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Calcium silicate hydrate (C-S-H) is the most abundant synthetic phase on the planet. However, its atomic-level structure remains only partially resolved. In the present study, the atomic-level structure, water content, and energetics of bulk C-S-H are investigated by molecular dynamics (MD). It is shown that experimentally observed water retention in the C-S-H structure is closely associated by the calcium oxygen coordination environment. This coordination environment affects the cohesion and hydration energetics of C-S-H. Close examination of the modeled interlayer region reveals three distinct interlayer calcium sites. In the absence of sufficient water content in the C-S-H interlayer, these sites coordinate with silicate oxygens of the calcium oxide sheet and consequently cause disorder of the mainlayer which was previously observed by 29Si NMR and XRD.