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Summary Geometry Related PDB entries

H5A

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C8	O2	sing	1.43Å	1.42Å
O2	C7	sing	1.36Å	1.37Å
O1	C1	sing	1.43Å	1.42Å
O1	C2	sing	1.36Å	1.37Å
O3	C9	sing	1.43Å	1.42Å
O3	C6	sing	1.36Å	1.37Å
C7	C2	doub	1.39Å	1.40Å	Aromatic
C7	C6	sing	1.39Å	1.40Å	Aromatic
C2	C3	sing	1.38Å	1.37Å	Aromatic
C6	C5	doub	1.38Å	1.37Å	Aromatic
C5	C4	sing	1.40Å	1.39Å	Aromatic
C3	C4	doub	1.40Å	1.39Å	Aromatic
C4	C10	sing	1.47Å	1.49Å
C10	O4	doub	1.22Å	1.24Å
C10	O5	sing	1.35Å	1.24Å
C5	H1	sing	1.08Å	1.08Å
C8	H2	sing	1.09Å	1.10Å
C8	H3	sing	1.09Å	1.10Å
C8	H4	sing	1.09Å	1.10Å
C1	H5	sing	1.09Å	1.10Å
C1	H6	sing	1.09Å	1.10Å
C1	H7	sing	1.09Å	1.10Å
C3	H8	sing	1.08Å	1.08Å
C9	H9	sing	1.09Å	1.10Å
C9	H10	sing	1.09Å	1.10Å
C9	H11	sing	1.09Å	1.10Å
O5	H12	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C8	O2	C7	112.9°	117.0°
O2	C8	H2	109.5°	109.5°
O2	C8	H3	109.5°	109.4°
O2	C8	H4	109.4°	109.5°
O2	C7	C2	119.2°	119.9°
O2	C7	C6	120.5°	120.0°
C1	O1	C2	117.4°	117.0°
O1	C1	H5	109.5°	109.4°
O1	C1	H6	109.5°	109.4°
O1	C1	H7	109.5°	109.4°
O1	C2	C7	114.8°	120.0°
O1	C2	C3	125.1°	120.0°
C9	O3	C6	118.8°	117.0°
O3	C9	H9	109.5°	109.5°
O3	C9	H10	109.5°	109.5°
O3	C9	H11	109.5°	109.5°
O3	C6	C7	115.6°	119.9°
O3	C6	C5	124.7°	120.0°
C2	C7	C6	120.3°	120.1°
C7	C2	C3	120.1°	120.0°
C7	C6	C5	119.6°	120.1°
C2	C3	C4	119.4°	119.9°
C2	C3	H8	120.3°	120.0°
C6	C5	C4	119.9°	120.0°
C6	C5	H1	120.0°	120.0°
C5	C4	C3	120.8°	119.9°
C5	C4	C10	119.2°	120.1°
C4	C5	H1	120.1°	120.0°
C3	C4	C10	120.0°	120.0°
C4	C3	H8	120.3°	120.0°
C4	C10	O4	117.5°	120.0°
C4	C10	O5	118.0°	120.0°
O4	C10	O5	124.5°	120.0°
C10	O5	H12	109.5°	117.0°
H2	C8	H3	109.5°	109.4°
H2	C8	H4	109.5°	109.5°
H3	C8	H4	109.5°	109.5°
H5	C1	H6	109.5°	109.5°
H5	C1	H7	109.5°	109.5°
H6	C1	H7	109.5°	109.5°
H9	C9	H10	109.5°	109.5°
H9	C9	H11	109.5°	109.5°
H10	C9	H11	109.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C8	O2	C7	C2	45.6°	90.0°
C8	O2	C7	C6	132.1°	90.3°
O2	C8	H2	H3	120.0°	120.0°
O2	C8	H2	H4	120.0°	120.0°
O2	C8	H3	H4	120.0°	120.0°
O2	C7	C2	O1	0.4°	0.4°
O2	C7	C6	O3	4.3°	0.3°
O2	C7	C2	C6	177.7°	179.6°
O2	C7	C2	C3	179.2°	180.0°
O2	C7	C6	C5	179.8°	179.7°
C7	O2	C8	H2	180.0°	60.0°
C7	O2	C8	H3	60.0°	60.0°
C7	O2	C8	H4	60.0°	180.0°
C1	O1	C2	C7	173.6°	179.9°
C1	O1	C2	C3	6.9°	0.3°
O1	C1	H5	H6	120.0°	120.0°
O1	C1	H5	H7	120.0°	119.9°
O1	C1	H6	H7	120.0°	120.0°
O1	C2	C7	C3	179.6°	179.6°
O1	C2	C7	C6	178.1°	180.0°
O1	C2	C3	C4	178.8°	179.7°
C2	O1	C1	H5	180.0°	60.0°
C2	O1	C1	H6	60.0°	60.0°
C2	O1	C1	H7	60.0°	180.0°
O1	C2	C3	H8	1.1°	0.3°
C9	O3	C6	C7	112.0°	179.9°
C9	O3	C6	C5	72.4°	0.0°
O3	C9	H9	H10	120.0°	120.0°
O3	C9	H9	H11	120.0°	120.0°
O3	C9	H10	H11	120.0°	120.0°
O3	C6	C7	C2	178.0°	180.0°
O3	C6	C7	C5	175.8°	180.0°
O3	C6	C5	C4	177.5°	180.0°
O3	C6	C5	H1	2.5°	0.1°
C6	O3	C9	H9	180.0°	180.0°
C6	O3	C9	H10	60.0°	60.0°
C6	O3	C9	H11	60.0°	60.0°
C2	C7	C6	C5	2.2°	0.1°
C7	C2	C3	C4	0.7°	0.6°
C7	C2	C3	H8	179.4°	180.0°
C6	C7	C2	C3	1.5°	0.4°
C7	C6	C5	C4	2.0°	0.1°
C7	C6	C5	H1	177.9°	179.9°
C2	C3	C4	C5	0.5°	0.6°
C2	C3	C4	H8	180.0°	179.4°
C2	C3	C4	C10	179.3°	179.7°
C6	C5	C4	H1	180.0°	180.0°
C6	C5	C4	C3	1.2°	0.3°
C6	C5	C4	C10	180.0°	180.0°
C5	C4	C3	C10	178.8°	179.7°
C5	C4	C10	O4	22.0°	0.0°
C5	C4	C10	O5	158.6°	180.0°
C5	C4	C3	H8	179.5°	180.0°
C3	C4	C10	O4	156.8°	179.7°
C3	C4	C10	O5	22.6°	0.3°
C3	C4	C5	H1	178.7°	179.7°
C4	C10	O4	O5	179.4°	179.9°
C10	C4	C5	H1	0.1°	0.0°
C10	C4	C3	H8	0.7°	0.3°
C4	C10	O5	H12	179.4°	179.9°
O4	C10	O5	H12	0.0°	0.1°
H2	C8	H3	H4	120.0°	120.0°
H5	C1	H6	H7	120.0°	120.1°
H9	C9	H10	H11	120.0°	120.0°

247536

PDB entries from 2026-01-14

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