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Summary Geometry Related PDB entries

A1DNU

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	C1	sing	1.43Å	1.43Å
C1	C2	sing	1.51Å	1.49Å
C2	C3	sing	1.39Å	1.41Å	Aromatic
C3	N1	doub	1.31Å	1.33Å	Aromatic
N1	N2	sing	1.40Å	1.37Å	Aromatic
N2	C4	sing	1.37Å	1.37Å	Aromatic
C4	C5	doub	1.35Å	1.35Å	Aromatic
C5	C6	sing	1.40Å	1.42Å	Aromatic
C6	C7	doub	1.36Å	1.35Å	Aromatic
C7	C8	sing	1.41Å	1.41Å	Aromatic
C2	C8	doub	1.39Å	1.38Å	Aromatic
N2	C8	sing	1.37Å	1.39Å	Aromatic
O1	H1	sing	0.97Å	0.95Å
C1	H2	sing	1.09Å	1.10Å
C1	H3	sing	1.09Å	1.10Å
C3	H4	sing	1.08Å	1.08Å
C4	H5	sing	1.08Å	1.08Å
C5	H6	sing	1.08Å	1.08Å
C6	H7	sing	1.08Å	1.08Å
C7	H8	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C1	C2	111.4°	109.4°
C1	O1	H1	109.5°	113.9°
O1	C1	H2	109.0°	109.5°
O1	C1	H3	109.0°	109.5°
C1	C2	C3	128.5°	126.2°
C1	C2	C8	125.7°	126.2°
C2	C1	H2	109.0°	109.5°
C2	C1	H3	109.0°	109.5°
C2	C3	N1	111.6°	109.0°
C3	C2	C8	105.7°	107.6°
C2	C3	H4	124.2°	125.5°
C3	N1	N2	105.5°	108.9°
N1	C3	H4	124.2°	125.5°
N1	N2	C4	126.8°	132.4°
N1	N2	C8	111.0°	107.4°
N2	C4	C5	118.7°	120.6°
C4	N2	C8	122.2°	120.2°
N2	C4	H5	120.6°	119.7°
C4	C5	C6	120.8°	120.5°
C5	C4	H5	120.6°	119.7°
C4	C5	H6	119.6°	119.8°
C5	C6	C7	120.4°	119.6°
C6	C5	H6	119.6°	119.8°
C5	C6	H7	119.8°	120.2°
C6	C7	C8	119.4°	119.2°
C7	C6	H7	119.8°	120.2°
C6	C7	H8	120.3°	120.4°
C7	C8	C2	135.3°	133.0°
C7	C8	N2	118.6°	119.9°
C8	C7	H8	120.3°	120.4°
C2	C8	N2	106.1°	107.1°
H2	C1	H3	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C1	C2	H2	120.3°	120.0°
O1	C1	C2	H3	120.3°	120.0°
O1	C1	C2	C3	60.2°	0.0°
O1	C1	C2	C8	117.4°	179.7°
O1	C1	H2	H3	119.2°	120.0°
C1	C2	C3	C8	178.0°	179.7°
C1	C2	C3	N1	178.5°	180.0°
C1	C2	C8	C7	1.6°	0.8°
C1	C2	C8	N2	178.2°	179.8°
C2	C1	O1	H1	180.0°	180.0°
C2	C1	H2	H3	119.1°	120.0°
C1	C2	C3	H4	1.5°	0.1°
C2	C3	N1	H4	180.0°	179.9°
C2	C3	N1	N2	0.6°	0.0°
C3	C2	C8	C7	179.6°	179.5°
C3	C2	C8	N2	0.2°	0.4°
C3	C2	C1	H2	60.1°	120.0°
C3	C2	C1	H3	179.5°	120.0°
C3	N1	N2	C4	179.3°	180.0°
N1	C3	C2	C8	0.5°	0.3°
C3	N1	N2	C8	0.5°	0.3°
N1	N2	C4	C8	179.9°	179.7°
N1	N2	C4	C5	179.3°	180.0°
N1	N2	C8	C7	179.9°	179.6°
N1	N2	C8	C2	0.2°	0.4°
N2	N1	C3	H4	179.3°	179.9°
N1	N2	C4	H5	0.7°	0.0°
N2	C4	C5	H5	180.0°	180.0°
N2	C4	C5	C6	0.7°	0.1°
C4	N2	C8	C7	0.2°	0.6°
C4	N2	C8	C2	179.7°	179.8°
N2	C4	C5	H6	179.3°	180.0°
C4	C5	C6	H6	180.0°	180.0°
C4	C5	C6	C7	0.2°	0.0°
C5	C4	N2	C8	0.6°	0.3°
C4	C5	C6	H7	179.9°	180.0°
C5	C6	C7	H7	180.0°	179.9°
C5	C6	C7	C8	0.6°	0.3°
C6	C5	C4	H5	179.3°	180.0°
C5	C6	C7	H8	179.5°	180.0°
C6	C7	C8	H8	180.0°	179.7°
C6	C7	C8	C2	179.0°	179.6°
C6	C7	C8	N2	0.7°	0.6°
C7	C6	C5	H6	179.9°	180.0°
C7	C8	C2	N2	179.8°	179.0°
C8	C7	C6	H7	179.4°	179.7°
C8	C2	C1	H2	122.3°	59.7°
C8	C2	C1	H3	2.9°	60.3°
C8	C2	C3	H4	179.4°	179.8°
C2	C8	C7	H8	0.9°	0.8°
C8	N2	C4	H5	179.4°	179.7°
N2	C8	C7	H8	179.3°	179.7°
H1	O1	C1	H2	59.8°	60.0°
H1	O1	C1	H3	59.7°	60.0°
H5	C4	C5	H6	0.7°	0.0°
H6	C5	C6	H7	0.1°	0.1°
H7	C6	C7	H8	0.6°	0.1°

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PDB entries from 2026-08-05

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