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SummaryGeometryRelated PDB entries

V5L

Bonds
First atomSecond atomBond order typeDistance
(experimental model)		Distance
(ideal model)		Properties
C04C05doub1.38Å1.38ÅAromatic
C04C03sing1.39Å1.38ÅAromatic
C05C06sing1.39Å1.38ÅAromatic
O02C03sing1.36Å1.41Å
O02C01sing1.43Å1.40Å
C03C08doub1.39Å1.39ÅAromatic
N10N09sing1.41Å1.35ÅAromatic
N10N11doub1.29Å1.38ÅAromatic
C06N09sing1.40Å1.31Å
C06C07doub1.39Å1.39ÅAromatic
N09C13sing1.35Å1.33ÅAromatic
N11N12sing1.28Å1.37ÅAromatic
C08C07sing1.38Å1.38ÅAromatic
C13N12doub1.31Å1.32ÅAromatic
C13H1sing1.08Å1.08Å
C01H2sing1.09Å1.10Å
C01H3sing1.09Å1.10Å
C01H4sing1.09Å1.10Å
C04H5sing1.08Å1.08Å
C05H6sing1.08Å1.08Å
C07H7sing1.08Å1.08Å
C08H8sing1.08Å1.08Å
Angles
First atomSecond atomThird atomAngle
(experimental model)		Angle
(ideal model)
C05C04C03121.0°120.1°
C04C05C06118.7°119.9°
C05C04H5119.5°120.0°
C04C05H6120.6°120.0°
C04C03O02119.0°120.0°
C04C03C08119.3°120.0°
C03C04H5119.5°119.9°
C05C06N09118.0°120.0°
C05C06C07121.4°120.0°
C06C05H6120.6°120.0°
C03O02C01115.1°117.0°
O02C03C08121.6°120.0°
O02C01H2109.5°109.5°
O02C01H3109.5°109.5°
O02C01H4109.5°109.5°
C03C08C07120.5°120.0°
C03C08H8119.8°120.0°
N09N10N11106.7°106.6°
N10N09C06127.1°127.4°
N10N09C13108.2°105.2°
N10N11N12107.4°110.2°
N09C06C07120.5°120.0°
C06N09C13124.7°127.4°
C06C07C08119.0°120.0°
C06C07H7120.5°120.0°
N09C13N12110.4°107.3°
N09C13H1124.8°126.4°
N11N12C13107.4°110.6°
C08C07H7120.5°120.0°
C07C08H8119.8°120.0°
N12C13H1124.8°126.3°
H2C01H3109.4°109.5°
H2C01H4109.5°109.4°
H3C01H4109.5°109.5°
Dihedrals
First atomSecond atomThird atomFourth atomTorsion
(experimental model)		Torsion
(ideal model)
C05C04C03H5180.0°180.0°
C04C05C06H6180.0°180.0°
C05C04C03O02179.9°179.8°
C05C04C03C080.8°0.0°
C04C05C06N09179.4°180.0°
C04C05C06C071.6°0.0°
C03C04C05C061.3°0.0°
C04C03O02C08179.0°179.8°
C04C03O02C01152.4°0.2°
C04C03C08C070.6°0.0°
C03C04C05H6178.7°180.0°
C04C03C08H8179.4°179.9°
C05C06N09N1035.1°0.0°
C05C06N09C07177.8°179.9°
C05C06N09C13143.4°180.0°
C05C06C07C081.4°0.1°
C06C05C04H5178.6°180.0°
C05C06C07H7178.6°180.0°
O02C03C08C07179.7°179.8°
C03O02C01H2180.0°60.0°
C03O02C01H360.0°60.0°
C03O02C01H460.0°180.0°
O02C03C04H50.1°0.2°
O02C03C08H80.3°0.3°
C01O02C03C0828.6°180.0°
O02C01H2H3120.0°120.1°
O02C01H2H4120.0°120.0°
O02C01H3H4120.0°120.0°
C03C08C07C060.9°0.1°
C03C08C07H8180.0°179.9°
C08C03C04H5179.1°180.0°
C03C08C07H7179.1°180.0°
N10N09C06C13178.5°179.9°
N10N09C06C07147.1°180.0°
N09N10N11N120.4°0.0°
N10N09C13N120.0°0.0°
N10N09C13H1180.0°179.8°
N11N10N09C06179.0°180.0°
N11N10N09C130.3°0.0°
N10N11N12C130.4°0.0°
N09C06C07C08179.2°180.0°
C06N09C13N12178.8°180.0°
C06N09C13H11.2°0.2°
N09C06C05H60.6°0.0°
N09C06C07H70.8°0.1°
C07C06N09C1334.4°0.1°
C06C07C08H7180.0°179.9°
C07C06C05H6178.4°180.0°
C06C07C08H8179.1°180.0°
N09C13N12N110.2°0.0°
N09C13N12H1180.0°179.8°
N11N12C13H1179.8°179.8°
H2C01H3H4120.0°119.9°
H5C04C05H61.4°0.0°
H7C07C08H80.9°0.1°

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PDB entries from 2026-04-08

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