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

V5K

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C7	N1	sing	1.35Å	1.34Å	Aromatic
C7	C6	doub	1.35Å	1.37Å	Aromatic
N1	N2	sing	1.28Å	1.36Å	Aromatic
C6	C5	sing	1.41Å	1.40Å	Aromatic
N2	C5	doub	1.32Å	1.35Å	Aromatic
C5	C4	sing	1.48Å	1.47Å
C4	O1	sing	1.35Å	1.35Å
C4	O2	doub	1.21Å	1.21Å
O1	C2	sing	1.45Å	1.48Å
C1	C2	sing	1.53Å	1.52Å
C2	C3	sing	1.53Å	1.52Å
N1	H1	sing	0.97Å	1.00Å
C2	H2	sing	1.09Å	1.10Å
C6	H3	sing	1.08Å	1.08Å
C1	H4	sing	1.09Å	1.10Å
C1	H5	sing	1.09Å	1.10Å
C1	H6	sing	1.09Å	1.10Å
C3	H7	sing	1.09Å	1.10Å
C3	H8	sing	1.09Å	1.10Å
C3	H9	sing	1.09Å	1.10Å
C7	H10	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N1	C7	C6	107.5°	107.2°
C7	N1	N2	111.4°	110.2°
C7	N1	H1	124.4°	124.8°
N1	C7	H10	126.3°	126.4°
C7	C6	C5	105.7°	105.5°
C7	C6	H3	127.2°	127.3°
C6	C7	H10	126.3°	126.4°
N1	N2	C5	105.3°	110.1°
N2	N1	H1	124.3°	124.9°
C6	C5	N2	109.7°	107.0°
C6	C5	C4	129.3°	126.5°
C5	C6	H3	127.1°	127.2°
N2	C5	C4	121.0°	126.5°
C5	C4	O1	111.2°	120.0°
C5	C4	O2	123.5°	120.0°
O1	C4	O2	125.2°	120.0°
C4	O1	C2	120.4°	117.0°
O1	C2	C1	106.1°	109.5°
O1	C2	C3	108.8°	109.5°
O1	C2	H2	109.9°	109.5°
C1	C2	C3	113.5°	109.5°
C1	C2	H2	109.3°	109.5°
C2	C1	H4	109.5°	109.4°
C2	C1	H5	109.5°	109.5°
C2	C1	H6	109.5°	109.5°
C3	C2	H2	109.2°	109.5°
C2	C3	H7	109.5°	109.5°
C2	C3	H8	109.4°	109.5°
C2	C3	H9	109.4°	109.5°
H4	C1	H5	109.4°	109.4°
H4	C1	H6	109.5°	109.5°
H5	C1	H6	109.5°	109.5°
H7	C3	H8	109.4°	109.4°
H7	C3	H9	109.5°	109.5°
H8	C3	H9	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N1	C7	C6	H10	180.0°	179.9°
C7	N1	N2	H1	180.0°	179.7°
N1	C7	C6	C5	4.6°	0.2°
C7	N1	N2	C5	6.6°	0.2°
N1	C7	C6	H3	175.4°	179.8°
C6	C7	N1	N2	7.1°	0.0°
C7	C6	C5	H3	180.0°	179.9°
C7	C6	C5	N2	0.7°	0.4°
C7	C6	C5	C4	178.4°	180.0°
C6	C7	N1	H1	172.9°	179.7°
N1	N2	C5	C6	3.4°	0.4°
N1	N2	C5	C4	174.5°	180.0°
N2	N1	C7	H10	172.8°	179.9°
C6	C5	N2	C4	178.0°	179.7°
C6	C5	C4	O1	169.2°	180.0°
C6	C5	C4	O2	6.8°	0.0°
C5	C6	C7	H10	175.3°	179.7°
N2	C5	C4	O1	8.3°	0.4°
N2	C5	C4	O2	175.6°	179.6°
C5	N2	N1	H1	173.4°	180.0°
N2	C5	C6	H3	179.3°	179.7°
C5	C4	O1	O2	176.0°	180.0°
C5	C4	O1	C2	173.5°	180.0°
C4	C5	C6	H3	1.6°	0.0°
C4	O1	C2	C1	172.4°	90.0°
C4	O1	C2	C3	65.1°	150.0°
C4	O1	C2	H2	54.4°	30.0°
O2	C4	O1	C2	2.5°	0.0°
O1	C2	C1	C3	119.5°	120.0°
O1	C2	C1	H2	118.4°	120.0°
O1	C2	C3	H2	119.9°	120.0°
O1	C2	C1	H4	180.0°	180.0°
O1	C2	C1	H5	60.0°	60.0°
O1	C2	C1	H6	60.0°	60.0°
O1	C2	C3	H7	180.0°	60.0°
O1	C2	C3	H8	60.0°	60.0°
O1	C2	C3	H9	60.0°	180.0°
C1	C2	C3	H2	122.2°	120.0°
C2	C1	H4	H5	120.0°	120.0°
C2	C1	H4	H6	120.0°	120.0°
C2	C1	H5	H6	120.0°	120.0°
C1	C2	C3	H7	62.1°	60.0°
C1	C2	C3	H8	177.9°	180.0°
C1	C2	C3	H9	57.9°	60.0°
C3	C2	C1	H4	60.5°	60.0°
C3	C2	C1	H5	59.5°	179.9°
C3	C2	C1	H6	179.5°	60.0°
C2	C3	H7	H8	120.0°	120.0°
C2	C3	H7	H9	120.0°	120.1°
C2	C3	H8	H9	120.0°	120.1°
H1	N1	C7	H10	7.2°	0.3°
H2	C2	C1	H4	61.6°	60.0°
H2	C2	C1	H5	178.4°	59.9°
H2	C2	C1	H6	58.4°	180.0°
H2	C2	C3	H7	60.1°	180.0°
H2	C2	C3	H8	59.9°	60.0°
H2	C2	C3	H9	179.9°	60.0°
H3	C6	C7	H10	4.7°	0.2°
H4	C1	H5	H6	120.0°	120.0°
H7	C3	H8	H9	120.0°	119.9°

222415

PDB entries from 2024-07-10

PDB statistics

PDBj update info

Contact PDBj

numon