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1YD

Bonds
First atomSecond atomBond order typeDistance
(experimental model)
Distance
(ideal model)
Properties
O4'C1'sing1.43Å1.39Å
O4'C4'sing1.43Å1.40Å
C1'N9sing1.46Å1.46Å
C1'C2'sing1.54Å1.55Å
N3C2doub1.32Å1.37ÅAromatic
N3C4sing1.33Å1.32ÅAromatic
C2N1sing1.32Å1.38ÅAromatic
O2'C2'sing1.43Å1.41Å
C4N9sing1.37Å1.31ÅAromatic
C4C5doub1.41Å1.33ÅAromatic
N9C8sing1.36Å1.32ÅAromatic
N1C6doub1.33Å1.33ÅAromatic
C2'C3'sing1.54Å1.46Å
C5C6sing1.41Å1.32ÅAromatic
C5N7sing1.35Å1.31ÅAromatic
C8N7doub1.30Å1.33ÅAromatic
C4'C5'sing1.53Å1.49Å
C4'C3'sing1.54Å1.47Å
C6N6sing1.38Å1.32Å
C5'O5'sing1.43Å1.42Å
C3'O3'sing1.43Å1.44Å
O5'PBSsing1.61Å1.51Å
OAEPBSdoub1.48Å1.45Å
PBSOAIsing1.61Å1.57Å
PBSOAZsing1.61Å1.56Å
O3'PBRsing1.61Å1.61Å
OAZCBMsing1.43Å1.44Å
PBROAHdoub1.48Å1.55Å
PBROAVsing1.61Å1.56Å
PBROADsing1.61Å1.46Å
OAVCANsing1.43Å1.41Å
CBMCBKsing1.54Å1.51Å
CBMCBIsing1.54Å1.48Å
CANCBKsing1.53Å1.50Å
CBKOAXsing1.42Å1.37Å
CBIOAGsing1.43Å1.42Å
CBICBOsing1.54Å1.57Å
CALNARdoub1.30Å1.32ÅAromatic
CALNBQsing1.36Å1.32ÅAromatic
NARCBEsing1.36Å1.32ÅAromatic
NBQCBOsing1.47Å1.48Å
NBQCBGsing1.37Å1.32ÅAromatic
OAXCBOsing1.43Å1.41Å
CBECBGdoub1.40Å1.33ÅAromatic
CBECBCsing1.41Å1.32Å
OACCBCdoub1.22Å1.22Å
CBGNASsing1.34Å1.33Å
CBCNATsing1.35Å1.36Å
NASCBAdoub1.31Å1.34Å
NATCBAsing1.36Å1.36Å
CBANAAsing1.37Å1.32Å
NATH1sing0.97Å1.00Å
NAAH2sing0.97Å1.00Å
NAAH3sing0.97Å1.00Å
CALH4sing1.08Å1.08Å
CBOH5sing1.09Å1.10Å
CBIH6sing1.09Å1.10Å
OAGH7sing0.97Å0.95Å
CBKH8sing1.09Å1.10Å
CANH9sing1.09Å1.10Å
CANH10sing1.09Å1.10Å
OADH11sing0.97Å0.95Å
CBMH12sing1.09Å1.10Å
OAIH13sing0.97Å0.95Å
C5'H14sing1.09Å1.10Å
C5'H15sing1.09Å1.10Å
C4'H16sing1.09Å1.10Å
C3'H17sing1.09Å1.10Å
C2'H18sing1.09Å1.10Å
O2'H19sing0.97Å0.95Å
C1'H20sing1.09Å1.10Å
C8H21sing1.08Å1.08Å
C2H22sing1.08Å1.08Å
N6H23sing0.97Å1.00Å
N6H24sing0.97Å1.00Å
Angles
First atomSecond atomThird atomAngle
(experimental model)
Angle
(ideal model)
C1'O4'C4'100.9°109.6°
O4'C1'N9104.9°109.8°
O4'C1'C2'102.5°107.9°
O4'C1'H20113.0°109.8°
O4'C4'C5'106.3°109.9°
O4'C4'C3'97.1°107.7°
O4'C4'H16112.8°109.8°
N9C1'C2'113.6°109.7°
C1'N9C4122.5°126.3°
C1'N9C8130.0°126.3°
N9C1'H20111.9°109.8°
C1'C2'O2'110.7°110.4°
C1'C2'C3'101.8°105.0°
C1'C2'H18111.6°110.4°
C2'C1'H20110.5°109.8°
C2N3C4119.9°120.7°
N3C2N1118.2°122.4°
N3C2H22120.9°118.8°
N3C4N9129.7°134.9°
N3C4C5121.2°119.0°
C2N1C6119.3°121.2°
N1C2H22120.9°118.8°
O2'C2'C3'104.9°110.3°
O2'C2'H18113.9°110.3°
C2'O2'H19109.5°114.0°
N9C4C5109.1°106.0°
C4N9C8107.5°107.4°
C4C5C6119.9°118.2°
C4C5N7107.3°107.1°
N9C8N7108.2°110.0°
N9C8H21125.9°125.0°
N1C6C5121.5°118.4°
N1C6N6120.5°120.8°
C2'C3'C4'97.8°105.0°
C2'C3'O3'113.6°110.3°
C2'C3'H17109.1°110.3°
C3'C2'H18113.0°110.3°
C6C5N7132.8°134.7°
C5C6N6118.0°120.8°
C5N7C8108.1°109.5°
N7C8H21126.0°125.0°
C5'C4'C3'116.9°109.9°
C4'C5'O5'102.5°109.5°
C4'C5'H14111.2°109.5°
C4'C5'H15111.2°109.4°
C5'C4'H16111.3°109.8°
C4'C3'O3'117.3°110.5°
C3'C4'H16111.6°109.8°
C4'C3'H17108.9°110.4°
C6N6H23109.5°120.0°
C6N6H24109.5°120.0°
C5'O5'PBS117.9°123.0°
O5'C5'H14111.2°109.5°
O5'C5'H15111.2°109.5°
C3'O3'PBR138.0°123.0°
O3'C3'H17109.4°110.2°
O5'PBSOAE109.0°109.4°
O5'PBSOAI109.7°109.5°
O5'PBSOAZ103.0°109.5°
OAEPBSOAI111.9°109.5°
OAEPBSOAZ110.5°109.5°
OAIPBSOAZ112.4°109.5°
PBSOAIH13109.5°114.1°
PBSOAZCBM135.8°123.0°
O3'PBROAH113.0°109.5°
O3'PBROAV105.3°109.5°
O3'PBROAD107.9°109.5°
OAZCBMCBK108.4°110.4°
OAZCBMCBI118.8°110.4°
OAZCBMH12111.3°110.2°
OAHPBROAV99.6°109.4°
OAHPBROAD117.1°109.5°
OAVPBROAD113.1°109.5°
PBROAVCAN125.1°123.0°
PBROADH11109.5°113.9°
OAVCANCBK100.2°109.4°
OAVCANH9111.8°109.5°
OAVCANH10111.7°109.5°
CBKCBMCBI96.2°105.1°
CBMCBKCAN115.8°109.7°
CBMCBKOAX103.0°108.1°
CBMCBKH8107.4°109.6°
CBKCBMH12110.3°110.4°
CBMCBIOAG103.4°110.5°
CBMCBICBO103.5°104.2°
CBMCBIH6113.4°110.6°
CBICBMH12110.7°110.3°
CANCBKOAX113.6°110.0°
CANCBKH8107.5°109.5°
CBKCANH9111.8°109.4°
CBKCANH10111.8°109.4°
CBKOAXCBO97.4°111.5°
OAXCBKH8109.2°109.9°
OAGCBICBO109.4°110.5°
OAGCBIH6114.4°110.4°
CBIOAGH7109.5°114.0°
CBICBONBQ112.5°109.8°
CBICBOOAX103.1°107.5°
CBICBOH5109.1°109.8°
CBOCBIH6111.9°110.4°
NARCALNBQ108.4°109.8°
CALNARCBE108.3°109.4°
NARCALH4125.8°125.1°
CALNBQCBO128.7°126.2°
CALNBQCBG107.6°107.5°
NBQCALH4125.8°125.1°
NARCBECBG107.7°107.2°
NARCBECBC132.0°134.1°
CBONBQCBG123.7°126.2°
NBQCBOOAX110.1°109.9°
NBQCBOH5110.4°109.9°
NBQCBGCBE108.1°106.1°
NBQCBGNAS131.1°134.2°
OAXCBOH5111.4°109.9°
CBGCBECBC120.3°118.6°
CBECBGNAS120.8°119.7°
CBECBCOAC123.0°120.8°
CBECBCNAT120.6°118.3°
OACCBCNAT116.4°120.8°
CBGNASCBA119.8°121.1°
CBCNATCBA118.2°120.4°
CBCNATH1120.9°119.8°
NASCBANAT120.3°121.9°
NASCBANAA123.2°119.1°
NATCBANAA116.5°119.1°
CBANATH1120.9°119.8°
CBANAAH2120.0°120.0°
CBANAAH3120.0°120.0°
H2NAAH3120.0°120.1°
H9CANH10109.5°109.5°
H14C5'H15109.5°109.4°
H23N6H24109.4°120.0°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)
Torsion
(ideal model)
O4'C1'N9C2'111.1°118.4°
O4'C1'N9H20122.9°120.8°
O4'C1'C2'H20120.7°119.6°
O4'C1'C2'O2'109.2°106.8°
O4'C1'N9C4165.1°156.8°
O4'C1'N9C815.6°23.6°
O4'C1'C2'C3'1.9°12.1°
C1'O4'C4'C5'178.2°142.2°
C1'O4'C4'C3'61.0°22.5°
C1'O4'C4'H1656.0°97.0°
O4'C1'C2'H18122.8°131.0°
C4'O4'C1'N980.4°97.7°
C4'O4'C1'C2'38.4°21.8°
O4'C4'C3'C2'57.7°13.9°
O4'C4'C5'C3'107.0°118.3°
O4'C4'C5'H16123.1°120.8°
O4'C4'C3'H16117.9°119.5°
O4'C4'C5'O5'84.6°127.5°
O4'C4'C3'O3'179.4°132.9°
O4'C4'C5'H1434.2°112.4°
O4'C4'C5'H15156.5°7.5°
O4'C4'C3'H1755.6°105.0°
C4'O4'C1'H20157.4°141.4°
N9C1'C2'H20126.7°120.8°
C1'N9C4N30.7°0.1°
N9C1'C2'O2'138.3°133.6°
C1'N9C4C8179.4°179.7°
C1'N9C4C5179.5°179.9°
N9C1'C2'C3'110.6°107.5°
C1'N9C8N7179.3°180.0°
N9C1'C2'H1810.2°11.4°
C1'N9C8H210.7°0.0°
C1'C2'O2'C3'109.1°115.6°
C1'C2'O2'H18126.8°122.3°
C2'C1'N9C483.7°84.9°
C2'C1'N9C895.5°94.8°
C1'C2'C3'H18119.8°119.0°
C1'C2'C3'C4'32.9°1.1°
C1'C2'C3'O3'157.4°120.1°
C1'C2'C3'H1780.3°117.8°
C1'C2'O2'H19180.0°64.4°
N3C2N1H22180.0°180.0°
C2N3C4N9179.5°180.0°
C2N3C4C50.2°0.2°
N3C2N1C60.5°0.5°
C4N3C2N10.7°0.0°
N3C4N9C5179.8°179.8°
N3C4N9C8179.9°179.8°
N3C4C5C60.5°0.1°
N3C4C5N7180.0°179.7°
C4N3C2H22179.3°180.0°
C2N1C6C50.2°0.7°
C2N1C6N6179.8°179.9°
O2'C2'C3'H18124.7°122.1°
O2'C2'C3'C4'148.4°120.0°
O2'C2'C3'O3'87.2°121.0°
O2'C2'C3'H1735.2°1.1°
O2'C2'C1'H2011.5°12.9°
N9C4C5C6179.7°179.8°
N9C4C5N70.2°0.4°
C4N9C8N70.0°0.3°
C4N9C1'H2042.3°35.9°
C4N9C8H21180.0°179.7°
C5C4N9C80.1°0.4°
C4C5C6N10.7°0.5°
C4C5C6N7179.4°179.8°
C4C5N7C80.2°0.2°
C4C5C6N6179.7°179.7°
N9C8N7C50.1°0.0°
N9C8N7H21180.0°180.0°
C8N9C1'H20138.5°144.5°
N1C6C5N6179.6°179.2°
N1C6C5N7179.9°179.3°
C6N1C2H22179.5°179.6°
N1C6N6H230.0°179.2°
N1C6N6H24120.0°0.8°
C2'C3'C4'C5'170.0°133.5°
C2'C3'C4'O3'121.8°119.0°
C2'C3'C4'H17113.3°118.9°
C2'C3'O3'H17122.2°122.1°
C2'C3'O3'PBR47.6°112.0°
C2'C3'C4'H1660.3°105.6°
C3'C2'O2'H1971.0°180.0°
C3'C2'C1'H20122.6°131.7°
C6C5N7C8179.6°180.0°
C5C6N6H23179.6°0.0°
C5C6N6H2459.7°180.0°
N7C5C6N60.3°0.0°
C5N7C8H21179.9°180.0°
C5'C4'C3'H16129.7°120.9°
C4'C5'O5'H14118.9°120.0°
C4'C5'O5'H15118.9°120.0°
C5'C4'C3'O3'68.2°107.5°
C4'C5'O5'PBS142.0°143.5°
C4'C5'H14H15123.2°119.9°
C5'C4'C3'H1756.7°14.7°
C3'C4'C5'O5'168.3°114.2°
C4'C3'O3'H17124.7°122.2°
C4'C3'O3'PBR65.6°132.4°
C3'C4'C5'H1472.8°5.9°
C3'C4'C5'H1549.5°125.8°
C4'C3'C2'H1886.9°117.9°
C6N6H23H24120.0°180.0°
C5'O5'PBSOAE79.9°7.1°
C5'O5'PBSOAI157.2°112.9°
C5'O5'PBSOAZ37.4°127.0°
O5'C5'H14H15123.3°120.0°
O5'C5'C4'H1638.5°6.7°
C3'O3'PBROAH28.2°115.1°
C3'O3'PBROAV79.5°125.0°
C3'O3'PBROAD159.4°5.0°
O3'C3'C4'H1661.5°13.4°
O3'C3'C2'H1837.5°1.1°
O5'PBSOAEOAI121.5°120.0°
O5'PBSOAEOAZ112.5°120.0°
O5'PBSOAIOAZ113.9°120.0°
O5'PBSOAZCBM139.3°118.4°
O5'PBSOAIH13121.1°59.9°
PBSO5'C5'H1499.1°23.5°
PBSO5'C5'H1523.2°96.5°
OAEPBSOAIOAZ125.0°120.0°
OAEPBSOAZCBM104.4°1.5°
OAEPBSOAIH130.0°60.0°
OAIPBSOAZCBM21.3°121.5°
PBSOAZCBMCBK120.1°129.2°
PBSOAZCBMCBI11.9°115.1°
PBSOAZCBMH12118.5°7.0°
OAZPBSOAIH13125.0°180.0°
O3'PBROAHOAV111.3°120.0°
O3'PBROAHOAD126.4°120.0°
O3'PBROAVOAD117.7°120.0°
O3'PBROAVCAN77.0°122.9°
O3'PBROADH11128.9°180.0°
PBRO3'C3'H17169.8°10.1°
OAZCBMCBKCBI123.2°119.0°
OAZCBMCBKH12122.1°122.1°
OAZCBMCBIH12130.6°122.1°
OAZCBMCBKCAN59.4°113.0°
OAZCBMCBKOAX176.0°127.0°
OAZCBMCBIOAG108.6°106.1°
OAZCBMCBICBO137.3°135.2°
OAZCBMCBIH615.8°16.4°
OAZCBMCBKH860.7°7.2°
OAHPBROAVOAD125.1°120.0°
OAHPBROAVCAN165.7°117.1°
OAHPBROADH110.0°60.0°
PBROAVCANCBK175.1°137.9°
PBROAVCANH956.6°102.2°
PBROAVCANH1066.4°17.9°
OAVPBROADH11115.0°60.0°
OADPBROAVCAN40.6°2.9°
OAVCANCBKCBM127.1°117.8°
OAVCANCBKH9118.5°120.0°
OAVCANCBKH10118.5°120.0°
OAVCANCBKOAX114.0°123.4°
OAVCANCBKH87.0°2.6°
OAVCANH9H10124.3°120.1°
CBKCBMCBIH12114.4°118.9°
CBMCBKCANOAX118.9°118.8°
CBMCBKCANH8120.1°120.3°
CBMCBKOAXH8113.9°119.6°
CBKCBMCBIOAG136.5°134.9°
CBKCBMCBICBO22.4°16.2°
CBMCBKOAXCBO61.6°4.4°
CBKCBMCBIH699.1°102.6°
CBMCBKCANH98.6°122.2°
CBMCBKCANH10114.4°2.2°
CBICBMCBKCAN177.4°128.0°
CBICBMCBKOAX52.8°8.0°
CBMCBIOAGCBO109.7°114.8°
CBMCBIOAGH6123.8°122.7°
CBMCBICBOH6122.4°118.8°
CBMCBICBONBQ107.4°138.8°
CBMCBICBOOAX11.1°19.2°
CBMCBICBOH5129.6°100.3°
CBMCBIOAGH7180.0°176.3°
CBICBMCBKH862.4°111.8°
CANCBKOAXH8120.1°120.6°
CANCBKOAXCBO172.4°115.4°
CBKCANH9H10124.3°120.0°
CANCBKCBMH1262.7°9.1°
CBKOAXCBOCBI43.1°15.1°
CBKOAXCBONBQ77.1°134.6°
CBKOAXCBOH5160.0°104.4°
OAXCBKCANH9127.5°3.5°
OAXCBKCANH104.5°116.5°
OAXCBKCBMH1261.9°110.9°
OAGCBICBOH6127.9°122.5°
OAGCBICBONBQ142.9°102.5°
OAGCBICBOOAX98.5°137.9°
OAGCBICBOH520.0°18.4°
OAGCBICBMH1222.0°16.0°
CBICBONBQCAL90.7°94.8°
CBICBONBQOAX114.4°118.1°
CBICBONBQH5122.2°120.9°
CBICBONBQCBG88.1°85.6°
CBICBOOAXH5116.9°119.5°
CBOCBIOAGH770.3°61.5°
CBOCBICBMH1292.1°102.8°
NARCALNBQH4180.0°179.8°
NARCALNBQCBO179.1°180.0°
NARCALNBQCBG0.2°0.3°
CALNARCBECBG0.1°0.0°
CALNARCBECBC179.7°179.4°
NBQCALNARCBE0.1°0.2°
CALNBQCBOCBG178.8°179.6°
CALNBQCBOOAX23.7°23.3°
CALNBQCBGCBE0.2°0.3°
CALNBQCBGNAS180.0°179.9°
CALNBQCBOH5147.1°144.3°
NARCBECBGNBQ0.2°0.2°
NARCBECBGCBC179.7°179.5°
NARCBECBCOAC0.3°0.4°
NARCBECBGNAS180.0°180.0°
NARCBECBCNAT179.9°179.9°
CBENARCALH4179.9°180.0°
NBQCBOOAXH5122.8°121.0°
CBONBQCBGCBE179.2°180.0°
CBONBQCBGNAS1.0°0.3°
CBONBQCALH40.9°0.2°
NBQCBOCBIH615.0°20.0°
CBGNBQCBOOAX157.5°156.3°
NBQCBGCBENAS179.8°179.8°
NBQCBGCBECBC179.9°179.7°
NBQCBGNASCBA180.0°180.0°
CBGNBQCALH4179.8°179.9°
CBGNBQCBOH534.1°35.3°
OAXCBOCBIH6133.5°99.6°
CBOOAXCBKH852.3°124.0°
CBGCBECBCOAC179.9°179.8°
CBGCBECBCNAT0.2°0.5°
CBECBGNASCBA0.3°0.2°
CBECBCOACNAT179.9°179.7°
CBCCBECBGNAS0.3°0.5°
CBECBCNATCBA0.1°0.3°
CBECBCNATH1179.9°179.8°
OACCBCNATCBA180.0°180.0°
OACCBCNATH10.0°0.1°
CBGNASCBANAT0.2°0.0°
CBGNASCBANAA178.7°180.0°
CBCNATCBANAS0.1°0.0°
CBCNATCBAH1180.0°179.9°
CBCNATCBANAA178.7°180.0°
NASCBANATNAA178.6°180.0°
NASCBANATH1179.9°180.0°
NASCBANAAH20.0°180.0°
NASCBANAAH3180.0°0.0°
NATCBANAAH2178.6°0.0°
NATCBANAAH31.4°180.0°
NAACBANATH11.3°0.1°
CBANAAH2H3180.0°180.0°
H5CBOCBIH6108.0°140.9°
H6CBIOAGH756.2°61.0°
H6CBICBMH12146.5°138.5°
H8CBKCANH9111.4°117.4°
H8CBKCANH10125.5°122.6°
H8CBKCBMH12177.2°129.3°
H14C5'C4'H16157.4°126.7°
H15C5'C4'H1680.4°113.3°
H16C4'C3'H17173.6°135.5°
H17C3'C2'H18159.9°123.2°
H18C2'O2'H1953.2°57.8°
H18C2'C1'H20116.5°109.3°

224931

PDB entries from 2024-09-11

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