I have a pdb file of a protein which contains a lysine residue bound to a ligand. The ligand has two conformations due to a cis/trans isomerisation. I have created a pdb file (also .mol and .mol2) of lysine attached to the cis form and would like to replace the lysine-ligand(trans) form which is currently in the protein structure with the lysine-ligand(cis) form. Does anyone know how to do this; mutagenesis only gives me the option of standard amino acids and also does not remove the existing ligand.
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