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Summary Geometry Related PDB entries

B1J

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C2	C1	doub	1.38Å	1.38Å	Aromatic
C2	C3	sing	1.38Å	1.38Å	Aromatic
CL1	C3	sing	1.74Å	1.74Å
C1	C6	sing	1.39Å	1.39Å	Aromatic
C3	C4	doub	1.38Å	1.38Å	Aromatic
N3	N1	sing	1.29Å	1.35Å	Aromatic
N3	N2	doub	1.29Å	1.31Å	Aromatic
C6	N1	sing	1.40Å	1.43Å
C6	C5	doub	1.39Å	1.38Å	Aromatic
C4	C5	sing	1.38Å	1.38Å	Aromatic
N1	C7	sing	1.36Å	1.35Å	Aromatic
N2	C8	sing	1.34Å	1.36Å	Aromatic
C7	C8	doub	1.35Å	1.36Å	Aromatic
C8	C9	sing	1.51Å	1.50Å
O1	C9	sing	1.43Å	1.42Å
C4	H1	sing	1.08Å	1.08Å
C5	H2	sing	1.08Å	1.08Å
C7	H3	sing	1.08Å	1.08Å
C1	H4	sing	1.08Å	1.08Å
C2	H5	sing	1.08Å	1.08Å
C9	H6	sing	1.09Å	1.10Å
C9	H7	sing	1.09Å	1.10Å
O1	H8	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	C2	C3	119.4°	120.0°
C2	C1	C6	119.5°	120.0°
C2	C1	H4	120.2°	120.0°
C1	C2	H5	120.3°	120.0°
C2	C3	CL1	119.7°	119.9°
C2	C3	C4	121.5°	120.1°
C3	C2	H5	120.3°	120.0°
CL1	C3	C4	118.7°	120.0°
C1	C6	N1	120.5°	120.0°
C1	C6	C5	120.3°	119.9°
C6	C1	H4	120.2°	120.0°
C3	C4	C5	119.2°	120.1°
C3	C4	H1	120.4°	120.0°
N1	N3	N2	106.9°	110.2°
N3	N1	C6	119.5°	125.9°
N3	N1	C7	110.2°	108.1°
N3	N2	C8	109.7°	109.1°
N1	C6	C5	119.0°	120.1°
C6	N1	C7	129.9°	126.0°
C6	C5	C4	120.0°	120.0°
C6	C5	H2	120.0°	120.0°
C5	C4	H1	120.4°	119.9°
C4	C5	H2	120.0°	120.0°
N1	C7	C8	105.3°	106.0°
N1	C7	H3	127.4°	127.0°
N2	C8	C7	107.8°	106.6°
N2	C8	C9	121.6°	126.7°
C7	C8	C9	130.6°	126.7°
C8	C7	H3	127.3°	127.0°
C8	C9	O1	112.7°	109.5°
C8	C9	H6	108.7°	109.5°
C8	C9	H7	108.7°	109.5°
O1	C9	H6	108.7°	109.4°
O1	C9	H7	108.7°	109.4°
C9	O1	H8	109.5°	114.0°
H6	C9	H7	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	C2	C3	H5	180.0°	179.8°
C1	C2	C3	CL1	179.6°	180.0°
C2	C1	C6	H4	180.0°	180.0°
C1	C2	C3	C4	0.5°	0.4°
C2	C1	C6	N1	176.9°	180.0°
C2	C1	C6	C5	2.4°	0.0°
C2	C3	CL1	C4	179.1°	179.6°
C3	C2	C1	C6	0.7°	0.2°
C2	C3	C4	C5	0.1°	0.4°
C2	C3	C4	H1	179.9°	179.8°
C3	C2	C1	H4	179.3°	179.8°
CL1	C3	C4	C5	179.1°	180.0°
CL1	C3	C4	H1	0.9°	0.2°
CL1	C3	C2	H5	0.4°	0.1°
C1	C6	N1	N3	23.6°	179.7°
C1	C6	N1	C5	174.5°	180.0°
C1	C6	C5	C4	2.9°	0.0°
C1	C6	N1	C7	163.8°	0.1°
C1	C6	C5	H2	177.1°	180.0°
C6	C1	C2	H5	179.3°	179.9°
C3	C4	C5	C6	1.7°	0.2°
C3	C4	C5	H1	180.0°	179.8°
C3	C4	C5	H2	178.3°	179.8°
C4	C3	C2	H5	179.5°	179.7°
N3	N1	C6	C7	172.6°	179.6°
N3	N1	C6	C5	151.0°	0.4°
N1	N3	N2	C8	2.7°	0.0°
N3	N1	C7	C8	3.2°	0.1°
N3	N1	C7	H3	176.7°	180.0°
N2	N3	N1	C6	177.7°	179.7°
N2	N3	N1	C7	3.7°	0.1°
N3	N2	C8	C7	0.7°	0.0°
N3	N2	C8	C9	178.1°	180.0°
N1	C6	C5	C4	177.4°	180.0°
C6	N1	C7	C8	176.4°	179.7°
N1	C6	C5	H2	2.6°	0.0°
C6	N1	C7	H3	3.6°	0.4°
N1	C6	C1	H4	3.1°	0.0°
C6	C5	C4	H2	180.0°	180.0°
C5	C6	N1	C7	21.6°	180.0°
C6	C5	C4	H1	178.3°	180.0°
C5	C6	C1	H4	177.6°	180.0°
N1	C7	C8	N2	1.6°	0.0°
N1	C7	C8	H3	180.0°	179.9°
N1	C7	C8	C9	179.8°	180.0°
N2	C8	C7	C9	178.6°	180.0°
N2	C8	C9	O1	78.9°	180.0°
N2	C8	C7	H3	178.4°	179.9°
N2	C8	C9	H6	41.6°	60.0°
N2	C8	C9	H7	160.7°	60.0°
C7	C8	C9	O1	102.7°	0.0°
C7	C8	C9	H6	136.8°	120.0°
C7	C8	C9	H7	17.8°	120.0°
C8	C9	O1	H6	120.5°	120.0°
C8	C9	O1	H7	120.5°	120.0°
C9	C8	C7	H3	0.2°	0.1°
C8	C9	H6	H7	118.5°	120.0°
C8	C9	O1	H8	180.0°	180.0°
O1	C9	H6	H7	118.5°	119.9°
H1	C4	C5	H2	1.7°	0.0°
H4	C1	C2	H5	0.7°	0.0°
H6	C9	O1	H8	59.5°	60.0°
H7	C9	O1	H8	59.5°	60.0°

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PDB entries from 2026-01-21

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