My template has a heme. Theoretically, the Fe in heme is attached to an oxygen atom, which is reactive and drives the reaction. However, the oxygen is not visible from pdb (maybe) cuz the ligand is in the middle of reaction and the reaction site of ligand directly form a covalent bond with Fe (~2A).
All papers i have on modelling this class of enzymes add O onto the heme manually before docking. If i want to add O to my heme, for my ctrl dock, should i modify the heme so that the Fe is attached to O or not? IF i modify it in ctrl dock, the RMSD will be very high; interaction btwn ligand and protein residues will be different from that of crystal structure because 1 O is added btwn ligand and heme. How do i justify my control? If my ctrl is without the O, how can i certain that my docking with oxygen-heme is accurate?
Besides that, my ctrl dock ligand's active site is N. In the native compound, its R-N=S-R; But in the crystal, its R-N-S-R (N form a single bond with Fe of heme). Should i ctrldock with R-N=S-R or R-N-S-R? The latter will creates a H on N when preparing pdbqt.
I wonder what is the real purpose of ctrl dock, as from what i heard+read, it was to:
1. make sure the parameter is suitable (read)
2. make sure the software is suitable for my system (heard)
IF it is the 1st case, how am i suppose to be confident that the parameter used in ctrl dock using my template is suitable for docking different ligands into my model?