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Summary Geometry Related PDB entries

3A9

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O2	C1	doub	1.22Å	1.35Å
C1	O1	sing	1.35Å	1.24Å
C1	C2	sing	1.47Å	1.43Å
O1	HO1	sing	0.97Å	0.95Å
C3	C2	doub	1.40Å	1.40Å	Aromatic
C2	C9	sing	1.40Å	1.41Å	Aromatic
C3	C4	sing	1.38Å	1.42Å	Aromatic
C3	H3	sing	1.08Å	1.08Å
C5	O3	sing	1.36Å	1.37Å
O3	C6	sing	1.44Å	1.45Å
C4	C5	doub	1.40Å	1.40Å	Aromatic
C4	H4	sing	1.08Å	1.08Å
C5	C8	sing	1.39Å	1.40Å	Aromatic
C7	C6	sing	1.55Å	1.57Å
C6	H6A	sing	1.09Å	1.10Å
C6	H6B	sing	1.09Å	1.10Å
C8	C7	sing	1.52Å	1.51Å
C7	H7A	sing	1.09Å	1.10Å
C7	H7B	sing	1.09Å	1.10Å
C9	C8	doub	1.37Å	1.36Å	Aromatic
C9	H9	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O2	C1	O1	117.9°	120.0°
O2	C1	C2	118.4°	120.0°
O1	C1	C2	123.7°	120.0°
C1	O1	HO1	109.5°	117.0°
C1	C2	C3	121.2°	120.3°
C1	C2	C9	115.6°	120.2°
C3	C2	C9	123.2°	119.5°
C2	C3	C4	119.1°	120.2°
C2	C3	H3	120.5°	119.9°
C2	C9	C8	117.8°	119.8°
C2	C9	H9	121.1°	120.1°
C4	C3	H3	120.5°	119.9°
C3	C4	C5	116.4°	120.5°
C3	C4	H4	121.8°	119.8°
C5	O3	C6	109.9°	109.3°
O3	C5	C4	124.5°	129.7°
O3	C5	C8	111.8°	111.1°
O3	C6	C7	106.9°	102.8°
O3	C6	H6A	110.1°	110.7°
O3	C6	H6B	110.1°	110.7°
C5	C4	H4	121.8°	119.8°
C4	C5	C8	123.7°	119.1°
C5	C8	C7	109.9°	107.0°
C5	C8	C9	119.9°	120.9°
C7	C6	H6A	110.1°	110.8°
C7	C6	H6B	110.1°	110.8°
C6	C7	C8	101.3°	101.9°
C6	C7	H7A	111.5°	110.9°
C6	C7	H7B	111.5°	110.9°
H6A	C6	H6B	109.5°	110.7°
C8	C7	H7A	111.5°	111.0°
C8	C7	H7B	111.5°	111.0°
C7	C8	C9	130.1°	132.1°
H7A	C7	H7B	109.5°	110.8°
C8	C9	H9	121.1°	120.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O2	C1	O1	C2	178.3°	179.8°
O2	C1	O1	HO1	0.0°	0.2°
O2	C1	C2	C3	18.2°	179.5°
O2	C1	C2	C9	164.7°	0.3°
O1	C1	C2	C3	160.0°	0.3°
O1	C1	C2	C9	17.0°	180.0°
C2	C1	O1	HO1	178.3°	180.0°
C1	C2	C3	C9	176.8°	179.8°
C1	C2	C3	C4	175.9°	179.9°
C1	C2	C3	H3	4.1°	0.2°
C1	C2	C9	C8	177.6°	179.7°
C1	C2	C9	H9	2.4°	0.0°
C2	C3	C4	H3	180.0°	179.9°
C2	C3	C4	C5	1.5°	0.1°
C2	C3	C4	H4	178.5°	179.9°
C3	C2	C9	C8	0.6°	0.5°
C3	C2	C9	H9	179.4°	179.7°
C9	C2	C3	C4	1.0°	0.1°
C9	C2	C3	H3	179.0°	179.9°
C2	C9	C8	C5	1.6°	0.8°
C2	C9	C8	C7	175.3°	179.3°
C2	C9	C8	H9	180.0°	179.7°
C3	C4	C5	O3	179.5°	179.4°
C3	C4	C5	H4	180.0°	180.0°
C3	C4	C5	C8	0.5°	0.1°
H3	C3	C4	C5	178.5°	179.9°
H3	C3	C4	H4	1.5°	0.1°
O3	C5	C4	C8	178.9°	179.5°
O3	C5	C4	H4	0.5°	0.6°
C5	O3	C6	C7	0.5°	27.8°
C5	O3	C6	H6A	120.1°	90.6°
C5	O3	C6	H6B	119.1°	146.3°
O3	C5	C8	C7	4.6°	0.9°
O3	C5	C8	C9	178.0°	179.0°
C6	O3	C5	C4	177.9°	161.5°
C6	O3	C5	C8	3.1°	19.0°
O3	C6	C7	H6A	119.6°	118.4°
O3	C6	C7	H6B	119.6°	118.3°
O3	C6	H6A	H6B	121.2°	123.2°
O3	C6	C7	C8	2.0°	25.4°
O3	C6	C7	H7A	120.7°	143.6°
O3	C6	C7	H7B	116.6°	92.8°
C4	C5	C8	C7	176.4°	179.5°
C4	C5	C8	C9	1.1°	0.6°
H4	C4	C5	C8	179.4°	179.9°
C5	C8	C7	C6	3.8°	15.5°
C5	C8	C7	C9	177.1°	180.0°
C5	C8	C7	H7A	122.5°	133.6°
C5	C8	C7	H7B	114.8°	102.6°
C5	C8	C9	H9	178.4°	179.5°
C7	C6	H6A	H6B	121.1°	123.4°
C6	C7	C8	H7A	118.7°	118.1°
C6	C7	C8	H7B	118.6°	118.2°
C6	C7	H7A	H7B	123.8°	123.7°
C6	C7	C8	C9	179.0°	164.5°
H6A	C6	C7	C8	117.6°	93.0°
H6A	C6	C7	H7A	1.0°	25.2°
H6A	C6	C7	H7B	123.7°	148.8°
H6B	C6	C7	C8	121.6°	143.8°
H6B	C6	C7	H7A	119.7°	98.1°
H6B	C6	C7	H7B	3.0°	25.6°
C8	C7	H7A	H7B	123.8°	123.8°
C7	C8	C9	H9	4.7°	0.5°
H7A	C7	C8	C9	60.4°	46.4°
H7B	C7	C8	C9	62.3°	77.3°

223532

PDB entries from 2024-08-07

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