Chem3D 8.0 Manual - CambridgeSoft

AdministratorNumberof AtomsNumberof Bonds19 MOLCyclohexanol 06 1 -1.3959 -0.4449 0.7768CAtomID19 MOLAtomTypeMoleculeNameXCoordYCoord3 1 7 1CenterZCoordAtom”) in column 2 and the Atom ID of theatom where the bond stops (the “To-Atom”) incolumn 3. The last column in the bond recordsis the bond type. Finally the last line in the fileis the Number of Features record, whichcontains the number of feature records in themolecule. Chem3D does not use thisinformation.FORTRAN FormatsThe FORTRAN format for each record of theSYBYL MOL File format is as follows:Numberof FeaturesBondNumber0 MOLFrom-Atom To-Atom BondTypeLine DescriptionNumber of Atoms/FileNameFORTRAN FormatI4,1X,'MOL',20A2,11X,I4The format for SYBYL MOL files is as follows:1. The first record in the SYBYL MOL Filecontains the number of atoms in the model, theword “MOL”, the name of the molecule, andthe center of the molecule.2. The atom records (lines 2–20 in thecyclohexanol example) contain the Atom ID incolumn 1, followed by the Atom Type incolumn 2, and the X, Y and Z Cartesiancoordinates of that atom in columns 3–5.3. The first record after the last atom recordscontains the number of bonds in the molecule,followed by the word “MOL”.4. The bond records (lines 22–40 in thecyclohexanol example) contain the BondNumber in column 1, followed by the Atom IDof the atom where the bond starts (the “From-Atom recordsNumber of Bonds recordBond recordsNumber of FeaturesrecordSYBYL MOL2 File2I4,3F9.4,2A2I4,1X,'MOL'3I4,9X,I4I4,1X,'MOL'The SYBYL MOL2 1 file format (SYBYL2) isdefined in Chapter 3, “File Formats”, pages 3033–3050, of the 1991 SYBYL Programming Manual.The following is a sample SYBYL MOL2 filecreated using Chem3D Pro. This file describes amodel of cyclohexanol (the line numbers are addedfor reference only):1. SYBYL is a product of TRIPOS Associates, Inc., asubsidiary of Evans & Sutherland.A60 • CambridgeSoftProtein Data Bank Files