We produced a set of gauge configurations generated with a new N_f=3+1 massive renormalization and improvement scheme for three degenerate light quarks with a mass that equals the average light quark mass in nature and a physical charm quark mass, and a non-perturbatively determined clover coefficient for dynamical Wilson quarks on the lattice. We present the details of the algorithmic setup and tuning procedure of ensembles with three different volumes. We determine the lattice spacings of the generated ensembles assuming decoupling of charm at low energies. We discuss finite volume effects and lattice artifacts and present physical results for the charmonium spectrum and dimensionless ratios of low energy scales in a first continuum limit study.