The fragment-based coupled-cluster (CC) theory utilizing the transferable functional groups through natural localized molecular orbital (NLMO), that is, the natural linear-scaled coupled-cluster (NLSCC) has been further developed to take the extra-fragment interactions into account. The correction to the interaction energies sacrificed during the fragmentation process for the previous NLSCC method is computed by a computationally efficient perturbation theory that maintains the original scaling. The new linear-scaled coupled-cluster for the singles and doubles (CCSD) method is applied to the analysis of relative energies of delicate conformational problems of polypeptides. By adding a perturbation correction, results accurate to less than a kcal/mol are obtained for the alanine tetramer.