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SummaryGeometryRelated PDB entries

YR5

Bonds
First atomSecond atomBond order typeDistance
(experimental model)		Distance
(ideal model)		Properties
C01C02doub1.38Å1.32ÅAromatic
C01C06sing1.39Å1.51ÅAromatic
C02C03sing1.38Å1.52ÅAromatic
C02F11sing1.35Å1.37Å
C03C04doub1.40Å1.34ÅAromatic
C04C05sing1.40Å1.51ÅAromatic
C04C07sing1.48Å1.52Å
C05C06doub1.39Å1.34ÅAromatic
C06N10sing1.40Å1.44Å
C07O08doub1.22Å1.26Å
C07O09sing1.35Å1.26Å
C12C13sing1.51Å1.52Å
C12N10sing1.46Å1.47Å
C13C14doub1.39Å1.48ÅAromatic
C13C20sing1.39Å1.32ÅAromatic
C14C15sing1.51Å1.54Å
C14C16sing1.38Å1.31ÅAromatic
C15O24sing1.43Å1.41Å
C16N17doub1.32Å1.48ÅAromatic
C18C19sing1.51Å1.54Å
C18C20doub1.39Å1.50ÅAromatic
C18N17sing1.32Å1.30ÅAromatic
C20O21sing1.36Å1.41Å
O23P22sing1.61Å1.51Å
O24P22sing1.61Å1.66Å
O25P22doub1.48Å1.43Å
O26P22sing1.61Å1.46Å
C01H011sing1.08Å1.08Å
C03H031sing1.08Å1.08Å
C05H051sing1.08Å1.08Å
C12H122sing1.09Å1.10Å
C12H121sing1.09Å1.10Å
C15H152sing1.09Å1.10Å
C15H151sing1.09Å1.10Å
C16H161sing1.08Å1.08Å
C19H192sing1.09Å1.10Å
C19H191sing1.09Å1.10Å
C19H193sing1.09Å1.10Å
N10H101sing0.97Å1.00Å
O09H1sing0.97Å0.95Å
O21H211sing0.97Å0.95Å
O23H2sing0.97Å0.95Å
O26H3sing0.97Å0.95Å
Angles
First atomSecond atomThird atomAngle
(experimental model)		Angle
(ideal model)
C02C01C06120.4°120.2°
C01C02C03121.6°120.2°
C01C02F11121.0°119.9°
C02C01H011119.8°119.9°
C01C06C05119.9°120.0°
C01C06N10117.8°120.0°
C06C01H011119.8°119.9°
C03C02F11117.4°119.9°
C02C03C04116.3°120.0°
C02C03H031121.8°120.0°
C03C04C05123.6°119.8°
C03C04C07116.2°120.1°
C04C03H031121.9°120.0°
C05C04C07120.2°120.1°
C04C05C06118.1°119.8°
C04C05H051121.0°120.1°
C04C07O08119.9°120.0°
C04C07O09117.8°120.0°
C05C06N10122.2°120.0°
C06C05H051121.0°120.1°
C06N10C12117.2°119.9°
C06N10H101107.5°120.0°
O08C07O09122.3°120.0°
C07O09H1109.5°117.0°
C13C12N10115.3°109.4°
C12C13C14119.7°120.8°
C12C13C20122.8°120.8°
C13C12H122108.0°109.4°
C13C12H121108.0°109.4°
N10C12H122108.0°109.5°
N10C12H121108.0°109.5°
C12N10H101107.5°120.0°
C14C13C20117.2°118.4°
C13C14C15119.6°120.4°
C13C14C16122.9°119.2°
C13C20C18119.6°119.1°
C13C20O21122.5°120.5°
C15C14C16117.5°120.4°
C14C15O24104.6°109.5°
C14C15H152110.7°109.5°
C14C15H151110.7°109.5°
C14C16N17119.7°120.9°
C14C16H161120.2°119.5°
C15O24P22113.3°123.0°
O24C15H152110.7°109.5°
O24C15H151110.7°109.5°
C16N17C18118.6°121.8°
N17C16H161120.2°119.5°
C19C18C20117.7°119.7°
C19C18N17120.5°119.7°
C18C19H192109.5°109.5°
C18C19H191109.5°109.5°
C18C19H193109.5°109.5°
C20C18N17121.8°120.6°
C18C20O21118.0°120.4°
C20O21H211109.5°114.0°
O23P22O24109.2°109.4°
O23P22O25109.0°109.4°
O23P22O26110.8°109.5°
P22O23H2109.5°114.0°
O24P22O25110.0°109.5°
O24P22O26106.7°109.5°
O25P22O26111.2°109.5°
P22O26H3109.5°114.0°
H122C12H121109.5°109.5°
H152C15H151109.4°109.4°
H192C19H191109.5°109.5°
H192C19H193109.4°109.4°
H191C19H193109.5°109.4°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)		Torsion
(ideal model)
C02C01C06H011180.0°179.8°
C01C02C03F11179.4°180.0°
C01C02C03C040.2°0.0°
C02C01C06C052.7°0.1°
C02C01C06N10180.0°180.0°
C01C02C03H031179.9°179.9°
C06C01C02C031.1°0.0°
C06C01C02F11178.3°180.0°
C01C06C05C043.0°0.1°
C01C06C05N10177.2°179.9°
C01C06N10C12154.3°0.0°
C01C06C05H051177.0°180.0°
C01C06N10H10184.6°180.0°
C02C03C04H031180.0°180.0°
C02C03C04C050.6°0.0°
C02C03C04C07178.8°179.9°
C03C02C01H011178.9°179.8°
F11C02C03C04179.2°180.0°
F11C02C01H0111.7°0.3°
F11C02C03H0310.8°0.0°
C03C04C05C07179.4°179.9°
C03C04C05C062.2°0.0°
C03C04C07O0827.9°180.0°
C03C04C07O09149.2°0.1°
C03C04C05H051177.8°179.9°
C04C05C06H051180.0°179.9°
C04C05C06N10179.7°180.0°
C05C04C07O08152.7°0.1°
C05C04C07O0930.2°180.0°
C05C04C03H031179.4°179.9°
C07C04C05C06177.2°179.9°
C04C07O08O09177.0°179.9°
C07C04C03H0311.2°0.0°
C07C04C05H0512.8°0.0°
C04C07O09H1177.0°180.0°
C05C06N10C1228.4°179.9°
C05C06C01H011177.3°179.7°
C05C06N10H10192.7°0.0°
C06N10C12C13160.6°180.0°
C06N10C12H101121.1°180.0°
N10C06C01H0110.0°0.2°
N10C06C05H0510.3°0.1°
C06N10C12H12278.5°60.1°
C06N10C12H12139.8°60.1°
O08C07O09H10.0°0.1°
C13C12N10H122120.9°120.0°
C13C12N10H121120.8°119.9°
C12C13C14C20174.8°179.7°
C12C13C14C152.3°0.3°
C12C13C14C16179.8°179.7°
C12C13C20C18179.0°179.7°
C12C13C20O210.4°0.3°
C13C12H122H121117.3°120.0°
C13C12N10H10178.3°0.0°
N10C12C13C14170.8°90.0°
N10C12C13C2014.8°90.3°
N10C12H122H121117.3°120.1°
C13C14C15C16178.0°179.9°
C13C14C15O2474.8°180.0°
C13C14C16N173.7°0.0°
C14C13C20C184.4°0.1°
C14C13C20O21175.0°180.0°
C14C13C12H12249.9°150.0°
C14C13C12H12168.4°30.0°
C13C14C15H152166.0°60.0°
C13C14C15H15144.4°60.0°
C13C14C16H161176.3°180.0°
C20C13C14C15177.1°179.9°
C20C13C14C165.0°0.0°
C13C20C18C19179.9°180.0°
C13C20C18O21179.5°179.9°
C13C20C18N173.2°0.1°
C20C13C12H122135.6°29.7°
C20C13C12H121106.1°149.7°
C13C20O21H211180.0°90.0°
C14C15O24H152119.2°120.0°
C14C15O24H151119.2°120.0°
C15C14C16N17178.3°180.0°
C14C15O24P22161.7°180.0°
C14C15H152H151122.3°120.0°
C15C14C16H1611.6°0.1°
C16C14C15O24103.3°0.1°
C14C16N17H161180.0°180.0°
C14C16N17C182.1°0.0°
C16C14C15H15216.0°120.1°
C16C14C15H151137.5°120.0°
C15O24P22O2340.5°175.0°
C15O24P22O2579.1°55.0°
C15O24P22O26160.2°65.0°
O24C15H152H151122.2°120.0°
C16N17C18C19178.6°180.0°
C16N17C18C201.7°0.1°
C19C18C20N17177.0°180.0°
C19C18C20O210.6°0.0°
C18C19H192H191120.0°120.1°
C18C19H192H193120.0°120.0°
C18C19H191H193120.0°120.0°
C20C18C19H192177.0°90.0°
C20C18C19H19163.0°149.9°
C20C18C19H19357.0°30.0°
C18C20O21H2110.6°90.0°
N17C18C20O21176.3°180.0°
C18N17C16H161177.9°180.0°
N17C18C19H1920.0°90.0°
N17C18C19H191120.0°30.0°
N17C18C19H193120.0°150.0°
O23P22O24O25119.5°120.0°
O23P22O24O26119.8°120.0°
O23P22O25O26122.4°120.0°
O23P22O26H3121.4°60.1°
O24P22O25O26117.9°120.1°
P22O24C15H15279.1°60.0°
P22O24C15H15142.4°60.0°
O24P22O23H2120.2°180.0°
O24P22O26H3119.9°59.9°
O25P22O23H20.0°60.0°
O25P22O26H30.0°180.0°
O26P22O23H2122.6°60.0°
H122C12N10H10142.6°120.0°
H121C12N10H101160.9°119.9°
H192C19H191H193120.0°119.9°

246704

PDB entries from 2025-12-24

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