The deployment of autonomous navigation systems on ships necessitates accurate motion prediction models tailored to individual vessels. Traditional physics-based models, while grounded in hydrodynamic principles, often fail to account for ship-specific behaviors under real-world conditions. Conversely, purely data-driven models offer specificity but lack interpretability and robustness in edge cases. This study proposes a data-driven physics-based model that integrates physics-based equations with data-driven parameter optimization, leveraging the strengths of both approaches to ensure interpretability and adaptability. The model incorporates physics-based components such as 3-DoF dynamics, rudder, and propeller forces, while parameters such as resistance curve and rudder coefficients are optimized using synthetic data. By embedding domain knowledge into the parameter optimization process, the fitted model maintains physical consistency. Validation of the approach is realized with two container ships by comparing, both qualitatively and quantitatively, predictions against ground-truth trajectories. The results demonstrate significant improvements, in predictive accuracy and reliability, of the data-driven physics-based models over baseline physics-based models tuned with traditional marine engineering practices. The fitted models capture ship-specific behaviors in diverse conditions with their predictions being, 51.6% (ship A) and 57.8% (ship B) more accurate, 72.36% (ship A) and 89.67% (ship B) more consistent.