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SummaryGeometryRelated PDB entries

D00

Bonds
First atomSecond atomBond order typeDistance
(experimental model)		Distance
(ideal model)		Properties
OP2Pdoub1.48Å1.48Å
C2'C3'sing1.55Å1.51Å
C2'C1'sing1.54Å1.51Å
C3'O3'sing1.43Å1.42Å
C3'C4'sing1.55Å1.50Å
O5'Psing1.61Å1.61Å
O5'C5'sing1.43Å1.42Å
OP1Psing1.61Å1.48Å
C6C5doub1.35Å1.35Å
C6N1sing1.36Å1.35Å
C5C4sing1.41Å1.44Å
C5'C4'sing1.53Å1.52Å
C4'O4'sing1.44Å1.42Å
C1'N1sing1.47Å1.48Å
C1'O4'sing1.44Å1.43Å
N1C2sing1.35Å1.38Å
C4N4sing1.38Å1.38Å
C4N3doub1.33Å1.35Å
C2N3sing1.33Å1.36Å
C2O2doub1.22Å1.23Å
N4C11sing1.47Å1.47Å
C11C10sing1.53Å1.35Å
POP3sing1.61Å1.61Å
OP1H1sing0.97Å0.95Å
C5'H5''sing1.09Å1.10Å
C5'H5'sing1.09Å1.10Å
C4'H4'sing1.09Å1.10Å
C3'H3'sing1.09Å1.10Å
O3'HO3'sing0.97Å0.95Å
C2'H2''sing1.09Å1.10Å
C2'H2'sing1.09Å1.10Å
C1'H1'sing1.09Å1.10Å
N4H41sing0.97Å1.00Å
C5H5sing1.08Å1.08Å
C6H6sing1.08Å1.08Å
C10H12sing1.09Å1.10Å
C10H11sing1.09Å1.10Å
C10H8sing1.09Å1.10Å
C11H13sing1.09Å1.10Å
C11H14sing1.09Å1.10Å
OP3H9sing0.97Å0.95Å
Angles
First atomSecond atomThird atomAngle
(experimental model)		Angle
(ideal model)
OP2PO5'108.0°109.4°
OP2POP1120.0°109.5°
OP2POP3108.0°109.4°
C3'C2'C1'103.0°104.2°
C2'C3'O3'112.9°110.9°
C2'C3'C4'100.8°102.1°
C2'C3'H3'108.9°111.0°
C3'C2'H2''111.1°110.5°
C3'C2'H2'111.0°110.5°
C2'C1'N1114.2°109.8°
C2'C1'O4'94.5°107.3°
C1'C2'H2''111.0°110.5°
C1'C2'H2'111.1°110.5°
C2'C1'H1'114.3°109.9°
O3'C3'C4'114.6°110.9°
O3'C3'H3'110.1°110.8°
C3'O3'HO3'109.5°114.0°
C3'C4'C5'120.2°110.6°
C3'C4'O4'104.6°103.4°
C3'C4'H4'106.7°110.8°
C4'C3'H3'109.0°110.9°
PO5'C5'116.9°123.0°
O5'POP1108.1°109.5°
O5'POP3103.3°109.5°
O5'C5'C4'111.8°109.5°
O5'C5'H5''108.9°109.5°
O5'C5'H5'108.9°109.4°
OP1POP3108.3°109.5°
POP1H1109.5°114.0°
C5C6N1121.9°119.3°
C6C5C4119.0°118.9°
C6C5H5120.5°120.5°
C5C6H6119.0°120.4°
C6N1C1'118.0°119.9°
C6N1C2120.7°120.3°
N1C6H6119.1°120.3°
C5C4N4118.4°120.2°
C5C4N3116.7°119.7°
C4C5H5120.5°120.6°
C5'C4'O4'110.5°110.6°
C4'C5'H5''108.9°109.5°
C4'C5'H5'108.9°109.4°
C5'C4'H4'106.5°110.6°
C4'O4'C1'109.2°107.0°
O4'C4'H4'107.7°110.6°
N1C1'O4'100.9°109.9°
C1'N1C2121.2°119.8°
N1C1'H1'114.8°109.8°
O4'C1'H1'115.7°110.0°
N1C2N3117.4°121.1°
N1C2O2121.6°119.4°
N4C4N3121.6°120.2°
C4N4C11123.6°120.0°
C4N4H41118.2°120.0°
C4N3C2124.3°120.7°
N3C2O2121.0°119.5°
N4C11C10129.3°109.5°
C11N4H41118.2°120.0°
N4C11H13104.3°109.5°
N4C11H14104.3°109.5°
C11C10H12109.5°109.4°
C11C10H11109.5°109.4°
C11C10H8109.5°109.5°
C10C11H13104.3°109.4°
C10C11H14104.3°109.4°
POP3H9109.5°114.0°
H5''C5'H5'109.5°109.5°
H2''C2'H2'109.5°110.6°
H12C10H11109.5°109.5°
H12C10H8109.5°109.5°
H11C10H8109.4°109.5°
H13C11H14109.5°109.5°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)		Torsion
(ideal model)
OP2PO5'OP1131.2°120.0°
OP2PO5'OP3114.2°120.0°
OP2PO5'C5'178.0°55.0°
OP2POP1OP3124.5°120.0°
OP2POP1H10.0°180.0°
OP2POP3H90.0°60.0°
C3'C2'C1'H2''119.0°118.7°
C3'C2'C1'H2'118.9°118.6°
C2'C3'O3'C4'114.6°112.7°
C2'C3'O3'H3'122.0°123.7°
C2'C3'C4'H3'114.5°118.3°
C2'C3'C4'C5'116.2°155.5°
C2'C3'C4'O4'8.7°37.0°
C3'C2'C1'N1154.8°121.5°
C3'C2'C1'O4'50.7°2.1°
C2'C3'C4'H4'122.6°81.5°
C2'C3'O3'HO3'180.0°67.3°
C3'C2'H2''H2'123.0°122.6°
C3'C2'C1'H1'70.1°117.6°
C1'C2'C3'O3'85.3°139.0°
C1'C2'C3'C4'37.5°20.9°
C2'C1'N1C646.9°114.7°
C2'C1'O4'C4'46.9°26.6°
C2'C1'N1O4'100.1°117.8°
C2'C1'N1H1'134.8°121.0°
C2'C1'O4'H1'119.7°119.5°
C2'C1'N1C2134.9°65.0°
C1'C2'C3'H3'152.0°97.3°
C1'C2'H2''H2'123.0°122.6°
O3'C3'C4'H3'124.0°123.5°
O3'C3'C4'C5'122.3°86.3°
O3'C3'C4'O4'112.9°155.2°
O3'C3'C4'H4'1.1°36.7°
O3'C3'C2'H2''155.8°102.3°
O3'C3'C2'H2'33.7°20.4°
C3'C4'C5'O5'69.3°179.5°
C3'C4'C5'O4'122.0°114.0°
C3'C4'C5'H4'121.3°123.1°
C3'C4'O4'H4'113.3°118.6°
C3'C4'O4'C1'25.3°40.1°
C3'C4'C5'H5''51.0°60.5°
C3'C4'C5'H5'170.4°59.5°
C4'C3'O3'HO3'65.4°180.0°
C4'C3'C2'H2''81.5°139.6°
C4'C3'C2'H2'156.4°97.8°
O5'POP1OP3111.3°120.0°
PO5'C5'C4'162.5°180.0°
O5'POP1H1124.2°60.0°
PO5'C5'H5''77.2°60.0°
PO5'C5'H5'42.2°60.0°
O5'POP3H9114.2°180.0°
C5'O5'POP150.9°65.0°
O5'C5'C4'H5''120.3°120.0°
O5'C5'C4'H5'120.3°119.9°
O5'C5'C4'O4'52.7°66.5°
C5'O5'POP363.8°175.0°
O5'C5'H5''H5'118.9°120.0°
O5'C5'C4'H4'169.4°56.4°
OP1POP3H9131.4°59.9°
C5C6N1H6180.0°179.5°
C6C5C4H5180.0°179.9°
C5C6N1C1'177.9°179.8°
C5C6N1C20.3°0.5°
C6C5C4N4159.6°179.7°
C6C5C4N30.4°0.1°
N1C6C5C40.1°0.4°
C6N1C1'C2178.2°179.7°
C6N1C1'O4'53.2°127.5°
C6N1C2N30.4°0.2°
C6N1C2O2179.2°179.7°
C6N1C1'H1'178.3°6.3°
N1C6C5H5179.8°179.7°
C5C4N4N3158.9°179.8°
C5C4N3C20.3°0.1°
C5C4N4C11142.0°179.9°
C5C4N4H4138.0°0.1°
C4C5C6H6179.9°180.0°
C5'C4'O4'H4'116.0°122.9°
C5'C4'O4'C1'156.0°158.6°
C4'C5'H5''H5'118.9°120.0°
C5'C4'C3'H3'1.7°37.2°
C4'O4'C1'N1162.6°145.9°
O4'C4'C5'H5''173.0°53.5°
O4'C4'C5'H5'67.6°173.6°
O4'C4'C3'H3'123.2°81.3°
C4'O4'C1'H1'72.8°93.0°
N1C1'O4'H1'124.5°121.1°
C1'N1C2N3177.8°180.0°
C1'N1C2O22.6°0.0°
N1C1'C2'H2''35.8°2.8°
N1C1'C2'H2'86.3°119.9°
C1'N1C6H62.1°0.2°
O4'C1'N1C2125.0°52.8°
C1'O4'C4'H4'88.0°78.5°
O4'C1'C2'H2''68.3°116.6°
O4'C1'C2'H2'169.6°120.7°
N1C2N3C40.1°0.1°
N1C2N3O2179.6°180.0°
C2N1C1'H1'0.1°174.0°
C2N1C6H6179.7°180.0°
N4C4N3C2159.0°179.9°
C4N4C11H41180.0°180.0°
C4N4C11C1098.5°180.0°
N4C4C5H520.4°0.2°
C4N4C11H13138.9°60.0°
C4N4C11H1424.1°60.1°
C4N3C2O2179.5°180.0°
N3C4N4C1159.1°0.1°
N3C4N4H41120.9°180.0°
N3C4C5H5179.6°180.0°
N4C11C10H13122.6°120.0°
N4C11C10H14122.6°120.0°
N4C11C10H12180.0°59.9°
N4C11C10H1160.0°60.0°
N4C11C10H860.0°180.0°
N4C11H13H14111.1°120.1°
C10C11N4H4181.5°0.0°
C11C10H12H11120.0°119.9°
C11C10H12H8120.0°120.1°
C11C10H11H8120.0°120.0°
C10C11H13H14111.2°119.9°
OP3POP1H1124.5°60.1°
H5''C5'C4'H4'70.2°176.4°
H5'C5'C4'H4'49.1°63.6°
H4'C4'C3'H3'122.9°160.3°
H3'C3'O3'HO3'58.0°56.4°
H3'C3'C2'H2''33.1°21.4°
H3'C3'C2'H2'89.0°144.0°
H2''C2'C1'H1'170.9°123.8°
H2'C2'C1'H1'48.8°1.1°
H41N4C11H1341.1°119.9°
H41N4C11H14155.9°120.0°
H5C5C6H60.2°0.1°
H12C10H11H8120.0°120.1°
H12C10C11H1357.4°179.9°
H12C10C11H1457.4°60.1°
H11C10C11H13177.4°60.0°
H11C10C11H1462.6°NaN°
H8C10C11H1362.6°60.0°
H8C10C11H14177.4°60.0°

223532

PDB entries from 2024-08-07

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