Chem3D Users Manual - CambridgeSoft

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Administrator Line 56 -2794 21139 6600 Line 57 2876 15736 11820 Line 58 -14029 20018 -10310 Line 59 -22477 3450 6965 Line 60 -806 -4365 16672 Line 61 14642 -18918 3566 Line 62 23341 -2014 -13035 Line 63 1740 5536 -22837 Each line is either a blank line, a block header line or a data record containing multiple fields of information about the structure. The SMD file is broken down into several blocks of information. The header for each block starts with a > sign. Individual fields are delimited by space(s) or a tab. The fields in the SMD format file used by Chem3D Pro are discussed below: 1. Line 1 starts the block named STRT. This block contains the molecule name. The molecule name is the file name when the file was created using Chem3D Pro. 2. Line 2 starts the block named DTCR. The information in this line includes the name of the application that created the file and the date and time when the file was generated. 3. Line 3 starts the block named CT which contains the connection table of the compound(s). Also on this line is a 10 character description of the connection table. This will be the same as the file name when the file is generated using Chem3D Pro. Finally, the number of records contained within the CT block is indicated, 39 in the above example. 4. Line 4 of the CT Block contains four fields. The first field is the number of atoms, the second field is the number of bonds, the third field is the FORTRAN format for the number of atoms, and the fourth field is the FORTRAN format for the number of bonds. 5. Lines 5–23 of the CT Block each contain 4 fields describing an atom. The first field is the element symbol (first letter uppercase, second lowercase). The second field is the total number of hydrogens attached to the atom, the third field is the stereo information about the atom and the fourth field is the formal charge of the atom. NOTE: If the file is created using Chem3D Pro, the number of hydrogens, the stereo information and the formal charge fields are not used, and will always contain zeros. 6. Lines 24–42 of the CT Block each contains 3 fields describing a bond between the two atoms. The first field is the serial number of the atom from which the bond starts, the second field is the serial number of atom where the bond ends, and the third field is the bond order. 7. Line 43 starts the block named CO, The information in this block includes the Cartesian coordinates of all the atoms from the CT block and indicates the type of coordinates used, Angstroms in this example. Also in this line is the number of lines in the block, 20 in this example. 8. Line 44 contains two fields. The first field contains the exponent used to convert the coordinates in the lines following to the 264• File Formats CambridgeSoft Protein Data Bank Files
coordinate type specified in line 43. The second field is the FORTRAN format of the atom coordinates. 9. Lines 45–65 each contains three fields describing the Cartesian coordinates of an atom indicated in the CT block. The first field is the X coordinate, the second field is the Y coordinate and the third field is the Z coordinate. SYBYL MOL File The SYBYL MOL File format (SYBYL) is defined in Chapter 9, “SYBYL File Formats”, pages 9–1 through 9–5, of the 1989 SYBYL Programming Manual. The following is an example of a file in SYBYL format produced from within Chem3D. This file describes a model of cyclohexanol. 19 MOL Cyclohexanol0 1 1 1.068 0.3581 -0.7007C 2 1 -0.207 1.2238 -0.7007C 3 1 -1.473 0.3737 -0.5185C 4 1 1.1286 -0.477 0.5913C 5 1 -0.139 -1.324 0.7800C 6 1 -1.396 -0.445 0.7768C 7 8 2.1708 1.2238 -0.7007O 8 13 1.0068 -0.343 -1.5689H 9 13 -0.284 1.7936 -1.6577H 10 13 -0.147 1.9741 0.1228H 11 13 -2.375 1.032 -0.4983H 12 13 -1.589 -0.314 -1.3895H 13 13 1.2546 0.202 1.4669H 14 13 2.0091 -1.161 0.5742H 15 13 -0.077 -1.893 1.7389H 16 13 -0.21 -2.076 -0.0419H 17 13 -2.308 -1.081 0.8816H 18 13 -1.372 0.2442 1.6545H 19 13 2.9386 0.6891 -0.8100H 19 MOL 1 1 2 1 2 1 4 1 3 1 7 1 4 1 8 1 5 2 3 1 6 2 9 1 Appendices ChemOffice 2005/Appendix File Formats • 265 Protein Data Bank Files
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