One of the main frontiers of Nuclear Physics is searching for violations of fundamental symmetries such as parity and time reversal. These symmetries have to be broken at the level above the Standard Model prediction, otherwise it will be hard to explain the observed amount of nuclear matter in the Universe. Measurements of the electric dipole moment (EDM) of nucleon, nuclei, and atoms are the most promising ways to observe CP-symmetry violations in the quark-gluon sector. Several experiments plan to improve the bound on the neutron EDM by two orders of magnitude in the next decade. Another vital condition for the baryogenesis is the violation of the baryon number, which, despite extensive several decade-long searches for proton decays and neutron oscillations, has never been observed. Interpreting these experimental limits in terms of fundamental particles and their interactions requires robust theoretical understanding of hadron structure. Thanks to mature numerical methods of solving QCD on a lattice, we can now investigate effects of non-Standard Model quark-gluon interactions on the properties of protons and neutrons. I will present our recent progress in calculations of nucleon EDM induced by quark-gluon color-electric dipole interaction (quark chromo-EDM) performed in QCD with physical masses of quarks and discretization preserving chiral symmetry. In addition, I will present results for the neutron-antineutron oscillation amplitudes and its implications for BSM phenomenology.