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We determine the ground-state phase diagram of the three-band Hubbard model across a range of model parameters using density matrix embedding theory. We study the atomic-scale nature of the antiferromagnetic (AFM) and superconducting (SC) orders, explicitly including the oxygen degrees of freedom. All parametrizations of the model display AFM and SC phases, but the decay of AFM order with doping is too slow compared to the experimental phase diagram, and further, coexistence of AFM and SC orders occurs in all parameter sets. The local magnetic moment localizes entirely at the copper sites. The magnetic phase diagram is particularly sensitive to $Δ_{pd}$ and $t_{pp}$, and existing estimates of the charge transfer gap $Δ_{pd}$ appear too large in so-called minimal model parametrizations. The electron-doped side of the phase diagram is qualitatively distinct from hole-doped side and we find an unusual two-peak structure in the SC in the full model parametrization. Examining the SC order at the atomic scale, within the larger scale $d_{x^2 - y^2}$-wave SC pairing order between Cu-Cu and O-O, we also observe a local $p_{x (y)}$ [or $d_{xz (yz)}$]-symmetry modulation of the pair density on the Cu-O bonds. Our work highlights some of the features that arise in a three-band versus one-band picture, the role of the oxygen degrees of freedom in new kinds of atomic-scale SC orders, and the necessity of re-evaluating current parametrizations of the three-band Hubbard model.