Without any extension Mulliken population analyses (MPA) are carried out for all densities present in the respective program, e.g. total (and spin) densities leading to Mulliken charges (and unpaired electrons) per atom in RHF(UHF)-type calculations in dscf or ridft, SCF+MP2 densities in rimp2 or mpgrad, excited state densities in egrad. Suboptions (see Section 15.2.17) also allow for calculation of Mulliken contributions of selectable atoms to selectable MOs including provision of data for graphical output (simulated density of states).
With $pop nbo a Natural Population Analysis (NPA)  is done. Currently only the resulting charges are calculated.
With $pop paboon a population analyses based on occupation numbers  is performed yielding "shared electron numbers (SENs)" and multicenter contributions. For this method always the total density is used, i.e. the sum of alpha and beta densities in case of UHF, the SCF+MP2-density in case of MP2 and the GHF total density for (two-component-)GHF. Note that the results of such an analysis may depend on the choice of the number of modified atomic orbitals ("MAOs"). By default, numbers of MAOs which are reasonable in most cases are taken (see Section 15.2.17). Nevertheless it is warmly recommended to carefully read the information concerning MAOs given in the output before looking at the numbers for atomic charges and shared electron numbers. For different ways of selecting MAOs see Section 15.2.17.