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

 

Figure 1-1. 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/achemistsguidetomaestro.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 1-2. Save Project panel.

6. Go to File > Save Project As
7. Change the File name to Maestro_chemist.
8. Click Save.
   • The project is now named Maestro_chemist.prj.

Figure 1-3. Import panel and selection.

9. Go to  File > Import Structures
10. Select 1fjs_prep_lig.mae, 4TVG.pdb, 4TVH.pdb, 4Z4X.pdb, LigandMCMM.mae
11. Click Open.
    • Structures are added in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Figure 1-4. Customize Mouse Actions option.

12. Navigate to Workspace > Customize Mouse Actions
13. Choose your appropriate mouse or trackpad preferences from the dropdown  and read through the corresponding mouse actions.  

Figure 2-1. The Ligand option in Quick Select.

1. Includethe entry is represented in the Workspace, the circle in the In column is blue 1fjs_prep_lig in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
2. Under Quick Select, click L.
   • The ligand is highlighted.

Figure 2-2. Copy option in Edit.

3. Go to Edit > Copy
   • The SMILES string of the ligand is ready to be pasted into an external document.
4. Go to Edit > Paste Special > By Placing
   • A banner appears.

Figure 2-3. Exit this mode by clicking the X.

5. Click in the Workspace.
   • A copy of the ligand is pasted into the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
6. Click X to close the banner.
   • Pasting function stops.

Figure 2-4. Clear selection option in Quick Select.

7. Under Quick Select, click Clear selection.
8. Type Z to fit structures to the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

Figure 2-5. Save Image panel with Options open.

9. Click Workspace > Save Image As
   • The Save Image panel opens.
10. Click Options >> to expand image details.
11. Check Transparent background and 300 DPI.
12. Change File name to 1fjs_ligands.
13. Click Save.
    • A .png image of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed is saved to your Working Directorythe location that files are saved.

 

Note: If an item is highlighted in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed, the image will be saved with the selection highlights.

 

Figure 2-6. Copy selected atoms to the new entry option in 3D Builder.

1. Includethe entry is represented in the Workspace, the circle in the In column is blue LigandMCMM in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Note: Fill in the blue circle to includethe entry is represented in the Workspace, the circle in the In column is blue an Entry in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed. Included entries can be interacted with. Selected Entries have the Title highlighted in blue. Typically this is done when preparing for a computational task.

2. Under Quick Select, click L.
   • The ligand is highlighted.
3. Click Build.
   • The 3D Builder panel opens.

Note: The 3D Builder panel can be moved by clicking and dragging on the panel name.

Figure 2-7. Banner prompt to change Entry title.

4. Choose Copy selected atoms to new entry.
   • A banner appears.
5. Change Entry title to ligand_copy and click the check.
   • A new entry ligand_copy is created in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Figure 2-8. Ligand_copy with piperidine selected.

6. Includethe entry is represented in the Workspace, the circle in the In column is blue ligand_copy in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
7. Use click and drag 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the piperidine group.

Note: If in Trackpad/PyMOL mode, use shift-click and drag 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries items in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 2-9. Delete selected atoms option.

8. In 3D Builder, click delete selected atoms.

Figure 2-10. Ligand_copy with terminal hydrogen selected.

9. Click a hydrogen on the terminal carbon.

Note: Use predictive highlighting to help when selecting items in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed before you commit to the selection by hovering over the atom of interest.

Figure 2-11. Fragments pane in the 3D Builder, with the cyclopentadiene option highlighted.

10. In 3D Builder, click Add Fragments.
    • The Fragments pane opens.
11. Choose cyclopentadiene.
    • A cyclopentadiene fragment is appended to the molecule in place of the 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries hydrogen.

Figure 2-12. Edit Fragment options.

12. Next to the attached fragment, click the Edit Fragment four-line icon.
13. Choose Change Connection Point.
    • Possible connection points are highlighted.

Figure 2-13. Possible sp³ carbon connection point (left). New connection point chosen (right).

14. Click the sp³ carbon.
    • The new connection point is marked with a green check.
15. Close the 3D Builder.

Optional: Select Measure in the favorites toolbar to measure bond distances and angles.

Optional: Rotate dihedrals using the 3D Builder by selecting from the Move dropdown menu.

Figure 3-1. View in 2D sketcher option in 2D Overlay.

1. Includethe entry is represented in the Workspace, the circle in the In column is blue ligand_copy in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
2. Right-click on the 2D Overlay and choose View in 2D Sketcher.
   • The 2D Workspace - 2D Sketcher opens.
   • If the 2D Overlay is not visible in your workspace, turn it on before proceeding with the previous step by clicking Window > 2D Overlay.

 

Note: Right-clicking is a functionality present in many different panels and areas of Maestro.

 

Optional: Read through the lists of options that appear as they can contain useful shortcuts.

Figure 3-2. Ligand_copy with hydroxyl groups changed to amines.

3. Choose N and click both hydroxyl groups.
   • The hydroxyl groups are changed to amines.
4. Click Save as New.
5. Name the Entry ligand_2DSketcher.
   • A new ligand is added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion with these modifications.
   • The Workspacethe 3D display area in the center of the main window, where molecular structures are displayed is rendered in a wire representation.
6. Close the 2D Sketcher.

Figure 3-3. Apply custom Preset style to the Workspace.

7. Double-click Presets.
   • The ligand is rendered as ball and stick.

Figure 3-4. Clear Workspace option in the Workspace tab.

8. Go to Workspace > Clear Workspace

 

Note: You can also right-click on empty Workspacethe 3D display area in the center of the main window, where molecular structures are displayed and choose Clear Workspace.

Figure 3-5. Draw and benzene options in the 2D Workspace - 2D Sketcher.

9. Go to Edit > 2D Sketcher
   • The 2D Workspace - 2D Sketcher opens.
   • You are still in Draw Mode.
10. In 2D Workspace - 2D Sketcher, click benzene and click in the 2D Workspace.
11. Draw this structure.
    • To add the alkyne, you may type “3” when hovering over an alkane, or use the alkyne drawing tool.
12. Click the green check mark indicating Cleanup to fix bond angles.
13. Click Save as New and change the Input Entry Title to fragment.
14. Click OK.
    • A new entry titled fragment is saved to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
    • The fragment is shown in 3D in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

Figure 3-6. Decrease Bond Order option.

15. Right-click on the alkyne bond.
16. Choose Decrease Bond Order.
    • The alkyne is now an alkene.
17. Under Quick Select, click All.
    • The fragment is highlighted.
18. Type Ctrl+M (Cmd-M) to minimize the selection.
    • The fragment is minimized.

Figure 3-7. Duplicate an entry In Place.

1. Right-click on ligand_2DSketcher in the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.
2. Choose Duplicate > In Place
3. Double click on the second ligand_2DSketcher entry and change the title to ligand1.
4. Includethe entry is represented in the Workspace, the circle in the In column is blue ligand1 in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 3-8. Fragment options in the 3D Builder.

5. In 3D Builder, click Add Fragments and choose a fragment of your choice.

 

Note: If you wish to explore all fragments included in the 3D Builder please click the three dots. You may also choose to create your own fragment library or click the pencil icon to draw directly on the 3D structure.

 

Note: The fragment shown in this example is a cyclopropane.

Figure 3-9. A cyclopropane is drawn and connected to the aniline of ligand1.

6. Shift-click to select an aniline carbon on the ligand and a fragment atom.
7. Right-click on one of the selected atoms and choose Add Bond.
   • Your fragment is now attached to the ligand.
8. Minimize this structure by selecting the whole molecule and clicking Minimize Selected Atoms in the Favorites Toolbar.
9. Close the 3D Builder Panel.

 

Note: If in Trackpad/PyMOL mode, use shift-click and drag to draw bonds.

Figure 4-1. Delete Atoms option in Multiple Atoms Selected menu.

1. Includethe entry is represented in the Workspace, the circle in the In column is blue 1fjs_prep_lig in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
2. Click R on your keyboard to switch to Residue selection mode.
3. Click on an atom of a copy of the ligand to select the structure.

 

Note: This ligand was copied earlier in Section 2.1. The copied structures need to be removed before the conformational search.

 

4. Right click on the selected ligand.
   • The Multiple Atoms Selected menu opens.
5. Choose Delete Atoms.
   • The ligand is deleted from the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
6. Ensure only one ligand 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.

Figure 4-2. Advanced Search option in Structure Analysis.

7. Go to Tasks and type Advanced Search.
8. Click on Advanced Search in the displayed results.
   • The Conformational Search panel opens.

Figure 4-3. Conformational Search panel with Mini tab selected.

9. For Use structures from, choose Workspace (included entries).
10. Click the Mini tab.
11. Set Maximum iterations to 100.
12. Change Job name to mmod_csearch_1fjs.
13. Click Run.
    • This job takes ~2 minutes.
    • A banner appears when the job is incorporated.
    • A new group titled mmod_csearch_1fjs-out is added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

Figure 4-4. All entries of the conformational search are selected, the first entry is included.

1. Click the mmod_csearch_1fjs-out group.
   • All entries are 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries.

2. Includethe entry is represented in the Workspace, the circle in the In column is blue the first 1fjs_prep_lig entry.
3. Go to Tasks > Browse > Structure Alignment > Superposition
   • The Superposition panel opens.

Figure 4-5. Selected entries and RMSD properties for Superposition panel.

4. For Entries to superimpose, choose Project Table (selected).
5. For Reference structure, choose           1fjs_prep_lig.
6. Check Add property to Project Table.
7. For Choose method, select Substructures.
8. For Define structures for superposition using, choose SMARTS.

 

Figure 4-6. Pyridine and two fluorines of 1fjs_prep_lig selected.

Note: In case you are still in Residue selection mode, type A on your keyboard to switch to Atom selection mode.

 

9. 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries the atoms of the pyridine and the two fluorines.

Figure 4-7. The SMARTS tab of the Superposition panel.

10. In the Superposition panel, click Get from Selection.
    • The SMARTS pattern is generated.
11. Click Superimpose Structures.
    • RMSD properties are calculated.  

Note: Click the Table icon in the upper right corner of the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed to view the RMSD values in 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.

Figure 4-8. Superposition of conformations of 1fjs_prep_lig aligned to the pyridine.

12. Right-click the mmod_csearch_1fjs-out group and choose Include.
13. Click Continue in the Warning window.
    • The conformations are superimposed in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
    • Conformations are aligned to the pyridine.
14. Close the Superposition panel.

Figure 5-1. Copy selected atoms to new entry option in 3D Builder.

1. Includethe entry is represented in the Workspace, the circle in the In column is blue LigandMCMM in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
2. Create a new entry of only the ligand titled ligand_phenol.

Note: See section 2.2 for details on creating a new entry.

Figure 5-2. Quick Align option in Tasks.

3. Includethe entry is represented in the Workspace, the circle in the In column is blue 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries ligand_phenol.
4. Ctrl-click (Cmd-click) to includethe entry is represented in the Workspace, the circle in the In column is blue 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries 1fjs_prep_lig.
5. Go to Tasks > Browse > Structure Alignment > Quick Align
   • The ligands are aligned.

Figure 5-3. Ligand_phenol (green) automatically aligned with 1fjs_prep_lig (gray).

6. Type Z to fit ligands to the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

 

Figure 5-4. 1fjs_prep_lig and ligand_phenol2 included in the Workspace.

 

7. Includethe entry is represented in the Workspace, the circle in the In column is blue LigandMCMM.
8. Create a new entry of only the ligand titled ligand_phenol2.
9. Ctrl-click (Cmd-click) to includethe entry is represented in the Workspace, the circle in the In column is blue both 1fjs_prep_lig and ligand_phenol2.

Figure 5-5. The Superposition panel using Atom Pairs from Included entries.

Note: Use the Move Atoms function to move the ligands closer, if desired. See Section 3.2 for more details.

 

10. Go to Tasks > Structure Alignment > Superposition
    • The Superposition panel opens.
11. For Superimpose entries from, choose Workspace.
12. For Reference structure, choose ligand_phenol2.
13. Click the Atom pairs option.

 

Note: The order of atom selection is important, always start a pair from the same molecule.

Figure 5-6. First atom pair.

14. Click the sulfur of ligand_phenol2.
    • The sulfur is highlighted with a pink box.
15. Click the oxygen 1 of 1fjs_prep_lig.
    • An orange line connects the atoms.

Figure 5-7. Selected atom pairs for superposition. Ligand_phenol2 is shown in green (right) and 1fjs_prep_lig is in gray (left).

16. Click the carbon 5 of ligand_phenol2.
17. Click the carbon 6 of 1fjs_prep_lig.
18. Click the carbon 4 of ligand_phenol2.
19. Click the carbon 1 of 1fjs_prep_lig.

 

Figure 5-8. Ligands after manual alignment.

20. Click Superimpose Structures.
    • The ligands are superimposed.
21. Use Move in the 3D Builder to break the alignment.

Figure 5-9. Ligand Alignment panel.

22. Ctrl-click (Cmd-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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries both 1fjs_prep_lig and ligand_phenol2.
23. Go to Tasks > Browse > Structure Alignment > Ligand Alignment
    • The Ligand Alignment panel opens.
24. For Align ligands from, choose Project Table.
25. For Reference, choose User-specified.
26. Under Reference, choose 1fjs_prep_lig.
27. Under Conformation, select Constrain common substructure and choose Largest common Bemis-Murcko scaffold.
28. Set Job name to align_ligands_1fjs.
29. Click Run.
    • This job takes a few seconds.
    • The align_ligands_1fjs group is added to the Entry List.

Figure 5-10. Ligands after alignment.

Note: At this point, you can inspect the alignment, and consider altering the parameters until you get something more preferable.

Figure 5-11. Create Binding Site Surfaces panel.

1. Includethe entry is represented in the Workspace, the circle in the In column is blue Ligand MCMM.
2. In the Favorites Toolbar, click Surface (Binding Site).
   • The Create Binding Site Surfaces panel opens.
3. For Surface type, choose Molecular Surface.

 

Note: The Interaction Map allows you to add a SiteMap surface map to your binding site.

 

4. For Truncate receptor surface at, type 7.0 Å from ligand.
5. For Color scheme, choose Electrostatic Potential.
6. Click OK.
   • A surface is added to the protein.
   • An ‘S’ is next to the entry.

Figure 5-12. 1fjs_prep_lig and LigandMCMM included in the Workspace.

7. Ctrl-click (Cmd-click) to includethe entry is represented in the Workspace, the circle in the In column is blue 1fjs_prep_lig.
8. Under Quick Select, click L.
   • Both ligands are 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entriesin the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Figure 5-13. ASL tab of Superposition.

9. Go to Tasks > Browse > Structure Alignment > Superposition
   • The Superposition panel opens.
10. For Superimpose entries from, choose Workspace.
11. For Reference structure, choose LigandMCMM.
12. For Choose method, choose Substructures.
13. For Define structures for superposition using, choose ASL.
14. Click Load Selection.
15. Click Superimpose Structures.
    • 1fjs_prep_lig is aligned to the ligand of LigandMCMM.

 

Figure 5-14. 1fjs_prep_lig (gray) is aligned to the receptor-bound ligand (green). Ligand surface is toggled off.

16. Type L to zoom to the ligands.

 

Note: You may choose to toggle off the surface for the Ligand. Click S and toggle off the Ligand surface.

 

Figure 6-1. Tile option toggled on in the Workspace Configuration panel.

1. Shift-click to includethe entry is represented in the Workspace, the circle in the In column is blue entries 4TVG, 4TVH, 4Z4X in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
2. In the Workspace Configuration Toolbar, click ➕.
3. Click Tile.
   • The Workspacethe 3D display area in the center of the main window, where molecular structures are displayed is tiled by entry to show all three proteins separately.
4. Under Quick Select, click P.
   • Proteins are 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries.
5. Type Z.

Figure 6-2. Add ribbons colored by entry.

6. Click the Style button.
7. Click Undisplay selected atoms.
   • The proteins residues are hidden.
8. Click Ribbons.
   • Ribbons are added to the protein structures.
9. Under Edit Ribbon, change the Color Scheme to Entry.
10. In the Workspace Configuration Toolbar, click ➕.
11. Click the Tile by button to turn off the tiling.
12. Type Z.
    • The Workspacethe 3D display area in the center of the main window, where molecular structures are displayed is zoomed to the entries.

Figure 6-3. Protein Structure Alignment panel.

13. Go to Tasks > Browse > Structure Alignment > Protein Structure Alignment
    • The Protein Structure Alignment panel opens.
14. Under Use proteins from, choose Workspace (included entries).
15. Uncheck Pick.
16. Click Align.
    • The Protein Structure Alignment Results panel opens.
    • Protein sequences, Alignment Scores, and RMSDs are shown.

Figure 6-4. Align Binding Sites panel.

1. Go to Tasks > Browse > Structure Alignment > Binding Site Alignment
   • The Align Binding Sites panel opens.
2. In the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion, 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 Entry List (and Project Table) and the row for the entry is highlighted. Project operations are performed on all selected entries entries 4TVG and 4TVH.
3. For Use proteins from, choose Workspace (2 included entries).
4. Change Job name to align_binding_sites_2proteins.
5. Click Run.
   • This job takes ~1 minute.
   • A new group is appended to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.

 

Note: Structure 4Z4X has no ligand bound.

Figure 6-5. Include 4TVG, 4TVH and 4Z4X.

6. Include binding site aligned 4TVG and 4TVH.
7. Include unaligned 4Z4X.

Figure 6-6. Tile the Workspace via the Workspace Configuration panel.

8. Toggle on Tile under Workspace Layout in the Workspace Configuration Toolbar.
9. Choose Group from the dropdown.

Figure 6-7. Aligned binding sites of proteins without a ligand (pink) and with a ligand (white and green).

Note: Notice the differences in the binding site area for the two aligned PDB files 4TVG and 4TVH with a ligand and the 4Z4X PDB file without a ligand.

10. Toggle off Tile by to return to the default Workspacethe 3D display area in the center of the main window, where molecular structures are displayed view.

Figure 7-1. Ligand Designer in Lead Optimization.

1. Includethe entry is represented in the Workspace, the circle in the In column is blue only LigandMCMM in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.
2. Go to Tasks > Browse > Lead Optimization > Ligand Designer
   • The Ligand Designer panel opens.

Figure 7-2. Analyze Workspace in Ligand Desinger panel.

5. Click Analyze Workspace.
   • New entries are added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion in the Ligand Designer group.
   • The Workspacethe 3D display area in the center of the main window, where molecular structures are displayed now has just a single ligand and a cloud surrounding it to represent the growth space.

Note: You can uncheck Adjust view and style when analyzing to retain the view that you currently have when working in the Ligand Designer.

Figure 7-3. 2D/3D Editing in Ligand Designer.

6. Under Display, select 2D/3D Editing.

Note: You can make edits either directly in the sketcher or in the Workspace using the 3D Builder. Any change you make in the Workspace with the 3D builder will be mirrored in the 2D sketcher.

7. Change the lower hydroxyl group to a fluorine.

Optional: View Ligand-Receptor Interactions.

 

Figure 7-4. Predict pose of the edited ligand.

8. Click Predict Pose.
   • A new entry is added to the Entry Lista simplified view of the Project Table that allows you to perform basic operations such as selection and inclusion.  

Figure 7-5. View ligand pose in the Workspace.

9. Include user_designed_ligand_1 and RAL 600 in the Workspacethe 3D display area in the center of the main window, where molecular structures are displayed.

Note: The modification is not predicted to affect the pose of the ligand in the binding pocket.