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8 Pharmaceutical Technology ® Regulating Innovation, Quality, and Risk eBook January 2024 PharmTech.com Regul ations FDA/CDER's Electronic Submissions Gateway (ESG) (4), with standardized associated data fields meet- ing Agency cheminformatics and cross-functional regulatory review needs. What is an SD File? The SD File belongs to a family of chemical-data file formats. The machine-readable data are interpreted as the corresponding structure and associated data fields, as shown in Figure 1. The SD File is in plain text and contains chemi- cal structure records and associated data fields. It is used as a standard exchange format for chemical information. The SD File's chemical table adheres to a strict format for representing multiple chemical str ucture records and associated data f ields. The chemical table file format stores information about the positions of the individual atoms (either in 2D or 3D space) that make up the molecule. The SD File is based on the MOL-file format; both the SD File and molecular file (MOL)-file formats were developed by Molecular Design Limited (MDL) (5, 6, 7). The orig- inal MOL-file format was designed to encode only a single structure, whereas the SD File format was designed to encode single or multiple structures and associated data fields with individual MOL-files sep- arated by lines consisting of four-dollar signs ($$$$, see Figures 1 and 2 "End of File") (6, 7). The individual MOL-files within the SD File con- ta i n speci f ic seg ments (Figure 2). A l l MOL-f i les have a header block and a count line block with a connection table (CTAB). The Header block has two lines. The first line gives the name of the molecule (if known) or an automatically generated name and is of variable format. The second line reports the software that generated the file, and if 2D or 3D coordinates are given. The Count Line Block is the first line in the CTAB and refers to how many atoms and bonds make up the molecule. For example, the count line in Figure 2 shows that caffeine has 14 atoms and 15 bonds. The count line also provides the version num- ber of the MOL-file. The Atom and Bond blocks describe t he atoms (mass difference, charge, stereochemistr y, and as- sociated hydrogens) and connectivit y (bond t y pe, stereochemistry, and topology (ring or open chain), Figure 1: Structure of Caffeine and its corresponding computer-readable SD File format. Structure FIGURE 1. Structure of caffeine and its corresponding computer-readable structure-data file (SD File) format. FIGURES COURTESY OF THE AUTHORS.