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Article ID: 785 - Last Modified:

How do I dock ligands that contain metals with Glide?

A ligand must be a single molecule in order to dock it with Glide. Glide can handle metal complexes as ligands, provided there is support for the metal in the force field. However, the OPLS force fields used by Glide for docking do not treat bonds to metals as covalent bonds; rather the metals must be treated as ions, and the bonds treated as ionic or dative. Therefore, to dock such a ligand you must turn the bonds between the metals and the ligating atoms into zero-order bonds, and adjust the formal charges on the atoms accordingly.

If there are single bonds to the metal in your structure, you can turn them into zero-order bonds by decreasing the bond orders by one (there is a button on the Build toolbar in Maestro that does this). If there are no bonds to coordinating atoms, you can draw in the bonds with the Draw tool and then change them to zero-order bonds. You can then adjust the formal charges with the buttons on the Build toolbar. It is helpful to label the atoms with formal charges first, from the Label toolbar. Note that atoms with no charge are not labeled.

The zero-order bonds essentially create constraints on the metal coordination geometry. This means that the input structure must have reasonable coordination geometry already. You might want to turn off the post-docking minimization step of Glide (on the Output tab), because minimization of strained initial poses could result in some distortion of the coordination geometry.

Keywords: metal ligands, inorganic complex, coordination complex

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