ABSTRACT We present hydrodynamic simulations of the interstellar medium (ISM) within the circumnuclear disc (CND) of a typical active galactic nucleus (AGN)-dominated galaxy influenced by mechanical feedback from an AGN. The simulations are coupled with the CHIMES non-equilibrium chemistry network to treat the radiative-cooling and AGN-heating. A focus is placed on the central 100 pc scale where AGN outflows are coupled to the ISM and constrained by observational Seyfert-2 galaxies. AGN-feedback models are implemented with different wind-velocity and mass-loading factors. We post-process the simulation snapshots with a radiative-transfer code to obtain the molecular emission lines. We find that the inclusion of an AGN promotes the formation of CO in clumpy and dense regions surrounding supermassive black holes (SMBHs). The CO(1-0) intensity maps (<6 Myr) in the CND seem to match well with observations of NGC 1068 with a best match for a model with 5000 km s−1 wind-velocity and a high mass-loading factor. We attempt to discern between competing explanations for the apparent counter-rotating gas disc in the NGC 1068 through an analysis of kinematic maps of the CO line emission. We suggest that mechanical AGN-feedback could explain the alignment-stability of position-angle across the different CND radii around the SMBH through momentum and energy loading of the wind. It is the wind-velocity that drives the disc out of alignment on a 100 pc scale for a long period of time. The position–velocity diagrams are in broad agreement with the predicted Keplerian rotation-curve in the model without AGN, but the AGN models exhibit a larger degree of scatter, in better agreement with NGC 1068 observations.