Large-language models (LLMs) and agentic systems present exciting opportunities to accelerate drug discovery. In this study, we examine the modularity of LLM-based agentic systems for drug discovery, i.e., whether parts of the system such as the LLM and type of agent are interchangeable, a topic that has received limited attention in drug discovery. We compare the performance of different LLMs and the effectiveness of tool-calling agents versus code-generating agents. Our case study, comparing performance in orchestrating tools for chemistry and drug discovery using an LLM-as-a-judge score, shows that Claude-3.5-Sonnet, Claude-3.7-Sonnet and GPT-4o outperform alternative language models such as Llama-3.1-8B, Llama-3.1-70B, GPT-3.5-Turbo, and Nova-Micro. Although we confirm that code-generating agents outperform the tool-calling ones on average, we show that this is highly question- and model-dependent. Furthermore, the impact of replacing system prompts is dependent on the question and model, underscoring that even in this particular domain one cannot just replace components of the system without re-engineering. Our study highlights the necessity of further research into the modularity of agentic systems to enable the development of reliable and modular solutions for real-world problems.