Protein-ligand interaction ontology

Last uploaded: November 3, 2014
Preferred Name

Hydrogen_bonding
Synonyms
ID

http://www.semanticweb.org/ontologies/2010/3/Ontology1271664172453.owl#Hydrogen_bonding

isDefinedBy

Strong intermolecular forces produced by the attraction of a hydrogen atom, already covalently bonded to one electronegative atom, to a second electronegative atom of the same molecule or an adjacent molecule; these bonds are found in compounds containing strong electronegative atoms such as fluorine, oxygen, nitrogen. The energy of a hydrogen bond lies in between the energies of covalent bonds and Vander Waals interactions, and is of the order of 2-10 kcal mol-1. The strength of the hydrogen bond is dependent on the distance between the donor and acceptor atoms, which in turn is dependent on their electronegativities. The standard hydrogen bond between the donor and acceptor atoms is of the order of 2.6Å - 3.5Å, with the optimum at 2.8Å. Distances may be less accurate at low resolution. The highest bonding energy for the hydrogen bond is obtained, when the two negative charges are approximately in line with the positive charge inbetween (O...H-O in water, O...H-N in the oxygen amide hydrogen bond). Deviations from linearity will reduce the bonding energy rapidly. It follows that the "best" hydrogen bond is "close" to linear.

prefixIRI

Ontology1271664172453:Hydrogen_bonding

prefLabel

Hydrogen_bonding

Reference

http://pipe.ibibiosolutions.com/Hydrogen%20Bond.html

software

MarvinSketch is an advanced, Java based chemical editor for drawing chemical structures, queries and reactions. http://www.chemaxon.com/marvin/sketch/index.php In this site go to Tools section after drawing the molecular structure: Other(H bond donor/ Hbond acceptor)

Synonym

hydrogen bonding H-bonds H-bond hydrogen-bonding interaction hydrogen bond interaction hydrogen bond interactions hydrogen-bonded interaction hydrogen-bonded interactions hydrogen bonds hydrogen bond

subClassOf

http://www.semanticweb.org/ontologies/2010/3/Ontology1271664172453.owl#Non_bonded_interaction

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