Avogadro

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Small Molecule Databases

Avogadro

Download a Small Molecule through PubChem

  1. Go to PubChem
    • It will look like this: 50pxClick to enlarge
  2. Make sure that the File:Pharm8050ModII2.png is selected.
  3. Type: acetaminophen in the search
    • Often called Tylenol
    • If you did it correctly, you will get: 50pxClick to enlarge
  4. Select the first entry.
    • If you did it correctly, you will get: 50pxClick to enlarge
  5. Now let's download the 3D SDF file. SDF --> 3D SDF: Save
    • It should look like: 50pxClick to enlarge
  6. Save the file to your Avogadro directory. The file name should be CID_1983.sdf.
    • CID stands for Compound IDentification Number
  7. Open the CID_1983 file in a text editor (TextWrangler for Mac and Notepad++ for Windows)

Download a Small Molecule through PDBeChem

  1. PDBeChem is a database of small molecules from the Protein Database (PDB) database
  2. Go to PDBeChem
    • It will look like this: 50pxClick to enlarge
  3. On the left side click File:Pharm8050ModII-2.png
    • It will look like this: 50pxClick to enlarge
  4. In another window or tab, go to the PDB database
    • It will look like this: 50pxClick to enlarge
  5. In the Search, put Aromatase Inhibitors, Click Enter and Scroll Down. The first entry should have the PDB ID 4GL7
    • It will look like this: 50pxClick to enlarge
  6. In the PDBeChem window, type in 4GL7, where it says PDB Entry ID.
    • It will look like this: 50pxClick to enlarge
  7. Click File:Pharm8050ModII-7.png
    • The output will look like: 50pxClick to enlarge
  8. Click 0XJ
    • The output will look like: 50pxClick to enlarge
  9. On the left, click Download Links
    • It will look like this: 50pxClick to enlarge
  10. Under Mole file hydrogens, click ideal.
    • It will look like this: 50pxClick to enlarge
  11. Save the OXJ file in a place that you can find it.
  12. You can look at the text file, as you did in PubChem above.

Download a Small Molecule through the ZINC Database

  • The ZINC Database is a free database of compounds that are available for virtual screening.
  1. Go to the ZINC Database
  2. Click Search and Structure
    • 50pxClick to enlarge
    • If you did it correctly, the output will look like: 50pxClick to enlarge
  3. Now, we will build a toluene molecule to search.
    1. Select the File:Pharm8050ModII-14.png icon for benzene.
    2. Click somewhere on the drawing window.
      • If you did it correctly, it should look like: 50pxClick to enlarge
    3. Select the File:Pharm8050ModII-16.png icon for a single carbon.
    4. Click on one of the carbons on the benzene ring.
      • If you did it correctly, it should look like: 50pxClick to enlarge
    5. At any time, if you get stuck, use the File:Pharm8050ModII-18.png and click the atoms that you need to delete.
  4. Once you have built your toluene molecule, click File:Pharm8050ModII-19.png
    • If you did it correctly, the output should look like: 50pxClick to enlarge
  5. Select the molecule that is furthest to the right and click on 1699890. 50pxClick to enlarge
    • If you did it correctly, the output should look like: 50pxClick to enlarge
  6. Click on SDF in File:Pharm8050ModII-23.png
  7. Save the zinc_169980.sdf in a location, where you can find it.
    • All ZINC structure files will begin with zinc.
  8. You can look at the text file, as you did in PubChem above.

Basic Use of Avogadro

  1. Open Avogadro
    • If you did it correctly, it should look like: 50pxClick to enlarge
  2. File-->Open
  3. Select CID_1983.SDF from your Avogadro directory
    • If you did it correctly, it should look like: 50pxClick to enlarge
  4. Click on the File:Pharm8050ModII9.png and File:Pharm8050ModII10.png to open and close the Tool and Display Settings..., respectively.
  5. Discription of the various icons
    File:Pharm8050ModII11.png Editing Tool
    • Used to draw atoms and make bonds.
    File:Pharm8050ModII12.png Navigation Tool
    • Used to translate and rotate the molecule.
    File:Pharm8050ModII13.png Bond Centric Manipulation Tool
    File:Pharm8050ModII14.png Manipulation tool
    • Allows you to manipulate the atoms
    File:Pharm8050ModII15.png Selection Tool
    • Select an atom or group of atoms.
    File:Pharm8050ModII16.png Autorotation Tool
    File:Pharm8050ModII17.png Autooptimization Tool
    • Optimize the geometry
    File:Pharm8050ModII18.png Measuring Tool
    • Measure bonds, angles and dihedrals, depending on which atoms are selected.
    File:Pharm8050ModII19.png Alignment Tool
    • Aligns with the X, Y and Z axes.
  6. Select File:Pharm8050ModII12.png
    • Left-Click rotates
    • Command Left-click or Right Click translates
    • Shift Left-Click zooms
    • Spend a few minutes playing around with this.
  7. Make sure that File:Pharm8050ModII10.png is blue
  8. Have only Ball and Stick Checked
    It should look like this: 50px Click to enlarge.
  9. Have only Simple Wireframe Checked
    It should look like this: 50px Click to enlarge.
  10. Have only Van der Waals Spheres Checked
    It should look like this: 50px Click to enlarge.
  11. Have only Stick Checked
    It should look like this: 50px Click to enlarge.
  12. Switch it back to Ball and Stick
  13. Check Label
  14. Click File:Pharm8050ModII24.png
    • If you did it correctly, the following dialog should come up 50px Click to enlarge
  15. Check the Atom Labels pull down menu
    • You have the following label options:50pxClick to enlarge
  16. Set Label Settings to Atom Number and Close
    • If you did it correctly, it should look like this:50pxClick to enlarge
  17. Now, let's do some measurements. Click on File:Pharm8050ModII18.png
  18. Click the carbonyl carbon (atom #10) and carbonyl oxygen (atom #2).
    • If you did it correctly, it should look like this:50pxClick to enlarge
    • The distance is in the lower left hand corner and should be 1.227 Å.
  19. Click the carbonyl carbon (atom #10) and carbonyl oxygen (atom #2) to reset them.
  20. Click the amide nitrogen (atom #3), carbonyl carbon (atom #10) and the carbonyl oxygen (atom #2).
    • If you did it correctly, it should look like this:50pxClick to enlarge
    • The Angle is 127.4o and the Distances are 1.401 Å and 1.227 Å.
  21. Click the amide nitrogen (atom #3), carbonyl carbon (atom #10) and the carbonyl oxygen (atom #2) to reset them.
  22. Click on the aromatic carbon (atom #4), amide nitrogen (atom #3), carbonyl carbon (atom #10) and carbonyl oxygen (atom #2)
    • If you did it correctly, it should look like this:50pxClick to enlarge
    • The Dihedral or Torsional Angle is 0.2o
  23. Click on the aromatic carbon (atom #4), amide nitrogen (atom #3), carbonyl carbon (atom #10) and carbonyl oxygen (atom #2) to reset
  24. Click on the aromatic carbon (atom #4), amide nitrogen (atom #3), carbonyl carbon (atom #10) and methyl carbon (atom #11)
    • If you did it correctly, it should look like this:50pxClick to enlarge
    • The Dihedral or Torsional Angle is -180o
  25. To save a picture of it, Go to File --> Export --> Graphics...
    • 50pxClick to enlarge
  26. After you have selected a place to save the file, click the Save button.
    • 50pxClick to enlarge

Building Acetaminophen

  1. In Avogadro, go to File-->New
  2. Click on File:Pharm8050ModII11.png (The Editing Tool)
  3. We are going to first build the aromatic ring.
  4. Make sure that the Draw Settings are set to Carbon (6) and Bond Order Single.
    • It should look like: 50pxClick to enlarge
  5. Click Avogadro and a methyl molecule should appear.
    • It should look like: 50pxClick to enlarge
  6. Select the carbon and drag to produce 2 atoms.
    • It should look like: 50pxClick to enlarge
  7. Click and drag carbons, until you produce a 6 carbon ring.
    • It should look like: 50pxClick to enlarge
  8. File-->Save
  9. Save the file to the Avogadro directory as Acetaminophen.pdb
  10. Now, let's add double bonds.
  11. Change the bond order from single to double
    • It should look like: 50pxClick to enlarge
  12. Left click on 1 carbon and drag it to the next carbon.
    • It should look like: 50pxClick to enlarge
  13. Do the same thing for every other pair of carbons.
    • It should look like: 50pxClick to enlarge
  14. The geometry is obviously messed up, so we need to do some geometric optimization.
  15. Click on File:Pharm8050ModII17.png (The Autooptimization Tool)
  16. Use the default settings
    • It should look like: 50pxClick to enlarge
  17. Once it has stabilized, click 50px
    • It should look like: 50pxClick to enlarge
  18. Now, let's accidentally, put an atom in there and then delete it.
  19. Click on File:Pharm8050ModII11.png (The Editing Tool)
  20. Put a carbon anywhere in the black space by left clicking.
    • It should look like: 50pxClick to enlarge
  21. Click File:Pharm8050ModII15.png (The Selection Tool)
  22. Left click on the middle atom. It will turn blue.
    • It should look like: 50pxClick to enlarge
  23. However, we missed the hydrogens. There are three ways that we can include the hydrogens.
    1. We can left click and drag, which will put a box around the protons.
    2. We can left click all the protons, while holding the shift key.
    3. We can change the selection mode Atom/Bond to Molecule
      • Using this last method, it looks 50pxClick to enlarge
    4. You can unselect everything by left clicking and dragging, where there are no atoms.
  24. To delete those atoms, click the delete or backspace key.
  25. Click on File:Pharm8050ModII11.png (The Editing Tool)
  26. Change the bond order as single. Click one of the aromatic carbons and drag a methyl from it.
    • If you did it correctly, it should look like: 50pxClick to enlarge
  27. Build the rest of the acetaminophen as a carbon scaffold. It does not have to be pretty.
    • Mine looks like: 50pxClick to enlarge
  28. Change the Element to Oxygen (8)
    • It should look like: 50pxClick to enlarge
  29. Left click atoms that are oxygens.
    • It should look like: 50pxClick to enlarge
  30. Change the bond order to double. Then left click and drag from the oxygen (atom #16 in my case) to the carbon (atom #13 in my case).
    • It should look like: 50pxClick to enlarge
  31. Change the Element to Nitrogen (7) and the Bond Order to Single
    • It should look like: 50pxClick to enlarge
  32. Left click on the atom that will be nitrogen (atom #11 in my case).
    • It should look like: 50pxClick to enlarge
  33. Click on File:Pharm8050ModII17.png (The Autooptimization Tool)
  34. Use the default settings
    • It should look like: 50pxClick to enlarge
  35. Once it has stabilized, click 50px
    • It should look like: 50pxClick to enlarge
  36. Click File-->Save. You have built your own acetaminophen.
  37. To save a picture of it, Go to File --> Export --> Graphics...
    • 50pxClick to enlarge
  38. After you have selected a place to save the file, click the Save button.
    • 50pxClick to enlarge