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Summary Geometry Related PDB entries

CIY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C6	C1	doub	1.40Å	1.45Å	Aromatic
C2	C1	sing	1.40Å	1.42Å	Aromatic
C1	C7	sing	1.47Å	1.47Å
C3	C2	doub	1.38Å	1.41Å	Aromatic
C2	H2	sing	1.08Å	1.08Å
C4	C3	sing	1.39Å	1.50Å	Aromatic
O3	C3	sing	1.36Å	1.36Å
O3	C3M	sing	1.43Å	1.44Å
O4	C4	sing	1.36Å	1.35Å
C4	C5	doub	1.39Å	1.45Å	Aromatic
O4	HO4	sing	0.97Å	0.95Å
C5	C6	sing	1.38Å	1.44Å	Aromatic
C5	H5	sing	1.08Å	1.08Å
C6	H6	sing	1.08Å	1.08Å
C7	C8	doub	1.36Å	1.31Å
C7	H7	sing	1.08Å	1.08Å
C8	C9	sing	1.41Å	1.43Å
C8	H8	sing	1.08Å	1.08Å
C9	O9	doub	1.21Å	1.21Å
C9	H9	sing	1.08Å	1.08Å
C3M	H3M	sing	1.09Å	1.10Å
C3M	H3MA	sing	1.09Å	1.10Å
C3M	H3MB	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C6	C1	C2	120.9°	119.8°
C6	C1	C7	123.0°	120.1°
C1	C6	C5	119.5°	120.0°
C1	C6	H6	120.2°	120.0°
C2	C1	C7	116.1°	120.1°
C1	C2	C3	120.9°	119.8°
C1	C2	H2	119.5°	120.1°
C1	C7	C8	122.7°	120.0°
C1	C7	H7	118.6°	120.0°
C3	C2	H2	119.5°	120.1°
C2	C3	C4	119.8°	120.0°
C2	C3	O3	120.7°	120.0°
C4	C3	O3	119.5°	120.0°
C3	C4	O4	119.0°	119.9°
C3	C4	C5	118.2°	120.2°
C3	O3	C3M	112.1°	117.0°
O3	C3M	H3M	109.5°	109.5°
O3	C3M	H3MA	109.5°	109.5°
O3	C3M	H3MB	109.5°	109.5°
O4	C4	C5	122.7°	119.9°
C4	O4	HO4	109.5°	114.0°
C4	C5	C6	120.6°	120.2°
C4	C5	H5	119.7°	119.9°
C6	C5	H5	119.7°	119.9°
C5	C6	H6	120.2°	120.0°
C8	C7	H7	118.6°	120.0°
C7	C8	C9	116.6°	120.0°
C7	C8	H8	121.7°	120.0°
C9	C8	H8	121.7°	120.0°
C8	C9	O9	119.6°	120.0°
C8	C9	H9	120.2°	120.0°
O9	C9	H9	120.2°	120.0°
H3M	C3M	H3MA	109.5°	109.5°
H3M	C3M	H3MB	109.5°	109.5°
H3MA	C3M	H3MB	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C6	C1	C2	C7	179.5°	179.7°
C6	C1	C2	C3	0.0°	0.2°
C6	C1	C2	H2	180.0°	179.8°
C1	C6	C5	C4	0.3°	0.5°
C1	C6	C5	H6	180.0°	179.4°
C1	C6	C5	H5	179.7°	179.8°
C6	C1	C7	C8	7.1°	0.3°
C6	C1	C7	H7	172.9°	179.7°
C1	C2	C3	H2	180.0°	180.0°
C1	C2	C3	C4	0.8°	0.0°
C1	C2	C3	O3	179.1°	180.0°
C2	C1	C6	C5	0.2°	0.5°
C2	C1	C6	H6	179.8°	180.0°
C2	C1	C7	C8	173.4°	180.0°
C2	C1	C7	H7	6.6°	0.0°
C7	C1	C2	C3	179.5°	180.0°
C7	C1	C2	H2	0.5°	0.0°
C7	C1	C6	C5	179.2°	179.7°
C7	C1	C6	H6	0.8°	0.3°
C1	C7	C8	H7	180.0°	180.0°
C1	C7	C8	C9	178.8°	180.0°
C1	C7	C8	H8	1.3°	0.0°
C2	C3	C4	O3	179.8°	180.0°
C2	C3	O3	C3M	81.2°	0.1°
C2	C3	C4	O4	179.6°	180.0°
C2	C3	C4	C5	1.3°	0.0°
H2	C2	C3	C4	179.2°	179.9°
H2	C2	C3	O3	0.9°	0.0°
C4	C3	O3	C3M	98.9°	180.0°
C3	C4	O4	C5	179.0°	180.0°
C3	C4	O4	HO4	180.0°	90.1°
C3	C4	C5	C6	1.1°	0.2°
C3	C4	C5	H5	178.9°	179.9°
O3	C3	C4	O4	0.5°	0.0°
O3	C3	C4	C5	178.5°	180.0°
C3	O3	C3M	H3M	180.0°	60.0°
C3	O3	C3M	H3MA	60.0°	180.0°
C3	O3	C3M	H3MB	60.0°	60.1°
O3	C3M	H3M	H3MA	120.0°	120.0°
O3	C3M	H3M	H3MB	120.0°	120.0°
O3	C3M	H3MA	H3MB	120.0°	120.0°
O4	C4	C5	C6	179.9°	179.7°
O4	C4	C5	H5	0.1°	0.0°
C5	C4	O4	HO4	1.0°	89.9°
C4	C5	C6	H5	180.0°	179.7°
C4	C5	C6	H6	179.6°	180.0°
H5	C5	C6	H6	0.4°	0.3°
C7	C8	C9	H8	180.0°	180.0°
C7	C8	C9	O9	179.7°	180.0°
C7	C8	C9	H9	0.3°	0.0°
H7	C7	C8	C9	1.2°	0.0°
H7	C7	C8	H8	178.7°	180.0°
C8	C9	O9	H9	180.0°	180.0°
H8	C8	C9	O9	0.3°	0.0°
H8	C8	C9	H9	179.7°	180.0°
H3M	C3M	H3MA	H3MB	120.0°	120.0°

224004

PDB entries from 2024-08-21

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