Chem3D Users Manual - CambridgeSoft

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Administrator Line 4e: C 1.53597 1 111.7012 1 55.3112 1 4 1 2 Line 4f: C 1.53424 1 110.7535 1 57.03175 1 3 2 1 Line 4g: O 1.40196 1 107.6989 1 -172.662 1 1 2 3 Line 4h: H 1.11739 1 107.8685 1 62.06751 1 1 2 3 Line 4I: H 1.11633 1 110.0751 1 -177.17 1 2 1 4 Line 4j: H 1.11566 1 109.4526 1 65.43868 1 2 1 4 Line 4k: H 1.11665 1 109.9597 1 178.6209 1 3 2 1 Line 4l: H 1.1161 1 109.5453 1 -63.9507 1 3 2 1 Line 4m: H 1.11542 1 109.4316 1 -66.0209 1 4 1 2 Line 4n: H 1.11499 1 110.549 1 176.0838 1 4 1 2 Line 4o: H 1.11671 1 109.93 1 -178.296 1 5 4 1 Line 4p: H 1.11615 1 109.4596 1 64.43501 1 5 4 1 Line 4q: H 1.11664 1 110.0104 1 -178.325 1 6 3 2 Line 4r: H 1.11604 1 109.6082 1 64.09581 1 6 3 2 Line 4s: H 0.94199 1 106.898 1 -173.033 1 7 1 2 The following illustrates the components of the MOPAC Output File from Chem3D for C(1) Through C(4) of Cyclohexanol 1st Atom 2nd Atom 3rd Atom 4th Atom Element Bond Symbol Lengths C C C C 0.000000 1.541519 1.535233 1.539734 Action Integers 0 1 1 1 Bond Angles 0.000000 0.000000 Action Integers 111.774673 1 Dihedral Angles 0.000000 0.000000 0.000000 Action Integers 109.711411 1 -55.695877 1 The internal coordinates section of the MOPAC Data-File format contains one line of text for each atom in the model. Each line contains bond lengths, bond angles, dihedral angles, action integers, and connectivity atoms. 0 0 0 0 0 Connectivity Atoms 0 0 0 1 0 0 2 1 0 1 2 3 As shown in the illustration above, C(1) is the origin atom. C(2) is connected to C(1) with a bond of length 1.541519 Å. C(3) is connected to C(2) with a bond of length 1.535233 Å, and is at a bond angle of 111.774673 degrees from C(1). C(4) is connected to C(1) with a bond of length 1.539734 Å, and is at a bond angle of 109.711411 degrees from C(2). C(4) also forms a dihedral angle of -55.695877 degrees with C(3). The action integers listed next to each measurement are instructions to MOPAC which are as follows: 1Optimize this internal coordinate 0Do not optimize this internal coordinate -1Reaction coordinate or grid index When you create a MOPAC file from within Chem3D, an action integer of 1 is automatically assigned to each non-zero bond length, bond angle, and dihedral angle for each atom record in the file. 258• File Formats CambridgeSoft MSI MolFile
FORTRAN Formats The description of the MOPAC Data-File format for each line is as follows: Line Number Description 1 Keywords for Calculation Instructions Read by Chem3D No Written by Chem3D No 2 Molecule Title No Yes 3 Comment No No A Protein Data Bank file can contain as many as 32 different record types. Only the COMPND, ATOM, HETATM, and CONECT records are used by Chem3D; all other records in a Protein Data Bank file are ignored. The COMPND record contains the name of the molecule and identifying information. The ATOM record contains atomic coordinate records for “standard” groups, and the HETATM record contains atomic coordinate records for “non-standard” groups. The CONECT record contains the atomic connectivity records. NOTE: The COMPND record is created by Chem3D to include the title of a Chem3D model only when you are saving a file using the Protein Data Bank file format. This record is not used when opening a file. 4a-s Internal coordinates for molecule Yes Yes The following is an example of a Protein Data Bank Output File from Chem3D for L-Alanine. 5 Blank line, terminates geometry definition Yes Protein Data Bank Files Yes The FORTRAN format for each line containing internal coordinate data in the MOPAC Data-File is FORMAT(1X, 2A, 3(F12.6, I3), 1X, 3I4). The Protein Data Bank file format (Protein DB) is taken from pages 3, 14–15, and 17–18 of the Protein Data Bank Atomic coordinate and Bibliographic Entry Format Description dated January, 1985. COMPND Alanine.pdb HETATM 1 N 0 -0.962 1 HETATM 2 C 0 -0.049 0 HETATM 3 C 0.6 0.834 -1 HETATM 4 C -2 0.834 1 HETATM 5 O 0.3 1.737 -1 HETATM 6 O 1.8 0.459 0 HETATM 7 H 0.9 -1.398 1 HETATM 13 H -1 -1.737 1 HETATM 8 H -1 -0.642 -1 HETATM 9 H -2 1.564 0 HETATM 10 H -1 1.41 1 HETATM 11 H -2 0.211 1 HETATM 12 H 2.4 1.06 -1 CONECT 1 2 7 13 CONECT 2 1 3 4 8 CONECT 3 2 5 6 Appendices ChemOffice 2005/Appendix File Formats • 259 Protein Data Bank Files
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Method Type Advantages Disadvantage
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The following table contains the ke
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