We report a computational study of the conformationally and tautomerically flexible cation-dianion complex of Na(+) with doubly deprotonated adenosine 5'-triphosphate (ATP) using a hierarchical selection method. The method uses molecular dynamics to generate initial conformeric structures, followed by a classification process that groups conformers into five "families" to ensure that a representative sample of structures is retained for further analysis, while very similar conformational structures are eliminated. Hierarchical ab initio calculations (DFT and MP2) of typical conformers of the families are then performed to identify the lowest-energy conformeric structures. The procedure described should provide a useful methodology for conducting higher-level ab initio calculations of medium-sized gas-phase biological molecules for interpreting contemporary laser spectroscopy measurements. For Na(+) x [ATP-2H](2) (considering tautomers where the phosphate chain of ATP is doubly deprotonated), the calculations reveal that the sodium cation interacts directly with the negatively charged phosphates (maximum distance = 2.54 A) in all of the low-energy conformers, while a number of the structures also display close cation-adenine interactions producing compact ball-like structures. These compact structures generally correspond to the lowest-energy conformers. The structural variation between the bare [ATP-2H](2-) molecular ion (Burke et al. J. Phys. Chem. A 2005 , 109 , 9775-9785) and the Na(+) x [ATP-2H](2-) cluster is discussed in detail, including the effect of sodiation on the intramolecular hydrogen-bonding network within ATP in a gas-phase environment.