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

3DM

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	O1	sing	1.36Å	1.34Å
O1	HO1	sing	0.97Å	0.95Å
C2	C1	doub	1.39Å	1.49Å	Aromatic
C1	C6	sing	1.39Å	1.50Å	Aromatic
O2	C2	sing	1.36Å	1.37Å
C3	C2	sing	1.39Å	1.40Å	Aromatic
C7	O2	sing	1.43Å	1.42Å
C7	H7	sing	1.09Å	1.10Å
C7	H7A	sing	1.09Å	1.10Å
C7	H7B	sing	1.09Å	1.10Å
C3	C4	doub	1.38Å	1.40Å	Aromatic
C3	H3	sing	1.08Å	1.08Å
C4	C5	sing	1.38Å	1.40Å	Aromatic
C4	H4	sing	1.08Å	1.08Å
C5	C6	doub	1.39Å	1.40Å	Aromatic
C5	H5	sing	1.08Å	1.08Å
C6	O3	sing	1.36Å	1.38Å
O3	C8	sing	1.43Å	1.43Å
C8	H8	sing	1.09Å	1.10Å
C8	H8A	sing	1.09Å	1.10Å
C8	H8B	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	O1	HO1	109.5°	114.0°
O1	C1	C2	119.5°	120.1°
O1	C1	C6	123.6°	120.1°
C2	C1	C6	116.9°	119.8°
C1	C2	O2	119.5°	120.0°
C1	C2	C3	120.1°	119.9°
C1	C6	C5	118.4°	119.9°
C1	C6	O3	125.1°	120.0°
O2	C2	C3	120.5°	120.0°
C2	O2	C7	120.0°	117.0°
C2	C3	C4	121.2°	120.1°
C2	C3	H3	119.4°	120.0°
O2	C7	H7	109.5°	109.4°
O2	C7	H7A	109.5°	109.4°
O2	C7	H7B	109.4°	109.4°
H7	C7	H7A	109.5°	109.5°
H7	C7	H7B	109.5°	109.5°
H7A	C7	H7B	109.5°	109.5°
C4	C3	H3	119.4°	119.9°
C3	C4	C5	121.0°	120.2°
C3	C4	H4	119.5°	119.9°
C5	C4	H4	119.5°	119.9°
C4	C5	C6	122.5°	120.1°
C4	C5	H5	118.8°	120.0°
C6	C5	H5	118.8°	120.0°
C5	C6	O3	116.5°	120.0°
C6	O3	C8	126.5°	117.0°
O3	C8	H8	109.5°	109.4°
O3	C8	H8A	109.5°	109.5°
O3	C8	H8B	109.4°	109.4°
H8	C8	H8A	109.5°	109.5°
H8	C8	H8B	109.5°	109.5°
H8A	C8	H8B	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C1	C2	C6	179.8°	179.7°
O1	C1	C2	O2	0.1°	0.1°
O1	C1	C2	C3	179.8°	180.0°
O1	C1	C6	C5	179.9°	179.7°
O1	C1	C6	O3	0.4°	0.0°
HO1	O1	C1	C2	178.3°	89.8°
HO1	O1	C1	C6	1.5°	90.0°
C1	C2	O2	C3	179.7°	179.9°
C1	C2	O2	C7	121.2°	180.0°
C1	C2	C3	C4	0.3°	0.0°
C1	C2	C3	H3	179.7°	180.0°
C2	C1	C6	C5	0.3°	0.6°
C2	C1	C6	O3	179.4°	179.8°
C6	C1	C2	O2	179.9°	179.7°
C6	C1	C2	C3	0.4°	0.2°
C1	C6	C5	C4	0.2°	0.6°
C1	C6	C5	O3	179.7°	179.7°
C1	C6	C5	H5	179.8°	179.7°
C1	C6	O3	C8	1.0°	180.0°
C2	O2	C7	H7	128.5°	180.0°
C2	O2	C7	H7A	8.5°	60.0°
C2	O2	C7	H7B	111.5°	60.0°
O2	C2	C3	C4	179.9°	180.0°
O2	C2	C3	H3	0.1°	0.1°
C3	C2	O2	C7	58.6°	0.1°
C2	C3	C4	H3	180.0°	180.0°
C2	C3	C4	C5	0.2°	0.0°
C2	C3	C4	H4	179.8°	179.9°
O2	C7	H7	H7A	120.0°	120.0°
O2	C7	H7	H7B	120.0°	120.0°
O2	C7	H7A	H7B	120.0°	120.0°
H7	C7	H7A	H7B	120.0°	120.1°
C3	C4	C5	H4	180.0°	179.9°
C3	C4	C5	C6	0.1°	0.3°
C3	C4	C5	H5	179.9°	179.9°
H3	C3	C4	C5	179.8°	180.0°
H3	C3	C4	H4	0.2°	0.1°
C4	C5	C6	H5	180.0°	179.7°
C4	C5	C6	O3	179.5°	179.7°
H4	C4	C5	C6	179.9°	179.8°
H4	C4	C5	H5	0.1°	0.0°
C5	C6	O3	C8	179.3°	0.3°
H5	C5	C6	O3	0.5°	0.0°
C6	O3	C8	H8	178.2°	60.0°
C6	O3	C8	H8A	58.2°	60.0°
C6	O3	C8	H8B	61.8°	180.0°
O3	C8	H8	H8A	120.0°	120.0°
O3	C8	H8	H8B	120.0°	120.0°
O3	C8	H8A	H8B	120.0°	120.0°
H8	C8	H8A	H8B	120.0°	120.1°

246704

PDB entries from 2025-12-24

PDB statistics

PDBj update info

Contact PDBj

numon