Is it possible to correct bond order and conectivity problems in an sdf file according to mol2 files? I was doing a Virtual Screening Search using Pharmer software. The .sdf output file contains a column in mol format and another column with Root Mean Square Deviations. I can see some bond order and connectivity problems in the mol column. I do have a mol2 file that contains the original molecules and I was wondering if I can use these mol2 files, to fix this. Can rdkit work in this case?
RDKit has a one line command to fix the bond order (docs)
 mol = Chem.MolFromMolFile('wonky.mol')
 template = Chem.MolFromMol2File('template.mol2')
 newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)

The problem is that the two need to be identical. I see a carboxylate in your screenshots, so you most likely did the correct thing and docked with the appropriate protonation for pH 7, i.e. as the conjugate base with a negative formal charge. If one does not then RDKit will fail.
Also, RDKit is &quot;not great&quot; with mol2 files. If you have the original SMILES that is better. If the problem is atom names, using a PDB is a better call. If you want to assign atom names, this blog post of mine may help.