Chem3D Users Manual - CambridgeSoft

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Administrator 13 * 3D displacement vector 14 0.000 0.000 0.000 15 * 3D rotation matrix 16 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 17 * 3D scale factor 18 0 19 * 2D scale factor 20 1 21 * 2D attributes 22 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 * 3D attributes 24 0 0 0 0 0 0 0 0 0 0 0 25 * Global display attributes 26 1 0 1 12 256 27 * Atom List 28 * Atom# Lbl Type x y x y z bits chrg ichrg frag istp lp chrl ring frad name seg grp FLAGS 29 1 C 10 0 0 -1 0.46 0.2 0 0 0 0 0 0 0 0 0 C 1 0 -1 0 0 0 0 0 0 [C] 30 2 C 10 0 0 1.2 -1.1 0.2 0 0 0 0 0 0 0 0 0 C 2 0 -1 0 0 0 0 0 0 [C] 30 2 C 10 0 0 1.2 -1.1 0.2 0 0 0 0 0 0 0 0 0 C 2 0 -1 0 0 0 0 0 0 [C] 31 3 C 10 0 0 0.1 -1.6 0.7 0 0 0 0 0 0 0 0 0 C 3 0 -1 0 0 0 0 0 0 [C] 32 4 C 10 0 0 1.3 -1.1 0 0 0 0000000C40-1000000[C] 33 5 C 10 0 0 1.2 0.48 0 0 0 0 0 0 0 0 0 0 C 5 0 -1 0 0 0 0 0 0 [C] 34 6 C 10 0 0 0 1.01 -1 0 0 0 0 0 0 0 0 0 C 6 0 -1 0 0 0 0 0 0 [C] 35 7 O 45 0 0 0 2.42 -1 0 0 0 0 0 0 0 0 0 O 7 0 -1 0 0 0 0 0 0 [O] 36 8 H 8 0 0 0.6 2.72 -1 0 0 0 0 0 0 0 0 0 H 7 0 -1 0 0 0 0 0 0 [H] 37 9 H 1 0 0 2.1 0.86 -1 0 0 0 0 0 0 0 0 0 H 8 0 -1 0 0 0 0 0 0 [H] 38 10 H 1 0 0 1.4 0.86 0.8 0 0 0 0 0 0 0 0 0 H 9 0 -1 0 0 0 0 0 0 [H] 39 11 H 1 0 0 1.1 -1.4 -1 0 0 0 0 0 0 0 0 0 H 10 0 -1 0 0 00 00[H] 40 12 H 1 0 0 2.2 -1.4 0.2 0 0 0 0 0 0 0 0 0 H 11 0 -1 0 0 0000 [H] 41 13 H 1 0 0 0 0.72 -2 0 0 0 0 0 0 0 0 0 H 12 0 -1 0 0000 0 [H] 42 14 H 1 0 0 0.1 -2.7 0.7 0 0 0 0 0 0 0 0 0 H 13 0 -1 0 0 0000 [H] 43 15 H 1 0 0 0.3 -1.3 1.7 0 0 0 0 0 0 0 0 0 H 14 0 -1 0 0 0 00 [H] 44 16 H 1 0 0 -1 -1.5 -1 0 0 0 0 0 0 0 0 0 H 15 0 -1 0 0 0000 [H] 45 17 H 1 0 0 -2 -1.5 0.9 0 0 0 0 0 0 0 0 0 H 16 0 -1 0 0 0000 [H] 46 18 H 1 0 0 -1 0.85 1.2 0 0 0 0 0 0 0 0 0 H 17 0 -1 0 0 0000 [H] 47 19 H 1 0 0 -2 0.83 0 0 0 0 0 0 0 0 0 0 H 18 0 -1 0 0 0000 [H] 254• File Formats <strong>CambridgeSoft</strong> MSI MolFile
48 * Bond List 49 * Bond# bond_type atom1 atom2 cis/trans length locked ring Sh_type Sh_nr Qorder Qtopol Qs 50 1 1 1 2 0 0.000 0 0 0 0 [S] 0 0 51 2 1 1 6 0 0.000 0 0 0 0 [S] 0 0 52 3 1 1 18 0 0.000 0 0 0 0 [S] 0 0 53 4 1 1 19 0 0.000 0 0 0 0 [S] 0 0 54 5 1 2 3 0 0.000 0 0 0 0 [S] 0 0 55 6 1 2 16 0 0.000 0 0 0 0 [S] 0 0 56 7 1 2 17 0 0.000 0 0 0 0 [S] 0 0 57 8 1 3 4 0 0.000 0 0 0 0 [S] 0 0 58 9 1 3 14 0 0.000 0 0 0 0 [S] 0 0 59 10 1 3 15 0 0.000 0 0 0 0 [S] 0 0 60 11 1 4 5 0 0.000 0 0 0 0 [S] 0 0 61 12 1 4 11 0 0.000 0 0 0 0 [S] 0 0 62 13 1 4 12 0 0.000 0 0 0 0 [S] 0 0 63 14 1 5 6 0 0.000 0 0 0 0 [S] 0 0 64 15 1 5 9 0 0.000 0 0 0 0 [S] 0 0 65 16 1 5 10 0 0.000 0 0 0 0 [S] 0 0 66 17 1 6 7 0 0.000 0 0 0 0 [S] 0 0 67 18 1 6 13 0 0.000 0 0 0 0 [S] 0 0 68 19 1 7 8 0 0.000 0 0 0 0 [S] 0 0 69 * Bond Angles 70 * bond1 bond2 angle locked 71 * Dihedral Angles 72 * at1-cons at1 at2 at2-cons angle locked 73 * Planarity data 74 * User data area 75 * End of File The MSI MolFile 1 format is broken up into several sections. Section headers are preceded by a “*”. Blank lines also contain a “*”. Each line is either a blank line, a header line or a data record containing one or more fields of information about the 1. Molecular Simulations MOLFILE (ChemNote) is a product of Molecular Simulations, Inc. structure. Individual fields are delimited by space(s) or a tab. The fields in the MSI MolFile format file used by <strong>Chem3D</strong> Pro are discussed below. Appendices ChemOffice 2005/Appendix File Formats • 255 MSI MolFile
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator provides a balance be
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Administrator the activation each t
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Administrator The following table d
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Administrator • Stereo Pairs—A
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator modes and color setti
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Administrator 30 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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3. Move the pointer over the C-C bo
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Administrator Add serial numbers an
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Administrator 5. Press the Enter ke
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. Administrator b. From the Structu
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Administrator In the Measurements t
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A molecule of Epinephrine appears.
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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The allyl radical, CH 2 =CHCH 2·,
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Administrator Determine the raw spi
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Administrator atoms are relatively
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To change the structural display ty
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Administrator When sizing by partia
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Administrator Depth Fading3D enhanc
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• Select Parallel to rotate the r
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Administrator • From the Computat
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Administrator Surface Type Solid De
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Administrator 2. Adjust the slider
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Administrator Density surface is ca
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Administrator 72 •Displaying Mode
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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Administrator copied into blank tab
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Administrator 3. Type the atom type
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Administrator Clean Up Structure or
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Setting Serial Numbers this step, y
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Administrator Refining a Model Afte
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Administrator Selecting Multiple At
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Administrator New in Chem3D version
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Administrator Dragging moves atoms
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator • Second Positioned
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Administrator For example, consider
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Administrator If you want to displa
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Administrator Example: To examine t
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Administrator Chem3D provides two o
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Administrator change a property. By
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Administrator To add to a group: 1.
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To stop spinning: • On the Movie
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Administrator If you want to … Th
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Administrator EPS The PostScript fi
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If you want the file to … Then cl
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Molecular Design Limited MolFile (.
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Administrator 7. Leave the last lin
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Administrator 128•Printing and Ex
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Administrator • Semiempirical Ext
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Method Type Advantages Disadvantage
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Administrator • A single point ca
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Administrator • Molecular mechani
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Administrator constant), while θ 0
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Administrator The van der Waals int
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Administrator 6. The modified value
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the same wave function and a consta
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Administrator A variety of other ba
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Administrator Molecular wave functi
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Administrator activation barriers.
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3. From the Calculations menu, poin
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minimizing a second model, the mini
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Administrator move to lower the ene
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. Administrator Molecular Dynamics
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Administrator If you want to … Th
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Administrator The Compute Propertie
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Administrator To run a previously c
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Administrator The procedures assume
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Administrator improvements in each
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Administrator • Overall errors in
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Administrator The following table c
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Administrator TRIPLET QUARTET QUINT
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Administrator Chemical symbol ++ ba
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Administrator 4. Click Run. A new m
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Administrator Minimizing Energy Min
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Administrator criteria, to optimize
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Administrator 6. Hold down the S ke
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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The following table contains the ke
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Administrator 3. Click in the model
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 198•MOPAC Computati
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Administrator If you want to … re
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Administrator In the Results In tex
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Page 284 and 285: Parameter Table Use Parameter Table
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Administrator density 67 editing 67
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Administrator editing 107 non-bonde
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Administrator repeating jobs 178 RH
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Administrator Rectification, when d
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Administrator all atoms 95 atoms or
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Administrator Translucent surface t
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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MANAGEMENT • E-Notebook Enterpris
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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