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Holomorphicity of vector bundles can stabilize complex structure moduli of a Calabi-Yau threefold in N = 1 supersymmetric heterotic compactifications. In principle, the Atiyah class determines the stabilized moduli. In this paper, we study how this mechanism works in the context of elliptically fibered Calabi-Yau manifolds where the complex structure moduli space contains two kinds of moduli, those from the base and those from the fibration. Defining the bundle with spectral data, we find threedoi:10.1007/jhep03(2021)281 fatcat:vuyyglacgvbnja2pm7xhkty6zu