Simplified quantum chemistry (sQC) methods can routinely compute excited states for very large systems in an "all-atom" fashion. They are viable alternatives to regular multiscale schemes. sQC methods have the advantage of accounting explicitly for all of the environment at a quantum mechanical (QM) level. The treatment of charge-transfer states is now improved by the native implementation of range-separated hybrid (RSH) exchange-correlation functionals into the eXact integral simplified time-dependent density functional theory (XsTD-DFT). After the RSH XsTD-DFT/TDA scheme was benchmarked, XsTD-DFT(/TDA) ultraviolet/visible absorption, circular dichroism (CD), and/or two-photon absorption (2PA) spectra were directly compared to the results of experiments for four challenging and increasingly large systems: eYFP model system, Λ-shaped multimodular D-π-A-π-D'-π-A-π-D chromophore, mixed donor/acceptor ligand Pd(II) double cage [3BF4@Pd4DmA8-m], and the photoactive yellow protein (PYP). Among the results, this study shows that an "all-atom" approach is unavoidable for reproducing absorption and CD spectra of PYP because one of the main transitions involves a local excitation on a tryptophan.