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The paper gives the investigation on organizational structure ontology. It presents a theoretical foundation for understanding organizational structure ontology by means of structural analysis. Also it discusses and provides an overview of advanced business modeling environment and enterprise modeling. The proposed solution architecture improves organizational structure of an enterprise in order to be more efficient and to be aligned with the current processes organization. The structural analysis based on Q-analysis method and using different measures like eccentricity and complexity of a system are described. It illustrates the use of structural analysis base on Q-analysis method by giving an illustration to prove how to ensure synchronization between formal organizational structure and emergent one, due to perceived changes in business processes.