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Summary Geometry Related PDB entries

8YO

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C10	O3	doub	1.21Å	1.21Å
C10	C9	sing	1.47Å	1.53Å
O7	C9	sing	1.35Å	1.37Å	Aromatic
O7	C6	sing	1.35Å	1.54Å	Aromatic
O1	C7	sing	1.43Å	1.39Å
O1	C1	sing	1.36Å	1.40Å
C9	C8	doub	1.36Å	1.26Å	Aromatic
C6	C1	doub	1.39Å	1.36Å	Aromatic
C6	C5	sing	1.41Å	1.44Å	Aromatic
C1	C2	sing	1.38Å	1.40Å	Aromatic
C8	C5	sing	1.46Å	1.31Å	Aromatic
C5	C4	doub	1.40Å	1.41Å	Aromatic
C2	C3	doub	1.39Å	1.40Å	Aromatic
C4	C3	sing	1.37Å	1.41Å	Aromatic
C2	H1	sing	1.08Å	1.08Å
C3	H2	sing	1.08Å	1.08Å
C4	H3	sing	1.08Å	1.08Å
C7	H4	sing	1.09Å	1.10Å
C7	H5	sing	1.09Å	1.10Å
C7	H6	sing	1.09Å	1.10Å
C8	H7	sing	1.08Å	1.08Å
C10	O2	sing	1.35Å	1.43Å
O2	H8	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O3	C10	C9	124.9°	120.1°
O3	C10	O2	122.8°	120.0°
C10	C9	O7	116.3°	125.2°
C10	C9	C8	132.4°	125.1°
C9	C10	O2	112.3°	119.9°
C9	O7	C6	99.3°	110.8°
O7	C9	C8	111.3°	109.7°
O7	C6	C1	126.6°	133.2°
O7	C6	C5	109.1°	107.7°
C7	O1	C1	116.8°	117.0°
O1	C7	H4	109.5°	109.5°
O1	C7	H5	109.4°	109.5°
O1	C7	H6	109.5°	109.4°
O1	C1	C6	114.5°	120.1°
O1	C1	C2	127.1°	120.1°
C9	C8	C5	120.4°	106.1°
C9	C8	H7	119.8°	127.0°
C1	C6	C5	124.3°	119.1°
C6	C1	C2	118.4°	119.8°
C6	C5	C8	99.9°	105.7°
C6	C5	C4	117.0°	120.1°
C1	C2	C3	119.6°	120.7°
C1	C2	H1	120.2°	119.7°
C8	C5	C4	143.1°	134.2°
C5	C8	H7	119.8°	126.9°
C5	C4	C3	118.4°	119.9°
C5	C4	H3	120.8°	120.1°
C2	C3	C4	122.3°	120.5°
C3	C2	H1	120.2°	119.7°
C2	C3	H2	118.8°	119.7°
C4	C3	H2	118.8°	119.8°
C3	C4	H3	120.8°	120.0°
H4	C7	H5	109.5°	109.5°
H4	C7	H6	109.5°	109.4°
H5	C7	H6	109.5°	109.5°
C10	O2	H8	109.5°	117.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O3	C10	C9	O2	179.5°	179.9°
O3	C10	C9	O7	172.8°	180.0°
O3	C10	C9	C8	10.3°	0.1°
O3	C10	O2	H8	0.0°	0.1°
C10	C9	O7	C8	177.6°	180.0°
C10	C9	O7	C6	178.4°	180.0°
C10	C9	C8	C5	178.4°	180.0°
C10	C9	C8	H7	1.6°	0.0°
C9	C10	O2	H8	179.5°	180.0°
C9	O7	C6	C1	179.4°	180.0°
C9	O7	C6	C5	0.2°	0.0°
O7	C9	C8	C5	1.4°	0.0°
O7	C9	C8	H7	178.6°	180.0°
O7	C9	C10	O2	7.7°	0.1°
O7	C6	C1	O1	0.2°	0.2°
C6	O7	C9	C8	0.8°	0.0°
O7	C6	C1	C5	179.5°	180.0°
O7	C6	C1	C2	179.4°	180.0°
O7	C6	C5	C8	0.5°	0.0°
O7	C6	C5	C4	179.6°	180.0°
C7	O1	C1	C6	158.3°	179.8°
C7	O1	C1	C2	22.2°	0.0°
O1	C7	H4	H5	120.0°	120.1°
O1	C7	H4	H6	120.0°	119.9°
O1	C7	H5	H6	120.0°	120.0°
O1	C1	C6	C2	179.5°	179.8°
O1	C1	C6	C5	179.7°	179.8°
O1	C1	C2	C3	179.7°	179.8°
O1	C1	C2	H1	0.3°	0.3°
C1	O1	C7	H4	180.0°	60.0°
C1	O1	C7	H5	60.0°	60.0°
C1	O1	C7	H6	60.0°	179.9°
C9	C8	C5	C6	1.1°	0.0°
C9	C8	C5	H7	180.0°	180.0°
C9	C8	C5	C4	179.0°	180.0°
C8	C9	C10	O2	169.2°	180.0°
C1	C6	C5	C8	179.9°	180.0°
C1	C6	C5	C4	0.0°	0.0°
C6	C1	C2	C3	0.2°	0.0°
C6	C1	C2	H1	179.8°	180.0°
C5	C6	C1	C2	0.1°	0.0°
C6	C5	C8	C4	179.9°	180.0°
C6	C5	C4	C3	0.1°	0.0°
C6	C5	C4	H3	179.9°	180.0°
C6	C5	C8	H7	178.9°	180.0°
C1	C2	C3	H1	180.0°	180.0°
C1	C2	C3	C4	0.2°	0.0°
C1	C2	C3	H2	179.8°	180.0°
C8	C5	C4	C3	180.0°	180.0°
C8	C5	C4	H3	0.0°	0.1°
C5	C4	C3	C2	0.0°	0.0°
C5	C4	C3	H3	180.0°	180.0°
C5	C4	C3	H2	180.0°	180.0°
C4	C5	C8	H7	1.0°	0.1°
C2	C3	C4	H2	180.0°	180.0°
C2	C3	C4	H3	180.0°	180.0°
C4	C3	C2	H1	179.9°	180.0°
H1	C2	C3	H2	0.1°	0.0°
H2	C3	C4	H3	0.0°	0.0°
H4	C7	H5	H6	120.0°	119.9°

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PDB entries from 2026-02-04

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