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Summary Geometry Related PDB entries

OPL

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	O1	sing	1.43Å	1.43Å
C1	C2	sing	1.53Å	1.48Å
C1	O2	sing	1.43Å	1.44Å
C2	C3	sing	1.53Å	1.30Å
C2	C5	sing	1.53Å	1.52Å
C2	H2	sing	1.09Å	1.10Å
C3	C4	sing	1.51Å	1.48Å
C3	O4	sing	1.43Å	1.34Å
C3	H3	sing	1.09Å	1.10Å
O3	C4	doub	1.21Å	1.30Å
C4	H4	sing	1.08Å	1.08Å
O4	HO4	sing	0.97Å	0.95Å
C5	H5	sing	1.09Å	1.10Å
C5	H5A	sing	1.09Å	1.10Å
C5	H5B	sing	1.09Å	1.10Å
O1	H8	sing	0.97Å	0.95Å
C1	H9	sing	1.09Å	1.10Å
O2	H10	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C1	C2	116.6°	109.4°
O1	C1	O2	117.1°	109.5°
C1	O1	H8	109.5°	114.0°
O1	C1	H9	102.7°	109.4°
C2	C1	O2	112.6°	109.5°
C1	C2	C3	120.1°	109.5°
C1	C2	C5	115.9°	109.5°
C1	C2	H2	102.5°	109.5°
C2	C1	H9	102.2°	109.5°
O2	C1	H9	102.6°	109.5°
C1	O2	H10	109.5°	114.0°
C3	C2	C5	109.2°	109.4°
C3	C2	H2	104.4°	109.5°
C2	C3	C4	116.9°	109.5°
C2	C3	O4	99.7°	109.5°
C2	C3	H3	112.7°	109.5°
C5	C2	H2	102.2°	109.4°
C2	C5	H5	109.5°	109.4°
C2	C5	H5A	109.5°	109.5°
C2	C5	H5B	109.5°	109.5°
C4	C3	O4	105.2°	109.5°
C4	C3	H3	109.7°	109.4°
C3	C4	O3	122.0°	120.0°
C3	C4	H4	119.0°	120.0°
O4	C3	H3	111.9°	109.5°
C3	O4	HO4	109.5°	114.0°
O3	C4	H4	119.0°	120.0°
H5	C5	H5A	109.5°	109.5°
H5	C5	H5B	109.5°	109.5°
H5A	C5	H5B	109.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C1	C2	O2	139.5°	120.0°
O1	C1	C2	H9	111.2°	120.0°
O1	C1	O2	H9	111.6°	120.0°
O1	C1	C2	C3	130.7°	180.0°
O1	C1	C2	C5	4.0°	60.0°
O1	C1	C2	H2	114.3°	60.0°
O1	C1	O2	H10	180.0°	60.0°
C2	C1	O2	H9	109.2°	120.1°
C1	C2	C3	C5	137.4°	120.0°
C1	C2	C3	H2	114.0°	120.1°
C1	C2	C5	H2	110.5°	120.1°
C1	C2	C3	C4	92.1°	175.0°
C1	C2	C3	O4	20.5°	65.0°
C1	C2	C3	H3	139.3°	55.0°
C1	C2	C5	H5	180.0°	60.0°
C1	C2	C5	H5A	60.0°	180.0°
C1	C2	C5	H5B	60.0°	59.9°
C2	C1	O1	H8	180.0°	180.0°
C2	C1	O2	H10	40.7°	59.9°
O2	C1	C2	C3	8.8°	60.0°
O2	C1	C2	C5	143.5°	180.0°
O2	C1	C2	H2	106.2°	60.0°
O2	C1	O1	H8	42.4°	60.0°
C3	C2	C5	H2	110.1°	120.0°
C2	C3	C4	O4	109.5°	120.0°
C2	C3	C4	H3	129.9°	120.0°
C2	C3	O4	H3	119.4°	120.0°
C2	C3	C4	O3	10.0°	120.0°
C2	C3	C4	H4	170.0°	59.9°
C2	C3	O4	HO4	180.0°	60.0°
C3	C2	C5	H5	40.6°	180.0°
C3	C2	C5	H5A	79.4°	60.0°
C3	C2	C5	H5B	160.6°	60.0°
C3	C2	C1	H9	118.1°	60.0°
C5	C2	C3	C4	45.2°	65.0°
C5	C2	C3	O4	157.9°	55.0°
C5	C2	C3	H3	83.3°	175.0°
C2	C5	H5	H5A	120.0°	120.0°
C2	C5	H5	H5B	120.0°	120.0°
C2	C5	H5A	H5B	120.0°	120.0°
C5	C2	C1	H9	107.2°	60.0°
H2	C2	C3	C4	153.8°	54.9°
H2	C2	C3	O4	93.5°	175.0°
H2	C2	C3	H3	25.3°	65.1°
H2	C2	C5	H5	69.5°	60.0°
H2	C2	C5	H5A	170.5°	60.0°
H2	C2	C5	H5B	50.5°	180.0°
H2	C2	C1	H9	3.2°	179.9°
C4	C3	O4	H3	119.1°	120.0°
C3	C4	O3	H4	180.0°	179.9°
C4	C3	O4	HO4	58.5°	60.0°
O4	C3	C4	O3	99.5°	0.0°
O4	C3	C4	H4	80.5°	180.0°
H3	C3	C4	O3	139.9°	120.0°
H3	C3	C4	H4	40.0°	60.1°
H3	C3	O4	HO4	60.6°	180.0°
H5	C5	H5A	H5B	120.0°	120.0°
H8	O1	C1	H9	69.1°	60.0°
H9	C1	O2	H10	68.4°	180.0°

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PDB entries from 2026-01-14

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