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Summary Geometry Related PDB entries

2MY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C8	C6	sing	1.51Å	1.53Å
C6	C5	doub	1.38Å	1.39Å	Aromatic
C6	C1	sing	1.39Å	1.40Å	Aromatic
C5	C4	sing	1.38Å	1.39Å	Aromatic
C4	C3	doub	1.38Å	1.39Å	Aromatic
C3	C2	sing	1.38Å	1.38Å	Aromatic
C2	C7	sing	1.51Å	1.53Å
C2	C1	doub	1.39Å	1.38Å	Aromatic
C1	O1	sing	1.36Å	1.35Å
C8	H8	sing	1.09Å	1.10Å
C8	H8A	sing	1.09Å	1.10Å
C8	H8B	sing	1.09Å	1.10Å
C5	H5	sing	1.08Å	1.08Å
C4	H4	sing	1.08Å	1.08Å
C3	H3	sing	1.08Å	1.08Å
C7	H7	sing	1.09Å	1.10Å
C7	H7A	sing	1.09Å	1.10Å
C7	H7B	sing	1.09Å	1.10Å
O1	HO1	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C8	C6	C5	121.7°	120.0°
C8	C6	C1	119.3°	120.1°
C6	C8	H8	109.5°	109.4°
C6	C8	H8A	109.5°	109.5°
C6	C8	H8B	109.4°	109.5°
C5	C6	C1	118.9°	119.9°
C6	C5	C4	119.4°	120.1°
C6	C5	H5	120.3°	119.9°
C6	C1	C2	121.3°	119.9°
C6	C1	O1	121.3°	120.0°
C5	C4	C3	121.6°	120.1°
C4	C5	H5	120.3°	120.0°
C5	C4	H4	119.2°	119.9°
C4	C3	C2	119.0°	120.1°
C3	C4	H4	119.2°	119.9°
C4	C3	H3	120.5°	120.0°
C3	C2	C7	120.8°	120.1°
C3	C2	C1	119.7°	119.9°
C2	C3	H3	120.5°	120.0°
C7	C2	C1	119.5°	120.0°
C2	C7	H7	109.5°	109.5°
C2	C7	H7A	109.5°	109.5°
C2	C7	H7B	109.5°	109.5°
C2	C1	O1	117.4°	120.1°
C1	O1	HO1	109.5°	114.0°
H8	C8	H8A	109.4°	109.4°
H8	C8	H8B	109.5°	109.5°
H8A	C8	H8B	109.5°	109.5°
H7	C7	H7A	109.5°	109.5°
H7	C7	H7B	109.4°	109.4°
H7A	C7	H7B	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C8	C6	C5	C1	175.5°	179.7°
C8	C6	C5	C4	178.5°	180.0°
C8	C6	C1	C2	178.5°	179.8°
C8	C6	C1	O1	2.5°	0.0°
C6	C8	H8	H8A	120.0°	120.0°
C6	C8	H8	H8B	120.0°	120.0°
C6	C8	H8A	H8B	120.0°	120.1°
C8	C6	C5	H5	1.5°	0.1°
C6	C5	C4	H5	180.0°	179.9°
C6	C5	C4	C3	1.7°	0.0°
C5	C6	C1	C2	2.8°	0.5°
C5	C6	C1	O1	178.2°	179.7°
C5	C6	C8	H8	7.0°	90.1°
C5	C6	C8	H8A	127.0°	150.0°
C5	C6	C8	H8B	113.0°	30.0°
C6	C5	C4	H4	178.3°	180.0°
C1	C6	C5	C4	3.0°	0.3°
C6	C1	C2	C3	1.2°	0.5°
C6	C1	C2	C7	178.8°	179.7°
C6	C1	C2	O1	179.0°	179.8°
C1	C6	C8	H8	177.4°	90.3°
C1	C6	C8	H8A	57.5°	29.7°
C1	C6	C8	H8B	62.5°	149.7°
C1	C6	C5	H5	177.0°	179.8°
C6	C1	O1	HO1	0.4°	90.0°
C5	C4	C3	H4	180.0°	180.0°
C5	C4	C3	C2	0.1°	0.0°
C5	C4	C3	H3	179.9°	180.0°
C4	C3	C2	H3	180.0°	180.0°
C4	C3	C2	C7	179.8°	180.0°
C4	C3	C2	C1	0.2°	0.3°
C3	C4	C5	H5	178.3°	180.0°
C3	C2	C7	C1	180.0°	179.7°
C3	C2	C1	O1	179.8°	179.7°
C2	C3	C4	H4	179.9°	180.0°
C3	C2	C7	H7	177.1°	90.0°
C3	C2	C7	H7A	62.9°	150.0°
C3	C2	C7	H7B	57.2°	30.0°
C7	C2	C1	O1	0.3°	0.0°
C7	C2	C3	H3	0.2°	0.0°
C2	C7	H7	H7A	120.0°	120.0°
C2	C7	H7	H7B	120.0°	120.0°
C2	C7	H7A	H7B	120.0°	120.0°
C1	C2	C3	H3	179.8°	179.7°
C1	C2	C7	H7	2.9°	89.7°
C1	C2	C7	H7A	117.1°	30.3°
C1	C2	C7	H7B	122.9°	150.3°
C2	C1	O1	HO1	178.7°	89.8°
H8	C8	H8A	H8B	120.0°	120.0°
H5	C5	C4	H4	1.7°	0.0°
H4	C4	C3	H3	0.1°	0.0°
H7	C7	H7A	H7B	120.0°	120.0°

225681

PDB entries from 2024-10-02

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