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Summary Geometry Related PDB entries

9MJ

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C	N	sing	1.35Å	1.33Å
C	O	doub	1.21Å	1.25Å
C	N1	sing	1.35Å	1.39Å
C1	N2	doub	1.31Å	1.33Å	Aromatic
C1	C3	sing	1.48Å	1.45Å
C1	N3	sing	1.34Å	1.38Å	Aromatic
N1	C2	sing	1.36Å	1.38Å	Aromatic
N1	N2	sing	1.40Å	1.38Å	Aromatic
O1	C3	sing	1.35Å	1.37Å	Aromatic
O1	C4	sing	1.34Å	1.38Å	Aromatic
C2	N3	doub	1.31Å	1.34Å	Aromatic
C2	N4	sing	1.38Å	1.33Å
C3	C6	doub	1.36Å	1.35Å	Aromatic
C4	C5	doub	1.35Å	1.32Å	Aromatic
C5	C6	sing	1.41Å	1.43Å	Aromatic
N	HN	sing	0.97Å	1.00Å
N	HNA	sing	0.97Å	1.00Å
C4	H4	sing	1.08Å	1.08Å
N4	HN4	sing	0.97Å	1.00Å
N4	HN4A	sing	0.97Å	1.00Å
C5	H5	sing	1.08Å	1.08Å
C6	H6	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N	C	O	124.8°	120.0°
N	C	N1	115.2°	120.0°
C	N	HN	120.0°	120.0°
C	N	HNA	120.0°	119.9°
O	C	N1	119.9°	120.0°
C	N1	C2	127.5°	126.9°
C	N1	N2	123.2°	126.8°
N2	C1	C3	121.3°	125.5°
N2	C1	N3	116.0°	109.1°
C1	N2	N1	102.5°	107.0°
C3	C1	N3	122.7°	125.4°
C1	C3	O1	117.6°	125.9°
C1	C3	C6	132.4°	126.0°
C1	N3	C2	102.2°	109.7°
C2	N1	N2	109.2°	106.3°
N1	C2	N3	110.0°	108.0°
N1	C2	N4	124.0°	126.0°
C3	O1	C4	106.3°	109.4°
O1	C3	C6	110.0°	108.1°
O1	C4	C5	110.6°	108.7°
O1	C4	H4	124.7°	125.7°
N3	C2	N4	125.9°	126.0°
C2	N4	HN4	109.5°	120.0°
C2	N4	HN4A	109.5°	120.0°
C3	C6	C5	106.3°	106.7°
C3	C6	H6	126.8°	126.6°
C4	C5	C6	106.8°	107.0°
C5	C4	H4	124.7°	125.6°
C4	C5	H5	126.6°	126.5°
C6	C5	H5	126.6°	126.5°
C5	C6	H6	126.8°	126.6°
HN	N	HNA	120.0°	120.1°
HN4	N4	HN4A	109.5°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N	C	O	N1	177.2°	179.8°
N	C	N1	C2	178.2°	180.0°
N	C	N1	N2	0.3°	0.4°
C	N	HN	HNA	180.0°	179.9°
O	C	N1	C2	4.3°	0.2°
O	C	N1	N2	177.8°	179.8°
O	C	N	HN	0.0°	0.0°
O	C	N	HNA	180.0°	180.0°
C	N1	N2	C1	178.8°	180.0°
C	N1	C2	N2	178.1°	179.7°
C	N1	C2	N3	179.9°	180.0°
C	N1	C2	N4	0.7°	0.1°
N1	C	N	HN	177.3°	179.8°
N1	C	N	HNA	2.7°	0.2°
N2	C1	C3	N3	178.1°	179.8°
C1	N2	N1	C2	0.6°	0.3°
N2	C1	C3	O1	179.8°	0.1°
N2	C1	N3	C2	1.9°	0.0°
N2	C1	C3	C6	1.3°	180.0°
C3	C1	N2	N1	179.0°	180.0°
C1	C3	O1	C6	178.8°	179.9°
C1	C3	O1	C4	179.3°	179.9°
C3	C1	N3	C2	180.0°	179.8°
C1	C3	C6	C5	179.9°	179.9°
C1	C3	C6	H6	0.1°	0.1°
C1	N3	C2	N1	2.1°	0.3°
N3	C1	N2	N1	0.8°	0.2°
N3	C1	C3	O1	1.7°	179.7°
C1	N3	C2	N4	178.5°	179.7°
N3	C1	C3	C6	176.8°	0.2°
N1	C2	N3	N4	179.4°	179.9°
N1	C2	N4	HN4	179.3°	0.1°
N1	C2	N4	HN4A	59.3°	180.0°
N2	N1	C2	N3	1.8°	0.4°
N2	N1	C2	N4	178.8°	179.5°
C3	O1	C4	C5	1.0°	0.0°
O1	C3	C6	C5	1.6°	0.0°
C3	O1	C4	H4	179.0°	180.0°
O1	C3	C6	H6	178.4°	180.0°
C4	O1	C3	C6	0.4°	0.0°
O1	C4	C5	H4	180.0°	180.0°
O1	C4	C5	C6	1.9°	0.0°
O1	C4	C5	H5	178.1°	180.0°
N3	C2	N4	HN4	0.0°	180.0°
N3	C2	N4	HN4A	120.0°	0.1°
C2	N4	HN4	HN4A	120.0°	179.9°
C3	C6	C5	C4	2.1°	0.0°
C3	C6	C5	H6	180.0°	179.9°
C3	C6	C5	H5	177.9°	180.0°
C4	C5	C6	H5	180.0°	180.0°
C4	C5	C6	H6	177.8°	180.0°
C6	C5	C4	H4	178.1°	180.0°
H4	C4	C5	H5	1.9°	0.0°
H5	C5	C6	H6	2.1°	0.0°

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PDB entries from 2024-08-07

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