After performing Glide docking you have to save your project file so that for each ligand the correct Ser/Thr/Cys rotamer is displayed in the pose viewer file. In order to include this information in your saved files, you have to follow this procedure:
1) Import the *_pv.maegz with your top-scored compounds in Maestro
2) In another Maestro window import the *.sdf file containing the exemplar compounds of each of the initial clusters.
3) In the Project Table of the first Maestro window, select (Control and right mouse click on the entry) AND include (Control and right mouse click on the box of the table entry so that it turns from empty full (black): the displayed atoms (i.e. the protein) plus each of the exemplar compounds that we see in the second Maestro window.
4) Export the selected/included entries into a *maegz file that MUST end with "_pv", e.g. "exemp1_pv.maegz", making also sure that the option "All properties" in the Export pop-up window is selected.