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SummaryGeometryRelated PDB entries

YTH

Bonds
First atomSecond atomBond order typeDistance
(experimental model)		Distance
(ideal model)		Properties
O1PPdoub1.48Å1.48Å
O2PPsing1.61Å1.69Å
PO3Psing1.61Å1.61Å
POG1sing1.61Å1.59Å
NCAsing1.47Å1.47Å
OG1CBsing1.43Å1.43Å
CBCAsing1.53Å1.56Å
CBCG2sing1.53Å1.54Å
CACsing1.51Å1.56Å
COdoub1.21Å1.24Å
COXTsing1.34Å1.34Å
NHsing1.01Å1.00Å
NH2sing1.01Å1.00Å
CAHAsing1.09Å1.10Å
CBHBsing1.09Å1.10Å
CG2HG21sing1.09Å1.10Å
CG2HG22sing1.09Å1.10Å
CG2HG23sing1.09Å1.10Å
O2PH9sing0.97Å0.95Å
O3PH10sing0.97Å0.95Å
OXTHXTsing0.97Å0.95Å
Angles
First atomSecond atomThird atomAngle
(experimental model)		Angle
(ideal model)
O1PPO2P113.3°109.5°
O1PPO3P110.7°109.4°
O1PPOG1119.7°109.4°
O2PPO3P110.8°109.5°
O2PPOG1103.7°109.5°
PO2PH9109.5°114.0°
O3PPOG197.4°109.5°
PO3PH10109.5°114.0°
POG1CB122.6°123.0°
NCACB108.7°109.5°
NCAC108.2°109.5°
CANH109.5°111.0°
CANH2109.5°111.0°
NCAHA107.4°109.4°
OG1CBCA110.4°109.5°
OG1CBCG2109.7°109.5°
OG1CBHB109.1°109.5°
CACBCG2112.2°109.5°
CBCAC119.0°109.4°
CBCAHA106.5°109.5°
CACBHB107.6°109.4°
CG2CBHB107.8°109.5°
CBCG2HG21109.5°109.5°
CBCG2HG22109.5°109.5°
CBCG2HG23109.5°109.4°
CACO122.8°120.0°
CACOXT112.6°120.0°
CCAHA106.5°109.5°
OCOXT123.5°120.0°
COXTHXT109.5°117.0°
HNH2109.5°111.0°
HG21CG2HG22109.5°109.5°
HG21CG2HG23109.5°109.4°
HG22CG2HG23109.5°109.5°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)		Torsion
(ideal model)
O1PPO2PO3P125.1°120.0°
O1PPO2POG1131.3°120.0°
O1PPO3POG1125.7°119.9°
O1PPOG1CB23.3°55.0°
O1PPO2PH90.0°180.0°
O1PPO3PH100.0°60.1°
O2PPO3POG1107.8°120.0°
O2PPOG1CB104.2°65.0°
O2PPO3PH10126.5°60.0°
O3PPOG1CB142.2°175.0°
O3PPO2PH9125.1°60.0°
POG1CBCA111.3°120.0°
POG1CBCG2124.5°120.0°
POG1CBHB6.7°0.0°
OG1PO2PH9131.3°60.0°
OG1PO3PH10125.7°180.0°
NCACBOG146.2°180.0°
NCACBC124.4°120.0°
NCACBHA115.5°120.0°
NCACBCG2168.9°60.0°
NCACHA115.2°120.0°
NCACO35.9°20.0°
NCACOXT132.8°159.9°
CANHH2120.0°124.0°
NCACBHB72.7°60.0°
OG1CBCACG2122.7°120.0°
OG1CBCAHB118.9°120.0°
OG1CBCG2HB118.7°120.0°
OG1CBCAC78.2°60.0°
OG1CBCAHA161.7°60.0°
OG1CBCG2HG21180.0°179.9°
OG1CBCG2HG2260.0°60.0°
OG1CBCG2HG2360.0°60.0°
CACBCG2HB118.3°120.0°
CBCACHA120.2°120.0°
CBCACO88.7°100.0°
CBCACOXT102.6°80.0°
CBCANH180.0°176.0°
CBCANH260.0°59.9°
CACBCG2HG2156.9°59.9°
CACBCG2HG22176.9°180.0°
CACBCG2HG2363.1°60.0°
CG2CBCAC44.5°180.0°
CG2CBCAHA75.6°60.0°
CBCG2HG21HG22120.0°120.0°
CBCG2HG21HG23120.0°119.9°
CBCG2HG22HG23120.0°120.0°
CACOOXT167.4°179.9°
CCANH49.5°64.0°
CCANH270.5°60.0°
CCACBHB162.9°60.0°
CACOXTHXT168.5°180.0°
OCCAHA151.1°139.9°
OCOXTHXT0.0°0.1°
OXTCCAHA17.5°40.0°
HNCAHA65.1°56.0°
H2NCAHA174.9°180.0°
HACACBHB42.8°180.0°
HBCBCG2HG2161.3°60.0°
HBCBCG2HG2258.7°60.1°
HBCBCG2HG23178.6°180.0°
HG21CG2HG22HG23120.0°120.0°

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PDB entries from 2024-08-07

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