Creating a sophisticated plant growth model that simulates the 3D structure of a plant while considering light distribution and energy production is a fascinating endeavor. While there might not be a single software that perfectly meets all your requirements out of the box, you can certainly leverage a combination of tools and technologies to achieve your goal.

Plant Simulation Software: To simulate the 3D structure of a plant, you could explore software like GroIMP, a modeling platform for 3D simulation of plants and ecosystems. It allows you to design complex plant structures and simulate their growth over time.

Light and Energy Simulation: Software such as DART (Dynamically Altered Radiation for Trees) can help simulate the interaction between light and plants. This can be crucial for modeling how light distribution affects energy production in leaves.

Radiative Transfer Models: These models simulate how light interacts with leaves and plant canopies. Tools like the DART model, mentioned earlier, use radiative transfer principles to simulate light absorption, reflection, and transmission in complex plant structures.

Python and R Programming: You can use programming languages like Python or R to develop your own simulation models. Libraries like PyTorch or TensorFlow could help you build custom models that integrate 3D plant growth, light distribution, and energy balance calculations.

3D Modeling Software: Consider using software like Blender or Maya to create detailed 3D plant structures. While these tools might not directly simulate plant growth, they can help you visualize and create the plant's 3D geometry.

Environmental Physics Simulation: Tools like EnergyPlus or Radiance, primarily used for building energy simulation and lighting design, could be adapted to model plant energy balance by treating leaves as surfaces.

Custom Simulation Development: Depending on the complexity of your project, you might need to develop a custom simulation framework that integrates all the aspects you mentioned. This approach provides the most flexibility but requires advanced programming skills.

Collaboration: Given the complexity of your project, collaborating with experts in plant physiology, botany, and computational biology could greatly enhance your model's accuracy and realism.

Remember that building such a comprehensive model might require integration of various tools and potentially custom code development. Be prepared for a steep learning curve and consider breaking down your project into manageable steps. Combining existing software with your own code might be the most effective way to achieve your ambitious plant growth simulation with accurate light-energy interactions.
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