We show that chiral matters in the minimal supersymmetric standard model (MSSM) with semi-realistic flavor structures can be obtained form 7-brane configurations of magnetized super Yang-Mills (SYM) theory on a toroidal orbifold , where background magnetic fluxes and Wilson-lines are turned on preserving four-dimensional supersymmetry. The zero-mode spectrum of chiral multiplets in total is just MSSM ones, except the existence of those for three generations of right-handed neutrino and extra generations of MSSM Higgs pairs. Hierarchical Yukawa couplings can be obtained from the overlap integrals of wavefunctions localized in extra dimensions, allowing semi-realistic patterns of flavor structures for quarks and charged leptons. We also develop a systematic way to embed additional 7-branes into the configuration, those are sequestered from the visible sector toward a hidden sector model building.

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