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Summary Geometry Related PDB entries

A1JDZ

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N	C1	sing	1.38Å	1.33Å	Aromatic
N	C12	sing	1.36Å	1.33Å	Aromatic
C	O	sing	1.36Å	1.39Å
C	C1	doub	1.35Å	1.39Å	Aromatic
C	N1	sing	1.34Å	1.32Å	Aromatic
C12	N1	doub	1.31Å	1.31Å	Aromatic
C12	O1	sing	1.35Å	1.40Å
C1	H11	sing	1.08Å	1.08Å
N	H1	sing	0.97Å	1.00Å
O	HO1	sing	0.97Å	0.95Å
O1	H12	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	N	C12	108.4°	107.0°
N	C1	C	105.9°	106.8°
N	C1	H11	127.0°	126.6°
C1	N	H1	125.8°	126.5°
N	C12	N1	109.8°	108.6°
N	C12	O1	126.8°	125.8°
C12	N	H1	125.8°	126.4°
O	C	C1	126.6°	125.9°
O	C	N1	125.5°	125.9°
C	O	HO1	109.5°	114.0°
C1	C	N1	107.9°	108.2°
C	C1	H11	127.0°	126.6°
C	N1	C12	107.9°	109.4°
N1	C12	O1	123.4°	125.7°
C12	O1	H12	109.5°	114.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	N	C12	H1	180.0°	180.0°
N	C1	C	O	179.8°	179.7°
N	C1	C	H11	180.0°	179.8°
N	C1	C	N1	0.2°	0.2°
C1	N	C12	N1	0.0°	0.2°
C1	N	C12	O1	179.7°	180.0°
C12	N	C1	C	0.1°	0.3°
N	C12	N1	C	0.2°	0.0°
N	C12	N1	O1	179.7°	179.8°
C12	N	C1	H11	179.9°	180.0°
N	C12	O1	H12	179.7°	89.9°
O	C	C1	N1	180.0°	180.0°
O	C	N1	C12	179.8°	179.8°
O	C	C1	H11	0.2°	0.0°
C1	C	N1	C12	0.2°	0.1°
C	C1	N	H1	179.9°	179.7°
C1	C	O	HO1	180.0°	90.0°
C	N1	C12	O1	179.6°	179.9°
N1	C	C1	H11	179.8°	180.0°
N1	C	O	HO1	0.0°	90.0°
N1	C12	N	H1	179.9°	179.8°
N1	C12	O1	H12	0.0°	89.9°
O1	C12	N	H1	0.3°	0.0°
H11	C1	N	H1	0.1°	0.0°

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PDB entries from 2026-02-04

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