Hi i am doing work on a protein which has Cu ion in it but the bond it is making with protein are not matching the reference protein making bond with Cu ion so is there any possible to change the bond type or bond formed by my Cu ion in protein. As shown in picture one the reference protein, Cu makes 3 solid bond and one H-bond with protein but our protein, Cu is 2 solid bond and 2 H-bond. So, there any way that we can change this bond formed in our protein file and make it exact like reference protein file?
Are these calculated (e.g. DFT) or XRD structures? If they are calculated, please see my answer to a similar question:
https://www.researchgate.net/post/Is_there_any_problem_if_we_get_a_double_bond_in_benzene_fragment_after_geometry_optimization_in_gaussian_LOG_file
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