How to work with SD files

The structural data file (SDF) belongs to a family of chemical-data file formats. It is based on the MOL-file format, both developed by Molecular Design Limited (MDL), now named Biovia (belongs Dassault Systèmes).

The SDF contains information on the chemical structure and associated data of compounds in plain text. The original MOL-file only encoded a single molecule, whereas files in SDF format can encode single or multiple molecules that are then delimited by lines consisting of four dollar signs ($$$$). SDF files are formatted ASCII files that store information about the positions of the individual atoms (either in 2D or 3D space) that make up the molecule. The data on connectivity and hybridization state are also encoded, although their use is less frequent and often inconsistent.

To browse, search, export and perform other operations with collections of molecules represented as SDF files, please, check out the software list below. Most of these programs are open-source with cross-platform availability. In many cases, basic associated  physicochemical parameters (such as molecular weight, exact mass, molecular formula, hydrogen bond acceptor and donor counts) are automatically calculated on import.

Figures 1-3 show an example of SD file of a compound from Life Chemicals HTS Compound Collection.

Free, open-source  and  cross-platform software/programs that open .SDF files

Available for Windows, macOS, and Linux

Available for Windows and Linux

License-based products that work with .SDF files

In some cases, a free trial version or academic license may be available

Structure of compound F2135-1207

Figure 1. Structure of compound F2135-1207

SDF file structure of F2135-1207 open in a text editor (NotePad)

Figure 2. SDF file structure of F2135-1207 open in a text editor (NotePad)

Information from the SDF file of F2135-1207 viewed in DataWarrior

Figure 3. Information from the SDF file of F2135-1207 viewed in DataWarrior

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