" badge signifies that an independent expert has evaluated the tool's logic to guarantee accuracy and alignment with the current consensus in the scientific community.