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Summary Geometry Related PDB entries

A1JDY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N	C12	doub	1.32Å	1.31Å	Aromatic
N	N1	sing	1.28Å	1.34Å	Aromatic
C	O	sing	1.36Å	1.40Å
C	C1	doub	1.39Å	1.42Å	Aromatic
C	C13	sing	1.39Å	1.41Å	Aromatic
C1	C12	sing	1.38Å	1.40Å	Aromatic
C13	N1	doub	1.32Å	1.31Å	Aromatic
C1	H11	sing	1.08Å	1.08Å
C13	H131	sing	1.08Å	1.08Å
O	HO1	sing	0.97Å	0.95Å
C12	H121	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C12	N	N1	122.0°	122.4°
N	C12	C1	120.8°	119.9°
N	C12	H121	119.6°	120.1°
N	N1	C13	122.1°	122.2°
O	C	C1	120.6°	121.0°
O	C	C13	120.7°	121.1°
C	O	HO1	109.5°	114.0°
C1	C	C13	118.7°	117.9°
C	C1	C12	117.1°	117.9°
C	C1	H11	121.4°	121.1°
C	C13	N1	119.3°	119.7°
C	C13	H131	120.4°	120.2°
C12	C1	H11	121.5°	121.0°
C1	C12	H121	119.6°	120.0°
N1	C13	H131	120.4°	120.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N	C12	C1	C	0.8°	0.3°
N	C12	C1	H121	180.0°	180.0°
C12	N	N1	C13	1.5°	0.6°
N	C12	C1	H11	179.2°	180.0°
N	N1	C13	C	1.5°	0.3°
N1	N	C12	C1	0.3°	0.6°
N	N1	C13	H131	178.5°	179.9°
N1	N	C12	H121	179.7°	179.4°
O	C	C1	C13	179.9°	179.9°
O	C	C1	C12	179.4°	180.0°
O	C	C13	N1	179.5°	180.0°
O	C	C1	H11	0.6°	0.4°
O	C	C13	H131	0.5°	0.3°
C	C1	C12	H11	180.0°	179.7°
C1	C	C13	N1	0.4°	0.0°
C1	C	C13	H131	179.6°	179.8°
C1	C	O	HO1	180.0°	90.0°
C	C1	C12	H121	179.2°	179.7°
C13	C	C1	C12	0.7°	0.0°
C	C13	N1	H131	180.0°	179.8°
C13	C	C1	H11	179.3°	179.7°
C13	C	O	HO1	0.1°	90.0°
H11	C1	C12	H121	0.8°	0.1°

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PDB entries from 2026-02-04

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