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PGD

Bonds
First atomSecond atomBond order typeDistance
(experimental model)
Distance
(ideal model)
Properties
PBO1Bdoub1.48Å1.71Å
PBO2Bsing1.61Å1.70Å
PBO3Bsing1.61Å1.62Å
PBO5'sing1.61Å1.72Å
O2BHOB2sing0.97Å0.95Å
O3BPAsing1.61Å1.62Å
O3APAsing1.61Å1.74Å
O3AC10sing1.43Å1.39Å
PAO1Adoub1.48Å1.70Å
PAO2Asing1.61Å1.69Å
O2AHOA2sing0.97Å0.95Å
O5'C5'sing1.43Å1.39Å
C5'C4'sing1.53Å1.54Å
C5'H5'1sing1.09Å1.11Å
C5'H5'2sing1.09Å1.12Å
C4'O4'sing1.44Å1.41Å
C4'C3'sing1.54Å1.52Å
C4'H4'sing1.09Å1.11Å
O4'C1'sing1.44Å1.44Å
C3'O3'sing1.43Å1.40Å
C3'C2'sing1.55Å1.51Å
C3'H3'sing1.09Å1.12Å
O3'HO3'sing0.97Å0.95Å
C2'O2'sing1.43Å1.41Å
C2'C1'sing1.55Å1.52Å
C2'H2'sing1.09Å1.12Å
O2'HO2'sing0.97Å0.95Å
C1'N9sing1.46Å1.46Å
C1'H1'sing1.09Å1.11Å
N9C8sing1.36Å1.36ÅAromatic
N9C4sing1.37Å1.34ÅAromatic
C8N7doub1.30Å1.36ÅAromatic
C8H8sing1.08Å1.10Å
N7C5sing1.35Å1.35ÅAromatic
C5C6sing1.42Å1.39Å
C5C4doub1.40Å1.36ÅAromatic
C6O6doub1.22Å1.22Å
C6N1sing1.35Å1.36Å
N1C2sing1.36Å1.38Å
N1HN1sing0.97Å1.02Å
C2N2sing1.37Å1.41Å
C2N3doub1.31Å1.37Å
N2HN21sing0.97Å1.02Å
N2HN22sing0.97Å1.02Å
N3C4sing1.34Å1.37Å
C10C11sing1.53Å1.55Å
C10H101sing1.09Å1.12Å
C10H102sing1.09Å1.12Å
C11O11sing1.43Å1.41Å
C11C12sing1.50Å1.51Å
C11H11sing1.09Å1.12Å
O11C23sing1.43Å1.40Å
C12S12sing1.76Å1.82Å
C12C13doub1.32Å1.35Å
S12H12sing1.34Å0.95Å
C13S13sing1.76Å1.79Å
C13C14sing1.51Å1.49Å
S13H13sing1.34Å0.95Å
C14N15sing1.47Å1.47Å
C14C23sing1.53Å1.56Å
C14H14sing1.09Å1.12Å
N15C16doub1.29Å1.44Å
C16C17sing1.49Å1.40Å
C16C21sing1.49Å1.39Å
C17O17doub1.22Å1.22Å
C17N18sing1.34Å1.36Å
N18C19doub1.32Å1.36Å
C19N19sing1.37Å1.42Å
C19N20sing1.34Å1.36Å
N19H191sing0.97Å1.02Å
N19H192sing0.97Å1.02Å
N20C21doub1.31Å1.36Å
C21N22sing1.37Å1.43Å
N22C23sing1.47Å1.45Å
N22H22sing0.97Å1.02Å
C23H23sing1.09Å1.12Å
Angles
First atomSecond atomThird atomAngle
(experimental model)
Angle
(ideal model)
O1BPBO2B115.0°109.4°
O1BPBO3B103.4°109.5°
O1BPBO5'113.2°109.5°
O2BPBO3B109.6°109.5°
O2BPBO5'109.8°109.5°
PBO2BHOB2115.0°106.8°
O3BPBO5'105.1°109.5°
PBO3BPA137.5°106.8°
PBO5'C5'115.9°106.8°
O3BPAO3A101.6°109.5°
O3BPAO1A109.4°109.5°
O3BPAO2A107.7°109.5°
PAO3AC10108.4°106.8°
O3APAO1A109.0°109.5°
O3APAO2A112.2°109.4°
O3AC10C11104.2°109.5°
O3AC10H101114.3°109.5°
O3AC10H102114.2°109.5°
O1APAO2A115.9°109.5°
PAO2AHOA2107.7°106.8°
O5'C5'C4'104.6°109.5°
O5'C5'H5'1114.0°109.4°
O5'C5'H5'2114.0°109.5°
C4'C5'H5'1114.1°109.5°
C4'C5'H5'2114.1°109.4°
C5'C4'O4'108.8°110.4°
C5'C4'C3'111.5°110.5°
C5'C4'H4'108.0°110.3°
H5'1C5'H5'296.4°109.5°
O4'C4'C3'107.7°104.8°
O4'C4'H4'111.8°110.4°
C4'O4'C1'103.1°105.3°
C3'C4'H4'109.1°110.3°
C4'C3'O3'109.1°110.6°
C4'C3'C2'104.1°104.1°
C4'C3'H3'114.6°110.5°
O4'C1'C2'103.9°104.9°
O4'C1'N9108.0°110.4°
O4'C1'H1'115.2°110.4°
O3'C3'C2'113.5°110.5°
O3'C3'H3'105.5°110.4°
C3'O3'HO3'109.0°106.8°
C2'C3'H3'110.3°110.6°
C3'C2'O2'113.5°110.5°
C3'C2'C1'101.0°104.0°
C3'C2'H2'112.6°110.5°
O2'C2'C1'110.0°110.8°
O2'C2'H2'104.1°110.5°
C2'O2'HO2'113.4°106.8°
C1'C2'H2'116.0°110.4°
C2'C1'N9113.0°110.3°
C2'C1'H1'110.4°110.4°
N9C1'H1'106.5°110.3°
C1'N9C8128.8°126.3°
C1'N9C4127.4°126.3°
C8N9C4103.7°107.4°
N9C8N7112.9°109.8°
N9C8H8123.7°125.1°
N9C4C5110.0°106.1°
N9C4N3125.6°134.2°
N7C8H8123.4°125.1°
C8N7C5103.8°109.3°
N7C5C6130.9°134.1°
N7C5C4109.6°107.3°
C6C5C4119.5°118.6°
C5C6O6126.5°120.8°
C5C6N1116.9°118.4°
C5C4N3124.3°119.7°
O6C6N1116.6°120.8°
C6N1C2122.4°120.3°
C6N1HN1118.3°119.8°
C2N1HN1119.4°119.8°
N1C2N2118.1°119.1°
N1C2N3120.9°121.9°
N2C2N3120.9°119.0°
C2N2HN21118.1°120.0°
C2N2HN22109.1°120.0°
C2N3C4115.9°121.1°
HN21N2HN22109.1°120.0°
C11C10H101114.1°109.5°
C11C10H102114.2°109.4°
C10C11O11105.8°109.2°
C10C11C12108.8°109.2°
C10C11H11113.6°109.2°
H101C10H10296.3°109.5°
O11C11C12113.0°110.7°
O11C11H11109.4°109.2°
C11O11C23110.3°107.1°
C12C11H11106.4°109.3°
C11C12S12122.7°118.8°
C11C12C13121.2°122.2°
O11C23C14111.0°109.2°
O11C23N22110.0°109.5°
O11C23H23107.6°109.5°
S12C12C13115.1°118.9°
C12S12H12122.7°100.1°
C12C13S13118.9°119.8°
C12C13C14121.7°120.6°
S13C13C14119.1°119.6°
C13S13H13118.9°100.0°
C13C14N15111.3°109.4°
C13C14C23105.9°109.2°
C13C14H14111.4°109.3°
N15C14C23111.6°111.0°
N15C14H14105.8°109.3°
C14N15C16116.8°122.4°
C23C14H14111.1°108.7°
C14C23N22107.7°109.6°
C14C23H23109.8°109.5°
N15C16C17123.3°122.6°
N15C16C21119.0°120.8°
C17C16C21117.7°116.6°
C16C17O17121.7°121.5°
C16C17N18119.7°116.9°
C16C21N20121.1°118.6°
C16C21N22121.6°118.2°
O17C17N18118.6°121.5°
C17N18C19121.4°122.0°
N18C19N19121.3°117.7°
N18C19N20119.9°124.7°
N19C19N20118.8°117.7°
C19N19H191121.3°120.0°
C19N19H192108.0°120.0°
C19N20C21120.3°121.2°
H191N19H192108.0°120.0°
N20C21N22117.3°123.2°
C21N22C23119.4°116.8°
C21N22H22108.7°121.6°
C23N22H22108.6°121.6°
N22C23H23110.9°109.5°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)
Torsion
(ideal model)
O1BPBO2BO3B116.0°120.0°
O1BPBO2BO5'129.0°120.0°
O1BPBO3BO5'118.9°120.0°
O1BPBO2BHOB2179.9°180.0°
O1BPBO3BPA177.0°60.0°
O1BPBO5'C5'58.6°60.0°
O2BPBO3BO5'117.9°120.0°
O2BPBO3BPA53.9°60.0°
O2BPBO5'C5'171.4°60.0°
O3BPBO2BHOB263.9°60.0°
PBO3BPAO3A156.4°180.0°
PBO3BPAO1A88.4°60.0°
PBO3BPAO2A38.4°60.0°
O3BPBO5'C5'53.6°180.0°
O5'PBO2BHOB251.1°60.0°
O5'PBO3BPA64.1°180.0°
PBO5'C5'C4'143.5°180.0°
PBO5'C5'H5'118.2°60.0°
PBO5'C5'H5'291.2°60.0°
O3BPAO3AO1A115.5°120.0°
O3BPAO3AO2A114.8°120.0°
O3BPAO3AC1073.7°180.0°
O3BPAO1AO2A122.0°120.0°
O3BPAO2AHOA2180.0°60.0°
O3APAO1AO2A127.7°120.0°
O3APAO2AHOA269.0°60.0°
PAO3AC10C11178.5°180.0°
PAO3AC10H10156.3°60.1°
PAO3AC10H10253.2°60.0°
C10O3APAO1A170.8°60.0°
C10O3APAO2A41.0°60.0°
O3AC10C11H101125.3°120.0°
O3AC10C11H102125.3°120.0°
O3AC10H101H102120.2°120.0°
O3AC10C11O1185.4°59.4°
O3AC10C11C12152.9°179.4°
O3AC10C11H1134.6°60.0°
O1APAO2AHOA257.1°180.0°
O5'C5'C4'H5'1125.3°120.0°
O5'C5'C4'H5'2125.3°120.1°
O5'C5'H5'1H5'2119.9°120.0°
O5'C5'C4'O4'50.2°61.5°
O5'C5'C4'C3'68.4°176.9°
O5'C5'C4'H4'171.8°60.8°
C4'C5'H5'1H5'2120.0°119.9°
C5'C4'O4'C3'121.0°119.0°
C5'C4'O4'H4'119.2°122.2°
C5'C4'C3'H4'119.2°122.3°
C5'C4'O4'C1'153.3°159.5°
C5'C4'C3'O3'112.4°98.4°
C5'C4'C3'C2'126.1°142.9°
C5'C4'C3'H3'5.5°24.2°
H5'1C5'C4'O4'175.5°178.5°
H5'1C5'C4'C3'56.8°63.1°
H5'1C5'C4'H4'63.0°59.2°
H5'2C5'C4'O4'75.1°58.6°
H5'2C5'C4'C3'166.3°56.9°
H5'2C5'C4'H4'46.5°179.2°
O4'C4'C3'H4'121.6°118.8°
O4'C4'C3'O3'128.3°142.8°
O4'C4'C3'C2'6.8°24.1°
O4'C4'C3'H3'113.8°94.7°
C4'O4'C1'C2'45.3°40.5°
C4'O4'C1'N9165.5°159.3°
C4'O4'C1'H1'75.5°78.4°
C3'C4'O4'C1'32.3°40.5°
C4'C3'O3'C2'115.6°114.7°
C4'C3'O3'H3'123.5°122.6°
C4'C3'C2'H3'123.4°118.7°
C4'C3'O3'HO3'180.0°180.0°
C4'C3'C2'O2'137.3°118.8°
C4'C3'C2'C1'19.6°0.1°
C4'C3'C2'H2'104.7°118.6°
H4'C4'O4'C1'87.5°78.3°
H4'C4'C3'O3'6.7°23.9°
H4'C4'C3'C2'114.7°94.8°
H4'C4'C3'H3'124.7°146.5°
O4'C1'C2'C3'40.0°23.9°
O4'C1'C2'O2'160.2°142.6°
O4'C1'C2'N9116.7°118.9°
O4'C1'C2'H1'124.1°118.9°
O4'C1'C2'H2'82.0°94.7°
O4'C1'N9H1'124.3°122.3°
O4'C1'N9C889.7°27.0°
O4'C1'N9C488.7°153.0°
O3'C3'C2'H3'118.1°122.6°
O3'C3'C2'O2'18.8°0.1°
O3'C3'C2'C1'98.8°118.8°
O3'C3'C2'H2'136.8°122.7°
C2'C3'O3'HO3'64.4°65.3°
C3'C2'O2'C1'112.3°114.7°
C3'C2'O2'H2'122.8°122.6°
C3'C2'C1'H2'122.0°118.6°
C3'C2'O2'HO2'180.0°61.5°
C3'C2'C1'N9156.8°142.7°
C3'C2'C1'H1'84.1°95.1°
H3'C3'O3'HO3'56.5°57.4°
H3'C3'C2'O2'99.3°122.5°
H3'C3'C2'C1'143.1°118.6°
H3'C3'C2'H2'18.7°0.1°
O2'C2'C1'H2'117.8°122.7°
O2'C2'C1'N983.1°98.5°
O2'C2'C1'H1'36.1°23.7°
C1'C2'O2'HO2'67.7°176.2°
C2'C1'N9H1'121.4°122.2°
C2'C1'N9C824.6°88.5°
C2'C1'N9C4157.0°91.6°
H2'C2'O2'HO2'57.2°61.1°
H2'C2'C1'N934.7°24.2°
H2'C2'C1'H1'153.9°146.4°
C1'N9C8C4178.7°179.9°
C1'N9C8N7178.9°179.9°
C1'N9C8H81.0°0.1°
C1'N9C4C5179.0°179.9°
C1'N9C4N31.3°0.0°
H1'C1'N9C8146.0°149.3°
H1'C1'N9C435.6°30.7°
N9C8N7H8179.9°180.0°
N9C8N7C50.1°0.0°
C8N9C4C50.3°0.0°
C8N9C4N3180.0°180.0°
C4N9C8N70.2°0.0°
C4N9C8H8179.7°180.0°
N9C4C5N70.2°0.0°
N9C4C5C6179.9°180.0°
N9C4C5N3179.7°180.0°
N9C4N3C2179.6°180.0°
C8N7C5C6179.7°180.0°
C8N7C5C40.1°0.0°
H8C8N7C5179.9°180.0°
N7C5C6C4179.6°180.0°
N7C5C6O60.1°0.0°
N7C5C6N1179.3°179.8°
N7C5C4N3180.0°180.0°
C5C6O6N1179.5°179.8°
C5C6N1C21.4°0.5°
C5C6N1HN1178.6°179.9°
C6C5C4N30.4°0.0°
C4C5C6O6179.7°180.0°
C4C5C6N10.3°0.2°
C5C4N3C20.1°0.1°
O6C6N1C2179.1°179.8°
O6C6N1HN11.0°0.2°
C6N1C2HN1180.0°179.6°
C6N1C2N2179.5°179.7°
C6N1C2N32.0°0.4°
N1C2N2N3178.5°179.8°
N1C2N2HN21180.0°179.8°
N1C2N2HN2254.7°0.5°
N1C2N3C41.3°0.1°
HN1N1C2N20.6°0.1°
HN1N1C2N3178.0°180.0°
C2N2HN21HN22125.3°179.7°
N2C2N3C4179.8°180.0°
N3C2N2HN211.4°0.0°
N3C2N2HN22126.7°179.6°
C11C10H101H102120.1°120.0°
C10C11O11C12118.9°120.3°
C10C11O11H11122.7°119.4°
C10C11C12H11122.7°119.4°
C10C11O11C23166.5°177.2°
C10C11C12S1258.0°38.3°
C10C11C12C13133.6°141.3°
H101C10C11O1139.9°60.6°
H101C10C11C1281.8°60.6°
H101C10C11H11159.8°180.0°
H102C10C11O11149.3°179.4°
H102C10C11C1227.6°59.4°
H102C10C11H1190.7°60.0°
O11C11C12H11120.0°120.3°
O11C11C12S12175.2°158.6°
O11C11C12C1316.4°21.1°
C11O11C23C1470.4°73.8°
C11O11C23N22170.6°166.2°
C11O11C23H2349.7°46.1°
C12C11O11C2347.6°57.0°
C11C12S12C13169.1°179.7°
C11C12S12H12180.0°95.4°
C11C12C13S13179.6°179.9°
C11C12C13C146.7°0.3°
H11C11O11C2370.8°63.4°
H11C11C12S1264.7°81.1°
H11C11C12C13103.7°99.3°
O11C23C14C1355.9°49.9°
O11C23C14N1565.3°70.7°
O11C23C14N22120.4°119.9°
O11C23C14H23118.8°119.9°
O11C23C14H14177.0°169.1°
O11C23N22C2180.9°70.5°
O11C23N22H23118.8°120.1°
O11C23N22H22153.8°109.5°
S12C12C13S1310.3°0.3°
S12C12C13C14176.0°180.0°
C13C12S12H1210.9°85.0°
C12C13S13C14173.9°179.8°
C12C13S13H13180.0°5.4°
C12C13C14N1596.9°108.1°
C12C13C14C2324.5°13.6°
C12C13C14H14145.3°132.3°
S13C13C14N1576.8°72.1°
S13C13C14C23161.8°166.2°
S13C13C14H1440.9°47.4°
C14C13S13H136.1°174.8°
C13C14N15C23118.1°120.6°
C13C14N15H14121.1°119.6°
C13C14C23H14121.1°119.1°
C13C14N15C16163.5°148.3°
C13C14C23N22176.3°169.9°
C13C14C23H2362.9°70.0°
N15C14C23H14117.7°120.2°
C14N15C16C17162.0°178.6°
C14N15C16C2117.3°1.8°
N15C14C23N2255.1°49.2°
N15C14C23H23175.9°169.3°
C23C14N15C1645.5°27.7°
C14C23N22C2140.2°49.3°
C14C23N22H23120.1°120.2°
C14C23N22H2285.1°130.7°
H14C14N15C1675.4°92.1°
H14C14C23N2262.6°71.0°
H14C14C23H2358.2°49.1°
N15C16C17C21179.3°179.5°
N15C16C17O171.5°0.5°
N15C16C17N18179.4°179.5°
N15C16C21N20178.9°179.3°
N15C16C21N220.0°1.0°
C16C17O17N18179.1°180.0°
C16C17N18C190.3°0.2°
C17C16C21N200.5°1.2°
C17C16C21N22179.4°178.5°
C21C16C17O17179.2°179.0°
C21C16C17N180.1°1.0°
C16C21N20C190.9°0.6°
C16C21N20N22179.0°179.7°
C16C21N22C2313.9°24.5°
C16C21N22H22111.4°155.5°
O17C17N18C19179.4°179.8°
C17N18C19N19179.5°179.5°
C17N18C19N200.2°0.5°
N18C19N19N20179.7°180.0°
N18C19N19H191179.9°0.1°
N18C19N19H19254.7°180.0°
N18C19N20C210.8°0.3°
C19N19H191H192125.2°179.9°
N19C19N20C21178.9°179.7°
N20C19N19H1910.4°179.9°
N20C19N19H192125.6°0.0°
C19N20C21N22179.9°179.1°
N20C21N22C23167.1°155.2°
N20C21N22H2267.6°24.8°
C21N22C23H22125.3°180.0°
C21N22C23H23160.3°169.4°
H22N22C23H2335.0°10.6°

222415

PDB entries from 2024-07-10

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