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Summary Geometry Related PDB entries

M3S

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O12	C11	doub	1.21Å	1.23Å
C11	O1	sing	1.34Å	1.35Å
C11	C13	sing	1.51Å	1.50Å
C2	O1	sing	1.36Å	1.38Å
C3	C2	doub	1.40Å	1.39Å	Aromatic
C2	C7	sing	1.39Å	1.41Å	Aromatic
C6	C7	doub	1.38Å	1.40Å	Aromatic
C7	C1	sing	1.51Å	1.53Å
C1	H1	sing	1.09Å	1.10Å
C1	H1A	sing	1.09Å	1.10Å
C1	H1B	sing	1.09Å	1.10Å
C5	C6	sing	1.39Å	1.40Å	Aromatic
C6	H6	sing	1.08Å	1.08Å
C4	C5	doub	1.38Å	1.41Å	Aromatic
C5	H5	sing	1.08Å	1.08Å
C4	C3	sing	1.40Å	1.40Å	Aromatic
C4	H4	sing	1.08Å	1.08Å
C8	C3	sing	1.47Å	1.58Å
O9	C8	doub	1.21Å	1.29Å
C8	O10	sing	1.35Å	1.31Å
O10	HO10	sing	0.97Å	0.95Å
C13	H13	sing	1.09Å	1.10Å
C13	H13A	sing	1.09Å	1.10Å
C13	H13B	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O12	C11	O1	116.8°	120.1°
O12	C11	C13	126.3°	120.0°
O1	C11	C13	116.9°	120.0°
C11	O1	C2	118.4°	117.0°
C11	C13	H13	109.5°	109.5°
C11	C13	H13A	109.4°	109.5°
C11	C13	H13B	109.5°	109.5°
O1	C2	C3	123.4°	120.1°
O1	C2	C7	116.1°	120.2°
C3	C2	C7	120.6°	119.7°
C2	C3	C4	120.7°	119.6°
C2	C3	C8	121.8°	120.2°
C2	C7	C6	119.0°	120.1°
C2	C7	C1	119.0°	120.0°
C6	C7	C1	122.0°	119.9°
C7	C6	C5	120.4°	120.4°
C7	C6	H6	119.8°	119.8°
C7	C1	H1	109.5°	109.4°
C7	C1	H1A	109.5°	109.5°
C7	C1	H1B	109.5°	109.5°
H1	C1	H1A	109.5°	109.5°
H1	C1	H1B	109.4°	109.4°
H1A	C1	H1B	109.5°	109.5°
C5	C6	H6	119.8°	119.8°
C6	C5	C4	120.5°	120.3°
C6	C5	H5	119.7°	119.9°
C4	C5	H5	119.7°	119.8°
C5	C4	C3	118.8°	119.9°
C5	C4	H4	120.6°	120.1°
C3	C4	H4	120.6°	120.1°
C4	C3	C8	117.4°	120.2°
C3	C8	O9	114.2°	120.0°
C3	C8	O10	115.6°	120.0°
O9	C8	O10	130.1°	120.0°
C8	O10	HO10	109.5°	117.0°
H13	C13	H13A	109.5°	109.4°
H13	C13	H13B	109.5°	109.5°
H13A	C13	H13B	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O12	C11	O1	C13	177.3°	179.7°
O12	C11	O1	C2	9.0°	0.0°
O12	C11	C13	H13	117.1°	90.1°
O12	C11	C13	H13A	2.9°	150.0°
O12	C11	C13	H13B	122.9°	30.0°
C11	O1	C2	C3	71.7°	90.3°
C11	O1	C2	C7	108.3°	90.0°
O1	C11	C13	H13	65.9°	90.3°
O1	C11	C13	H13A	174.1°	29.7°
O1	C11	C13	H13B	54.0°	149.7°
C13	C11	O1	C2	173.8°	179.7°
C11	C13	H13	H13A	120.0°	120.0°
C11	C13	H13	H13B	120.0°	120.0°
C11	C13	H13A	H13B	120.0°	120.0°
O1	C2	C3	C7	180.0°	179.7°
O1	C2	C7	C6	179.9°	180.0°
O1	C2	C7	C1	0.1°	0.0°
O1	C2	C3	C4	179.9°	179.7°
O1	C2	C3	C8	0.2°	0.3°
C3	C2	C7	C6	0.1°	0.3°
C3	C2	C7	C1	179.9°	179.7°
C2	C3	C4	C5	0.1°	0.5°
C2	C3	C4	C8	179.8°	179.5°
C2	C3	C4	H4	179.9°	179.7°
C2	C3	C8	O9	139.3°	0.5°
C2	C3	C8	O10	38.3°	179.5°
C2	C7	C6	C1	179.9°	180.0°
C2	C7	C1	H1	176.6°	90.0°
C2	C7	C1	H1A	63.4°	150.0°
C2	C7	C1	H1B	56.6°	29.9°
C2	C7	C6	C5	0.3°	0.0°
C2	C7	C6	H6	179.7°	180.0°
C7	C2	C3	C4	0.1°	0.6°
C7	C2	C3	C8	179.8°	180.0°
C6	C7	C1	H1	3.3°	90.0°
C6	C7	C1	H1A	116.7°	30.0°
C6	C7	C1	H1B	123.3°	150.0°
C7	C6	C5	H6	180.0°	180.0°
C7	C6	C5	C4	0.3°	0.0°
C7	C6	C5	H5	179.7°	180.0°
C7	C1	H1	H1A	120.0°	120.0°
C7	C1	H1	H1B	120.0°	120.0°
C7	C1	H1A	H1B	120.0°	120.0°
C1	C7	C6	C5	179.8°	180.0°
C1	C7	C6	H6	0.2°	0.0°
H1	C1	H1A	H1B	120.0°	120.0°
C6	C5	C4	H5	180.0°	180.0°
C6	C5	C4	C3	0.0°	0.2°
C6	C5	C4	H4	180.0°	180.0°
H6	C6	C5	C4	179.8°	180.0°
H6	C6	C5	H5	0.2°	0.0°
C5	C4	C3	H4	180.0°	179.8°
C5	C4	C3	C8	179.9°	180.0°
H5	C5	C4	C3	179.9°	179.8°
H5	C5	C4	H4	0.0°	0.0°
C4	C3	C8	O9	40.5°	180.0°
C4	C3	C8	O10	141.9°	0.0°
H4	C4	C3	C8	0.1°	0.2°
C3	C8	O9	O10	177.2°	180.0°
C3	C8	O10	HO10	177.1°	180.0°
O9	C8	O10	HO10	0.0°	0.0°
H13	C13	H13A	H13B	120.0°	120.0°

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PDB entries from 2024-08-07

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