Hi,

maybe you can do this with RDKit:

from rdkit import Chem

from rdkit.Chem import rdChemReactions

rxn = rdChemReactions.ReactionFromSmarts(([#6]-[#16:1]-[#6].[#8:2]=[#8:3])>>[#6]-[#16:1](=[#8:2])(=[#8:3])-[#6])

reacts = (Chem.MolFromSmiles('C(C(O)=O)(N)CCSC'), Chem.MolFromSmiles('O=O'))

products = rxn.RunReactants(reacts)

Here the example is methionine. You can just pass yout structure as input, run the reaction and then save again as PDB.

If you want to use a GUI, you can try VMD (molefacture), Schrödinger or MOE.