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Summary Geometry Related PDB entries

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Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
P1	O1	sing	1.62Å	1.45Å
P1	O2	doub	1.50Å	1.47Å
P1	C1	sing	1.78Å	1.79Å
O1	HO1	sing	0.98Å	0.95Å
C1	H1	sing	1.09Å	1.12Å
C1	H2	sing	1.09Å	1.11Å
C1	H3	sing	1.09Å	1.11Å
O3	P1	sing	1.62Å	88.00Å
O3	HO3	sing	1.43Å	0.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	P1	O2	109.6°	115.0°
O1	P1	C1	109.3°	103.4°
P1	O1	HO1	109.6°	119.0°
O1	P1	O3	172.7°	103.6°
O2	P1	C1	109.7°	114.5°
O2	P1	O3	64.8°	115.4°
P1	C1	H1	109.3°	110.1°
P1	C1	H2	112.3°	110.1°
P1	C1	H3	112.3°	110.1°
C1	P1	O3	69.7°	103.3°
H1	C1	H2	112.3°	108.9°
H1	C1	H3	112.2°	108.8°
H2	C1	H3	98.2°	108.8°
P1	O3	HO3	90.0°	111.3°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	P1	O2	C1	120.0°	119.6°
O1	P1	O2	O3	174.9°	120.6°
O1	P1	C1	O3	172.3°	107.8°
O1	P1	C1	H1	180.0°	65.8°
O1	P1	C1	H2	54.7°	174.1°
O1	P1	C1	H3	54.8°	54.1°
O1	P1	O3	HO3	90.0°	72.4°
O2	P1	C1	O3	52.1°	126.3°
O2	P1	O1	HO1	180.0°	52.1°
O2	P1	C1	H1	59.8°	60.0°
O2	P1	C1	H2	174.9°	60.0°
O2	P1	C1	H3	65.4°	180.0°
O2	P1	O3	HO3	90.0°	54.2°
C1	P1	O1	HO1	59.7°	177.7°
P1	C1	H1	H2	125.3°	120.8°
P1	C1	H1	H3	125.2°	120.7°
P1	C1	H2	H3	118.2°	120.7°
C1	P1	O3	HO3	90.0°	180.0°
HO1	O1	P1	O3	140.9°	74.8°
H1	C1	H2	H3	118.2°	118.5°
H1	C1	P1	O3	7.7°	173.7°
H2	C1	P1	O3	133.0°	66.3°
H3	C1	P1	O3	117.5°	53.7°

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PDB entries from 2026-02-18

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