We present results for the moments of nucleon isovector vector and axial generalised parton distribution functions computed within lattice QCD. Three ensembles of maximally twisted mass clover-improved fermions simulated with a physical value of the pion mass are analyzed. Two of these ensembles are generated using two degenerate light quarks. A third ensemble is used having, in addition to the light quarks, strange and charm quarks in the sea. A careful analysis of the convergence to the ground state is carried out that is shown to be essential for extracting the correct nucleon matrix elements. This allows a controlled determination of the unpolarised, helicity and tensor second Mellin moments. The vector and axial-vector generalised form factors are also computed as a function of the momentum transfer square up to about 1 GeV$^2$. The three ensembles allow us to check for unquenching effects and to assess lattice finite volume effects.