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

HQD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N1	C2	sing	1.36Å	1.41Å
N1	C9	sing	1.38Å	1.43Å
N1	H1N	sing	0.97Å	1.00Å
C2	C3	doub	1.35Å	1.50Å
C2	C	sing	1.51Å	1.50Å
C3	C4	sing	1.42Å	1.41Å
C3	O3	sing	1.36Å	1.37Å
C4	C10	sing	1.47Å	1.44Å
C4	O13	doub	1.22Å	1.29Å
C5	C6	doub	1.37Å	1.43Å	Aromatic
C5	C10	sing	1.40Å	1.37Å	Aromatic
C6	C7	sing	1.39Å	1.44Å	Aromatic
C7	C8	doub	1.38Å	1.41Å	Aromatic
C8	C9	sing	1.39Å	1.40Å	Aromatic
C9	C10	doub	1.41Å	1.48Å	Aromatic
C	HC1	sing	1.09Å	1.10Å
C	HC2	sing	1.09Å	1.10Å
C	HC3	sing	1.09Å	1.10Å
O3	H3	sing	0.97Å	0.95Å
C5	H5	sing	1.08Å	1.08Å
C6	H6	sing	1.08Å	1.08Å
C7	H7	sing	1.08Å	1.08Å
C8	H8	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	N1	C9	120.2°	121.6°
C2	N1	H1N	119.9°	119.2°
N1	C2	C3	120.1°	122.4°
N1	C2	C	120.0°	118.8°
C9	N1	H1N	119.9°	119.2°
N1	C9	C8	120.0°	121.1°
N1	C9	C10	120.1°	119.6°
C3	C2	C	120.0°	118.7°
C2	C3	C4	119.9°	120.0°
C2	C3	O3	120.0°	120.0°
C2	C	HC1	109.5°	109.5°
C2	C	HC2	109.5°	109.5°
C2	C	HC3	109.5°	109.4°
C4	C3	O3	120.1°	120.0°
C3	C4	C10	119.8°	117.8°
C3	C4	O13	120.0°	121.1°
C3	O3	H3	109.5°	114.0°
C10	C4	O13	120.1°	121.1°
C4	C10	C5	120.0°	121.4°
C4	C10	C9	119.9°	118.5°
C6	C5	C10	120.0°	119.7°
C5	C6	C7	120.1°	120.5°
C6	C5	H5	120.0°	120.1°
C5	C6	H6	119.9°	119.7°
C5	C10	C9	120.0°	120.1°
C10	C5	H5	120.0°	120.2°
C6	C7	C8	120.0°	120.7°
C7	C6	H6	120.0°	119.8°
C6	C7	H7	120.0°	119.6°
C7	C8	C9	120.0°	119.7°
C8	C7	H7	120.0°	119.7°
C7	C8	H8	120.0°	120.1°
C8	C9	C10	119.9°	119.3°
C9	C8	H8	120.0°	120.1°
HC1	C	HC2	109.4°	109.5°
HC1	C	HC3	109.5°	109.5°
HC2	C	HC3	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	N1	C9	H1N	180.0°	179.7°
N1	C2	C3	C	178.6°	180.0°
N1	C2	C3	C4	1.9°	0.0°
N1	C2	C3	O3	179.7°	180.0°
C2	N1	C9	C8	179.3°	180.0°
C2	N1	C9	C10	0.5°	0.0°
N1	C2	C	HC1	116.6°	89.9°
N1	C2	C	HC2	3.4°	150.0°
N1	C2	C	HC3	123.5°	30.1°
C9	N1	C2	C3	1.5°	0.0°
C9	N1	C2	C	179.9°	180.0°
N1	C9	C10	C4	0.2°	0.0°
N1	C9	C10	C5	177.8°	180.0°
N1	C9	C8	C7	178.7°	180.0°
N1	C9	C8	C10	179.8°	180.0°
N1	C9	C8	H8	1.3°	0.0°
H1N	N1	C2	C3	178.5°	179.7°
H1N	N1	C2	C	0.1°	0.2°
H1N	N1	C9	C8	0.7°	0.3°
H1N	N1	C9	C10	179.5°	179.7°
C2	C3	C4	O3	178.4°	180.0°
C2	C3	C4	C10	1.2°	0.0°
C2	C3	C4	O13	178.7°	179.9°
C3	C2	C	HC1	64.8°	90.0°
C3	C2	C	HC2	175.2°	30.0°
C3	C2	C	HC3	55.2°	150.0°
C2	C3	O3	H3	65.6°	180.0°
C	C2	C3	C4	179.5°	180.0°
C	C2	C3	O3	1.1°	0.0°
C2	C	HC1	HC2	120.0°	120.1°
C2	C	HC1	HC3	120.0°	120.0°
C2	C	HC2	HC3	120.0°	119.9°
C3	C4	C10	O13	179.9°	179.9°
C3	C4	C10	C5	177.4°	180.0°
C3	C4	C10	C9	0.2°	0.0°
C4	C3	O3	H3	112.8°	0.0°
O3	C3	C4	C10	179.6°	180.0°
O3	C3	C4	O13	0.3°	0.1°
C4	C10	C5	C6	179.7°	180.0°
C4	C10	C5	C9	177.6°	180.0°
C4	C10	C9	C8	180.0°	180.0°
C4	C10	C5	H5	0.3°	0.1°
O13	C4	C10	C5	2.6°	0.1°
O13	C4	C10	C9	179.7°	179.9°
C6	C5	C10	H5	180.0°	179.9°
C5	C6	C7	H6	180.0°	179.9°
C5	C6	C7	C8	1.2°	0.0°
C6	C5	C10	C9	2.6°	0.0°
C5	C6	C7	H7	178.7°	180.0°
C10	C5	C6	C7	2.1°	0.1°
C5	C10	C9	C8	2.4°	0.0°
C10	C5	C6	H6	177.9°	180.0°
C6	C7	C8	H7	180.0°	180.0°
C6	C7	C8	C9	0.9°	0.0°
C7	C6	C5	H5	177.9°	180.0°
C6	C7	C8	H8	179.0°	180.0°
C7	C8	C9	H8	180.0°	180.0°
C7	C8	C9	C10	1.5°	0.1°
C8	C7	C6	H6	178.8°	180.0°
C9	C8	C7	H7	179.0°	180.0°
C9	C10	C5	H5	177.3°	179.9°
C10	C9	C8	H8	178.5°	179.9°
HC1	C	HC2	HC3	120.0°	120.0°
H5	C5	C6	H6	2.1°	0.1°
H6	C6	C7	H7	1.3°	0.0°
H7	C7	C8	H8	1.0°	0.0°

247947

PDB entries from 2026-01-21

PDB statistics

PDBj update info

Contact PDBj

numon