I am doing molecular docking with a flavoprotein, but the results show that the cofactor is not being taken into account, since the spaces are overlapping as shown in the image. I am using Autodock VINA. How can I make the software consider the FAD? Or, what other software do you recommend to make this docking? I am interested in the interaction with the FAD because the inhibition forms a covalent bond with the cofactor, although I do not see the formation of bonds, I am interested in it being in the interaction calculations

Thank you very much for your help.