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Summary Geometry Related PDB entries

D1Y

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
CL16	C15	sing	1.74Å	1.72Å
O08	C07	doub	1.22Å	1.20Å
C15	C14	doub	1.38Å	1.38Å	Aromatic
C15	C09	sing	1.40Å	1.39Å	Aromatic
C14	C12	sing	1.39Å	1.39Å	Aromatic
C07	C09	sing	1.47Å	1.49Å
C07	C06	sing	1.47Å	1.45Å
C09	C10	doub	1.40Å	1.39Å	Aromatic
O05	C04	sing	1.35Å	1.35Å
C12	O13	sing	1.36Å	1.36Å
C12	C11	doub	1.39Å	1.40Å	Aromatic
C10	C11	sing	1.38Å	1.38Å	Aromatic
C04	C06	doub	1.35Å	1.35Å
C04	C02	sing	1.48Å	1.54Å
O03	C02	doub	1.21Å	1.24Å
C02	O01	sing	1.35Å	1.25Å
C10	H1	sing	1.08Å	1.08Å
C06	H3	sing	1.08Å	1.08Å
C11	H5	sing	1.08Å	1.08Å
C14	H6	sing	1.08Å	1.08Å
O01	H7	sing	0.97Å	0.95Å
O05	H8	sing	0.97Å	0.95Å
O13	H9	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
CL16	C15	C14	117.8°	120.1°
CL16	C15	C09	120.1°	120.0°
O08	C07	C09	116.8°	120.1°
O08	C07	C06	124.1°	120.0°
C14	C15	C09	122.1°	119.9°
C15	C14	C12	118.6°	120.1°
C15	C14	H6	120.7°	120.0°
C15	C09	C07	121.4°	120.1°
C15	C09	C10	118.2°	119.8°
C14	C12	O13	118.9°	119.9°
C14	C12	C11	120.6°	120.2°
C12	C14	H6	120.7°	119.9°
C09	C07	C06	119.1°	119.9°
C07	C09	C10	120.4°	120.2°
C07	C06	C04	119.1°	120.0°
C07	C06	H3	120.5°	120.0°
C09	C10	C11	121.2°	120.0°
C09	C10	H1	119.4°	120.0°
O05	C04	C06	119.2°	120.0°
O05	C04	C02	116.2°	120.0°
C04	O05	H8	109.5°	114.0°
O13	C12	C11	120.5°	119.9°
C12	O13	H9	109.5°	114.0°
C12	C11	C10	119.3°	120.1°
C12	C11	H5	120.3°	120.0°
C11	C10	H1	119.4°	120.0°
C10	C11	H5	120.3°	119.9°
C06	C04	C02	121.1°	120.0°
C04	C06	H3	120.5°	120.0°
C04	C02	O03	117.9°	120.0°
C04	C02	O01	113.3°	120.0°
O03	C02	O01	128.7°	120.1°
C02	O01	H7	109.5°	116.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
CL16	C15	C14	C09	179.8°	179.2°
CL16	C15	C14	C12	180.0°	180.0°
CL16	C15	C09	C07	0.1°	0.3°
CL16	C15	C09	C10	179.9°	179.7°
CL16	C15	C14	H6	0.0°	0.7°
O08	C07	C09	C15	52.8°	0.0°
O08	C07	C09	C06	178.6°	180.0°
O08	C07	C09	C10	127.0°	180.0°
O08	C07	C06	C04	4.9°	0.0°
O08	C07	C06	H3	175.1°	180.0°
C15	C14	C12	H6	180.0°	179.3°
C14	C15	C09	C07	179.7°	179.5°
C14	C15	C09	C10	0.2°	0.5°
C15	C14	C12	O13	180.0°	179.4°
C15	C14	C12	C11	0.2°	0.5°
C09	C15	C14	C12	0.2°	0.8°
C15	C09	C07	C10	179.8°	180.0°
C15	C09	C07	C06	128.6°	180.0°
C15	C09	C10	C11	0.2°	0.0°
C15	C09	C10	H1	179.8°	179.7°
C09	C15	C14	H6	179.8°	180.0°
C14	C12	O13	C11	179.8°	179.9°
C14	C12	C11	C10	0.2°	0.1°
C14	C12	C11	H5	179.8°	180.0°
C14	C12	O13	H9	180.0°	90.0°
C07	C09	C10	C11	179.7°	180.0°
C09	C07	C06	C04	173.5°	180.0°
C07	C09	C10	H1	0.3°	0.3°
C09	C07	C06	H3	6.4°	0.0°
C06	C07	C09	C10	51.6°	0.0°
C07	C06	C04	O05	35.3°	0.0°
C07	C06	C04	H3	180.0°	180.0°
C07	C06	C04	C02	122.7°	180.0°
C09	C10	C11	C12	0.2°	0.3°
C09	C10	C11	H1	180.0°	179.7°
C09	C10	C11	H5	179.8°	179.8°
O05	C04	C06	C02	158.0°	180.0°
O05	C04	C02	O03	32.5°	180.0°
O05	C04	C02	O01	147.6°	0.0°
O05	C04	C06	H3	144.7°	180.0°
O13	C12	C11	C10	180.0°	179.9°
O13	C12	C11	H5	0.1°	0.1°
O13	C12	C14	H6	0.0°	0.1°
C12	C11	C10	H5	180.0°	180.0°
C12	C11	C10	H1	179.8°	180.0°
C11	C12	C14	H6	179.8°	179.8°
C11	C12	O13	H9	0.2°	90.1°
C06	C04	C02	O03	126.1°	0.1°
C06	C04	C02	O01	53.8°	180.0°
C06	C04	O05	H8	29.4°	180.0°
C04	C02	O03	O01	179.9°	179.9°
C02	C04	C06	H3	57.3°	0.0°
C04	C02	O01	H7	179.9°	179.9°
C02	C04	O05	H8	129.7°	0.0°
O03	C02	O01	H7	0.0°	0.0°
H1	C10	C11	H5	0.2°	0.1°

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PDB entries from 2024-07-17

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