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Geometrical Preferences of the Hydrogen Bonds on Protein-Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations
Alternative TitleGeometrical Preferences of the Hydrogen Bonds on Protein-Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations
Liu ZG(刘治国); Wang GT(王贵涛); Li ZT(黎占亭); Wang RX(王任小)
2008
Source PublicationJ. Chem. Theory Comput.
ISSN1549-9618
Volume4Issue:11Pages:1959-1973
AbstractWe have conducted potential of mean force (PMF) analyses to derive the geometrical parameters of various types of hydrogen bonds on protein-ligand binding interface. Our PMF analyses are based on a set of 4535 high-quality protein-ligand complex structures, which are compiled through a systematic mining of the entire Protein Data Bank. Hydrogen bond donor and acceptor atoms are classified into several basic types. Both distance- and angle-dependent statistical potentials are derived for each donor-acceptor pair, from which distance and angle cutoffs are obtained in an objective, unambiguous manner. These donor-acceptor pairs are also studied by quantum mechanics (QM) calculations at the MP2/6-311++G** level on model molecules. Comparison of the outcomes of PMF analyses and QM calculations suggests that QM calculation may serve as an alternative approach for characterizing hydrogen bond geometry. Both of our PMF analyses and QM calculations indicate that C-H center dot center dot center dot O hydrogen bonds are relatively weak as compared to common hydrogen bonds formed between nitrogen and oxygen atoms. A survey on the protein-ligand complex structures in our data set has revealed that C-alpha-H center dot center dot center dot O hydrogen bonds observed in protein-ligand binding are frequently accompanied by bifurcate N-H center dot center dot center dot O hydrogen bonds. Thus, the C-alpha-H center dot center dot center dot O hydrogen bonds in such cases would better be interpreted as secondary interactions.
Subject Area物理有机化学
Department中科院上海有机化学研究所
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Indexed BySCI
Language英语
WOS IDWOS:000260851300016
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Document Type期刊论文
Identifierhttp://ir.sioc.ac.cn/handle/331003/20863
Collection物理有机化学研究室
Corresponding AuthorWang RX(王任小)
Recommended Citation
GB/T 7714
Liu ZG,Wang GT,Li ZT,et al. Geometrical Preferences of the Hydrogen Bonds on Protein-Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations[J]. J. Chem. Theory Comput.,2008,4(11):1959-1973.
APA 刘治国,王贵涛,黎占亭,&王任小.(2008).Geometrical Preferences of the Hydrogen Bonds on Protein-Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations.J. Chem. Theory Comput.,4(11),1959-1973.
MLA 刘治国,et al."Geometrical Preferences of the Hydrogen Bonds on Protein-Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations".J. Chem. Theory Comput. 4.11(2008):1959-1973.
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