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A second order accurate (in time) numerical scheme is proposed and analyzed for the Poisson-Nernst-Planck equation (PNP) system, reformulated as a non-constant mobility $H^{-1}$ gradient flow in the Energetic Variational Approach (EnVarA). The centered finite difference is taken as the spatial discretization. Meanwhile, the highly nonlinear and singular nature of the logarithmic energy potentials has always been the essential difficulty to design a second order accurate scheme in time, while preserving the variational energetic structures. The mobility function is updated with a second order accurate extrapolation formula, for the sake of unique solvability. A modified Crank-Nicolson scheme is used to approximate the logarithmic term, so that its inner product with the discrete temporal derivative exactly gives the corresponding nonlinear energy difference; henceforth the energy stability is ensured for the logarithmic part. In addition, nonlinear artificial regularization terms are added in the numerical scheme, so that the positivity-preserving property could be theoretically proved, with the help of the singularity associated with the logarithmic function. Furthermore, an optimal rate convergence analysis is provided in this paper, in which the higher order asymptotic expansion for the numerical solution, the rough error estimate and refined error estimate techniques have to be included to accomplish such an analysis. This work combines the following theoretical properties for a second order accurate numerical scheme for the PNP system: (i) second order accuracy in both time and space, (ii) unique solvability and positivity, (iii) energy stability, and (iv) optimal rate convergence. A few numerical results are also presented.