English 日本語简体中文繁體中文 한국어

✖

Menu

RCSB PDB PDBe BMRB Adv. Search Search help

Summary Geometry Related PDB entries

DHY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	doub	1.38Å	1.43Å	Aromatic
C1	C6	sing	1.38Å	1.41Å	Aromatic
C1	C7	sing	1.51Å	1.55Å
C2	C3	sing	1.39Å	1.36Å	Aromatic
C2	H2	sing	1.08Å	1.10Å
C3	C4	doub	1.39Å	1.39Å	Aromatic
C3	O3	sing	1.36Å	1.37Å
C4	C5	sing	1.39Å	1.40Å	Aromatic
C4	O4	sing	1.36Å	1.38Å
C5	C6	doub	1.38Å	1.42Å	Aromatic
C5	H5	sing	1.08Å	1.10Å
C6	H6	sing	1.08Å	1.10Å
C7	C8	sing	1.51Å	1.58Å
C7	H71	sing	1.09Å	1.12Å
C7	H72	sing	1.09Å	1.11Å
C8	O1	doub	1.21Å	1.27Å
C8	O2	sing	1.34Å	1.24Å
O2	HO2	sing	0.97Å	0.95Å
O3	HO3	sing	0.97Å	0.95Å
O4	HO4	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	C1	C6	121.1°	120.2°
C2	C1	C7	119.7°	119.9°
C1	C2	C3	117.9°	120.0°
C1	C2	H2	123.5°	120.1°
C6	C1	C7	118.9°	119.9°
C1	C6	C5	118.8°	120.1°
C1	C6	H6	120.1°	120.0°
C1	C7	C8	113.6°	109.5°
C1	C7	H71	110.7°	109.5°
C1	C7	H72	110.7°	109.5°
C3	C2	H2	118.6°	120.0°
C2	C3	C4	122.4°	119.8°
C2	C3	O3	121.8°	120.1°
C4	C3	O3	115.8°	120.1°
C3	C4	C5	121.0°	119.9°
C3	C4	O4	114.4°	120.1°
C3	O3	HO3	121.8°	106.9°
C5	C4	O4	124.5°	120.1°
C4	C5	C6	118.7°	120.0°
C4	C5	H5	119.7°	120.1°
C4	O4	HO4	114.5°	106.9°
C6	C5	H5	121.6°	119.9°
C5	C6	H6	121.1°	119.9°
C8	C7	H71	110.7°	109.4°
C8	C7	H72	110.7°	109.5°
C7	C8	O1	114.4°	119.9°
C7	C8	O2	120.9°	120.1°
H71	C7	H72	99.6°	109.4°
O1	C8	O2	124.7°	120.0°
C8	O2	HO2	120.9°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	C1	C6	C7	173.9°	179.7°
C1	C2	C3	H2	180.0°	179.5°
C1	C2	C3	C4	0.2°	0.5°
C1	C2	C3	O3	177.7°	179.8°
C2	C1	C6	C5	0.6°	0.3°
C2	C1	C6	H6	179.5°	179.7°
C2	C1	C7	C8	105.0°	90.4°
C2	C1	C7	H71	20.2°	149.7°
C2	C1	C7	H72	129.7°	29.8°
C6	C1	C2	C3	0.4°	0.5°
C6	C1	C2	H2	179.6°	179.9°
C1	C6	C5	C4	0.5°	0.1°
C1	C6	C5	H6	179.9°	180.0°
C1	C6	C5	H5	179.4°	180.0°
C6	C1	C7	C8	69.0°	90.0°
C6	C1	C7	H71	165.8°	30.0°
C6	C1	C7	H72	56.3°	149.9°
C7	C1	C2	C3	174.2°	179.8°
C7	C1	C2	H2	5.8°	0.2°
C7	C1	C6	C5	174.4°	180.0°
C7	C1	C6	H6	5.6°	0.0°
C1	C7	C8	H71	125.2°	120.0°
C1	C7	C8	H72	125.3°	120.1°
C1	C7	H71	H72	116.5°	120.0°
C1	C7	C8	O1	89.6°	0.1°
C1	C7	C8	O2	90.5°	180.0°
C2	C3	C4	O3	177.6°	179.7°
C2	C3	C4	C5	0.2°	0.3°
C2	C3	C4	O4	178.1°	179.8°
C2	C3	O3	HO3	180.0°	89.8°
H2	C2	C3	C4	179.8°	180.0°
H2	C2	C3	O3	2.3°	0.2°
C3	C4	C5	O4	178.1°	180.0°
C3	C4	C5	C6	0.4°	0.1°
C3	C4	C5	H5	179.6°	180.0°
C4	C3	O3	HO3	2.4°	90.0°
C3	C4	O4	HO4	180.0°	90.0°
O3	C3	C4	C5	177.8°	180.0°
O3	C3	C4	O4	0.4°	0.0°
C4	C5	C6	H5	179.9°	179.9°
C4	C5	C6	H6	179.5°	180.0°
C5	C4	O4	HO4	1.8°	90.0°
O4	C4	C5	C6	177.7°	180.0°
O4	C4	C5	H5	2.3°	0.0°
H5	C5	C6	H6	0.5°	0.0°
C8	C7	H71	H72	116.6°	120.0°
C7	C8	O1	O2	180.0°	179.9°
C7	C8	O2	HO2	180.0°	179.9°
H71	C7	C8	O1	35.7°	120.1°
H71	C7	C8	O2	144.3°	60.0°
H72	C7	C8	O1	145.1°	120.0°
H72	C7	C8	O2	34.8°	59.9°
O1	C8	O2	HO2	0.0°	0.0°

218853

PDB entries from 2024-04-24

PDB statistics

PDBj update info

Contact PDBj

numon