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Summary Geometry Related PDB entries

AMR

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N1	C1	doub	1.33Å	1.34Å	Aromatic
N1	C5	sing	1.31Å	1.35Å	Aromatic
C1	C3	sing	1.47Å	1.58Å
C1	C2	sing	1.40Å	1.40Å	Aromatic
C3	N5	sing	1.35Å	1.40Å
C3	O1	doub	1.22Å	1.24Å
N5	C6	sing	1.38Å	1.30Å
N5	HN5	sing	0.97Å	1.02Å
C6	N7	sing	1.37Å	1.31Å
C6	N6	doub	1.30Å	1.30Å
N7	HN71	sing	0.97Å	1.02Å
N7	HN72	sing	0.97Å	1.02Å
N6	HN6	sing	0.97Å	1.02Å
C2	N4	sing	1.38Å	1.41Å
C2	N3	doub	1.33Å	1.35Å	Aromatic
N4	HN41	sing	0.97Å	1.02Å
N4	HN42	sing	0.97Å	1.02Å
N3	C4	sing	1.33Å	1.36Å	Aromatic
C4	N2	sing	1.38Å	1.42Å
C4	C5	doub	1.40Å	1.41Å	Aromatic
N2	HN21	sing	0.97Å	1.02Å
N2	HN22	sing	0.97Å	1.02Å
C5	CL1	sing	1.74Å	1.74Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	N1	C5	121.5°	120.1°
N1	C1	C3	117.1°	120.1°
N1	C1	C2	119.8°	119.9°
N1	C5	C4	119.3°	120.2°
N1	C5	CL1	118.0°	119.9°
C3	C1	C2	123.2°	120.0°
C1	C3	N5	116.8°	120.0°
C1	C3	O1	120.2°	120.0°
C1	C2	N4	122.2°	120.2°
C1	C2	N3	119.6°	119.8°
N5	C3	O1	123.0°	120.0°
C3	N5	C6	124.1°	120.0°
C3	N5	HN5	121.7°	120.0°
C6	N5	HN5	114.2°	120.0°
N5	C6	N7	122.5°	120.0°
N5	C6	N6	118.2°	120.0°
N7	C6	N6	119.3°	120.0°
C6	N7	HN71	122.5°	120.0°
C6	N7	HN72	107.5°	120.0°
C6	N6	HN6	108.7°	120.0°
HN71	N7	HN72	107.5°	120.0°
N4	C2	N3	118.2°	120.0°
C2	N4	HN41	122.2°	120.1°
C2	N4	HN42	107.7°	119.9°
C2	N3	C4	120.6°	119.9°
HN41	N4	HN42	107.7°	120.0°
N3	C4	N2	118.0°	119.9°
N3	C4	C5	119.3°	120.1°
N2	C4	C5	122.7°	119.9°
C4	N2	HN21	118.0°	119.9°
C4	N2	HN22	109.2°	120.0°
C4	C5	CL1	122.7°	119.9°
HN21	N2	HN22	109.2°	120.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N1	C1	C3	C2	179.8°	179.7°
N1	C1	C3	N5	9.5°	6.2°
N1	C1	C3	O1	169.7°	173.9°
N1	C1	C2	N4	179.9°	180.0°
N1	C1	C2	N3	0.1°	0.6°
C1	N1	C5	C4	0.0°	0.1°
C1	N1	C5	CL1	179.9°	180.0°
C5	N1	C1	C3	179.9°	180.0°
C5	N1	C1	C2	0.1°	0.4°
N1	C5	C4	N3	0.1°	0.1°
N1	C5	C4	N2	180.0°	180.0°
N1	C5	C4	CL1	179.9°	179.9°
C1	C3	N5	O1	179.2°	179.9°
C1	C3	N5	C6	173.1°	174.1°
C1	C3	N5	HN5	6.8°	5.9°
C3	C1	C2	N4	0.1°	0.3°
C3	C1	C2	N3	179.9°	179.8°
C2	C1	C3	N5	170.7°	174.2°
C2	C1	C3	O1	10.1°	5.7°
C1	C2	N4	N3	180.0°	179.4°
C1	C2	N4	HN41	180.0°	174.9°
C1	C2	N4	HN42	54.7°	5.1°
C1	C2	N3	C4	0.1°	0.6°
C3	N5	C6	HN5	180.0°	180.0°
C3	N5	C6	N7	0.6°	5.3°
C3	N5	C6	N6	179.5°	174.7°
O1	C3	N5	C6	6.1°	5.8°
O1	C3	N5	HN5	174.0°	174.2°
N5	C6	N7	N6	179.9°	180.0°
N5	C6	N7	HN71	180.0°	174.4°
N5	C6	N7	HN72	54.8°	6.0°
N5	C6	N6	HN6	157.8°	5.0°
HN5	N5	C6	N7	179.4°	174.7°
HN5	N5	C6	N6	0.5°	5.3°
C6	N7	HN71	HN72	125.2°	179.7°
N7	C6	N6	HN6	22.3°	175.0°
N6	C6	N7	HN71	0.1°	5.6°
N6	C6	N7	HN72	125.1°	174.0°
C2	N4	HN41	HN42	125.3°	180.0°
N4	C2	N3	C4	179.9°	180.0°
N3	C2	N4	HN41	0.0°	5.7°
N3	C2	N4	HN42	125.3°	174.3°
C2	N3	C4	N2	179.9°	179.7°
C2	N3	C4	C5	0.0°	0.3°
N3	C4	N2	C5	179.9°	180.0°
N3	C4	N2	HN21	179.9°	0.0°
N3	C4	N2	HN22	54.7°	179.9°
N3	C4	C5	CL1	179.9°	180.0°
C4	N2	HN21	HN22	125.4°	179.9°
N2	C4	C5	CL1	0.0°	0.1°
C5	C4	N2	HN21	0.0°	179.9°
C5	C4	N2	HN22	125.4°	0.1°

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PDB entries from 2026-02-11

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