how to calculate the covalent binding energy?



hello all members:
 I need your help!!!
 When I want to calculate the binding energy of the protein and ligand,I find my
 ligand  covalently combined with the protein. how can we tackle this problem?
 Does any one know the
 empirical method to calculate it?any reference or answers will be helpful!
 thanks again !!
 Best regards!
             bxiong ^at^ mail.shcnc.ac.cn
 Xiong Bin
 Shanghai Institute of Materia Medica, C.A.S.
 phone:021-64311833-222(office)