Convert SDF to XLS

Laboratories often need compound records in .xls because a legacy LIMS, reporting template, or customer accepts only Excel 97–2003 workbooks. The useful result is usually a spreadsheet of SDF properties and identifiers, not a chemically editable replacement for the source file.

What an SDF file can contain

.sdf is ambiguous. Most commonly, it means Structure Data File, an MDL Molfile-based chemistry format used by chemists, compound vendors, screening databases, ChemDraw, BIOVIA software, ChemAxon tools, DataWarrior, Open Babel, and RDKit workflows.

A chemical SDF is plain text containing one or more molecule records. Each record can contain a molecular connection table, coordinates, a title, and named SD tags such as CAS_NUMBER, IC50, or Supplier; records normally end with $$$$. Molecule blocks may use V2000 or V3000 syntax.

An .sdf file can instead be a binary Microsoft SQL Server Compact database. SQL Server Compact is not SQL Server, and its database file must be queried and exported with SQL Server Compact-compatible software rather than opened by chemical-format tools.

What the XLS format provides

.xls is the binary Excel 97–2003 workbook format. Unlike CSV, it can retain worksheets, basic formulas, cell formatting, and multiple tables, which is useful when a recipient requires an older Excel workbook.

Use XLS only when required. It is limited to 65,536 rows and 256 columns per worksheet. .xlsx supports far larger worksheets and is the better default for current Excel-compatible systems.

Converting a chemical SDF file

1. Open the SDF in a chemistry-aware desktop application such as DataWarrior. Use File → Open, then verify that the application recognizes the molecule records and exposes the SD tags as data columns.
2. Check field names, missing values, units, and multiline tag values. Preserve a structure identifier and, when the recipient needs machine-readable structures, add a SMILES or InChI column before export.
3. Export the table as tab-delimited text or CSV using DataWarrior’s File → Save As or export command. Do not rely on a generic document converter to interpret molecular records and SD tags.
4. Open the text file in Microsoft Excel or LibreOffice Calc. In the import dialog, select the correct delimiter and explicitly set CAS numbers, catalog numbers, leading-zero codes, and long numeric identifiers to Text.
5. Use File → Save As and select Excel 97–2003 (.xls). Check the compatibility warning, worksheet dimensions, and a sample of imported values before distributing the workbook.

For repeatable processing, use RDKit or another chemistry toolkit to extract selected SD tags and generate a CSV with a SMILES column, then convert that CSV in Excel or LibreOffice. Open Babel can also inspect and transform SDF files, but validate its generated columns against the source because available property and descriptor output depends on the selected format and options.

For nonconfidential, already-tabular CSV files, CloudConvert can be used to create an XLS workbook after local SDF extraction. It should not be treated as a chemistry-aware SDF parser, and proprietary structures, assay data, and supplier data should not be uploaded unless the organization permits that transfer.

Exporting a SQL Server Compact SDF database

Open a database SDF with SQL Server Compact Toolbox or another tool using a compatible SQL Server Compact provider. Supply the database password if the file is encrypted, run a query for the required tables and columns, and export the result as CSV. Import that CSV into Excel or LibreOffice Calc and save it as .xls.

SQL Server Compact is a retired Microsoft product, so a current database application may not open the file without the appropriate legacy provider. A database SDF cannot be converted correctly by DataWarrior, RDKit, or Open Babel.

Compatibility checks

XLS does not natively store an editable SDF connection table. Keep the original SDF for chemical exchange and archiving; place SMILES, InChI, or molfile text in spreadsheet cells only when downstream software needs a machine-readable structure. Rendered structure images are suitable for review but are not chemical data.

Excel may automatically change values resembling dates or scientific notation. Text import settings prevent losses such as 001234 becoming 1234 and long numeric identifiers being rounded. Also check multiline SD tags and text exceeding Excel’s 32,767-character cell limit, which may require truncation, splitting, or retention in the original SDF.