Obviously there must be a set of fundamental fragments that are not defined in terms of smaller fragments. Therefore ADF has two modes of execution: the normal mode, using fragments, and the create mode, in which a fundamental fragment is generated. Such a fundamental fragment must be a single atom, spherically symmetric and spin-restricted (i.e. spin-α and spin-β orbitals are spatially identical, they are equally occupied, and fractional occupations are applied, if necessary, to distribute the electrons equally over symmetry-degenerate states). Such a fundamental fragment is denoted a basic atom. The basic atoms are the smallest building blocks from which any 'real' calculations are started.
One should realize that the basic atoms are artificial objects that are convenient in the computational approach but that do not necessarily represent real atoms very well (in fact, usually not at all). The bonding energy of a molecule with respect to basic atoms, for instance, should be corrected for this discrepancy in order to get a decent comparison against experimental data. See ref. [1] for a discussion and for examples of applicable values.
A basic atom is computed in the conventional way. The one-electron orbitals are determined as linear combinations of basis functions; the frozen core approximation may be applied for the inner atomic states; a particular type of density functional can be chosen, et cetera. You may have, for instance, different basic Copper atoms by using different basis sets, by choosing different levels of frozen core approximations, or by applying different density functionals.
