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Summary Geometry Related PDB entries

5QM

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	C2	sing	1.43Å	1.42Å
O1	HO1	sing	0.97Å	0.95Å
C2	C3	sing	1.47Å	1.47Å
C2	H2	sing	1.09Å	1.10Å
C2	H2A	sing	1.09Å	1.10Å
C3	C4	trip	1.17Å	1.20Å
C4	C5	sing	1.43Å	1.44Å
C5	C6	doub	1.41Å	1.40Å	Aromatic
C5	C14	sing	1.39Å	1.40Å	Aromatic
C6	C7	sing	1.36Å	1.38Å	Aromatic
C6	H6	sing	1.08Å	1.08Å
C7	C8	doub	1.40Å	1.42Å	Aromatic
C7	H7	sing	1.08Å	1.08Å
C8	C9	sing	1.41Å	1.41Å	Aromatic
C8	C13	sing	1.42Å	1.42Å	Aromatic
C9	C10	doub	1.36Å	1.38Å	Aromatic
C9	H9	sing	1.08Å	1.08Å
C10	N11	sing	1.33Å	1.34Å	Aromatic
C10	H10	sing	1.08Å	1.08Å
N11	C12	doub	1.31Å	1.34Å	Aromatic
C12	C13	sing	1.41Å	1.41Å	Aromatic
C12	H12	sing	1.08Å	1.08Å
C13	C14	doub	1.40Å	1.40Å	Aromatic
C14	H14	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	O1	HO1	109.5°	114.0°
O1	C2	C3	112.2°	109.5°
O1	C2	H2	108.8°	109.5°
O1	C2	H2A	108.8°	109.5°
C3	C2	H2	108.8°	109.5°
C3	C2	H2A	108.8°	109.4°
C2	C3	C4	180.0°	180.0°
H2	C2	H2A	109.5°	109.5°
C3	C4	C5	180.0°	180.0°
C4	C5	C6	120.2°	119.7°
C4	C5	C14	120.3°	119.7°
C6	C5	C14	119.5°	120.6°
C5	C6	C7	120.8°	120.9°
C5	C6	H6	119.6°	119.5°
C5	C14	C13	121.2°	119.3°
C5	C14	H14	119.4°	120.3°
C7	C6	H6	119.6°	119.5°
C6	C7	C8	120.4°	119.8°
C6	C7	H7	119.8°	120.1°
C8	C7	H7	119.8°	120.1°
C7	C8	C9	123.2°	122.0°
C7	C8	C13	119.0°	119.8°
C9	C8	C13	117.8°	118.2°
C8	C9	C10	119.2°	118.7°
C8	C9	H9	120.4°	120.6°
C8	C13	C12	117.9°	118.5°
C8	C13	C14	119.2°	119.5°
C10	C9	H9	120.4°	120.7°
C9	C10	N11	123.1°	121.9°
C9	C10	H10	118.4°	119.0°
N11	C10	H10	118.4°	119.0°
C10	N11	C12	118.9°	122.8°
N11	C12	C13	123.0°	119.9°
N11	C12	H12	118.5°	120.1°
C13	C12	H12	118.5°	120.0°
C12	C13	C14	122.9°	121.9°
C13	C14	H14	119.4°	120.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C2	C3	H2	120.4°	120.0°
O1	C2	C3	H2A	120.4°	120.0°
O1	C2	H2	H2A	118.7°	120.1°
O1	C2	C3	C4	44.3°	0.0°
HO1	O1	C2	C3	180.0°	180.0°
HO1	O1	C2	H2	59.6°	60.0°
HO1	O1	C2	H2A	59.6°	60.0°
C3	C2	H2	H2A	118.7°	119.9°
C2	C3	C4	C5	152.8°	180.0°
H2	C2	C3	C4	164.7°	120.0°
H2A	C2	C3	C4	76.1°	120.0°
C3	C4	C5	C6	36.0°	0.0°
C3	C4	C5	C14	144.7°	179.8°
C4	C5	C6	C14	179.3°	179.8°
C4	C5	C6	C7	179.8°	180.0°
C4	C5	C6	H6	0.2°	0.1°
C4	C5	C14	C13	179.0°	179.7°
C4	C5	C14	H14	1.0°	0.0°
C5	C6	C7	H6	180.0°	179.9°
C5	C6	C7	C8	0.8°	0.0°
C5	C6	C7	H7	179.2°	180.0°
C6	C5	C14	C13	1.7°	0.5°
C6	C5	C14	H14	178.3°	179.8°
C14	C5	C6	C7	0.5°	0.2°
C14	C5	C6	H6	179.5°	179.7°
C5	C14	C13	C8	1.7°	0.5°
C5	C14	C13	C12	179.9°	179.8°
C5	C14	C13	H14	180.0°	179.7°
C6	C7	C8	H7	180.0°	180.0°
C6	C7	C8	C9	178.7°	179.9°
C6	C7	C8	C13	0.8°	0.0°
H6	C6	C7	C8	179.3°	180.0°
H6	C6	C7	H7	0.8°	0.1°
C7	C8	C9	C13	177.9°	179.9°
C7	C8	C9	C10	179.8°	180.0°
C7	C8	C9	H9	0.2°	0.2°
C7	C8	C13	C12	178.9°	180.0°
C7	C8	C13	C14	0.5°	0.2°
H7	C7	C8	C9	1.3°	0.1°
H7	C7	C8	C13	179.2°	180.0°
C8	C9	C10	H9	180.0°	179.8°
C8	C9	C10	N11	1.7°	0.1°
C8	C9	C10	H10	178.3°	180.0°
C9	C8	C13	C12	0.9°	0.0°
C9	C8	C13	C14	177.6°	179.7°
C13	C8	C9	C10	2.2°	0.1°
C13	C8	C9	H9	177.7°	179.9°
C8	C13	C12	N11	1.2°	0.0°
C8	C13	C12	C14	178.4°	179.7°
C8	C13	C12	H12	178.8°	180.0°
C8	C13	C14	H14	178.3°	179.8°
C9	C10	N11	H10	180.0°	180.0°
C9	C10	N11	C12	0.3°	0.0°
H9	C9	C10	N11	178.3°	179.9°
H9	C9	C10	H10	1.7°	0.1°
C10	N11	C12	C13	1.8°	0.0°
C10	N11	C12	H12	178.2°	180.0°
H10	C10	N11	C12	179.6°	180.0°
N11	C12	C13	H12	180.0°	180.0°
N11	C12	C13	C14	179.5°	179.7°
C12	C13	C14	H14	0.1°	0.1°
H12	C12	C13	C14	0.5°	0.3°

223532

PDB entries from 2024-08-07

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