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GPD

Bonds
First atomSecond atomBond order typeDistance
(experimental model)
Distance
(ideal model)
Properties
C4GN4Asing1.47Å1.45Å
N4AHN4Asing1.01Å1.00Å
N4AHN4Bsing1.01Å1.00Å
C3GC4Gsing1.53Å1.52Å
C4GC5Gsing1.53Å1.52Å
C4GH4Gsing1.09Å1.10Å
O5GC5Gsing1.43Å1.43Å
C5GC6Gsing1.53Å1.53Å
C5GH5Gsing1.09Å1.10Å
C6GH6Gsing1.09Å1.10Å
C6GH6GAsing1.09Å1.10Å
C6GH6GBsing1.09Å1.10Å
C1GO5Gsing1.43Å1.41Å
C2GC3Gsing1.53Å1.51Å
C3GH3Gsing1.09Å1.10Å
C3GH3GAsing1.09Å1.10Å
O2GC2Gsing1.43Å1.42Å
C1GC2Gsing1.53Å1.51Å
C2GH2Gsing1.09Å1.10Å
O2GHO2Gsing0.97Å0.95Å
C1GO1Gsing1.43Å1.41Å
C1GH1Gsing1.09Å1.10Å
P2O1Gsing1.61Å1.59Å
OPPP2sing1.61Å1.61Å
O3PP2doub1.48Å1.50Å
P2O4Psing1.61Å1.51Å
O4PHO4Psing0.97Å0.95Å
POPPsing1.61Å1.61Å
O5'Psing1.61Å1.61Å
O2PPdoub1.48Å1.49Å
PO1Psing1.61Å1.50Å
O1PHO1Psing0.97Å0.95Å
O5'C5'sing1.43Å1.42Å
C4'C5'sing1.53Å1.51Å
C5'H5'sing1.09Å1.10Å
C5'H5'Asing1.09Å1.10Å
O4'C4'sing1.44Å1.44Å
C3'C4'sing1.54Å1.52Å
C4'H4'sing1.09Å1.10Å
C1'O4'sing1.44Å1.42Å
C2'C3'sing1.55Å1.52Å
O3'C3'sing1.43Å1.43Å
C3'H3'sing1.09Å1.10Å
O3'HO3'sing0.97Å0.95Å
O2'C2'sing1.43Å1.43Å
C1'C2'sing1.55Å1.52Å
C2'H2'sing1.09Å1.10Å
O2'HO2'sing0.97Å0.95Å
N9C1'sing1.47Å1.47Å
C1'H1'sing1.09Å1.10Å
C4N9sing1.37Å1.33ÅAromatic
N9C8sing1.36Å1.33ÅAromatic
N7C8doub1.30Å1.35ÅAromatic
C8H8sing1.08Å1.08Å
C5N7sing1.36Å1.35ÅAromatic
N3C4sing1.34Å1.35Å
C5C4doub1.40Å1.38ÅAromatic
C6C5sing1.41Å1.40Å
N1C6sing1.35Å1.34Å
O6C6doub1.22Å1.24Å
C2N3doub1.31Å1.34Å
N2C2sing1.37Å1.36Å
N1C2sing1.36Å1.35Å
N1HN1sing0.97Å1.00Å
N2HN2sing0.97Å1.00Å
N2HN2Asing0.97Å1.00Å
Angles
First atomSecond atomThird atomAngle
(experimental model)
Angle
(ideal model)
C4GN4AHN4A109.5°111.0°
C4GN4AHN4B109.4°111.0°
N4AC4GC3G106.3°109.5°
N4AC4GC5G109.9°109.5°
N4AC4GH4G112.1°109.5°
HN4AN4AHN4B109.5°111.0°
C3GC4GC5G111.8°109.2°
C3GC4GH4G110.2°109.6°
C4GC3GC2G109.8°109.0°
C4GC3GH3G109.3°109.5°
C4GC3GH3GA109.3°109.6°
C5GC4GH4G106.6°109.6°
C4GC5GO5G115.9°109.4°
C4GC5GC6G113.2°109.5°
C4GC5GH5G102.2°109.5°
O5GC5GC6G110.7°109.5°
O5GC5GH5G105.3°109.5°
C5GO5GC1G113.8°114.1°
C6GC5GH5G108.6°109.5°
C5GC6GH6G109.5°109.5°
C5GC6GH6GA109.5°109.5°
C5GC6GH6GB109.4°109.5°
H6GC6GH6GA109.5°109.5°
H6GC6GH6GB109.5°109.4°
H6GAC6GH6GB109.5°109.5°
O5GC1GC2G112.2°109.4°
O5GC1GO1G108.8°109.5°
O5GC1GH1G105.2°109.5°
C2GC3GH3G109.4°109.5°
C2GC3GH3GA109.3°109.6°
C3GC2GO2G111.1°109.5°
C3GC2GC1G114.3°109.2°
C3GC2GH2G103.4°109.6°
H3GC3GH3GA109.8°109.5°
O2GC2GC1G104.1°109.5°
O2GC2GH2G113.7°109.5°
C2GO2GHO2G109.5°114.0°
C1GC2GH2G110.5°109.5°
C2GC1GO1G98.5°109.5°
C2GC1GH1G114.5°109.6°
O1GC1GH1G117.6°109.4°
C1GO1GP2126.8°123.0°
O1GP2OPP101.4°109.5°
O1GP2O3P107.0°109.4°
O1GP2O4P101.9°109.5°
OPPP2O3P113.4°109.5°
OPPP2O4P110.6°109.5°
P2OPPP124.1°134.0°
O3PP2O4P120.1°109.5°
P2O4PHO4P109.5°114.0°
OPPPO5'104.3°109.5°
OPPPO2P106.9°109.4°
OPPPO1P111.2°109.5°
O5'PO2P106.5°109.5°
O5'PO1P110.8°109.5°
PO5'C5'122.5°123.0°
O2PPO1P116.4°109.4°
PO1PHO1P109.5°113.9°
O5'C5'C4'107.8°109.5°
O5'C5'H5'110.0°109.5°
O5'C5'H5'A110.4°109.5°
C4'C5'H5'110.0°109.5°
C4'C5'H5'A110.4°109.5°
C5'C4'O4'109.4°109.9°
C5'C4'C3'109.2°109.9°
C5'C4'H4'108.8°109.9°
H5'C5'H5'A108.2°109.4°
O4'C4'C3'106.5°107.4°
O4'C4'H4'111.4°109.9°
C4'O4'C1'109.9°107.0°
C3'C4'H4'111.6°109.9°
C4'C3'C2'104.8°104.2°
C4'C3'O3'106.9°110.5°
C4'C3'H3'113.4°110.5°
O4'C1'C2'105.8°103.5°
O4'C1'N9110.8°110.6°
O4'C1'H1'111.8°110.6°
C2'C3'O3'107.4°110.6°
C2'C3'H3'112.9°110.5°
C3'C2'O2'110.3°110.9°
C3'C2'C1'102.5°102.1°
C3'C2'H2'113.8°110.9°
O3'C3'H3'111.0°110.4°
C3'O3'HO3'109.5°114.1°
O2'C2'C1'110.5°111.0°
O2'C2'H2'106.3°110.7°
C2'O2'HO2'109.5°114.0°
C1'C2'H2'113.6°110.9°
C2'C1'N9111.7°110.8°
C2'C1'H1'110.9°110.5°
N9C1'H1'106.0°110.7°
C1'N9C4124.5°126.2°
C1'N9C8126.4°126.3°
C4N9C8109.1°107.5°
N9C4N3132.4°134.2°
N9C4C5107.5°106.1°
N9C8N7108.3°109.8°
N9C8H8125.9°125.0°
N7C8H8125.8°125.2°
C8N7C5108.6°109.4°
N7C5C4106.5°107.2°
N7C5C6134.3°134.1°
N3C4C5120.1°119.7°
C4N3C2119.7°121.1°
C4C5C6119.2°118.6°
C5C6N1118.2°118.3°
C5C6O6123.9°120.9°
N1C6O6117.8°120.8°
C6N1C2122.0°120.3°
C6N1HN1119.0°119.9°
N3C2N2121.5°119.0°
N3C2N1120.7°121.9°
N2C2N1117.8°119.1°
C2N2HN2110.4°120.0°
C2N2HN2A124.9°120.0°
C2N1HN1119.0°119.8°
HN2N2HN2A124.8°120.0°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)
Torsion
(ideal model)
C4GN4AHN4AHN4B120.0°123.9°
N4AC4GC3GC5G119.9°119.9°
N4AC4GC3GH4G121.7°120.1°
N4AC4GC5GH4G121.7°120.1°
N4AC4GC5GO5G171.3°177.5°
N4AC4GC5GC6G59.2°62.5°
N4AC4GC5GH5G57.4°57.5°
N4AC4GC3GC2G159.3°176.9°
N4AC4GC3GH3G80.7°63.3°
N4AC4GC3GH3GA39.5°56.9°
HN4AN4AC4GC3G91.7°60.4°
HN4AN4AC4GC5G29.4°180.0°
HN4AN4AC4GH4G147.8°59.8°
HN4BN4AC4GC3G28.3°175.7°
HN4BN4AC4GC5G149.4°56.1°
HN4BN4AC4GH4G92.2°64.1°
C3GC4GC5GH4G120.5°120.0°
C3GC4GC5GO5G53.6°57.6°
C3GC4GC5GC6G177.0°177.6°
C3GC4GC5GH5G60.3°62.4°
C4GC3GC2GH3G120.0°119.8°
C4GC3GC2GH3GA119.9°120.0°
C4GC3GH3GH3GA119.8°120.2°
C4GC3GC2GO2G129.3°62.9°
C4GC3GC2GC1G11.8°57.0°
C4GC3GC2GH2G108.4°176.9°
C4GC5GO5GC6G130.6°120.0°
C4GC5GO5GH5G112.2°120.0°
C4GC5GC6GH5G112.8°120.0°
C4GC5GC6GH6G53.6°60.0°
C4GC5GC6GH6GA173.6°180.0°
C4GC5GC6GH6GB66.4°60.0°
C4GC5GO5GC1G8.4°61.2°
C5GC4GC3GC2G39.5°57.0°
C5GC4GC3GH3G159.4°176.9°
C5GC4GC3GH3GA80.4°63.0°
H4GC4GC5GO5G66.9°62.4°
H4GC4GC5GC6G62.5°57.6°
H4GC4GC5GH5G179.1°177.6°
H4GC4GC3GC2G78.9°63.0°
H4GC4GC3GH3G41.0°56.9°
H4GC4GC3GH3GA161.2°177.0°
O5GC5GC6GH5G115.1°120.0°
O5GC5GC6GH6G78.5°60.0°
O5GC5GC6GH6GA41.5°60.1°
O5GC5GC6GH6GB161.5°179.9°
C5GO5GC1GC2G45.7°61.1°
C5GO5GC1GO1G153.7°58.8°
C5GO5GC1GH1G79.4°178.8°
C5GC6GH6GH6GA120.0°120.1°
C5GC6GH6GH6GB119.9°120.0°
C5GC6GH6GAH6GB120.0°120.0°
C6GC5GO5GC1G139.0°178.8°
H5GC5GC6GH6G166.4°180.0°
H5GC5GC6GH6GA73.6°60.0°
H5GC5GC6GH6GB46.4°60.1°
H5GC5GO5GC1G103.8°58.8°
H6GC6GH6GAH6GB120.0°119.9°
O5GC1GC2GC3G57.8°57.6°
O5GC1GC2GO2G179.2°62.4°
O5GC1GC2GO1G114.4°120.0°
O5GC1GC2GH1G119.9°120.0°
O5GC1GC2GH2G58.3°177.6°
O5GC1GO1GH1G119.5°120.0°
O5GC1GO1GP2107.6°90.0°
C2GC3GH3GH3GA119.9°120.3°
C3GC2GO2GC1G123.5°119.7°
C3GC2GO2GH2G116.2°120.2°
C3GC2GC1GH2G116.1°120.0°
C3GC2GO2GHO2G96.3°180.0°
C3GC2GC1GO1G172.2°62.4°
C3GC2GC1GH1G62.1°177.6°
H3GC3GC2GO2G9.3°56.9°
H3GC3GC2GC1G108.2°176.8°
H3GC3GC2GH2G131.6°63.2°
H3GAC3GC2GO2G110.9°177.1°
H3GAC3GC2GC1G131.6°63.0°
H3GAC3GC2GH2G11.5°56.9°
O2GC2GC1GH2G122.4°120.1°
O2GC2GC1GO1G66.3°177.7°
O2GC2GC1GH1G59.4°57.7°
C1GC2GO2GHO2G140.2°60.3°
C2GC1GO1GH1G123.5°120.1°
C2GC1GO1GP2135.3°150.1°
H2GC2GO2GHO2G19.9°59.8°
H2GC2GC1GO1G56.1°57.6°
H2GC2GC1GH1G178.2°62.4°
C1GO1GP2OPP69.5°175.0°
C1GO1GP2O3P49.5°55.0°
C1GO1GP2O4P176.4°64.9°
H1GC1GO1GP211.8°30.0°
O1GP2OPPO3P114.4°120.0°
O1GP2OPPO4P107.5°120.0°
O1GP2O3PO4P115.3°120.0°
O1GP2O4PHO4P159.5°60.1°
O1GP2OPPP171.6°160.0°
OPPP2O3PO4P133.8°120.0°
OPPP2O4PHO4P52.4°60.0°
P2OPPPO5'112.5°160.0°
P2OPPPO2P135.0°40.0°
P2OPPPO1P6.9°80.0°
O3PP2O4PHO4P82.6°180.0°
O3PP2OPPP74.0°40.0°
O4PP2OPPP64.1°80.0°
OPPPO5'O2P112.8°120.0°
OPPPO5'O1P119.7°120.1°
OPPPO2PO1P124.9°119.9°
OPPPO1PHO1P165.5°60.0°
OPPPO5'C5'77.1°175.0°
O5'PO2PO1P124.1°120.0°
O5'PO1PHO1P50.0°60.0°
PO5'C5'C4'130.1°180.0°
PO5'C5'H5'10.1°60.0°
PO5'C5'H5'A109.3°59.9°
O2PPO1PHO1P71.8°179.9°
O2PPO5'C5'170.1°55.0°
O1PPO5'C5'42.6°64.9°
O5'C5'C4'H5'120.0°120.0°
O5'C5'C4'H5'A120.7°120.0°
O5'C5'H5'H5'A120.7°120.0°
O5'C5'C4'O4'55.7°66.7°
O5'C5'C4'C3'60.4°175.3°
O5'C5'C4'H4'177.6°54.3°
C4'C5'H5'H5'A120.7°120.0°
C5'C4'O4'C3'117.9°119.5°
C5'C4'O4'H4'120.3°121.0°
C5'C4'C3'H4'120.3°121.0°
C5'C4'O4'C1'127.1°145.9°
C5'C4'C3'C2'106.2°121.5°
C5'C4'C3'O3'140.0°119.7°
C5'C4'C3'H3'17.4°2.8°
H5'C5'C4'O4'175.7°53.3°
H5'C5'C4'C3'59.6°64.6°
H5'C5'C4'H4'62.4°174.3°
H5'AC5'C4'O4'64.9°173.3°
H5'AC5'C4'C3'178.9°55.3°
H5'AC5'C4'H4'56.9°65.7°
O4'C4'C3'H4'121.7°119.5°
O4'C4'C3'C2'11.8°1.9°
O4'C4'C3'O3'102.0°120.8°
O4'C4'C3'H3'135.4°116.7°
C4'O4'C1'C2'26.8°39.9°
C4'O4'C1'N9148.0°158.6°
C4'O4'C1'H1'94.1°78.4°
C3'C4'O4'C1'9.2°26.4°
C4'C3'C2'O3'113.4°118.8°
C4'C3'C2'H3'123.9°118.7°
C4'C3'O3'H3'124.1°122.5°
C4'C3'O3'HO3'114.3°179.9°
C4'C3'C2'O2'144.3°139.2°
C4'C3'C2'C1'26.6°20.9°
C4'C3'C2'H2'96.5°97.3°
H4'C4'O4'C1'112.6°93.1°
H4'C4'C3'C2'133.5°117.5°
H4'C4'C3'O3'19.7°1.3°
H4'C4'C3'H3'102.9°123.8°
O4'C1'C2'C3'32.8°36.9°
O4'C1'C2'O2'150.3°155.2°
O4'C1'C2'N9120.6°118.6°
O4'C1'C2'H1'121.5°118.4°
O4'C1'C2'H2'90.4°81.3°
O4'C1'N9H1'121.5°122.9°
O4'C1'N9C4138.3°156.7°
O4'C1'N9C842.6°23.6°
C2'C3'O3'H3'123.9°122.6°
C2'C3'O3'HO3'2.3°65.2°
C3'C2'O2'C1'112.6°112.8°
C3'C2'O2'H2'123.7°123.6°
C3'C2'C1'H2'123.2°118.2°
C3'C2'O2'HO2'133.8°61.4°
C3'C2'C1'N9153.4°155.5°
C3'C2'C1'H1'88.7°81.5°
O3'C3'C2'O2'30.8°20.4°
O3'C3'C2'C1'86.8°97.9°
O3'C3'C2'H2'150.1°143.9°
H3'C3'O3'HO3'121.6°57.4°
H3'C3'C2'O2'91.9°102.2°
H3'C3'C2'C1'150.5°139.5°
H3'C3'C2'H2'27.4°21.3°
O2'C2'C1'H2'119.3°123.6°
O2'C2'C1'N989.1°86.2°
O2'C2'C1'H1'28.8°36.8°
C1'C2'O2'HO2'21.3°174.1°
C2'C1'N9H1'120.9°122.9°
C2'C1'N9C4104.1°89.1°
C2'C1'N9C875.1°90.6°
H2'C2'O2'HO2'102.4°62.2°
H2'C2'C1'N930.2°37.3°
H2'C2'C1'H1'148.1°160.3°
C1'N9C4C8179.3°179.7°
C1'N9C8N7179.3°180.0°
C1'N9C8H80.7°0.0°
C1'N9C4N31.1°0.0°
C1'N9C4C5179.3°179.9°
H1'C1'N9C416.8°33.8°
H1'C1'N9C8164.1°146.5°
C4N9C8N70.1°0.2°
C4N9C8H8179.9°179.8°
N9C4C5N70.0°0.4°
N9C4N3C5179.6°179.8°
N9C4C5C6180.0°179.8°
N9C4N3C2179.7°180.0°
N9C8N7H8180.0°180.0°
N9C8N7C50.1°0.0°
C8N9C4N3179.7°179.7°
C8N9C4C50.0°0.4°
C8N7C5C40.1°0.3°
C8N7C5C6180.0°180.0°
H8C8N7C5179.9°180.0°
N7C5C4N3179.7°179.7°
N7C5C4C6179.9°179.8°
N7C5C6N1179.9°179.9°
N7C5C6O61.3°0.0°
N3C4C5C60.3°0.1°
C4N3C2N2179.4°180.0°
C4N3C2N11.0°0.8°
C4C5C6N10.0°0.2°
C4C5C6O6178.6°179.7°
C5C4N3C20.8°0.2°
C5C6N1O6178.7°179.9°
C5C6N1C20.2°0.8°
C5C6N1HN1179.8°180.0°
C6N1C2N30.7°1.1°
C6N1C2N2179.6°179.6°
C6N1C2HN1180.0°179.2°
O6C6N1C2178.9°179.1°
O6C6N1HN11.1°0.1°
N3C2N2N1179.6°179.3°
N3C2N1HN1179.3°179.7°
N3C2N2HN2180.0°0.0°
N3C2N2HN2A0.0°180.0°
N2C2N1HN10.4°0.5°
C2N2HN2HN2A180.0°180.0°
N1C2N2HN20.3°179.3°
N1C2N2HN2A179.6°0.8°

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PDB entries from 2024-07-17

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