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SummaryGeometryRelated PDB entries

Y4I

Bonds
First atomSecond atomBond order typeDistance
(experimental model)		Distance
(ideal model)		Properties
OP1Psing1.61Å1.53Å
SPPdoub1.86Å1.96Å
O5'Psing1.61Å1.59Å
PN14sing1.68Å1.79Å
C5'O5'sing1.43Å1.46Å
C4'C5'sing1.53Å1.51Å
C4'O4'sing1.44Å1.47Å
C3'C4'sing1.55Å1.54Å
O4'C1'sing1.44Å1.43Å
O3'C3'sing1.43Å1.41Å
C2'C3'sing1.55Å1.51Å
C1'C2'sing1.54Å1.52Å
N1C1'sing1.46Å1.52Å
N1C2sing1.35Å1.39Å
C6N1sing1.37Å1.36Å
O2C2doub1.22Å1.19Å
C2N3sing1.35Å1.36Å
N3C4sing1.35Å1.37Å
O4C4doub1.22Å1.23Å
C4C5sing1.42Å1.44Å
C5MC5sing1.51Å1.52Å
C5C6doub1.35Å1.35Å
O11C12sing1.43Å1.42Å
O11C16sing1.43Å1.43Å
C13C12sing1.53Å1.53Å
C12N17sing1.46Å1.48Å
O12C18doub1.22Å1.23Å
N14C13sing1.47Å1.46Å
C20O13doub1.22Å1.24Å
C15N14sing1.47Å1.46Å
C16C15sing1.53Å1.52Å
O15C23sing1.43Å1.43Å
C23C16sing1.53Å1.50Å
N17C18sing1.35Å1.39Å
N17C22sing1.37Å1.39Å
C18N19sing1.35Å1.38Å
N19C20sing1.35Å1.39Å
C21C20sing1.42Å1.45Å
C22C21doub1.35Å1.34Å
N19H1sing0.97Å1.00Å
C21H2sing1.08Å1.08Å
C22H22sing1.08Å1.08Å
C12H12sing1.09Å1.10Å
C13H131sing1.09Å1.10Å
C13H132sing1.09Å1.10Å
C15H151sing1.09Å1.10Å
C15H152sing1.09Å1.10Å
C16H16sing1.09Å1.10Å
C23H231sing1.09Å1.10Å
C23H232sing1.09Å1.10Å
O15HO15sing0.97Å0.95Å
OP1HOP1sing0.97Å0.95Å
C5'H5'2sing1.09Å1.10Å
C5'H5'1sing1.09Å1.10Å
C4'H4'sing1.09Å1.10Å
C3'H3'sing1.09Å1.10Å
O3'HO3'sing0.97Å0.95Å
C2'H2'2sing1.09Å1.10Å
C2'H2'1sing1.09Å1.10Å
C1'H1'sing1.09Å1.10Å
C6H6sing1.08Å1.08Å
C5MH5M3sing1.09Å1.10Å
C5MH5M1sing1.09Å1.10Å
C5MH5M2sing1.09Å1.10Å
N3H3sing0.97Å1.00Å
Angles
First atomSecond atomThird atomAngle
(experimental model)		Angle
(ideal model)
OP1PSP112.7°109.5°
OP1PO5'109.0°109.5°
OP1PN14118.7°109.5°
POP1HOP1109.5°114.0°
SPPO5'108.6°109.5°
SPPN14109.6°109.4°
O5'PN1496.8°109.5°
PO5'C5'122.5°123.0°
PN14C13105.2°111.0°
PN14C15135.3°111.0°
O5'C5'C4'107.9°109.5°
O5'C5'H5'2109.9°109.5°
O5'C5'H5'1109.9°109.5°
C5'C4'O4'110.0°110.6°
C5'C4'C3'117.5°110.6°
C4'C5'H5'2109.8°109.5°
C4'C5'H5'1109.8°109.5°
C5'C4'H4'107.5°110.5°
O4'C4'C3'106.2°103.5°
C4'O4'C1'109.5°107.0°
O4'C4'H4'108.0°110.6°
C4'C3'O3'108.5°110.9°
C4'C3'C2'104.0°102.1°
C3'C4'H4'107.3°110.8°
C4'C3'H3'111.0°110.9°
O4'C1'C2'106.6°107.3°
O4'C1'N1106.7°110.0°
O4'C1'H1'110.6°109.8°
O3'C3'C2'108.4°110.9°
O3'C3'H3'113.1°110.8°
C3'O3'HO3'109.5°114.0°
C3'C2'C1'103.3°104.2°
C2'C3'H3'111.4°110.9°
C3'C2'H2'2111.0°110.4°
C3'C2'H2'1110.9°110.5°
C2'C1'N1114.2°109.9°
C1'C2'H2'2111.0°110.5°
C1'C2'H2'1111.0°110.6°
C2'C1'H1'109.4°109.9°
C1'N1C2116.9°119.7°
C1'N1C6120.7°119.7°
N1C1'H1'109.4°109.9°
C2N1C6122.5°120.6°
N1C2O2125.2°119.5°
N1C2N3114.8°121.0°
N1C6C5122.6°119.7°
N1C6H6118.7°120.2°
O2C2N3119.9°119.6°
C2N3C4125.2°120.3°
C2N3H3117.4°119.9°
N3C4O4117.5°120.3°
N3C4C5117.7°119.4°
C4N3H3117.4°119.9°
O4C4C5124.6°120.3°
C4C5C5M118.1°120.4°
C4C5C6117.1°119.1°
C5MC5C6124.7°120.5°
C5C5MH5M3109.5°109.5°
C5C5MH5M1109.5°109.5°
C5C5MH5M2109.5°109.5°
C5C6H6118.7°120.1°
C12O11C16108.7°113.7°
O11C12C13112.7°109.2°
O11C12N17109.6°109.5°
O11C12H12110.2°109.5°
O11C16C15107.0°109.2°
O11C16C23109.2°109.5°
O11C16H16109.1°109.5°
C13C12N17106.4°109.5°
C12C13N14113.5°109.2°
C13C12H12108.6°109.6°
C12C13H131108.5°109.5°
C12C13H132108.4°109.5°
C12N17C18118.0°119.7°
C12N17C22119.4°119.7°
N17C12H12109.3°109.5°
O12C18N17123.6°119.5°
O12C18N19122.1°119.5°
C13N14C15114.1°110.8°
N14C13H131108.4°109.5°
N14C13H132108.5°109.6°
O13C20N19119.1°120.3°
O13C20C21125.4°120.3°
N14C15C16106.4°109.3°
N14C15H151110.2°109.5°
N14C15H152110.2°109.5°
C15C16C23115.3°109.5°
C16C15H151110.3°109.5°
C16C15H152110.2°109.6°
C15C16H16108.0°109.5°
O15C23C16107.1°109.5°
O15C23H231110.1°109.4°
O15C23H232110.1°109.4°
C23O15HO15109.5°114.0°
C23C16H16108.2°109.5°
C16C23H231110.1°109.5°
C16C23H232110.1°109.5°
C18N17C22122.5°120.6°
N17C18N19114.2°121.0°
N17C22C21121.7°119.7°
N17C22H22119.1°120.1°
C18N19C20126.6°120.2°
C18N19H1116.7°119.9°
N19C20C21115.5°119.5°
C20N19H1116.7°119.9°
C20C21C22119.4°119.1°
C20C21H2120.3°120.5°
C22C21H2120.3°120.4°
C21C22H22119.1°120.2°
H131C13H132109.5°109.6°
H151C15H152109.5°109.5°
H231C23H232109.5°109.5°
H5'2C5'H5'1109.5°109.4°
H2'2C2'H2'1109.5°110.5°
H5M3C5MH5M1109.4°109.5°
H5M3C5MH5M2109.5°109.5°
H5M1C5MH5M2109.4°109.4°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)		Torsion
(ideal model)
OP1PSPO5'120.8°120.0°
OP1PSPN14134.6°120.0°
OP1PO5'N14123.5°120.0°
OP1PO5'C5'59.6°65.0°
OP1PN14C1325.3°60.0°
OP1PN14C15176.5°176.4°
SPPO5'N14113.4°119.9°
SPPO5'C5'177.3°55.0°
SPPN14C13106.1°60.0°
SPPN14C1545.0°63.6°
SPPOP1HOP10.0°180.0°
PO5'C5'C4'156.4°180.0°
O5'PN14C13141.4°180.0°
O5'PN14C1567.5°56.3°
O5'POP1HOP1120.6°60.0°
PO5'C5'H5'283.8°60.0°
PO5'C5'H5'136.7°60.0°
N14PO5'C5'63.9°175.0°
PN14C13C12160.6°177.6°
PN14C13C15158.2°123.8°
PN14C15C16156.5°177.6°
PN14C13H13140.0°57.7°
PN14C13H13278.8°62.5°
PN14C15H15137.0°57.7°
PN14C15H15284.0°62.4°
N14POP1HOP1130.1°60.0°
O5'C5'C4'H5'2119.8°120.0°
O5'C5'C4'H5'1119.8°120.0°
O5'C5'C4'O4'76.5°66.4°
O5'C5'C4'C3'45.1°179.5°
O5'C5'H5'2H5'1120.7°120.0°
O5'C5'C4'H4'166.1°56.4°
C5'C4'O4'C3'128.1°118.5°
C5'C4'O4'H4'117.1°122.8°
C5'C4'C3'H4'121.1°122.9°
C5'C4'O4'C1'128.6°158.6°
C5'C4'C3'O3'140.3°86.2°
C5'C4'C3'C2'104.5°155.5°
C4'C5'H5'2H5'1120.7°120.0°
C5'C4'C3'H3'15.5°37.4°
O4'C4'C3'H4'115.3°118.6°
O4'C4'C3'O3'96.1°155.3°
O4'C4'C3'C2'19.1°37.0°
C4'O4'C1'C2'20.0°26.5°
C4'O4'C1'N1142.4°146.0°
O4'C4'C5'H5'2163.7°53.6°
O4'C4'C5'H5'143.3°173.5°
O4'C4'C3'H3'139.0°81.1°
C4'O4'C1'H1'98.8°92.9°
C3'C4'O4'C1'0.5°40.1°
C4'C3'O3'C2'112.4°112.7°
C4'C3'O3'H3'123.6°123.6°
C4'C3'C2'H3'119.7°118.2°
C4'C3'C2'C1'30.2°20.9°
C3'C4'C5'H5'274.7°60.5°
C3'C4'C5'H5'1164.9°59.5°
C4'C3'O3'HO3'180.0°180.0°
C4'C3'C2'H2'288.8°139.5°
C4'C3'C2'H2'1149.2°97.9°
O4'C1'C2'C3'31.5°2.0°
O4'C1'C2'N1117.6°119.6°
O4'C1'C2'H1'119.6°119.4°
O4'C1'N1H1'119.6°121.1°
O4'C1'N1C2141.1°52.9°
O4'C1'N1C639.6°126.8°
C1'O4'C4'H4'114.3°78.6°
O4'C1'C2'H2'287.5°116.6°
O4'C1'C2'H2'1150.5°120.8°
O3'C3'C2'H3'125.0°123.6°
O3'C3'C2'C1'85.1°139.1°
O3'C3'C4'H4'19.2°36.7°
O3'C3'C2'H2'2155.9°102.3°
O3'C3'C2'H2'133.9°20.3°
C3'C2'C1'H2'2119.0°118.6°
C3'C2'C1'H2'1119.0°118.8°
C3'C2'C1'N1149.0°121.6°
C2'C3'C4'H4'134.4°81.6°
C2'C3'O3'HO3'67.6°67.3°
C3'C2'H2'2H2'1122.8°122.6°
C3'C2'C1'H1'88.1°117.4°
C2'C1'N1H1'122.9°121.0°
C2'C1'N1C2101.4°65.0°
C2'C1'N1C677.9°115.3°
C1'C2'C3'H3'149.9°97.3°
C1'C2'H2'2H2'1122.9°122.7°
C1'N1C2C6179.3°179.7°
C1'N1C2O22.6°0.0°
C1'N1C2N3179.7°179.7°
C1'N1C6C5179.0°180.0°
N1C1'C2'H2'230.0°3.0°
N1C1'C2'H2'192.0°119.6°
C1'N1C6H61.0°0.1°
N1C2O2N3177.6°179.8°
N1C2N3C42.7°0.6°
C2N1C6C51.7°0.3°
C2N1C1'H1'21.5°174.0°
C2N1C6H6178.3°179.8°
N1C2N3H3177.3°179.8°
C6N1C2O2176.7°179.7°
C6N1C2N31.0°0.5°
N1C6C5C43.6°0.1°
N1C6C5C5M179.4°180.0°
N1C6C5H6180.0°179.9°
C6N1C1'H1'159.2°5.7°
O2C2N3C4175.2°179.7°
O2C2N3H34.8°0.0°
C2N3C4H3180.0°179.6°
C2N3C4O4179.4°179.7°
C2N3C4C54.7°0.4°
N3C4O4C5174.3°179.9°
N3C4C5C5M177.9°180.0°
N3C4C5C64.9°0.1°
O4C4C5C5M3.7°0.1°
O4C4C5C6179.2°180.0°
O4C4N3H30.6°0.1°
C4C5C5MC6176.9°179.9°
C4C5C6H6176.4°180.0°
C4C5C5MH5M3180.0°89.9°
C4C5C5MH5M160.0°30.1°
C4C5C5MH5M260.0°150.1°
C5C4N3H3175.3°180.0°
C5MC5C6H60.5°0.2°
C5C5MH5M3H5M1120.0°120.0°
C5C5MH5M3H5M2120.0°120.0°
C5C5MH5M1H5M2120.0°120.0°
C6C5C5MH5M33.1°89.9°
C6C5C5MH5M1116.9°150.0°
C6C5C5MH5M2123.1°30.1°
O11C12C13N17120.1°119.9°
O11C12C13H12122.4°120.0°
O11C12N17H12120.9°120.1°
O11C12C13N1440.9°56.9°
C12O11C16C1571.0°58.7°
C12O11C16C23163.7°178.6°
O11C12N17C18139.6°125.0°
O11C12N17C2243.5°55.2°
O11C12C13H131161.5°176.8°
O11C12C13H13279.7°63.1°
C12O11C16H1645.6°61.3°
C16O11C12C1356.1°58.7°
C16O11C12N17174.3°178.6°
O11C16C15N1468.9°56.9°
O11C16C15C23121.6°119.9°
O11C16C15H16117.4°119.9°
O11C16C23O15163.4°65.0°
O11C16C23H16118.6°120.1°
C16O11C12H1265.4°61.3°
O11C16C15H151171.6°176.8°
O11C16C15H15250.6°63.1°
O11C16C23H23143.8°175.0°
O11C16C23H23276.9°54.9°
C13C12N17H12117.1°120.2°
C12C13N14H131120.6°119.9°
C12C13N14H132120.6°119.9°
C12C13N14C1541.2°58.7°
C13C12N17C1898.4°115.2°
C13C12N17C2278.5°64.5°
C12C13H131H132118.2°120.1°
C12N17C18O122.9°0.0°
N17C12C13N14161.0°176.8°
C12N17C18C22176.8°179.8°
C12N17C18N19177.9°180.0°
C12N17C22C21177.7°180.0°
C12N17C22H222.3°0.0°
N17C12C13H13178.5°63.3°
N17C12C13H13240.3°56.8°
O12C18N17N19179.2°180.0°
O12C18N17C22179.8°179.7°
O12C18N19C20179.8°180.0°
O12C18N19H10.2°0.0°
C13N14C15C1654.2°58.7°
N14C13C12H1281.5°63.1°
N14C13H131H132118.2°120.2°
C13N14C15H151173.7°178.6°
C13N14C15H15265.3°61.4°
O13C20N19C18179.9°180.0°
O13C20N19C21179.9°179.7°
O13C20C21C22179.9°180.0°
O13C20N19H10.1°0.0°
O13C20C21H20.1°0.0°
N14C15C16H151119.5°119.9°
N14C15C16H152119.5°120.0°
N14C15C16C23169.5°176.8°
C15N14C13H131161.8°178.5°
C15N14C13H13279.4°61.3°
N14C15H151H152121.4°120.1°
N14C15C16H1648.5°63.1°
C15C16C23O1576.2°175.3°
C15C16C23H16120.9°120.1°
C16C15H151H152121.5°120.2°
C15C16C23H231164.2°55.3°
C15C16C23H23243.5°64.8°
O15C23C16H231119.6°120.0°
O15C23C16H232119.7°119.9°
O15C23C16H1644.8°55.1°
O15C23H231H232121.1°119.9°
C23C16C15H15150.0°63.3°
C23C16C15H15271.0°56.8°
C16C23H231H232121.1°120.0°
C16C23O15HO15180.0°180.0°
N17C18N19C200.6°0.0°
C18N17C22C210.9°0.2°
N17C18N19H1179.4°180.0°
C18N17C22H22179.1°179.7°
C18N17C12H1218.7°4.9°
C22N17C18N191.1°0.3°
N17C22C21C200.2°0.1°
N17C22C21H22180.0°179.9°
N17C22C21H2179.7°180.0°
C22N17C12H12164.4°175.3°
C18N19C20H1180.0°180.0°
C18N19C20C210.0°0.3°
N19C20C21C220.2°0.3°
N19C20C21H2179.8°179.7°
C20C21C22H2180.0°180.0°
C21C20N19H1180.0°179.7°
C20C21C22H22179.8°180.0°
H2C21C22H220.3°0.0°
H12C12C13H13139.1°56.8°
H12C12C13H132157.9°177.0°
H151C15C16H1671.0°56.8°
H152C15C16H16168.0°176.9°
H16C16C23H23174.9°64.9°
H16C16C23H232164.4°175.1°
H231C23O15HO1560.4°60.0°
H232C23O15HO1560.3°60.0°
H5'2C5'C4'H4'46.3°176.4°
H5'1C5'C4'H4'74.1°63.6°
H4'C4'C3'H3'105.6°160.3°
H3'C3'O3'HO3'56.4°56.4°
H3'C3'C2'H2'230.9°21.3°
H3'C3'C2'H2'191.1°143.9°
H2'2C2'C1'H1'152.9°124.0°
H2'1C2'C1'H1'30.9°1.4°
H5M3C5MH5M1H5M2120.0°120.0°

225158

PDB entries from 2024-09-18

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