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Summary Geometry Related PDB entries

M8O

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C7	C1	doub	1.35Å	1.35Å
C1	C3	sing	1.48Å	1.55Å
C1	H1	sing	1.08Å	1.08Å
C2	O1	sing	1.34Å	1.24Å
O1	HO1	sing	0.97Å	0.95Å
C4	C2	sing	1.51Å	1.55Å
O3	C2	doub	1.21Å	1.25Å
C3	O2	sing	1.35Å	1.25Å
O2	HO2	sing	0.97Å	0.95Å
C3	O4	doub	1.22Å	1.25Å
C5	C4	sing	1.51Å	1.54Å
C4	H4	sing	1.09Å	1.10Å
C4	H4A	sing	1.09Å	1.10Å
C6	C5	sing	1.51Å	1.54Å
O5	C5	doub	1.21Å	1.23Å
C50	C6	sing	1.51Å	1.33Å
C6	H6	sing	1.09Å	1.10Å
C6	H6A	sing	1.09Å	1.10Å
O6	C50	doub	1.21Å	1.38Å
C7	C50	sing	1.47Å	1.56Å
C7	H7	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C7	C1	C3	127.7°	120.0°
C7	C1	H1	116.1°	120.0°
C1	C7	C50	123.2°	120.0°
C1	C7	H7	118.4°	120.0°
C3	C1	H1	116.2°	119.9°
C1	C3	O2	119.0°	120.0°
C1	C3	O4	117.6°	120.0°
C2	O1	HO1	109.5°	117.0°
O1	C2	C4	118.4°	120.0°
O1	C2	O3	121.1°	120.0°
C4	C2	O3	120.4°	120.0°
C2	C4	C5	117.4°	109.5°
C2	C4	H4	107.5°	109.5°
C2	C4	H4A	107.5°	109.4°
C3	O2	HO2	109.5°	117.0°
O2	C3	O4	123.4°	120.0°
C5	C4	H4	107.5°	109.5°
C5	C4	H4A	107.5°	109.5°
C4	C5	C6	121.2°	120.0°
C4	C5	O5	118.1°	120.0°
H4	C4	H4A	109.5°	109.4°
C6	C5	O5	116.9°	120.0°
C5	C6	C50	122.3°	109.5°
C5	C6	H6	106.2°	109.5°
C5	C6	H6A	106.2°	109.5°
C50	C6	H6	106.1°	109.4°
C50	C6	H6A	106.2°	109.5°
C6	C50	O6	116.6°	120.0°
C6	C50	C7	120.7°	120.0°
H6	C6	H6A	109.5°	109.4°
O6	C50	C7	121.8°	120.0°
C50	C7	H7	118.4°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C7	C1	C3	H1	180.0°	179.7°
C7	C1	C3	O2	157.0°	173.2°
C7	C1	C3	O4	23.8°	6.7°
C1	C7	C50	C6	65.9°	156.7°
C1	C7	C50	O6	125.4°	23.4°
C1	C7	C50	H7	180.0°	179.9°
C1	C3	O2	O4	179.2°	179.9°
C1	C3	O2	HO2	179.2°	180.0°
C3	C1	C7	C50	80.9°	20.9°
C3	C1	C7	H7	99.1°	159.0°
H1	C1	C3	O2	23.0°	6.5°
H1	C1	C3	O4	156.2°	173.5°
H1	C1	C7	C50	99.1°	158.8°
H1	C1	C7	H7	80.9°	21.3°
O1	C2	C4	O3	176.9°	180.0°
O1	C2	C4	C5	119.5°	180.0°
O1	C2	C4	H4	119.4°	59.9°
O1	C2	C4	H4A	1.7°	60.0°
HO1	O1	C2	C4	176.9°	180.0°
HO1	O1	C2	O3	0.0°	0.1°
C2	C4	C5	H4	121.1°	120.1°
C2	C4	C5	H4A	121.2°	120.0°
C2	C4	H4	H4A	116.4°	120.0°
C2	C4	C5	C6	59.4°	180.0°
C2	C4	C5	O5	143.3°	0.0°
O3	C2	C4	C5	63.6°	0.0°
O3	C2	C4	H4	57.5°	120.0°
O3	C2	C4	H4A	175.2°	120.0°
HO2	O2	C3	O4	0.0°	0.1°
C5	C4	H4	H4A	116.4°	120.0°
C4	C5	C6	O5	157.6°	180.0°
C4	C5	C6	C50	151.1°	180.0°
C4	C5	C6	H6	29.3°	60.0°
C4	C5	C6	H6A	87.2°	60.0°
H4	C4	C5	C6	61.7°	60.0°
H4	C4	C5	O5	95.6°	120.0°
H4A	C4	C5	C6	179.4°	60.0°
H4A	C4	C5	O5	22.1°	120.0°
C5	C6	C50	H6	121.8°	120.0°
C5	C6	C50	H6A	121.8°	120.1°
C5	C6	H6	H6A	114.2°	120.0°
C5	C6	C50	O6	139.3°	0.1°
C5	C6	C50	C7	29.9°	180.0°
O5	C5	C6	C50	51.4°	0.0°
O5	C5	C6	H6	173.1°	120.0°
O5	C5	C6	H6A	70.4°	120.0°
C50	C6	H6	H6A	114.2°	119.9°
C6	C50	O6	C7	169.1°	179.9°
C6	C50	C7	H7	114.1°	23.2°
H6	C6	C50	O6	98.9°	120.1°
H6	C6	C50	C7	91.8°	60.0°
H6A	C6	C50	O6	17.5°	120.0°
H6A	C6	C50	C7	151.7°	59.9°
O6	C50	C7	H7	54.6°	156.7°

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PDB entries from 2024-09-11

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