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Summary Geometry Related PDB entries

VR

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C4	C3	sing	1.53Å	1.53Å
C3	C5	sing	1.53Å	1.47Å
C3	C2	sing	1.53Å	1.52Å
C2	O2	sing	1.43Å	1.37Å
O2	P1	sing	1.61Å	1.56Å
P1	C1	sing	1.82Å	1.84Å
P1	O1	doub	1.48Å	1.48Å
P1	O3	sing	1.61Å	1.67Å
C4	H41C	sing	1.09Å	1.10Å
C4	H42C	sing	1.09Å	1.10Å
C4	H43C	sing	1.09Å	1.10Å
C3	H3	sing	1.09Å	1.10Å
C5	H51C	sing	1.09Å	1.10Å
C5	H52C	sing	1.09Å	1.10Å
C5	H53C	sing	1.09Å	1.10Å
C2	H21C	sing	1.09Å	1.10Å
C2	H22C	sing	1.09Å	1.10Å
C1	H11C	sing	1.09Å	1.10Å
C1	H12C	sing	1.09Å	1.10Å
C1	H13C	sing	1.09Å	1.10Å
O3	H30	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C4	C3	C5	110.5°	109.5°
C4	C3	C2	108.4°	109.5°
C3	C4	H41C	109.5°	109.5°
C3	C4	H42C	109.4°	109.5°
C3	C4	H43C	109.5°	109.4°
C4	C3	H3	108.1°	109.5°
C5	C3	C2	104.8°	109.5°
C5	C3	H3	111.5°	109.4°
C3	C5	H51C	109.5°	109.5°
C3	C5	H52C	109.5°	109.5°
C3	C5	H53C	109.4°	109.5°
C3	C2	O2	103.3°	109.5°
C2	C3	H3	113.5°	109.5°
C3	C2	H21C	111.6°	109.5°
C3	C2	H22C	112.9°	109.5°
C2	O2	P1	119.3°	123.0°
O2	C2	H21C	111.6°	109.5°
O2	C2	H22C	112.9°	109.5°
O2	P1	C1	104.1°	109.5°
O2	P1	O1	126.1°	109.5°
O2	P1	O3	100.9°	109.5°
C1	P1	O1	106.9°	109.4°
C1	P1	O3	101.3°	109.4°
P1	C1	H11C	109.5°	109.5°
P1	C1	H12C	109.4°	109.5°
P1	C1	H13C	109.5°	109.4°
O1	P1	O3	114.6°	109.5°
P1	O3	H30	109.5°	114.0°
H41C	C4	H42C	109.5°	109.5°
H41C	C4	H43C	109.5°	109.4°
H42C	C4	H43C	109.5°	109.5°
H51C	C5	H52C	109.5°	109.5°
H51C	C5	H53C	109.5°	109.4°
H52C	C5	H53C	109.5°	109.4°
H21C	C2	H22C	104.8°	109.4°
H11C	C1	H12C	109.5°	109.5°
H11C	C1	H13C	109.4°	109.5°
H12C	C1	H13C	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C4	C3	C5	C2	116.5°	120.0°
C4	C3	C5	H3	120.3°	120.0°
C4	C3	C2	H3	120.1°	120.0°
C4	C3	C2	O2	78.8°	175.0°
C3	C4	H41C	H42C	120.0°	120.0°
C3	C4	H41C	H43C	120.0°	119.9°
C3	C4	H42C	H43C	120.0°	120.0°
C4	C3	C5	H51C	125.8°	180.0°
C4	C3	C5	H52C	5.7°	60.0°
C4	C3	C5	H53C	114.2°	60.0°
C4	C3	C2	H21C	41.2°	65.0°
C4	C3	C2	H22C	159.0°	54.9°
C5	C3	C2	H3	121.9°	120.0°
C5	C3	C2	O2	163.3°	65.0°
C5	C3	C4	H41C	37.6°	59.9°
C5	C3	C4	H42C	157.6°	179.9°
C5	C3	C4	H43C	82.5°	60.0°
C3	C5	H51C	H52C	120.0°	120.1°
C3	C5	H51C	H53C	120.0°	120.0°
C3	C5	H52C	H53C	120.0°	120.0°
C5	C3	C2	H21C	76.7°	55.1°
C5	C3	C2	H22C	41.0°	175.0°
C3	C2	O2	H21C	120.0°	120.0°
C3	C2	O2	H22C	122.3°	120.0°
C3	C2	O2	P1	137.8°	180.0°
C2	C3	C4	H41C	76.7°	180.0°
C2	C3	C4	H42C	43.3°	60.0°
C2	C3	C4	H43C	163.3°	60.0°
C2	C3	C5	H51C	9.3°	60.0°
C2	C3	C5	H52C	110.8°	180.0°
C2	C3	C5	H53C	129.3°	60.0°
C3	C2	H21C	H22C	122.5°	120.0°
C2	O2	P1	C1	114.7°	175.0°
C2	O2	P1	O1	8.9°	55.0°
C2	O2	P1	O3	140.6°	65.0°
O2	C2	C3	H3	41.4°	55.0°
O2	C2	H21C	H22C	122.5°	120.0°
O2	P1	C1	O1	135.4°	120.0°
O2	P1	C1	O3	104.4°	120.0°
O2	P1	O1	O3	126.2°	120.1°
P1	O2	C2	H21C	102.2°	60.0°
P1	O2	C2	H22C	15.5°	60.0°
O2	P1	C1	H11C	45.8°	60.0°
O2	P1	C1	H12C	165.9°	180.0°
O2	P1	C1	H13C	74.1°	60.0°
O2	P1	O3	H30	38.3°	60.0°
C1	P1	O1	O3	111.3°	119.9°
P1	C1	H11C	H12C	120.0°	120.0°
P1	C1	H11C	H13C	120.0°	119.9°
P1	C1	H12C	H13C	120.0°	119.9°
C1	P1	O3	H30	68.6°	60.0°
O1	P1	C1	H11C	178.8°	180.0°
O1	P1	C1	H12C	58.8°	59.9°
O1	P1	C1	H13C	61.2°	60.0°
O1	P1	O3	H30	176.7°	180.0°
O3	P1	C1	H11C	58.5°	60.0°
O3	P1	C1	H12C	61.5°	60.0°
O3	P1	C1	H13C	178.5°	180.0°
H41C	C4	H42C	H43C	120.0°	120.0°
H41C	C4	C3	H3	159.9°	60.0°
H42C	C4	C3	H3	80.1°	60.0°
H43C	C4	C3	H3	39.8°	180.0°
H3	C3	C5	H51C	113.9°	60.0°
H3	C3	C5	H52C	126.0°	60.0°
H3	C3	C5	H53C	6.0°	180.0°
H3	C3	C2	H21C	161.4°	175.0°
H3	C3	C2	H22C	80.9°	65.1°
H51C	C5	H52C	H53C	120.0°	119.9°
H11C	C1	H12C	H13C	120.0°	120.1°

218500

PDB entries from 2024-04-17

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