The Species-Based Extended Coherent Flamelet Model (SB-ECFM) was developed and previously validated for 3D Reynolds-Averaged Navier-Stokes (RANS) modeling of a spark-ignited gasoline direct injection engine. In this work, we seek to extend the SB-ECFM model to the large eddy simulation (LES) framework and validate the model in a homogeneous charge spark-ignited engine. In the SB-ECFM, which is a recently developed improvement of the ECFM, the progress variable is defined as a function of real species instead of tracer species. This adjustment alleviates discrepancies that may arise when the numerical treatment of real species is different than that of the tracer species. Furthermore, the species-based formulation also allows for the use of second-order numeric, which can be necessary in LES cases. The transparent combustion chamber (TCC) engine is the configuration used here for validating the SB-ECFM. It has been extensively characterized with detailed experimental measurements and the data are widely available for model benchmarking. Moreover, several of the boundary conditions leading to the engine are also measured experimentally. These measurements are used in the corresponding computational setup of LES calculations with SB-ECFM. Since the engine is spark ignited, the Imposed Stretch Spark Ignition Model (ISSIM) is utilized to model this physical process. The mesh for the current study is based on a configuration that has been validated in a previous LES study of the corresponding motored setup of the TCC engine. However, this mesh was constructed without considering the additional cells needed to sufficiently resolve the flame for the fired case. Thus, it is enhanced with value-based Adaptive Mesh Refinement (AMR) on the progress variable to better capture the flame front in the fired case. As one facet of model validation, the ensemble average of the measured cylinder pressure is compared against the LES/SB-ECFM prediction. Secondly, the predicted cycle-to-cycle variation by LES is compared with the variation measured in the experimental setup. To this end, the LES computation is required to span a sufficient number of engine cycles to provide statistical convergence to evaluate the coefficient of variation (COV) in peak cylinder pressure. Due to the higher computational cost of LES, the runtime required to compute a sufficient number of engine cycles sequentially can be intractable. The concurrent perturbation method (CPM) is deployed in this study to obtain the required number of cycles in a reasonable time frame. Lastly, previous numerical and experimental analyses of the TCC engine have shown that the flow dynamics at the time of ignition is correlated with the cycle-to-cycle variability. Hence, similar analysis is performed on the current simulation results to determine if this correlation effect is well-captured by the current modeling approach.