Use of numerical simulations at early stage of engine and aftertreatment systems development helps in evaluating their different concepts and reducing the need for costly building of prototypes. In this work, we explore the feasibility of fully physical and chemical-based tool-chain for co-simulating engine in-cylinder and aftertreatment processes. Detailed gas-phase reaction kinetics and surface chemistry mechanisms are applied for the modeling of combustion, pollutants formation and aftertreatment, respectively. Engine in-cylinder performance parameters are simulated using a stochastic reactor model and multi-component fuel surrogate. The engine model is coupled with an aftertreatment model capable of simulating diesel oxidation catalyst (DOC), selective catalytic reduction catalyst, lean NOx trap, ammonia slip catalyst, and three-way catalyst. Both the engine and aftertreatment models are embedded within the Simulink framework. They work in co-simulation and are coupled using Functional Mock-up Interface (FMI) technology. The coupled framework acts as a virtual test bench that is developed given its application for X-in-the-Loop (XiL) simulations. The framework can be applied to engine steady state or transient operating conditions. Here, exemplary calculations are performed using a Model-in-the-Loop (MiL) approach. Simulations are conducted under transient conditions of Worldwide Harmonized Light Vehicle Test Cycle for a compression ignition engine coupled with a DOC. The presented framework is considered a first step towards complex engine plant modeling using detailed chemistry for the virtualization of the development of engine, fuels and aftertreatment systems.