These are step-by-step instructions on how to download a pdf file from the Protein Data Bank and select the metal-active site on a metalloenzyme, examine the metal's coordination sphere, and build a rudimentary model in Spartan. Each step has a screenshot associated with the step.
1. Go the Protein Data Bank and download a .pdb file of your metalloenzyme. Screenshot 1
2. Save as a pdf file format. Screenshot 2
3. Save the file. If you have already downloaded Mercury (recommended), then the file should appear as Mercury file (yellow disk with three red spheres). Screenshot 3
4. Saved "Mercury" file type in whatever folder you have designated as where your downloads end up. Screenshot4
5. Open the file in Mercury. Screenshot 5
6. Change the color of the metal atom so you can find it! Screenshot 6
7. I chose green for zinc. Screenshot 7
8. Expand to see the metal environment. Screenshot 8
9. Change "Picking Mode:" to "Measure Distance." Screenshot 9
10. There are four atoms attached to the zinc atom. Clicking one then the zinc gives the bond distance. repeat for all attached atoms. Screenshot 10
11. Change "Picking Mode:" to "Measure Angles." This time you'll need to pick the three atoms that form the angle that you are interested in. There are 6 angles with a 4-coordinate central atom. Write them down and note their relative positions. Screenshot 11
12. Total of 4 distances (in angstroms) and 6 angles for the four coordinate zinc. Screenshot 12
13. Open Spartan and select "Build New" under the File tab. Screenshot 13
14. Model kit "Inorganic" (on right), pick zinc and 4-coordinate, tetrahedral. Screenshot 14
15. Double click on the Spartan desktop to get tetrahedral zinc. Screenshot 15
16. Click "ligands" and select water and click on one of the valences on the zinc. Then change "Ligands" to ammonia and click on the other three empty valences. Screenshot 16
17. Under the Geometry tab, pick "Measure Distance," and click on the oxygen and then the zinc atoms and on the bottom right of the screen you'll see the current bond distance. Change it to reflect the pdf file's distances. Screenshot 17
18. Under the Geometry tab select "Measure Angles," this time you need to select three atoms, and change them to reflect the pdf file measurements. Screenshot 18
19. Select "Calculation" under the Spartan Setup tab. Change "Equilibrium Geometry" to "Energy." The default should have "Density Functional" calculation with "wB97X-D" functional and "6-31G*" basis set. All good. You'll need to change the "Total Charge" to diction and the "Unpaired Electrons" at 0 is good. Screenshot 19
20. Check the boxes below to "Compute" UV-Vis, NMR, QSAR, etc,... Screenshot 20
21. Click "Submit" and you will be prompted to save the file. Use your initials, and a description of the calculation. Screenshot 21
22. To see that the file is being calculated, select "Monitor" under the Options tab. Screenshot 22
23. Under the Display tab you can select "Output" and then "Verbose Output" to see calculations in action. Screenshot 23
24. When the calculation is complete, select "Surfaces" under the Setup tab and add any orbitals that you want to see. Usually we are interested in the frontier orbitals, the HOMO and LUMO. What I'm really interested in is the zinc active site with a vacancy. So, under the Build tab (or you can just click the erasure, I can eliminate the water ligand. Before doing that, I'll duplicate my saved file and open the copy. I can rename it later on instead of "..._copy.spartan" I can name it "...._3coord.spartan". With the copied file open, perform the same calculation (i.e., energy, DFT, wB97X-D, 6-31G*, etc,...). When the calculation is complete, generate the LUMO. The LUMO, presumably, is the orbital that the incoming substrate will interact with. What is the shape and direction of the LUMO? Does it make sense?