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SummaryGeometryRelated PDB entries

VDM

Bonds
First atomSecond atomBond order typeDistance
(experimental model)		Distance
(ideal model)		Properties
O7C7sing1.42Å1.43Å
O7H7sing0.97Å0.95Å
C7C5sing1.50Å1.50Å
C7H7C1sing1.09Å1.12Å
C7H7C2sing1.09Å1.12Å
C5C6doub1.35Å1.35Å
C5C4sing1.51Å1.52Å
C6C1sing1.50Å1.53Å
C6H6sing1.09Å1.10Å
C4O4sing1.43Å1.42Å
C4C3sing1.54Å1.51Å
C4H4sing1.10Å1.11Å
O4HAsing0.97Å0.95Å
C3O3sing1.43Å1.43Å
C3C2sing1.53Å1.53Å
C3H3sing1.10Å1.12Å
O3HBsing0.97Å0.95Å
C2O2sing1.43Å1.43Å
C2C1sing1.54Å1.55Å
C2H2sing1.10Å1.11Å
O2HCsing0.97Å0.95Å
C1N1'sing1.47Å1.47Å
C1H1sing1.10Å1.12Å
N1'C1'sing1.47Å1.47Å
N1'H1'sing1.02Å1.02Å
C1'HDsing1.10Å1.11Å
C1'C2'sing1.54Å1.53Å
C1'C6'sing1.53Å1.55Å
C2'H2'sing1.10Å1.11Å
C2'O2'sing1.43Å1.43Å
C2'C3'sing1.53Å1.53Å
O2'HEsing0.97Å0.95Å
C6'H6'1sing1.10Å1.12Å
C6'H6'2sing1.10Å1.11Å
C6'C5'sing1.54Å1.53Å
C5'H5'sing1.10Å1.11Å
C5'C7'sing1.53Å1.53Å
C5'C4'sing1.54Å1.54Å
C7'H7'1sing1.09Å1.11Å
C7'H7'2sing1.09Å1.11Å
C7'O7'sing1.41Å1.44Å
O7'H7'sing0.97Å0.95Å
C4'H4'sing1.10Å1.11Å
C4'O4'sing1.43Å1.43Å
C4'C3'sing1.53Å1.53Å
O4'HFsing0.97Å0.95Å
C3'H3'sing1.10Å1.11Å
C3'O3'sing1.43Å1.43Å
O3'HGsing0.97Å0.95Å
Angles
First atomSecond atomThird atomAngle
(experimental model)		Angle
(ideal model)
C7O7H7104.3°107.2°
O7C7C5104.3°109.6°
O7C7H7C1114.2°109.4°
O7C7H7C2114.2°109.0°
C5C7H7C1114.2°110.0°
C5C7H7C2114.2°109.3°
C7C5C6118.8°120.9°
C7C5C4118.0°117.1°
H7C1C7H7C296.3°109.6°
C6C5C4123.1°122.1°
C5C6C1122.3°124.1°
C5C6H6112.5°119.1°
C5C4O4113.2°110.3°
C5C4C3112.7°114.5°
C5C4H4103.8°108.6°
C1C6H6125.1°116.7°
C6C1C2107.8°111.5°
C6C1N1'109.2°109.3°
C6C1H1112.3°109.1°
O4C4C3107.0°106.8°
O4C4H4109.8°106.5°
C4O4HA113.2°106.4°
C3C4H4110.4°109.9°
C4C3O3106.5°108.4°
C4C3C2109.1°111.3°
C4C3H3113.1°111.6°
O3C3C2113.4°108.2°
O3C3H3108.7°106.0°
C3O3HB106.5°106.4°
C2C3H3106.2°111.1°
C3C2O2110.6°109.4°
C3C2C1108.6°111.5°
C3C2H2110.9°109.5°
O2C2C1113.7°110.4°
O2C2H2105.4°106.0°
C2O2HC113.7°106.4°
C1C2H2107.6°109.8°
C2C1N1'113.6°111.7°
C2C1H1107.8°108.1°
N1'C1H1106.4°107.1°
C1N1'C1'120.9°110.6°
C1N1'H1'108.1°109.7°
C1'N1'H1'108.1°108.6°
N1'C1'HD104.5°106.9°
N1'C1'C2'113.6°111.1°
N1'C1'C6'113.9°110.0°
HDC1'C2'105.6°109.1°
HDC1'C6'105.2°109.7°
C2'C1'C6'112.9°110.0°
C1'C2'H2'107.2°109.2°
C1'C2'O2'111.3°110.1°
C1'C2'C3'111.9°112.8°
C1'C6'H6'1109.8°109.9°
C1'C6'H6'2109.8°108.8°
C1'C6'C5'116.1°112.6°
H2'C2'O2'107.8°106.0°
H2'C2'C3'107.1°109.4°
O2'C2'C3'111.3°109.1°
C2'O2'HE111.2°106.4°
C2'C3'C4'108.8°111.8°
C2'C3'H3'109.1°111.4°
C2'C3'O3'110.7°107.5°
H6'1C6'H6'2100.4°106.3°
H6'1C6'C5'109.8°109.6°
H6'2C6'C5'109.8°109.4°
C6'C5'H5'108.1°109.4°
C6'C5'C7'110.9°110.1°
C6'C5'C4'111.6°111.3°
H5'C5'C7'107.0°106.2°
H5'C5'C4'106.2°108.6°
C7'C5'C4'112.6°111.1°
C5'C7'H7'1112.0°109.5°
C5'C7'H7'2112.0°109.6°
C5'C7'O7'110.1°108.3°
C5'C4'H4'109.4°110.3°
C5'C4'O4'110.8°108.3°
C5'C4'C3'109.2°112.6°
H7'1C7'H7'298.4°110.1°
H7'1C7'O7'112.0°109.6°
H7'2C7'O7'112.0°109.6°
C7'O7'H7'110.1°107.2°
H4'C4'O4'107.3°106.7°
H4'C4'C3'108.9°109.8°
O4'C4'C3'111.3°108.9°
C4'O4'HF111.3°106.3°
C4'C3'H3'110.4°111.1°
C4'C3'O3'109.5°108.8°
H3'C3'O3'108.4°105.9°
C3'O3'HG110.8°106.2°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)		Torsion
(ideal model)
O7C7C5H7C1125.3°120.3°
O7C7C5H7C2125.3°119.4°
O7C7H7C1H7C2120.1°119.5°
O7C7C5C6100.1°119.7°
O7C7C5C475.7°58.9°
H7O7C7C5180.0°71.3°
H7O7C7H7C154.7°49.4°
H7O7C7H7C254.7°169.2°
C5C7H7C1H7C2120.1°120.1°
C7C5C6C4175.6°178.6°
C7C5C6C1179.8°177.2°
C7C5C6H60.2°2.0°
C7C5C4O450.1°52.4°
C7C5C4C3171.7°172.8°
C7C5C4H468.9°64.0°
H7C1C7C5C625.2°120.0°
H7C1C7C5C4159.0°61.4°
H7C2C7C5C6134.7°0.3°
H7C2C7C5C449.5°178.3°
C5C6C1H6180.0°179.2°
C6C5C4O4134.4°129.0°
C6C5C4C312.7°8.5°
C6C5C4H4106.7°114.7°
C5C6C1C226.6°18.2°
C5C6C1N1'97.2°105.8°
C5C6C1H1145.1°137.5°
C4C5C6C14.3°1.4°
C4C5C6H6175.7°179.4°
C5C4O4C3124.8°124.9°
C5C4O4H4115.4°117.7°
C5C4C3H4115.5°122.5°
C5C4O4HA180.0°64.7°
C5C4C3O3166.5°156.7°
C5C4C3C243.7°37.7°
C5C4C3H374.2°87.0°
C6C1C2C357.4°47.3°
C6C1C2O2179.1°169.2°
C6C1C2N1'121.1°122.6°
C6C1C2H1121.4°119.9°
C6C1C2H262.7°74.3°
C6C1N1'H1121.3°118.0°
C6C1N1'C1'34.6°60.2°
C6C1N1'H1'90.6°180.0°
H6C6C1C2153.4°161.0°
H6C6C1N1'82.8°75.0°
H6C6C1H134.9°41.8°
O4C4C3H4119.4°115.1°
O4C4C3O368.5°80.9°
O4C4C3C2168.8°160.1°
O4C4C3H350.9°35.4°
C3C4O4HA55.2°60.3°
C4C3O3C2119.9°120.9°
C4C3O3H3122.2°119.9°
C4C3C2H3122.2°124.9°
C4C3O3HB180.0°131.5°
C4C3C2O2166.2°179.8°
C4C3C2C168.3°57.8°
C4C3C2H249.7°64.0°
H4C4O4HA64.6°177.7°
H4C4C3O351.0°34.2°
H4C4C3C271.8°84.8°
H4C4C3H3170.3°150.5°
O3C3C2H3119.4°116.0°
O3C3C2O247.8°60.7°
O3C3C2C1173.2°176.9°
O3C3C2H268.8°55.1°
C2C3O3HB60.1°107.6°
C3C2O2C1122.5°123.1°
C3C2O2H2119.9°118.0°
C3C2C1H2120.1°121.6°
C3C2O2HC57.5°86.2°
C3C2C1N1'63.7°75.3°
C3C2C1H1178.7°167.2°
H3C3O3HB57.8°11.6°
H3C3C2O271.6°55.3°
H3C3C2C153.9°67.1°
H3C3C2H2171.8°171.1°
O2C2C1H2116.3°116.5°
O2C2C1N1'59.9°46.6°
O2C2C1H157.7°71.0°
C1C2O2HC180.0°150.7°
C2C1N1'H1118.4°118.1°
C2C1N1'C1'154.9°176.0°
C2C1N1'H1'29.6°56.2°
H2C2O2HC62.4°31.8°
H2C2C1N1'176.2°163.1°
H2C2C1H158.6°45.6°
C1N1'C1'H1'125.3°120.4°
C1N1'C1'HD27.6°58.6°
C1N1'C1'C2'142.2°177.5°
C1N1'C1'C6'86.6°60.5°
H1C1N1'C1'86.7°57.8°
H1C1N1'H1'148.0°61.9°
N1'C1'HDC2'120.1°120.2°
N1'C1'HDC6'120.2°119.2°
N1'C1'C2'C6'131.7°122.0°
N1'C1'C2'H2'159.0°171.1°
N1'C1'C2'O2'41.3°55.1°
N1'C1'C2'C3'83.9°67.1°
N1'C1'C6'H6'133.7°55.4°
N1'C1'C6'H6'2143.1°171.4°
N1'C1'C6'C5'91.6°67.2°
H1'N1'C1'HD97.6°179.0°
H1'N1'C1'C2'16.9°62.1°
H1'N1'C1'C6'148.1°59.9°
HDC1'C2'C6'114.5°120.4°
HDC1'C2'H2'45.1°53.5°
HDC1'C2'O2'72.6°62.5°
HDC1'C2'C3'162.2°175.3°
HDC1'C6'H6'180.1°61.9°
HDC1'C6'H6'229.3°54.2°
HDC1'C6'C5'154.6°175.6°
C1'C2'H2'O2'119.9°118.6°
C1'C2'H2'C3'120.2°123.9°
C1'C2'O2'C3'125.5°124.3°
C1'C2'O2'HE180.0°169.6°
C2'C1'C6'H6'1165.2°178.0°
C2'C1'C6'H6'285.4°65.9°
C2'C1'C6'C5'39.9°55.5°
C1'C2'C3'C4'61.1°53.4°
C1'C2'C3'H3'59.3°71.6°
C1'C2'C3'O3'178.5°172.8°
C6'C1'C2'H2'69.4°66.9°
C6'C1'C2'O2'173.0°177.1°
C6'C1'C2'C3'47.7°54.9°
C1'C6'H6'1H6'2115.6°117.6°
C1'C6'H6'1C5'128.8°124.3°
C1'C6'H6'2C5'128.8°123.4°
C1'C6'C5'H5'72.1°65.6°
C1'C6'C5'C7'170.9°178.1°
C1'C6'C5'C4'44.4°54.4°
H2'C2'O2'C3'117.2°117.7°
H2'C2'O2'HE62.8°72.3°
H2'C2'C3'C4'56.1°68.4°
H2'C2'C3'H3'176.5°166.7°
H2'C2'C3'O3'64.3°51.0°
O2'C2'C3'C4'173.7°176.2°
O2'C2'C3'H3'65.9°51.2°
O2'C2'C3'O3'53.3°64.5°
C3'C2'O2'HE54.4°45.3°
C2'C3'C4'C5'65.1°51.5°
C2'C3'C4'H4'54.3°71.9°
C2'C3'C4'O4'172.4°171.7°
C2'C3'C4'H3'119.6°125.1°
C2'C3'C4'O3'121.2°118.6°
C2'C3'H3'O3'120.7°116.6°
C2'C3'O3'HG180.0°28.9°
H6'1C6'H6'2C5'115.6°118.3°
H6'1C6'C5'H5'53.2°57.1°
H6'1C6'C5'C7'63.8°59.2°
H6'1C6'C5'C4'169.7°177.1°
H6'2C6'C5'H5'162.7°173.3°
H6'2C6'C5'C7'45.6°57.0°
H6'2C6'C5'C4'80.9°66.7°
C6'C5'H5'C7'119.5°118.8°
C6'C5'H5'C4'119.9°121.6°
C6'C5'C7'C4'126.0°123.8°
C6'C5'C7'H7'166.2°60.0°
C6'C5'C7'H7'2175.6°60.9°
C6'C5'C7'O7'59.1°179.5°
C6'C5'C4'H4'62.7°71.2°
C6'C5'C4'O4'179.3°172.4°
C6'C5'C4'C3'56.4°51.9°
H5'C5'C7'C4'116.4°117.9°
H5'C5'C7'H7'1176.2°58.3°
H5'C5'C7'H7'266.7°179.2°
H5'C5'C7'O7'58.6°61.2°
H5'C5'C4'H4'179.8°168.3°
H5'C5'C4'O4'61.7°51.9°
H5'C5'C4'C3'61.2°68.6°
C5'C7'H7'1H7'2117.9°120.6°
C5'C7'H7'1O7'124.2°118.7°
C5'C7'H7'2O7'124.2°118.7°
C5'C7'O7'H7'180.0°33.7°
C7'C5'C4'H4'62.9°51.9°
C7'C5'C4'O4'55.1°64.5°
C7'C5'C4'C3'178.0°175.0°
C4'C5'C7'H7'159.8°176.2°
C4'C5'C7'H7'249.7°62.9°
C4'C5'C7'O7'174.9°56.7°
C5'C4'H4'O4'120.2°117.5°
C5'C4'H4'C3'119.3°124.7°
C5'C4'O4'C3'121.7°122.8°
C5'C4'O4'HF58.3°69.7°
C5'C4'C3'H3'54.6°73.6°
C5'C4'C3'O3'173.8°170.2°
H7'1C7'H7'2O7'117.9°120.7°
H7'1C7'O7'H7'54.7°85.8°
H7'2C7'O7'H7'54.8°153.2°
H4'C4'O4'C3'119.0°118.4°
H4'C4'O4'HF61.0°171.6°
H4'C4'C3'H3'174.0°163.0°
H4'C4'C3'O3'66.8°46.8°
O4'C4'C3'H3'68.0°46.6°
O4'C4'C3'O3'51.2°69.6°
C3'C4'O4'HF180.0°53.1°
C4'C3'H3'O3'119.9°118.0°
C4'C3'O3'HG60.1°92.4°
H3'C3'O3'HG60.4°148.1°

224931

PDB entries from 2024-09-11

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