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SummaryGeometryRelated PDB entries

JDT

Bonds
First atomSecond atomBond order typeDistance
(experimental model)		Distance
(ideal model)		Properties
PO5'sing1.61Å1.59Å
POP1doub1.48Å1.49Å
POP2sing1.61Å1.49Å
POP3sing1.61Å1.61Å
N1C2sing1.35Å1.38Å
N1C6sing1.37Å1.38Å
N1C1'sing1.46Å1.48Å
C2O2doub1.22Å1.22Å
C2N3sing1.35Å1.37Å
N3C4sing1.35Å1.38Å
C4O4doub1.22Å1.23Å
C4C5sing1.42Å1.45Å
C5C6doub1.35Å1.34Å
C5C7sing1.51Å1.49Å
C7C72sing1.53Å1.50Å
C1'C2'sing1.54Å1.53Å
C1'O4'sing1.44Å1.43Å
C2'C3'sing1.55Å1.52Å
C3'O3'sing1.43Å1.43Å
C3'C4'sing1.55Å1.52Å
C4'O4'sing1.44Å1.44Å
C4'C5'sing1.53Å1.51Å
C5'O5'sing1.43Å1.43Å
N3HN3sing0.97Å1.00Å
C6H6sing1.08Å1.08Å
C7H71sing1.09Å1.10Å
C7H72sing1.09Å1.10Å
C1'H1'sing1.09Å1.10Å
C2'H2'sing1.09Å1.10Å
C2'H2''sing1.09Å1.10Å
C3'H3'sing1.09Å1.10Å
O3'HO3'sing0.97Å0.95Å
C4'H4'sing1.09Å1.10Å
C5'H5'sing1.09Å1.10Å
C5'H5''sing1.09Å1.10Å
C72H72Asing1.09Å1.10Å
C72H72Bsing1.09Å1.10Å
C72H72Csing1.09Å1.10Å
OP2HOP2sing0.97Å0.95Å
OP3HOP3sing0.97Å0.95Å
Angles
First atomSecond atomThird atomAngle
(experimental model)		Angle
(ideal model)
O5'POP1108.3°109.5°
O5'POP2107.7°109.4°
O5'POP3104.2°109.5°
PO5'C5'121.3°123.0°
OP1POP2119.5°109.5°
OP1POP3108.9°109.5°
OP2POP3107.1°109.5°
POP2HOP2109.5°114.0°
POP3HOP3109.5°114.0°
C2N1C6121.4°120.6°
C2N1C1'118.2°119.7°
N1C2O2123.2°119.5°
N1C2N3114.7°120.9°
C6N1C1'120.4°119.7°
N1C6C5123.1°119.7°
N1C6H6118.4°120.1°
N1C1'C2'114.1°109.9°
N1C1'O4'108.2°109.9°
N1C1'H1'106.5°109.8°
O2C2N3122.1°119.5°
C2N3C4127.2°120.2°
C2N3HN3116.4°119.9°
N3C4O4119.8°120.3°
N3C4C5115.1°119.4°
C4N3HN3116.4°119.9°
O4C4C5125.1°120.3°
C4C5C6118.4°119.1°
C4C5C7119.4°120.4°
C6C5C7122.0°120.5°
C5C6H6118.5°120.2°
C5C7C72120.1°109.5°
C5C7H71106.1°109.5°
C5C7H72106.1°109.4°
C72C7H71106.1°109.5°
C72C7H72106.1°109.5°
C7C72H72A109.4°109.5°
C7C72H72B109.5°109.5°
C7C72H72C109.5°109.4°
C2'C1'O4'107.2°107.3°
C1'C2'C3'103.9°104.2°
C2'C1'H1'107.5°109.9°
C1'C2'H2'111.4°110.5°
C1'C2'H2''111.4°110.5°
C1'O4'C4'109.0°107.0°
O4'C1'H1'113.5°110.0°
C2'C3'O3'111.4°110.9°
C2'C3'C4'102.4°102.1°
C3'C2'H2'111.4°110.5°
C3'C2'H2''111.3°110.5°
C2'C3'H3'113.1°110.9°
O3'C3'C4'110.4°110.9°
O3'C3'H3'105.6°110.8°
C3'O3'HO3'109.5°114.0°
C3'C4'O4'103.9°103.5°
C3'C4'C5'114.9°110.6°
C4'C3'H3'114.1°111.0°
C3'C4'H4'110.0°110.6°
O4'C4'C5'110.6°110.6°
O4'C4'H4'114.4°110.6°
C4'C5'O5'110.1°109.4°
C5'C4'H4'103.3°110.7°
C4'C5'H5'109.3°109.5°
C4'C5'H5''109.3°109.5°
O5'C5'H5'109.2°109.5°
O5'C5'H5''109.2°109.5°
H71C7H72112.6°109.4°
H2'C2'H2''107.5°110.5°
H5'C5'H5''109.7°109.5°
H72AC72H72B109.5°109.5°
H72AC72H72C109.5°109.5°
H72BC72H72C109.5°109.4°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)		Torsion
(ideal model)
O5'POP1OP2123.8°119.9°
O5'POP1OP3112.8°120.0°
O5'POP2OP3111.6°120.0°
PO5'C5'C4'101.1°180.0°
PO5'C5'H5'138.9°60.0°
PO5'C5'H5''18.9°60.0°
O5'POP2HOP2124.1°180.0°
O5'POP3HOP3115.4°60.0°
OP1POP2OP3124.3°120.1°
OP1PO5'C5'90.4°55.0°
OP1POP2HOP20.0°60.0°
OP1POP3HOP30.0°180.0°
OP2PO5'C5'139.0°175.0°
OP2POP3HOP3130.6°60.0°
OP3PO5'C5'25.4°65.0°
OP3POP2HOP2124.3°60.0°
C2N1C6C1'179.6°179.8°
N1C2O2N3180.0°180.0°
N1C2N3C40.0°0.0°
C2N1C6C50.9°0.1°
C2N1C1'C2'98.4°65.0°
C2N1C1'O4'142.4°52.8°
N1C2N3HN3180.0°180.0°
C2N1C6H6179.2°180.0°
C2N1C1'H1'20.0°174.0°
C6N1C2O2179.7°180.0°
C6N1C2N30.3°0.0°
N1C6C5C41.0°0.1°
N1C6C5H6180.0°179.9°
N1C6C5C7174.0°180.0°
C6N1C1'C2'81.2°114.7°
C6N1C1'O4'37.9°127.4°
C6N1C1'H1'160.3°6.2°
C1'N1C2O20.6°0.2°
C1'N1C2N3179.3°179.7°
C1'N1C6C5178.8°179.7°
N1C1'C2'O4'119.7°119.5°
N1C1'C2'H1'117.9°121.0°
N1C1'O4'H1'118.0°121.1°
N1C1'C2'C3'108.1°121.5°
N1C1'O4'C4'135.6°145.9°
C1'N1C6H61.2°0.2°
N1C1'C2'H2'131.9°119.8°
N1C1'C2'H2''11.9°2.8°
O2C2N3C4180.0°180.0°
O2C2N3HN30.0°0.0°
C2N3C4HN3180.0°179.9°
C2N3C4O4179.0°180.0°
C2N3C4C50.2°0.0°
N3C4O4C5179.2°179.9°
N3C4C5C60.7°0.1°
N3C4C5C7174.5°180.0°
O4C4C5C6178.5°180.0°
O4C4C5C76.3°0.1°
O4C4N3HN31.0°0.1°
C4C5C6C7175.0°179.9°
C4C5C7C7298.6°85.0°
C5C4N3HN3179.8°180.0°
C4C5C6H6179.0°180.0°
C4C5C7H7121.4°35.1°
C4C5C7H72141.4°155.0°
C6C5C7C7276.3°94.9°
C6C5C7H71163.7°145.0°
C6C5C7H7243.7°25.1°
C5C7C72H71120.0°120.0°
C5C7C72H72120.0°119.9°
C7C5C6H66.0°0.1°
C5C7H71H72115.6°119.9°
C5C7C72H72A60.0°180.0°
C5C7C72H72B60.0°59.9°
C5C7C72H72C180.0°60.0°
C72C7H71H72115.6°120.0°
C7C72H72AH72B120.0°120.0°
C7C72H72AH72C120.0°120.0°
C7C72H72BH72C120.0°119.9°
C2'C1'O4'H1'118.6°119.5°
C1'C2'C3'H2'120.0°118.7°
C1'C2'C3'H2''120.0°118.7°
C1'C2'C3'O3'147.2°139.1°
C1'C2'C3'C4'29.3°20.9°
C2'C1'O4'C4'12.1°26.5°
C1'C2'H2'H2''122.3°122.6°
C1'C2'C3'H3'94.0°97.4°
O4'C1'C2'C3'11.6°2.0°
C1'O4'C4'C3'31.0°40.0°
C1'O4'C4'C5'154.9°158.5°
O4'C1'C2'H2'108.4°120.7°
O4'C1'C2'H2''131.6°116.7°
C1'O4'C4'H4'89.0°78.5°
C2'C3'O3'C4'113.1°112.7°
C2'C3'O3'H3'123.2°123.6°
C2'C3'C4'H3'122.6°118.2°
C2'C3'C4'O4'37.0°37.0°
C2'C3'C4'C5'158.0°155.5°
C3'C2'C1'H1'134.0°117.6°
C3'C2'H2'H2''122.2°122.6°
C2'C3'O3'HO3'180.0°61.4°
C2'C3'C4'H4'86.0°81.5°
O3'C3'C4'H3'118.7°123.6°
O3'C3'C4'O4'155.7°155.2°
O3'C3'C4'C5'83.3°86.3°
O3'C3'C2'H2'27.2°20.4°
O3'C3'C2'H2''92.7°102.2°
O3'C3'C4'H4'32.7°36.7°
C3'C4'O4'C5'123.9°118.5°
C3'C4'O4'H4'120.0°118.5°
C3'C4'C5'H4'119.9°123.0°
C3'C4'C5'O5'134.9°175.0°
C4'C3'C2'H2'90.7°97.8°
C4'C3'C2'H2''149.3°139.6°
C4'C3'O3'HO3'66.9°174.1°
C3'C4'C5'H5'14.9°55.0°
C3'C4'C5'H5''105.1°65.0°
O4'C4'C5'H4'122.8°123.0°
O4'C4'C5'O5'107.8°70.9°
C4'O4'C1'H1'106.4°93.0°
O4'C4'C3'H3'85.7°81.2°
O4'C4'C5'H5'132.2°169.1°
O4'C4'C5'H5''12.2°49.0°
C4'C5'O5'H5'120.0°120.0°
C4'C5'O5'H5''120.0°120.0°
C5'C4'C3'H3'35.4°37.3°
C4'C5'H5'H5''119.7°120.0°
O5'C5'C4'H4'15.0°52.0°
O5'C5'H5'H5''119.7°120.0°
H71C7C72H72A180.0°60.0°
H71C7C72H72B60.0°180.0°
H71C7C72H72C60.0°60.0°
H72C7C72H72A60.0°60.0°
H72C7C72H72B180.0°60.0°
H72C7C72H72C60.0°179.9°
H1'C1'C2'H2'14.0°1.1°
H1'C1'C2'H2''106.0°123.7°
H2'C2'C3'H3'146.0°143.9°
H2''C2'C3'H3'26.0°21.3°
H3'C3'O3'HO3'56.8°62.1°
H3'C3'C4'H4'151.4°160.3°
H4'C4'C5'H5'105.0°67.9°
H4'C4'C5'H5''135.0°172.0°
H72AC72H72BH72C120.0°120.0°

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PDB entries from 2024-09-11

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