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Administrator 14 13 H 2.197 -0.8229 0.3289 15 14 H 2.7422 0.7763 -0.282 16 15 H 1.5961 0.9769 1.9574 17 16 H 0.7156 1.8784 0.679 18 17 H -0.8718 0.6068 2.0941 19 18 H -0.004 -0.9319 1.7721 20 19 H -2.7422 -0.593 0.9688 21 1 1 2 SINGLE 22 2 1 6 SINGLE 23 3 1 7 SINGLE 24 4 1 8 SINGLE 25 5 2 3 SINGLE 26 6 2 9 SINGLE 27 7 2 10 SINGLE 28 8 3 4 SINGLE 29 9 3 11 SINGLE 30 10 3 12 SINGLE 31 11 4 5 SINGLE 32 12 4 13 SINGLE 33 13 4 14 SINGLE 34 14 5 6 SINGLE 35 15 5 15 SINGLE 36 16 5 16 SINGLE 37 17 6 17 SINGLE 38 18 6 18 SINGLE 40 19 7 19 SINGLE Each line represents a data record containing one or more fields of information about the molecule. Each field is delimited by spaces or a tab. The fields used by Chem3D are described below: 1. Line 1 contains two fields. The first field is the total number of atoms in the molecule and the second field is the total number of bonds. 2. Lines 2–20 each contain 5 fields of information about each of the atom in the molecule. The first field is the serial number of the atom. The second field is the atom type, the third field is the X coordinate, the fourth field is the Y coordinate and the fifth field is the Zcoordinate. NOTE: Atom types in the Alchemy file format are user-definable. See “Editing File Format Atom Types” on page 619 for instructions on modifying or creating an atom type. 3. Lines 21–40 each contain 4 fields describing information about each of the bonds in the molecule. The first field is the bond number (ranging from 1 to the number of bonds), the second field is the serial number of the atom where the bond begins, the third field is the serial number of the atom where the bond ends, and the fourth field is the bond type. The possible bond types are: SINGLE, DOUBLE, TRIPLE, AMIDE, or AROMATIC. Note that all the bond order names are padded on the right with spaces to eight characters. FORTRAN Formats The FORTRAN format for each record of the Alchemy file is as follows: Line Number Description 1 number of atoms, number of bonds 2–20 atom serial number, type, and coordinates 21–40 bond id, from atom, to atom, bond type FORTRAN Format I5, 1X, ATOMS,1X,I5, 1X, BONDS I6,A4,3(F9.4) I6,I5,I6,2X,A8 620• File Formats <strong>CambridgeSoft</strong> File Format Examples
Cartesian Coordinate Files The Cartesian coordinate file format (Cart Coords, Cart Coords 2) interprets text files that specify models in terms of the X, Y, and Z coordinates of the atoms. This file format can also interpret fractional cell coordinates in orthogonal or nonorthogonal coordinate systems. Atom Types in Cartesian Coordinate Files Two file formats are supplied with Chem3D that interpret Cartesian coordinate files. The difference between the two file formats are the codes used to convert atom type numbers in the file into atom types used by Chem3D. In Cartesian coordinates 1, atom types are numbered according to the numbering used by N.L. Allinger in MM2. These numbers are also generally followed by the program PC Model. In Cartesian coordinates 2, the atom type number for all atom types is computed by multiplying the atomic number of the element by 10 and adding the number of valences as specified by the geometry of the atom type. These numbers are also generally followed by the program MacroModel. For example, the atom type number for C Alkane (a tetrahedral carbon atom) is 64. To examine the atom types described by a file format, see “Editing File Format Atom Types” on page 619. The Cartesian Coordinate File Format The format for Cartesian coordinate files is as follows: 1. The first line of data contains the number of atoms in the model. Optionally, you can follow the number of atoms in the file with crystal cell parameters for the crystal structure: a, b, c, α, β, and γ. Following the cell parameters, you can also include an exponent. If you include an exponent, then all of the fractional cell coordinates will be divided by 10 raised to the power of the exponent. 2. The first line of a Cartesian coordinate file is followed by one line of data for each atom in the model. Each line describing an atom begins with the symbol for the atom. This symbol must correspond to a symbol in the Elements table. The symbol can include a charge, such as N+. The symbol is followed by the serial number. 3. The serial number is followed by the three coordinates of the atom. If you have specified crystal cell parameters in the first line of the file, then these numbers are the fractional cell coordinates. Otherwise, the three numbers are X, Y, and Z Cartesian coordinates. 4. Following the coordinates is the atom type number of the atom type for this atom. This number must correspond to the code of an atom type record specified in the file format atom type table. For more information, see “Editing File Format Atom Types” on page 619. 5. Following the atom type number is the connection table for the atom. You can specify up to ten other atoms. The connection table for a Cartesian coordinate file can be listed in one of two ways: by serial number or by position. Connection tables by serial number use the serial number of each atom to determine the number that appears in the connection table of other atoms. All serial numbers must, therefore, be unique. Appendices <strong>ChemOffice</strong> 2005/Appendix File Formats • 621 File Format Examples
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KNOWLEDGE 21CFR11 Compliance Electr
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