Glasses are often described as supercooled liquids, whose structures are topologically disordered like a liquid, but nevertheless retain short-range structural order. Structural complexity is often associated with complicated electron-charge distributions in glassy systems, making a detailed investigation challenging even for short-range structural order, let alone their atomic dynamics. This is particularly problematic for lone-pair-rich, semiconducting materials, such as phase-change materials (PCMs). Here, this study shows that analytical methods for studying bonding, based on the electron-charge density, rather than a conventional atomic pair-correlation-function approach, allows an in-depth investigation into the chemical-bonding network, as well as lone pairs, of the prototypical PCM, Ge$2$Sb$2$Te$5$ (GST). It is demonstrated that the structurally flexible building units of the amorphous GST network, intimately linked to the presence of distinctly coexisting weak covalent and lone-pair interactions, give rise to cooperative structural-ordering processes, by which ultrafast crystal growth becomes possible. This finding may universally apply to other PCMs.