Intrinsically disordered proteins (IDPs) are known as proteins without a defined secondary structure and linked with many neurological diseases. Exploring the conformational space of IDPs is one of the major challenges faced by the experimental and computational studies due to its disordered nature. Obtaining an accurate conformational space is very important to identify the structural properties of IDPs linked with these biological phenomena. RNA polymerase II (Pol II) C-terminal domain (CTD) is an intrinsically disordered low complexity domain that has a heptapeptide repeating sequence with number of repeats varies according to the organism. CTD was documented to undergo liquid-liquid phase separation, which is affected by its length and phosphorylation level. In this study, we investigated the conformational space of CTD and the effects of phosphorylation to its conformation using enhanced sampling molecular dynamics (MD) simulations. We used CTD models with two repeating units with non-phosphorylated and phosphorylated states. In addition, we study a longer synthetic CTD sequence, which has available experimental observables as a reference point to compare with the simulations. Our results suggested that phosphorylation has complex effects on the conformations of the CTD that depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination and interactions with the nearby residues. With this study we provide a detailed explanation of conformational changes of CTD models upon their phosphorylation.