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Summary Geometry Related PDB entries

A1AYX

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
CL1	C1	sing	1.74Å	1.74Å
C1	C2	doub	1.38Å	1.38Å	Aromatic
C1	C9	sing	1.38Å	1.38Å	Aromatic
C2	C3	sing	1.38Å	1.38Å	Aromatic
C3	C4	doub	1.38Å	1.38Å	Aromatic
C4	C5	sing	1.39Å	1.39Å	Aromatic
C5	N1	sing	1.40Å	1.41Å
C5	C9	doub	1.39Å	1.39Å	Aromatic
N1	C6	sing	1.35Å	1.35Å
C6	O1	doub	1.21Å	1.22Å
C6	C7	sing	1.51Å	1.52Å
C7	C8	sing	1.47Å	1.45Å
C8	N2	trip	1.14Å	1.14Å
C2	H2	sing	1.08Å	1.08Å
C3	H3	sing	1.08Å	1.08Å
C4	H4	sing	1.08Å	1.08Å
C7	H73	sing	1.09Å	1.10Å
C7	H72	sing	1.09Å	1.10Å
C9	H9	sing	1.08Å	1.08Å
N1	H1	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
CL1	C1	C2	119.1°	120.0°
CL1	C1	C9	118.7°	120.0°
C2	C1	C9	122.2°	120.0°
C1	C2	C3	118.6°	120.1°
C1	C2	H2	120.7°	120.0°
C1	C9	C5	118.6°	119.9°
C1	C9	H9	120.7°	120.0°
C2	C3	C4	120.7°	120.1°
C3	C2	H2	120.7°	119.9°
C2	C3	H3	119.7°	120.0°
C3	C4	C5	120.0°	120.0°
C4	C3	H3	119.6°	120.0°
C3	C4	H4	120.0°	120.0°
C4	C5	N1	119.1°	120.1°
C4	C5	C9	119.9°	119.9°
C5	C4	H4	120.0°	120.0°
N1	C5	C9	121.0°	120.1°
C5	N1	C6	128.4°	120.0°
C5	N1	H1	115.8°	120.0°
C5	C9	H9	120.7°	120.0°
N1	C6	O1	123.2°	120.0°
N1	C6	C7	115.1°	120.0°
C6	N1	H1	115.8°	120.0°
O1	C6	C7	121.6°	120.0°
C6	C7	C8	111.1°	109.5°
C6	C7	H73	109.1°	109.5°
C6	C7	H72	109.1°	109.5°
C7	C8	N2	178.9°	180.0°
C8	C7	H73	109.1°	109.5°
C8	C7	H72	109.1°	109.5°
H73	C7	H72	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
CL1	C1	C2	C9	180.0°	179.7°
CL1	C1	C2	C3	179.8°	179.7°
CL1	C1	C9	C5	179.9°	179.7°
CL1	C1	C2	H2	0.1°	0.3°
CL1	C1	C9	H9	0.0°	0.3°
C1	C2	C3	H2	180.0°	180.0°
C1	C2	C3	C4	0.2°	0.0°
C2	C1	C9	C5	0.1°	0.0°
C1	C2	C3	H3	179.8°	180.0°
C2	C1	C9	H9	180.0°	180.0°
C9	C1	C2	C3	0.2°	0.0°
C1	C9	C5	C4	0.3°	0.0°
C1	C9	C5	N1	179.4°	180.0°
C1	C9	C5	H9	180.0°	180.0°
C9	C1	C2	H2	179.9°	180.0°
C2	C3	C4	H3	180.0°	180.0°
C2	C3	C4	C5	0.1°	0.0°
C2	C3	C4	H4	179.9°	180.0°
C3	C4	C5	H4	180.0°	180.0°
C3	C4	C5	N1	179.4°	180.0°
C3	C4	C5	C9	0.3°	0.0°
C4	C3	C2	H2	179.9°	180.0°
C4	C5	N1	C9	179.1°	180.0°
C4	C5	N1	C6	39.8°	33.3°
C5	C4	C3	H3	180.0°	180.0°
C4	C5	C9	H9	179.7°	180.0°
C4	C5	N1	H1	140.2°	146.7°
C5	N1	C6	H1	180.0°	180.0°
C5	N1	C6	O1	7.3°	5.2°
C5	N1	C6	C7	168.6°	174.7°
N1	C5	C4	H4	0.6°	0.0°
N1	C5	C9	H9	0.7°	0.0°
C9	C5	N1	C6	141.2°	146.7°
C9	C5	C4	H4	179.7°	180.0°
C9	C5	N1	H1	38.8°	33.3°
N1	C6	O1	C7	175.7°	179.9°
N1	C6	C7	C8	61.9°	180.0°
N1	C6	C7	H73	177.9°	60.0°
N1	C6	C7	H72	58.4°	60.0°
O1	C6	C7	C8	122.1°	0.1°
O1	C6	C7	H73	1.8°	120.1°
O1	C6	C7	H72	117.7°	119.9°
O1	C6	N1	H1	172.7°	174.8°
C6	C7	C8	H73	120.2°	120.0°
C6	C7	C8	H72	120.2°	120.0°
C6	C7	C8	N2	63.9°	27.2°
C6	C7	H73	H72	119.3°	120.0°
C7	C6	N1	H1	11.4°	5.3°
C8	C7	H73	H72	119.3°	120.0°
N2	C8	C7	H73	56.3°	92.9°
N2	C8	C7	H72	175.8°	147.2°
H2	C2	C3	H3	0.2°	0.0°
H3	C3	C4	H4	0.1°	0.0°

250059

PDB entries from 2026-03-04

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