Chem3D 8.0 Manual - CambridgeSoft

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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
Line 1 # Name: CYCLOHEXANOLLine 2Line 3 @MOLECULELine 4 CYCLOHEXANOLLine 5 19 19 0 0 0Line 6 SMALLLine 7 NO_CHARGESLine 8Line 9Line 10 @ATOMLine 11 1 C -1.349 0.195 1.032 C.3Line 12 2 C -0.407 -0.896 1.563 C.3Line 13 3 C 0.562 -1.378 0.473 C.3Line 14 4 C 1.351 -0.205 -0.128 C.3Line 15 5 C 0.42 0.9 -0.652 C.3Line 16 6 C -0.559 1.37 0.436 C.3Line 17 7 H -2.021 -0.239 0.253 HLine 18 8 H -1.005 -1.759 1.944 HLine 19 9 H 0.175 -0.496 2.427 HLine 20 10 H 1.27 -2.128 0.9 HLine 21 11 H -0.01 -1.898 -0.331 HLine 22 12 H 2.021 0.225 0.655 HLine 23 13 H 2.008 -0.569 -0.953 HLine 24 14 H 1.03 1.766 -1.016 HLine 25 15 O -0.3 0.427 -1.757 O.spLine 26 16 H -1.262 2.128 0.014 HLine 27 17 H 0.014 1.876 1.249 HLine 28 18 H -2.005 0.562 1.857 HLine 29 19 H 0.329 0.223 -2.427 H.spAppendixChem3D 8Protein Data Bank Files• A61
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ChemOffice.Com®ChemOffice®Chem3D,
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CS Product RegistrationRegistering
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User’s GuideCS Chem3D 8.0for Wind
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CambridgeSoft Software License1. Gr
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No Waiver. The failure of either pa
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The failure of either party to asse
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ContentsIntroduction . . . . . . .
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Rotating Fragments. . . . . . . . .
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Choosing a Hamiltonian . . . . . .
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Appendix D: MM2 . . . . . . . . . .
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Administrator• Faster graphics-3D
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AdministratorInstallation and Syste
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AdministratorModel WindowThe Model
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Table ElementDescriptionObjectDescr
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To specify the rendering type, atom
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AdministratorYou can also build mod
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AdministratorElementBound-to orderS
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Customizing the UserInterfaceAdmini
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AdministratoroptionUse BackBuffer f
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AdministratorExamine the atoms and
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Administrator2. Release the mouse b
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AdministratorReplacing AtomsTo chan
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Change the model display type:Build
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You will also save the frames you c
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Tutorial 4: SearchingFor Conformati
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Administrator3. Click in the model
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Administrator5. In the Theory tab,
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AdministratorFor phenol, the greate
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Creating a Model UsingTemplatesChem
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The Cartesian Coordinates Options d
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Saving a Model with a Different Nam
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Administrator44 • Chapter 3: Crea
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AdministratorThe following table de
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After you have the backbone, you ca
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AdministratorThe interpretation of
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AdministratorTo use a substructure
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AdministratorThe standard measureme
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AdministratorTo change the bond ord
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Administratorvalues are the standar
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AdministratorTo remove the formal c
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AdministratorRefining a ModelAfter
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AdministratorSelecting Atoms in a G
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AdministratorWhen you choose Show A
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AdministratorTo perform a rotation
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To move three atoms to a plane and
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Administratorit and other atoms. Al
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AdministratorIf an atom is position
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AdministratorModel TypesThe followi
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AdministratorColoring DisplaysYou c
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To change one of the colors in the
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AdministratorAll atoms currently in
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AdministratorDisplaying MolecularSu
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AdministratorMolecular Surface Colo
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AdministratorSolvent Accessible Sur
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AdministratorTo display a Connolly
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previously computed surface. If you
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If you want todisplay …Then Selec
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Administrator• From the Edit menu
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AdministratorShowing Dihedral Angle
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Administrator5. Select the C(2)-C(3
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AdministratorThe color of the atoms
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AdministratorTo begin the docking c
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AdministratorTo perform an overlay,
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To remove all frames after the fram
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Administrator106 • Chapter 7: Ins
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If you want to …Then select …Fi
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AdministratorBMPThe Bitmap file for
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When you save a file as a Connectio
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AdministratorIf you want to …buil
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Administratorexports .PDB. The .PDB
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Administrator116 • Chapter 8: Pri
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AdministratorComputational Chemistr
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AdministratorThe following table su
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Administrator• A single point cal
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Administrator• Potential energy f
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AdministratorE Stretch= 71.94 ∑ K
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Administratorinclude interactions w
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Administratorwhich are used to scal
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AdministratorQuantum mechanical met
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AdministratorLinear Combination of
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AdministratorUHFThe UHF method trea
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Administrator• Hypervalent compou
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Administrator138 • Chapter 9: Com
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AdministratorIf you want to …spec
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AdministratorThe Total Steric Energ
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AdministratorThe conformation you c
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.AdministratorSticks < Ball and Sti
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AdministratorThe simulation ends wh
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AdministratorThe units are kcal/mol
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AdministratorRepeating an MM2Comput
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AdministratorChoose the appropriate
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AdministratorTo determine the appro
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AdministratorFirst excited quintet:
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AdministratorMOPAC uses its default
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AdministratorThe following contains
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The heat of formation is composed o
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AdministratorComparing Cation Stabi
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Administratormeta>para>ortho, where
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Administrator3. Click in the model
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Form ofglycine∆H(kcal/mole)Solven
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AdministratorThe following table co
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AdministratorThe Message window dis
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AdministratorDescriptionVibrational
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You can create a structure from the
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AdministratorIf you want to …reco
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AdministratorSave a customized job
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Administrator2. Type the full path
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Administrator3. From the Basis Set
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AdministratorA new model window is
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PropertyDescriptionPropertyDescript
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PropertyDescriptionError MessageCau
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PropertyDescriptionThe GAMESS serve
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The property filters are:Administra
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AdministratorTo perform property ca
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The Select Descriptors dialog box a
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Administrator• Sum• Standard de
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To access Browse ChemStore.com:The
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AdministratorTo access the ChemOffi
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AdministratorDefining Substructures
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AdministratorA4 • CambridgeSoftDe
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AdministratorIf an atom can be assi
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AdministratorExample 3In Example 3,
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Page 328 and 329: CAMBRIDGESOFTChemOffice Desktop toK
Page 330 and 331: CS ChemOfficeSoftware SuitesChemOff
Page 332 and 333: DESKTOPCS E-NotebookElectronic Jour
Page 334 and 335: DESKTOPCS ChemDrawChemical Structur
Page 336 and 337: DESKTOPCS Chem3DMolecular Modeling
Page 338 and 339: DESKTOPCS ChemFinderSearching and I
Page 340 and 341: DESKTOPCS ChemInfoReference and Che
Page 342 and 343: ENTERPRISEChemOffice WebServerEnter
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KNOWLEDGEE-Notebook EnterpriseDeskt
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KNOWLEDGEDocument ManagerDesktop to
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KNOWLEDGE21CFR11 ComplianceElectron
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RESEARCH&Registration SystemChemica
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RESEARCH&Inventory ManagerChemical
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RESEARCH&CombiChem EnterpriseDeskto
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RESEARCH&BioAssay HTSBiological Ass
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RESEARCH&BioSAR BrowserBiological a
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CHEMICALChemACX DatabaseAvailable C
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CHEMICALThe Merck IndexChemistry’
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CHEMICALChemical DatabasesReference
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CONSULTING &Consulting & ServicesDe
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Administrator
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MENUSCreate a new model window.Open
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WORKING WITH SELECTIONSIf you want
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CS ChemOffice®Desktop to Enterpris
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