Aims. Supernovae offer the unique possibility to probe diffuse extra-galactic sightlines via observation of the optical transitions of atoms, molecules and the diffuse interstellar bands (DIBs). Through optical spectroscopy the presence of (complex) molecules in distant galaxies can be established. Methods. High resolution optical (3300 -- 6800 Angstrom) spectra of SN2006X at different phase obtained with UVES on the VLT were reduced and analysed. Results. In addition to previously detected atomic (NaI and CaII) and molecular (CN) transitions we present detections of DIBs (6196, 6283 Angstrom), diatomic molecules (CH, CH+) and neutral atoms (CaI) in the spectra of SN2006X taken at different phases (at 2 days before and 14 and 61 days after the brightness maximum). An analysis of the absorption profiles shows no variation between phases in the abundance, nor the central velocities (within 3-sigma error bars) of the (dense) gas tracers (CH, CH+ and CaI) and the DIBs. This is consistent with the conclusion in the literature that SN2006X exploded behind a dense interstellar cloud (inferred from strong atomic sodium and calcium lines and CN transitions) which caused strong photometric reddening but whose material was not directly affected by the supernova explosion. The CH and CN column densities correspond to a reddening of one magnitude following the Galactic correlation derived previously. The 6196 and 6283 lines detected in the M100 ISM are under-abundant by factor of 2.5 to 3.5 (assuming a visual extinction of ~2 mag) compared to the average Galactic ISM relationship. Upper limits for 6379 and 6613 DIBs show that these are at least a factor of seven weaker. Therefore, the Galactic DIB-reddening relation does not seem to hold in M100, although the lower gas-to-dust ratio may further reduce this discrepancy. ; Comment: 4 pages, including 7 figures, accepted for A&A Letters