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Summary Geometry Related PDB entries

Y1L

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C07	C08	doub	1.37Å	1.36Å	Aromatic
C07	C06	sing	1.40Å	1.40Å	Aromatic
C08	C09	sing	1.39Å	1.40Å	Aromatic
C06	S05	sing	1.76Å	1.74Å	Aromatic
C06	C12	doub	1.40Å	1.40Å	Aromatic
S05	C04	sing	1.75Å	1.66Å	Aromatic
C09	CL10	sing	1.74Å	1.73Å
C09	C11	doub	1.36Å	1.40Å	Aromatic
C12	C11	sing	1.41Å	1.39Å	Aromatic
C12	C03	sing	1.45Å	1.43Å	Aromatic
C04	C03	doub	1.32Å	1.47Å	Aromatic
C03	C02	sing	1.51Å	1.56Å
C02	O01	sing	1.43Å	1.44Å
C02	H1	sing	1.09Å	1.10Å
C02	H2	sing	1.09Å	1.10Å
C04	H3	sing	1.08Å	1.08Å
C07	H4	sing	1.08Å	1.08Å
C08	H5	sing	1.08Å	1.08Å
C11	H6	sing	1.08Å	1.08Å
O01	H7	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C08	C07	C06	120.3°	120.2°
C07	C08	C09	120.3°	120.2°
C08	C07	H4	119.9°	119.9°
C07	C08	H5	119.9°	119.9°
C07	C06	S05	132.8°	130.5°
C07	C06	C12	120.3°	119.7°
C06	C07	H4	119.8°	119.9°
C08	C09	CL10	118.5°	119.7°
C08	C09	C11	119.9°	120.6°
C09	C08	H5	119.9°	119.9°
S05	C06	C12	107.0°	109.7°
C06	S05	C04	99.2°	92.2°
C06	C12	C11	119.0°	118.9°
C06	C12	C03	113.5°	111.8°
S05	C04	C03	106.2°	111.4°
S05	C04	H3	126.9°	124.3°
CL10	C09	C11	121.6°	119.7°
C09	C11	C12	120.3°	120.4°
C09	C11	H6	119.8°	119.8°
C11	C12	C03	127.4°	129.3°
C12	C11	H6	119.9°	119.8°
C12	C03	C04	114.1°	114.9°
C12	C03	C02	123.8°	122.6°
C04	C03	C02	122.1°	122.5°
C03	C04	H3	126.9°	124.3°
C03	C02	O01	109.9°	109.5°
C03	C02	H1	109.4°	109.5°
C03	C02	H2	109.4°	109.5°
O01	C02	H1	109.4°	109.5°
O01	C02	H2	109.4°	109.5°
C02	O01	H7	109.5°	114.1°
H1	C02	H2	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C08	C07	C06	H4	180.0°	179.9°
C07	C08	C09	H5	180.0°	179.9°
C08	C07	C06	S05	179.8°	180.0°
C08	C07	C06	C12	0.5°	0.0°
C07	C08	C09	CL10	179.7°	179.9°
C07	C08	C09	C11	0.5°	0.0°
C06	C07	C08	C09	0.6°	0.0°
C07	C06	S05	C12	179.7°	180.0°
C07	C06	S05	C04	179.8°	180.0°
C07	C06	C12	C11	0.4°	0.0°
C07	C06	C12	C03	179.9°	179.8°
C06	C07	C08	H5	179.4°	180.0°
C08	C09	CL10	C11	179.9°	179.9°
C08	C09	C11	C12	0.3°	0.0°
C09	C08	C07	H4	179.5°	180.0°
C08	C09	C11	H6	179.7°	180.0°
S05	C06	C12	C11	179.9°	180.0°
S05	C06	C12	C03	0.2°	0.2°
C06	S05	C04	C03	0.0°	0.2°
C06	S05	C04	H3	180.0°	179.8°
S05	C06	C07	H4	0.2°	0.1°
C12	C06	S05	C04	0.1°	0.0°
C06	C12	C11	C09	0.3°	0.0°
C06	C12	C11	C03	179.7°	179.8°
C06	C12	C03	C04	0.2°	0.3°
C06	C12	C03	C02	179.7°	180.0°
C12	C06	C07	H4	179.5°	180.0°
C06	C12	C11	H6	179.7°	180.0°
S05	C04	C03	C12	0.1°	0.3°
S05	C04	C03	H3	180.0°	180.0°
S05	C04	C03	C02	179.8°	180.0°
CL10	C09	C11	C12	179.8°	180.0°
CL10	C09	C08	H5	0.3°	0.0°
CL10	C09	C11	H6	0.2°	0.0°
C09	C11	C12	H6	180.0°	180.0°
C09	C11	C12	C03	180.0°	179.8°
C11	C09	C08	H5	179.5°	179.9°
C11	C12	C03	C04	179.9°	179.9°
C11	C12	C03	C02	0.0°	0.2°
C12	C03	C04	C02	179.9°	179.7°
C12	C03	C02	O01	45.6°	179.7°
C12	C03	C02	H1	74.4°	60.2°
C12	C03	C02	H2	165.7°	59.7°
C12	C03	C04	H3	179.9°	179.7°
C03	C12	C11	H6	0.1°	0.2°
C04	C03	C02	O01	134.5°	0.0°
C04	C03	C02	H1	105.4°	120.0°
C04	C03	C02	H2	14.4°	120.0°
C03	C02	O01	H1	120.1°	120.0°
C03	C02	O01	H2	120.1°	120.0°
C03	C02	H1	H2	119.8°	120.0°
C02	C03	C04	H3	0.3°	0.0°
C03	C02	O01	H7	180.0°	180.0°
O01	C02	H1	H2	119.8°	119.9°
H1	C02	O01	H7	59.9°	60.0°
H2	C02	O01	H7	59.9°	60.0°
H4	C07	C08	H5	0.6°	0.1°

250359

PDB entries from 2026-03-11

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