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

VBR

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	C7	doub	1.22Å	1.24Å
CL1	C8	sing	1.74Å	1.74Å
O2	C7	sing	1.35Å	1.25Å
C7	C6	sing	1.47Å	1.51Å
C8	C6	doub	1.40Å	1.40Å	Aromatic
C8	C9	sing	1.36Å	1.38Å	Aromatic
C6	C5	sing	1.39Å	1.40Å	Aromatic
C9	C10	doub	1.39Å	1.39Å	Aromatic
C5	C4	doub	1.39Å	1.40Å	Aromatic
C10	C4	sing	1.41Å	1.41Å	Aromatic
C10	N1	sing	1.37Å	1.37Å	Aromatic
C4	C3	sing	1.47Å	1.43Å	Aromatic
N1	C2	sing	1.37Å	1.38Å	Aromatic
C3	C2	doub	1.34Å	1.36Å	Aromatic
C2	C1	sing	1.51Å	1.49Å
N1	H1	sing	0.97Å	1.00Å
C5	H2	sing	1.08Å	1.08Å
C1	H3	sing	1.09Å	1.10Å
C1	H4	sing	1.09Å	1.10Å
C1	H5	sing	1.09Å	1.10Å
C3	H6	sing	1.08Å	1.08Å
C9	H7	sing	1.08Å	1.08Å
O2	H8	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C7	O2	124.1°	120.0°
O1	C7	C6	118.1°	119.9°
CL1	C8	C6	120.8°	119.7°
CL1	C8	C9	117.9°	119.7°
O2	C7	C6	117.8°	120.0°
C7	O2	H8	109.5°	117.0°
C7	C6	C8	120.9°	120.0°
C7	C6	C5	118.8°	119.9°
C6	C8	C9	121.4°	120.6°
C8	C6	C5	120.3°	120.0°
C8	C9	C10	117.9°	120.3°
C8	C9	H7	121.1°	119.8°
C6	C5	C4	119.5°	119.4°
C6	C5	H2	120.3°	120.3°
C9	C10	C4	122.2°	119.7°
C9	C10	N1	130.3°	133.3°
C10	C9	H7	121.0°	119.9°
C5	C4	C10	118.7°	120.0°
C5	C4	C3	135.1°	134.0°
C4	C5	H2	120.2°	120.3°
C4	C10	N1	107.6°	107.1°
C10	C4	C3	106.1°	106.0°
C10	N1	C2	109.7°	110.0°
C10	N1	H1	125.2°	125.0°
C4	C3	C2	108.3°	106.9°
C4	C3	H6	125.9°	126.5°
N1	C2	C3	108.3°	110.0°
N1	C2	C1	120.7°	125.0°
C2	N1	H1	125.1°	125.0°
C3	C2	C1	131.0°	125.0°
C2	C3	H6	125.8°	126.6°
C2	C1	H3	109.5°	109.5°
C2	C1	H4	109.5°	109.5°
C2	C1	H5	109.5°	109.5°
H3	C1	H4	109.4°	109.5°
H3	C1	H5	109.5°	109.4°
H4	C1	H5	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C7	O2	C6	178.8°	179.9°
O1	C7	C6	C8	113.3°	0.8°
O1	C7	C6	C5	67.3°	180.0°
O1	C7	O2	H8	0.0°	0.1°
CL1	C8	C6	C7	1.2°	0.7°
CL1	C8	C6	C9	179.3°	179.3°
CL1	C8	C6	C5	179.4°	180.0°
CL1	C8	C9	C10	179.9°	179.7°
CL1	C8	C9	H7	0.1°	0.4°
O2	C7	C6	C8	67.8°	179.3°
O2	C7	C6	C5	111.5°	0.1°
C7	C6	C8	C5	179.4°	179.2°
C7	C6	C8	C9	179.5°	179.9°
C7	C6	C5	C4	179.0°	180.0°
C7	C6	C5	H2	1.0°	0.1°
C6	C7	O2	H8	178.8°	180.0°
C6	C8	C9	C10	0.6°	0.3°
C8	C6	C5	C4	0.3°	0.7°
C8	C6	C5	H2	179.6°	179.3°
C6	C8	C9	H7	179.4°	179.7°
C9	C8	C6	C5	0.2°	0.7°
C8	C9	C10	H7	180.0°	180.0°
C8	C9	C10	C4	0.5°	0.0°
C8	C9	C10	N1	179.7°	180.0°
C6	C5	C4	H2	180.0°	180.0°
C6	C5	C4	C10	0.4°	0.4°
C6	C5	C4	C3	179.8°	179.9°
C9	C10	C4	C5	0.0°	0.1°
C9	C10	C4	N1	179.8°	179.9°
C9	C10	C4	C3	179.8°	179.8°
C9	C10	N1	C2	179.7°	180.0°
C9	C10	N1	H1	0.3°	0.2°
C5	C4	C10	C3	179.8°	179.7°
C5	C4	C10	N1	179.9°	180.0°
C5	C4	C3	C2	179.8°	180.0°
C5	C4	C3	H6	0.2°	0.3°
C4	C10	N1	C2	0.1°	0.0°
C10	C4	C3	C2	0.0°	0.4°
C4	C10	N1	H1	179.9°	179.7°
C10	C4	C5	H2	179.6°	179.6°
C10	C4	C3	H6	180.0°	180.0°
C4	C10	C9	H7	179.5°	180.0°
N1	C10	C4	C3	0.0°	0.2°
C10	N1	C2	H1	180.0°	179.8°
C10	N1	C2	C3	0.1°	0.2°
C10	N1	C2	C1	179.3°	179.8°
N1	C10	C9	H7	0.3°	0.1°
C4	C3	C2	N1	0.1°	0.4°
C4	C3	C2	H6	180.0°	179.6°
C4	C3	C2	C1	179.2°	179.7°
C3	C4	C5	H2	0.2°	0.0°
N1	C2	C3	C1	179.3°	180.0°
N1	C2	C1	H3	89.7°	89.9°
N1	C2	C1	H4	150.3°	150.0°
N1	C2	C1	H5	30.3°	30.0°
N1	C2	C3	H6	180.0°	180.0°
C3	C2	N1	H1	179.9°	180.0°
C3	C2	C1	H3	89.5°	90.0°
C3	C2	C1	H4	30.5°	30.0°
C3	C2	C1	H5	150.4°	150.0°
C1	C2	N1	H1	0.7°	0.0°
C2	C1	H3	H4	120.0°	120.0°
C2	C1	H3	H5	120.0°	120.0°
C2	C1	H4	H5	120.0°	120.0°
C1	C2	C3	H6	0.7°	0.0°
H3	C1	H4	H5	120.0°	119.9°

250359

PDB entries from 2026-03-11

PDB statistics

PDBj update info

Contact PDBj

numon