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Administrator Line 16 6 C -0.559 1.37 0.436 C.3 Line 17 7 H -2.021 -0.239 0.253 H Line 18 8 H -1.005 -1.759 1.944 H Line 19 9 H 0.175 -0.496 2.427 H Line 20 10 H 1.27 -2.128 0.9 H Line 21 11 H -0.01 -1.898 -0.331 H Line 22 12 H 2.021 0.225 0.655 H Line 23 13 H 2.008 -0.569 -0.953 H Line 24 14 H 1.03 1.766 -1.016 H Line 25 15 O -0.3 0.427 -1.757 O.sp Line 26 16 H -1.262 2.128 0.014 H Line 27 17 H 0.014 1.876 1.249 H Line 28 18 H -2.005 0.562 1.857 H Line 29 19 H 0.329 0.223 -2.427 H.sp Line 30 @BOND Line 31 1 31 2 1 Line 32 2 1 6 1 Line 33 3 1 7 1 Line 34 4 1 18 1 Line 35 5 2 3 1 Line 36 6 2 8 1 Line 37 7 2 9 1 Line 38 8 3 4 1 Line 39 9 3 10 1 Line 40 10 3 11 1 Line 41 11 4 5 1 Line 42 12 4 12 1 Line 43 13 4 13 1 Line 44 14 5 6 1 Line 45 15 5 14 1 Line 46 16 5 15 1 Line 47 17 6 16 1 Line 48 18 6 17 1 Line 49 19 15 19 1 646• File Formats <strong>CambridgeSoft</strong> Protein Data Bank Files
Each line is either a blank line, a section header or a data record containing multiple fields of information about the compound. The SYBYL MOL2 file is broken down into several sections of information. Record type indicators (RTI) break the information about the molecule into sections. RTI’s are always preceded by an “@” sign. Individual fields are delimited by space(s) or a tab. of substructures, the fourth field is the number of features and the fifth field is the number of sets. NOTE: Chem3D Pro ignores the following fields: number of substructures, number of features and number of sets. These fields will contain zeros if the file was created using Chem3D Pro. The fields in the SYBYL MOL2 format file used by Chem3D Pro are as follows: 1. Line 1 is a comment field. The pound sign preceding the text indicates a comment line. Name: is a field designating the name of molecule. The molecule name is the file name when the file is created using Chem3D Pro. 2. Line 2 is a blank line. 3. Line 3, “@MOLECULE”, is a Record Type Indicator (RTI) which begins a section containing information about the molecule(s) contained in the file. NOTE: There are many additional RTIs in the SYBYL MOL2 format. Chem3D Pro uses only @MOLECULE, @ATOM and @BOND. 4. Line 4 contains the name of the molecule. The name on line 4 is the same as the name on line 1. 5. Line 5 contains 5 fields describing information about the molecule: The first field is the number of atoms, the second field is the number of bonds, the third field is the number 6. Line 6 describes the molecule type. This field contains SMALL if the file is created using Chem3D Pro. 7. Line 7 describes the charge type associated with the molecule. This field contains NO_CHARGES if the file is created using Chem3D Pro. 8. Line 8, blank in the above example, might contain internal SYBYL status bits associated with the molecule. 9. Line 9, blank in the above example, might contain comments associated with the molecule. NOTE: Four asterisks appear in line 8 when there are no status bits associated with the molecule but there is a comment in Line 9. 10. Line 10, “@ATOM”, is a Record Type Indicator (RTI) which begins a section containing information about each of the atoms associated with the molecule. 11. Lines 11–29 each contain 6 fields describing information about an atom: the first field is the atom id, the second field is the atom name, the third field is the X coordinate, the fourth field is the Y coordinate, the fifth field is the Z coordinate and the sixth field is the atom type. NOTE: Atom types are user-definable See “Editing File Format Atom Types” on page 619 for instructions on modifying or creating an atom type. Appendices <strong>ChemOffice</strong> 2005/Appendix File Formats • 647 Protein Data Bank Files
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