This paper discusses the framework methodology behind the proposed simulation-based HAZOP tool. Simulation-based approach is one of the many ways to support conventional HAZOP by its automation. Compared to knowledge-based and other approaches, a HAZOP software tool based on deviations simulation is able to examine the investigated process more into detail and so find root causes of hazardous consequences. Another advantage is the ability to identify also potential hazards which did not occur in the past and might be overlooked. The presented framework methodology uses a layer of protection analysis (LOPA) concept of independent protection layers (IPLs) testing. Control system integrated into the raw process design represents the first of various protection layers of the LOPA concept. As a case study, a CSTR chemical production with nonlinear behavior under Proportional-Integral-Derivative (PID) actions as the predominant type of classical feedback control strategy is used. The presented tool identifies hazardous regimes under conditions when control loop introduces hazardous consequences or even acts synergically with existing hazardous events. Risk derived from different consequences is ranked by the risk assessment matrix (RAM) as a part of the conventional quantitative HAZOP study.