Iron-phthalocyanine molecules deposited on the Au(110) reconstructed channels assemble into one-dimensional molecular chains, whose spatial distribution evolves into different structural phases at increasing molecular density. The plasticity of the Au channels first induces an ordered phase with a 5X5 symmetry, followed by a second long-range ordered structure composed by denser chains with a 5X7 periodicity with respect to the bare Au surface, as observed in the low-energy electron-diffraction (LEED) and grazing incidence X-ray diffraction (GIXRD) patterns. The geometry of the FePc molecular assemblies in the Au nanorails is determined by scanning tunneling microscopy (STM). For the 5X7 phases, the GIXRD analysis identifies a "4-3" rows profile along the [001] direction in the Au surface and an on-top FePc adsorption site, further confirmed by density functional theory (DFT) calculations. The latter also reveals the electronic mixing of the interface states. The chain assembly is driven by the molecule-molecule interaction and the chains interact with the Au nanorails via the central metal atom, while the chain-chain distance in the different structural phases is primarily driven by the plasticity of the Au surface.