Conformational Analysis for Small Molecules Using MacroModel and ConfGen

1. Double click the Maestro icon to start Maestro.
   • (No icon? See Starting Maestro)

Figure 2-1. Change Working Directory option.

2. Go to File > Change Working Directory.
3. Find your directory, and click Choose.
4. Pre-generated input and results files are included for running jobs or examining output. Download the zip file here: https://www.schrodinger.com/sites/default/files/s3/release/current/Tutorials/zip/macromodel_confgen.zip
5. After downloading the zip file, unzip the contents in your Working Directorythe location that files are saved for ease of access throughout the tutorial.

Figure 2-2. The Open Project dialog box.

6. Go to File > Open Project.
7. Select the file Torsional MM_Confgen.prjzip.
8. Click Open.
   • Structures are shown in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
   • A structure is includedthe entry is represented in the Workspace, the circle in the In column is blue in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Note: Please see the Glossary of Terms for the distinction between includedthe entry is represented in the Workspace, the circle in the In column is blue and selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries .

Figure 2-3. Warning box to save scratch project.

9. In the Save scratch project warning box, click OK.

Figure 2-4. Saving the project.

10. Go to File > Save Project As.
11. Change the File name to MM_Confgen_tutorial.
12. Click Save.
    • The project is named MM_Confgen_tutorial.prj.

Figure 3-1. Opening the Coordinate Scan panel from the Tasks.

1. Make sure the Ddrive entry is selected(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and includedthe entry is represented in the Workspace, the circle in the In column is blue in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Note: Atom number labels were added from the Style toolbox by clicking the  Apply Labels arrow and choosing Element + Atom Number.

2. Find and open the Coordinate Scan panel from the Tasks.

Figure 3-2. Choosing Dihedral as Coordinate Type.

3. For Use structures from, choose Workspace (included entry).
4. Switch to the Scan tab.
5. For Coordinate Type, choose Dihedral.

Figure 3-3. Selecting Torsion 1 dihedrals.

6. In the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed, select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries atom numbers 1, 14, 15, and 16.
   • Atoms are highlighted in cubes.
   • Torsion 1 is defined.

Figure 3-4. Selecting Torsion 2 dihedrals.

7. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries atom numbers 1, 6, 25, and 26.
   • Torsion 2 is defined.

Figure 3-5. Setting solvent to ‘none’ for the gas phase.

8. In the Coordinate Scan panel, switch to the Potential tab.
9. For Solvent, choose None.
   • A gas phase minimization will be run.
10. For Job name, type mmod_Ddrive.
11. Click Run.
    • This job takes a few seconds to complete.
    • A new group mmod_Ddrive-out is added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Note: In this example we have run the job with no solvent. You may choose to run this job in water and then chloroform to compare intramolecular interactions in the conformations.

12. Close the Coordinate Scan panel.

Figure 3-6. Choosing to show properties in the Entries table.

13. In the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, click the Change table settings icon (three vertical dots) and choose Show Property.
    • The Show Properties in Table dialog box opens.

Figure 3-7. Adding properties in the Entries table.

14. In the dialog box, click Choose.
15. Find and select Potential Energy-S-OPLS and Relative Energy-S-OPLS.
16. Click OK.
    • The Relative Energy and Potential Energy properties are added to the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
    • You may need to click and drag the edge of the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion table toward right to see the added properties.

Note: Both properties are given in kJ/mol.

Note: OPLS4 calculations will still use this OPLS3 property category for the time being while we update the remainder of the panel. Notice that once imported, the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion property headings are more general.

Figure 3-8. The Minimum E. structure.

Note: The last entry in the mmod_Ddrive-out

group is the lowest energy structure found from scanning the two dihedrals. You may have to expand the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion to view properties.

Note: The lowest energy structure gives us an indication of how adaptable the molecule is and how much strain is needed for it to adopt a particular conformation.

Figure 3-9. Renaming the Ddrive entry and moving it into the mmod_Ddrive-out group.

17. Double-click the original Ddrive entry header and rename it to Ddrive Starting Structure.
18. Move it to the top of the mmod_Ddrive-out group by right-clicking, Move to > Other Row > [Row Number of first mmod_Ddrive-out group entry].

Note: In this example row 10 would be chosen.

19. Click Move.

Figure 3-10. Opening the Superposition panel from the Tasks.

20. Select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the mmod_Ddrive-out group in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion and includethe entry is represented in the Workspace, the circle in the In column is blue the DDrive Starting Structure in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
21. Find and open the Superposition panel from the Tasks.
    • The Superposition panel opens.

Figure 3-11. Superimposing by selected entries.

22. For Entries to superimpose, choose Project Table (selected).
23. For Reference structure, choose             9: Ddrive Starting Structure.
24. Check Add property to Project Table.
25. For Choose Method, select Substructures.
26. For Define structures for superposition using, choose SMARTS.
27. Return to the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 3-12. Selecting the pyrimidine core.

28. Type A.
    • Atom selection mode is activated.
29. In the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed, use shift+click to select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries all atoms in the pyrimidine core (as shown in the adjacent figure).
30. In the Superposition panel, click Get from Selection.
31. Click Superimpose Structures.
    • The selected structures are aligned to the pyrimidine core.
    • RSMDs for the structures are shown at the bottom of the panel.

Figure 3-13. Fixing the starting structure and stepping through the results.

32. In the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, double-click the In circle next to Ddrive Starting Structure.
    • The structure is fixed in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
33. Includethe entry is represented in the Workspace, the circle in the In column is blue the second entry in the mmod_Ddrive-out group.
34. Use the left and right arrow keys to step through the conformations.

Figure 3-14. Including multiple entries in the Workspace.

Note: Use shift+click to include contiguous entries or ctrl+click (cmd+click) to includethe entry is represented in the Workspace, the circle in the In column is blue non-contiguous entries in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. The 300 lowest energy conformations are shown in the adjacent figure.

35. Close the Superposition panel.

Figure 3-15. Opening the Plot Coordinate Scan Results panel from the Tasks.

36. Find and open the Plot Coordinate Scan panel from the Tasks.
    • The Plot Coordinate Scan Results panel opens.

Note: The potential energy surface of a compound can help with understanding key aspects of a molecule's behavior.

Figure 3-16. Opening the coordinate scan output.

37. At the top of the panel, click Load Results.
38. Double-click mmod_Ddrive and choose mmod_Ddrive-out.grd.
39. Click Open.
    • The potential energy landscape is shown, colored rainbow.
    • Low energies are shown in blue, high energies are shown in red.

Figure 3-17. The Plot Coordinate Scan Results panel.

40. At the bottom of the panel, click Energy Options dropdown and set the Energy scale to Absolute.

Note: The energy scale is absolute because we are only studying a single molecule, rather than comparing several molecules.

Note: This plot shows there are large patches of lower energy with relatively sparse contour spacing between them. This suggests a reasonable freedom of movement of the two torsions relative to each other.

41. Close the Plot Coordinate Scan Results panel.

Figure 3-18. Applying CPK representation to the starting and lowest energy structures.

42. Includethe entry is represented in the Workspace, the circle in the In column is blue the last entry in the group, Minimum E. structure during drive.
    • The Ddrive Starting Structure should still be fixed in the Workspace.
43. Go to the Style toolbox and choose Apply CPK representation.

Figure 3-19. Tiled view of a low and high energy conformation, showing a CH₂ steric clash in yellow.

44. Click the + icon in the bottom right corner and choose Tile to tile the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
    • The Workspacethe 3D display area in the center of the main window, where molecular structures are displayed is tiled.
    • The steric clash between the CH₂ group and phenyl ring can be visualized.

Figure 3-20. Un-tiling the Workspace.

45. Un-tile the Workspace by deselecting Tile by.
46. Right-click empty Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and choose Clear Workspace.

Figure 3-21. Toggle properties on and off with the Property Tree.

47. Type ctrl+T (cmd+T) to open the Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data.

In the Property Tree, different calculated properties can be toggled on and off. You may click the arrow next to each application to view more properties.

48. In the Property Tree, double-click the All box.
    • All the properties are now hidden.
49. Expand All and then further expand MacroModel > Secondary.
50. Under Secondary, check Bend Energy-S-OPLS, RMS Derivative-S-OPLS and Van der Waal Energy- S-OPLS
    • The Project Tabledisplays the contents of a project and is also an interface for performing operations on selected entries, viewing properties, and organizing structures and data is updated with the chosen properties.

Figure 4-1. Including the Phenyl-linker-Pyridyl group.

1. Right-click anywhere in the empty Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and choose Clear Workspace.
2. In the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, expand and select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the group Phenyl-linker-Pyridyl.
3. Right-click the selection and choose include to includethe entry is represented in the Workspace, the circle in the In column is blue the entire group in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 4-2. Opening the ConfGen panel from the Tasks.

4. Find and open the Bioactive Search panel from the Tasks.
   • The ConfGen panel opens.

Figure 4-3. Setting the two dihedral angles.

5. For Use structures from, choose Workspace (4 entries).
6. Click Load.
7. For Target number of conformations, type 50.
8. Change the Job name to Phenyl-linker-Pyridyl_ConfGen.
9. Click Run.
   • This job takes a few seconds to complete.

Figure 4-4. Comparing the Ph-S-Py and Ddrive Starting Structure in the Workspace.

10. In the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, includethe entry is represented in the Workspace, the circle in the In column is blue a generated conformation of Ph-S-Py and the Ddrive Starting Structure
    • C-S has a greater bond length than the original C-S bond and the original Ph-S-Py compound.

Optional: Select Measure to measure and compare bond lengths in the structures.

Figure 4-5. Showing ConfGen energy properties.

1. Click Choose.
2. Find and select Energy.
3. Click Choose again. Find and select Relative Energy.
4. Click OK
   • The Energy and Relative Energy properties are shown in the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
   • You may need to click and drag the edge of the Entriesa simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion table toward right to see the added properties.

Note: Both properties are given in kJ/mol.

Figure 4-6. Sorting energy ascending.

5. Right-click energy and choose Sort Selected (Ascending).

Figure 4-7. Grouping the ConfGen result groups.

6. Right click the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and choose Clear Workspace.
7. Right-click to includethe entry is represented in the Workspace, the circle in the In column is blue the group Phenyl-linker-Pyridyl_ConfGen in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
8. Click Continue to the warning box that appears.
9. Using the Workspace toggles, tile your Workspacethe 3D display area in the center of the main window, where molecular structures are displayed by group.
   • Four groups with overlaid structures are present in your Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 4-8. Showing all ConfGen results by group in Tile view.

10. Rotate the molecules in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed
11. Right-click and select Clear Workspace.

Note: These structures are not aligned, but already you can see differences in the conformation due to changes in the linker atoms.

Optional: Align each group in turn to a common phenyl core to more easily see changes in one conformation to the next.

Figure 4-9. Tile view of only the four energy minimized conformations.

12. Using cmd/ctrl-click, includethe entry is represented in the Workspace, the circle in the In column is blue the lowest energy conformer in Ph-NH2-Py, Ph-CH2-Py, and Ph-S-Py groups using the energy property.
13. Double click the Presets button to apply Maestro presets to these compounds.
    • Notice differences in these active conformations.
14. Un-tile the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed by expanding the + toggle and deselecting Tile by.

Figure 4-10. Superimposing included entries by SMARTS.

15. With the lowest energy conformations still included in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed, find and open the Superimposition panel from the Tasks.
16. Under Entries to superimpose, choose Workspace.
17. For Reference Structure, choose Ph-NH2-Py.
18. For Choose Method, select Substructures.
19. For Define structures for superposition using, choose SMARTS.
20. In the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed, use shift-click to select(1) the atoms are chosen in the Workspace. These atoms are referred to as "the selection" or "the atom selection". Workspace operations are performed on the selected atoms. (2) The entry is chosen in the Entries (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries all pyridine carbons.
21. In the Superposition panel, click Get from Selection.
22. Choose Superimpose Structure.

Figure 4-11. The lowest energy active conformations of the linker series compounds superimposed.

Note: Changing the linker from an oxygen (in the structure with grey carbons) to a sulfur (in the structure with green carbons), alters the phenyl ring orientation with respect to the pyridyl nitrogen. The CH₂ linker induces the least planar conformation, due to sterics, while the NH₂ linker is most coplanar with the pyridyl ring.

Note: This was done via ConfGen so that only active conformations were chosen. Different results will be returned if the same comparison is done using MacroModel.

Figure 4-12. The Phenyl-O-Group in the Entries table.

Optional: A Phenyl-O-Group has also been included in the Entry List. If you would like more practice with MacroModel or ConfGen please use these structures to investigate the CH3,CFH2,CF2H, and CF3 groups and how they affect torsion parameters and active conformations of these ligands.