Chem3D 8.0 Manual - CambridgeSoft

AdministratorAlchemy FileThe following is a sample Alchemy file 1 (Alchemy)created using Chem3D for a model of cyclohexanol.The numbers in the first column are line numbersthat are added for reference only.1 19ATOMS19BONDS2 1 C3 -1.1236 -0.177 0.0593 2 C3 -0.26 -0.856 -1.02244 3 C3 1.01 -0.0491 -1.32675 4 C3 1.838 0.1626 -0.05266 5 C3 0.9934 0.8543 1.02527 6 C3 -0.2815 0.0527 1.32758 7 O3 -2.1621 -1.0585 0.39079 8 H -1.4448 0.8185 -0.333810 9 H -0.8497 -0.979 -1.962311 10 H 0.0275 -1.8784 -0.680612 11 H 1.6239 -0.5794 -2.094113 12 H 0.729 0.9408 -1.758914 13 H 2.197 -0.8229 0.328915 14 H 2.7422 0.7763 -0.28216 15 H 1.5961 0.9769 1.957417 16 H 0.7156 1.8784 0.67918 17 H -0.8718 0.6068 2.094119 18 H -0.004 -0.9319 1.772120 19 H -2.7422 -0.593 0.968821 1 1 2 SINGLE22 2 1 6 SINGLE23 3 1 7 SINGLE24 4 1 8 SINGLE1. Alchemy III is a registered trademark of TriposAssociates, Inc.25 5 2 3 SINGLE26 6 2 9 SINGLE27 7 2 10 SINGLE28 8 3 4 SINGLE29 9 3 11 SINGLE30 10 3 12 SINGLE31 11 4 5 SINGLE32 12 4 13 SINGLE33 13 4 14 SINGLE34 14 5 6 SINGLE35 15 5 15 SINGLE36 16 5 16 SINGLE37 17 6 17 SINGLE38 18 6 18 SINGLE40 19 7 19 SINGLEEach line represents a data record containing one ormore fields of information about the molecule. Eachfield is delimited by spaces or a tab. The fields usedby Chem3D are described below:1. Line 1 contains two fields. The first field is thetotal number of atoms in the molecule and thesecond field is the total number of bonds.2. Lines 2–20 each contain 5 fields of informationabout each of the atom in the molecule. The firstfield is the serial number of the atom. Thesecond field is the atom type, the third field isthe X coordinate, the fourth field is theY coordinate and the fifth field is theZ coordinate.NOTE: Atom types in the Alchemy file formatare user-definable. See “Editing File FormatAtom Types” on page 33 for instructions onmodifying or creating an atom type.A34 • CambridgeSoftFile Format Examples