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Summary Geometry Related PDB entries

OXQ

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O9	C6	sing	1.35Å	1.21Å
O9	HO9	sing	0.97Å	0.95Å
C6	O8	doub	1.21Å	1.22Å
C6	C2	sing	1.48Å	1.45Å
C2	C1	sing	1.48Å	1.47Å	Aromatic
C2	N3	doub	1.31Å	1.30Å	Aromatic
C1	O7	sing	1.36Å	1.29Å
C1	N5	doub	1.31Å	1.32Å	Aromatic
O7	HO7	sing	0.97Å	0.95Å
N3	O4	sing	1.21Å	1.39Å	Aromatic
O4	N5	sing	1.21Å	1.39Å	Aromatic

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C6	O9	HO9	125.4°	120.0°
O9	C6	O8	125.5°	120.0°
O9	C6	C2	112.5°	120.1°
O8	C6	C2	122.0°	120.0°
C6	C2	C1	129.8°	128.8°
C6	C2	N3	123.1°	128.7°
C1	C2	N3	107.2°	102.5°
C2	C1	O7	124.2°	128.7°
C2	C1	N5	108.4°	102.7°
C2	N3	O4	108.3°	109.3°
O7	C1	N5	127.4°	128.7°
C1	O7	HO7	124.2°	106.9°
C1	N5	O4	106.7°	109.4°
N3	O4	N5	109.5°	116.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O9	C6	O8	C2	176.8°	179.9°
O9	C6	C2	C1	152.8°	179.8°
O9	C6	C2	N3	27.8°	0.0°
HO9	O9	C6	O8	179.9°	0.2°
HO9	O9	C6	C2	2.9°	180.0°
O8	C6	C2	C1	30.0°	0.3°
O8	C6	C2	N3	149.4°	179.9°
C6	C2	C1	N3	179.5°	179.8°
C6	C2	C1	O7	1.2°	0.2°
C6	C2	C1	N5	179.8°	179.9°
C6	C2	N3	O4	179.6°	180.0°
C2	C1	O7	N5	178.4°	179.6°
C2	C1	O7	HO7	179.9°	90.5°
C1	C2	N3	O4	0.0°	0.2°
C2	C1	N5	O4	1.0°	0.3°
N3	C2	C1	O7	179.3°	180.0°
N3	C2	C1	N5	0.7°	0.3°
C2	N3	O4	N5	0.6°	0.0°
O7	C1	N5	O4	179.6°	180.0°
N5	C1	O7	HO7	1.7°	89.9°
C1	N5	O4	N3	1.0°	0.2°

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PDB entries from 2024-08-07

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