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Administrator 32 3 12 1 0 0 0 33 3 13 1 6 0 0 34 4 5 1 0 0 0 35 4 14 1 1 0 0 36 4 15 1 6 0 0 37 5 6 1 1 0 0 38 5 7 1 6 0 0 39 5 16 1 0 0 0 40 6 17 1 0 0 0 41 6 18 1 1 0 0 42 7 19 1 6 0 0 Each line represents either a blank line, or a data record containing one or more fields of information about the structure. Each field is delimited by a space(s) or a tab. The fields in the MDL MolFile format used by Chem3D Pro are discussed below: 1. Line 1 starts the header block, which contains the name of the molecule. The molecule name is the file name when the file was created using Chem3D Pro. 2. Line 2 continues the Header block, and is a blank line. 3. Line 3 continues the Header block, and is another blank line. 4. Line 4 (the Counts line) contains 5 fields which describes the molecule: The first field is the number of atoms, the second field is the number of bonds, the third field is the number of atom lists, the fourth field is an unused field and the fifth field is the stereochemistry. NOTE: Chem3D Pro ignores the following fields: number of atom lists, the unused field and stereochemistry. These fields will always contain a zero if the file was created using Chem3D Pro. 5. Lines 5–23 (the Atom block) each contain 9 fields which describes an atom in the molecule: The first field is the X coordinate, the second field is the Y coordinate, the third field is the Z coordinate, the fourth field is the atomic symbol, the fifth field is the mass difference, the sixth field is the charge, the seventh field is the stereo parity designator, the eighth field is the number of hydrogens and the ninth field is the center. NOTE: Chem3D Pro ignores the following fields: mass difference, charge, stereo parity designator, number of hydrogens, and center. These fields contain zeros if the file was created using Chem3D Pro. 6. Lines 24–42 (the Bond block) each contain 6 fields which describe a bond in the molecule: the first field is the from-atom id, the second field is the to-atom id, the third field is the bond type, the fourth field is the bond stereo designator, the fifth field is an unused field and the sixth field is the topology code. NOTE: Chem3D Pro ignores the unused field and topology code. These fields will contain zeros if the file was created using Chem3D Pro. 630• File Formats <strong>CambridgeSoft</strong> File Format Examples
Limitations The MDL MolFile format does not support non-integral charges in the same way as Chem3D Pro. For example, in a typical MDL MolFile format file, the two oxygens in a nitro functional group (NO 2 ) contain different charges: -1 and 0. In Chem3D models, the oxygen atoms each contain a charge of -0.500. FORTRAN Formats The FORTRAN format for each record of the MDL MolFile format is as follows: Line Number Description 1 Molecule name (file name) 2 Blank line FORTRAN Format A 4 Number of atoms Number of bonds 5–23 Atom coordinates, atomic symbol 24–42 Bond id, from atom, to atom, and bond type MSI MolFile 5I3 3F10.4,1X,A2,5I3 6(1X,I2) The MSI MolFile is defined in Chapter 4, “Chem-Note File Format” in the Centrum: Chem-Note Application documentation, pages 4-1 to 4-5. The following is a sample MSI MolFile file created using Chem3D Pro for cyclohexanol (the line numbers are added for purposes of discussion only): 3 Blank line 1 ! Polygen 133 2 Polygen Corporation: ChemNote molecule file (2D) 3 * File format version number 4 90.0928 5 * File update version number 6 92.0114 7 * molecule name 8 cyclohexanol-MSI 9 empirical formula 10 Undefined Empirical Formula 11 * need 3D conversion? 12 0 Appendices <strong>ChemOffice</strong> 2005/Appendix File Formats • 631 MSI MolFile
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