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Administrator The field value for Carbon 6 from the example file is included in parentheses for reference: 1. Line 1 is a standard header line for MSI MolFile format files. 2. Line 2 normally indicates the application which created the file. 3. Line 3 is the header for the File format version number section. 4. Line 4 indicates the file format version number. The format for this field is YY.MMDD. 5. Line 5 is the header for the File update version number section. 6. Line 6 indicates the file update version number. The format for this field is YY.MMDD. 7. Line 7 is the header for the molecule name section. 8. Line 8 contains the field molecule name. This field contains either the file name, or “Undefined Name”. 9. Line 9 is the header for the empirical formula. 10. Line 10 contains the empirical formula field. This field contains either the empirical formula or “Undefined Empirical Formula”. 11. Lines 11–24 each contains information concerning conversions from 3D to 2D. 12. Line 25 is the header for the Global display attributes section. 13. Line 26 contains 5 fields describing the global display attributes: Line thickness (1), font style (0), type face (1), type size (12), font (256). These values are specific to the platform that is generating the file. 14. .Line 27 contains the header for the Atom Lists section. 15. Line 28 contains a listing of all the possible fields for the atom list section. When the file is created using Chem3D Pro the following fields are used: Atom#,Lbl, Type, and x,y,z. 16. Lines 29–47 each contains 28 fields describing information about each of the atoms in the structure: the first field is the atom number (6), the second field is the atom label (C), the third field is the atom type (10), the fourth field and fifth fields contain 2D coordinates, and contain zeros when the file is created using Chem3D Pro, the sixth field is the X coordinate (-0.113) and the fifth field is the Y coordinate (1.005), the sixth field is the Z coordinate (-0.675), the seventh through fifteenth fields are ignored and contain zeros when the file is created by Chem3D Pro, the sixteenth field is, again, the atom label (C), the eighteenth field is, again, the atom number (6), the nineteenth field is the segment field, the twentieth field is the coordination field, the twenty first field is ignored, the twenty-second field is called the saturation field: if the atom is attached to any single, double or delocalized bonds this field is 1 (not saturated) otherwise this field is 0. The twenty-third through the twenty-sixth fields are ignored and contain zeros when the file is created using Chem3D Pro, the twentyseventh field is, again, the atom label (C). NOTE: Atom types in the Molecular Simulations MolFile format are user-definable. For more information, see “Editing File Format Atom Types” on page 619. 17. Line 48 contains the header for the Bond List section. 18. Line 49 contains a listing of all the possible fields for the bond list section. When the file is created by Chem3D Pro the following fields are used: Bond#, Bond_type, atom 1, atom 2 and cis/trans and Qorder. 19. Lines 50–68 each contain 4 fields describing information about each of the bonds in the structure: the first field is the internal bond number (6), the second field is the bond type (1), the third and fourth fields are the atom 634• File Formats <strong>CambridgeSoft</strong> MSI MolFile
serial numbers for the atoms involved in the bond [atom 1 (2), atom 2 (16)], the fifth field is the cis/trans designator (this is 0 if it does not apply), the sixth through tenth fields are ignored, and contain zeros if the file is created using Chem3D Pro, the eleventh field contains the bond order ([S] meaning single), the twelfth and thirteenth fields are ignored and contain zeros if the file is created using Chem3D Pro. 20. Lines 69–73 are each a section header for 3D conversion use. This section only contains the header name only (as shown) when the file is created using Chem3D Pro. 21. Line 74 is a header for the section User data area. This section contains the header name only (as shown) when the file is created using Chem3D Pro. 22. Line 75 is a header that indicates the End of File. FORTRAN Formats The FORTRAN format for each record of the Molecular Simulations MolFile format is as follows: 29-47 atom list, field value 50-68 bond list, field values MOPAC I,1X,A,3(1X,I),3F9. 3,1X,I,F4.1,7(1X,I), 1X,A,I,8(1X,I), “[“,A, “] “ I,4(1X,I),F9.3,4(2X ,I),1X, “[“,A1, “] “,2(1X,I) The specific format of the MOPAC files used by Chem3D is the MOPAC Data-File format. This format is described on pages 1-5 through 1-7 of the “Description of MOPAC” section and page 3-5 of the “Geometry Specification” section in the MOPAC Manual (fifth edition). For further details about the MOPAC Data-File format, please refer to the above publication. The following is a sample MOPAC output file from Chem3D for cyclohexanol: Line Number Description FORTRAN Format Line 1: Line 2: Cyclohexanol Line 3: Line 4a: C 0 0 0 0 0 0 0 0 0 Line 4b: C 1.54152 1 0 0 0 0 1 0 0 Line 4c: C 1.53523 1 111.7747 1 0 0 2 1 0 Line 4d: C 1.53973 1 109.7114 1 -55.6959 1 1 2 3 Appendices <strong>ChemOffice</strong> 2005/Appendix File Formats • 635 MSI MolFile
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Administrator Tutorial 7: Docking M
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Administrator xxxviii• CambridgeS
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CAMBRIDGESOFT ChemOffice Desktop to
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DESKTOP CS E-Notebook Electronic Jo
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DESKTOP CS Chem3D Molecular Modelin
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ENTERPRISE ChemOffice WebServer Ent
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ENTERPRISE Oracle Cartridge Enterpr
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KNOWLEDGE E-Notebook Enterprise Des
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KNOWLEDGE Document Manager Desktop
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KNOWLEDGE 21CFR11 Compliance Electr
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