Accurate potential energy models are necessary for reliable atomistic simulations of chemical phenomena. In the realm of biomolecular modeling, large systems like proteins comprise very many noncovalent interactions (NCIs) that can contribute to the protein’s stability and structure. This work presents two high-quality chemical databases of common fragment interactions in biomolecular systems as extracted from high-resolution Protein DataBank crystal structures: 3380 sidechain-sidechain interactions and 100 backbone-backbone interactions that inaugurate the BioFragment Database (BFDb). Absolute interaction energies are generated with a computationally tractable explicitly correlated coupled cluster with perturbative triples [CCSD(T)-F12] “silver standard” (0.05 kcal/mol average error) for NCI that demands only a fraction of the cost of the conventional “gold standard,” CCSD(T) at the complete basis set limit. By sampling extensively from biological environments, BFDb spans the natural diversity of protein NCI motifs and orientations. In addition to supplying a thorough assessment for lower scaling force-field (2), semi-empirical (3), density functional (244), and wavefunction (45) methods (comprising $>$1M interaction energies), BFDb provides interactive tools for running and manipulating the resulting large datasets and offers a valuable resource for potential energy model development and validation.

中文翻译：

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BioFragment 数据库 (BFDb)：用于非共价相互作用计算化学分析的开放数据平台


准确的势能模型对于化学现象的可靠原子模拟是必要的。在生物分子建模领域，蛋白质等大型系统包含许多非共价相互作用 (NCI)，这些相互作用有助于蛋白质的稳定性和结构。这项工作提出了从高分辨率蛋白质数据库晶体结构中提取的生物分子系统中常见片段相互作用的两个高质量化学数据库：3380 个侧链-侧链相互作用和 100 个主链-主链相互作用，这开启了生物片段数据库 (BFDb)。绝对相互作用能量是通过计算上易于处理的显式相关耦合簇与扰动三元组 [CCSD(T)-F12] NCI 的“银标准”（0.05 kcal/mol 平均误差）生成的，其成本仅为传统“银标准”的一小部分黄金标准”，CCSD(T) 处于完整基差设定限额。通过从生物环境中广泛采样，BFDb 涵盖了蛋白质 NCI 基序和方向的自然多样性。除了提供对低尺度力场 (2)、半经验 (3)、密度泛函 (244) 和波函数 (45) 方法（包括1M 交互能量），BFDb 提供了用于运行和操作生成的大型数据集的交互工具，并为势能模型开发和验证提供了宝贵的资源。