In a recent paper (J. Chem. Phys. 139, 064111, 2013), an antisymmetrised product of strongly orthogonal geminals with the expansion coefficients explicitly expressed by means of the occupation numbers was used to generate the Piris natural orbital functional 5 (PNOF5). This functional describes most of the non-dynamical effects, but also an important part of the intrapair (intrageminal) electron correlation. Second-order corrections to the generating PNOF5 wave function were derived using the multiconfigurational perturbation theory size consistent at the second order (SC2-MCPT) to include the missing interpair (intergeminal) electron correlation. A modified version of the SC2-MCPT involving double excitations only from different geminals was introduced and denoted as PNOF5-PT2. In this paper, the ground-state energies of 36 closed-shell species belonging to the G2/97 test set of molecules are studied by the PNOF5-PT2 and PNOF5-SC2-MCPT methods. The numerical performance of both methods on eight dimers, with different strength of hydrogen bonds, and 13 isogyric reactions is also assessed. The results are in reasonable agreement with those obtained using the complete active space second-order perturbation theory and coupled-cluster method with singles, doubles, and noniterative triples corrections.