A multiscale simulation approach is presented, which concurrently combines ab-initio quantum mechanical techniques (QM), classical molecular mechanics (MM) and quasi-continuum mechanics (QC) simulations. The atomic and the electronic structures of defect-free and vacancy defective semiconducting carbon nanotubes (CNT) were investigated by using a full scale QC/MM/QM multiscale simulation and the results were compared with the QC/MM and the first-principles simulation results. Though the overall geometries obtained by using a full scale simulation are similar to those obtained in QC/MM simulations, the bonding configuration changes near the vacancy site are correctly represented only in a full scale simulation due to the quantum nature of bond breaking and creation. For an adequate description of the electronic behavior at the center of the QM region, the QM cluster must be large enough to neglect the edge states from dangling carbon atoms and passivating hydrogen atoms at the interface between the QM and the MM regions. We have determined the minimum size of the QM cluster for the correct simulation by investigating the residual edge states at the center of the cluster. We have also studied the electronic properties coupled with the mechanical deformation of the CNT. We have found that the electrical properties of the CNT could drastically change with mechanical bending, initially transforming the semiconducting CNT into the metal.