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Summary Geometry Related PDB entries

N5J

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O	C1	doub	1.22Å	0.00Å
C1	N1	sing	1.36Å	0.00Å
C1	C7	sing	1.47Å	0.00Å
N1	C2	sing	1.36Å	0.00Å
C2	N2	doub	1.30Å	0.00Å
N2	C3	sing	1.36Å	0.00Å
C3	C4	doub	1.40Å	0.00Å	Aromatic
C3	C7	sing	1.41Å	0.00Å	Aromatic
N3	C4	sing	1.32Å	0.00Å	Aromatic
N3	C5	doub	1.32Å	0.00Å	Aromatic
C5	C6	sing	1.38Å	0.00Å	Aromatic
C6	C7	doub	1.39Å	0.00Å	Aromatic
N1	HN1	sing	0.97Å	0.00Å
C2	H2	sing	1.08Å	0.00Å
C4	H4	sing	1.08Å	0.00Å
C5	H5	sing	1.08Å	0.00Å
C6	H6	sing	1.08Å	0.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O	C1	N1	90.0°	121.4°
O	C1	C7	90.0°	121.4°
N1	C1	C7	90.0°	117.2°
C1	N1	C2	90.0°	120.6°
C1	N1	HN1	90.0°	119.7°
C1	C7	C3	90.0°	118.2°
C1	C7	C6	90.0°	122.9°
N1	C2	N2	90.0°	123.6°
C2	N1	HN1	90.0°	119.8°
N1	C2	H2	90.0°	118.2°
C2	N2	C3	90.0°	121.5°
N2	C2	H2	90.0°	118.2°
N2	C3	C4	90.0°	122.5°
N2	C3	C7	90.0°	119.0°
C4	C3	C7	90.0°	118.5°
C3	C4	N3	90.0°	120.0°
C3	C4	H4	90.0°	120.0°
C3	C7	C6	90.0°	118.9°
C4	N3	C5	90.0°	122.8°
N3	C4	H4	90.0°	120.0°
N3	C5	C6	90.0°	121.4°
N3	C5	H5	90.0°	119.3°
C5	C6	C7	90.0°	118.4°
C6	C5	H5	90.0°	119.3°
C5	C6	H6	90.0°	120.8°
C7	C6	H6	90.0°	120.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O	C1	N1	C7	90.0°	179.7°
O	C1	N1	C2	90.0°	180.0°
O	C1	C7	C3	90.0°	179.8°
O	C1	C7	C6	90.0°	0.0°
O	C1	N1	HN1	90.0°	0.0°
C1	N1	C2	HN1	90.0°	180.0°
C1	N1	C2	N2	90.0°	0.0°
N1	C1	C7	C3	90.0°	0.5°
N1	C1	C7	C6	90.0°	179.7°
C1	N1	C2	H2	90.0°	180.0°
C7	C1	N1	C2	90.0°	0.3°
C1	C7	C3	N2	90.0°	0.5°
C1	C7	C3	C4	90.0°	179.8°
C1	C7	C3	C6	90.0°	179.8°
C1	C7	C6	C5	90.0°	179.3°
C7	C1	N1	HN1	90.0°	179.8°
C1	C7	C6	H6	90.0°	0.0°
N1	C2	N2	H2	90.0°	180.0°
N1	C2	N2	C3	90.0°	0.0°
C2	N2	C3	C4	90.0°	180.0°
C2	N2	C3	C7	90.0°	0.3°
N2	C2	N1	HN1	90.0°	180.0°
N2	C3	C4	C7	90.0°	179.7°
N2	C3	C4	N3	90.0°	180.0°
N2	C3	C7	C6	90.0°	179.7°
C3	N2	C2	H2	90.0°	180.0°
N2	C3	C4	H4	90.0°	0.0°
C3	C4	N3	H4	90.0°	180.0°
C3	C4	N3	C5	90.0°	0.0°
C4	C3	C7	C6	90.0°	0.0°
C7	C3	C4	N3	90.0°	0.2°
C3	C7	C6	C5	90.0°	0.5°
C7	C3	C4	H4	90.0°	179.8°
C3	C7	C6	H6	90.0°	179.7°
C4	N3	C5	C6	90.0°	0.5°
C4	N3	C5	H5	90.0°	180.0°
N3	C5	C6	H5	90.0°	179.5°
N3	C5	C6	C7	90.0°	0.7°
C5	N3	C4	H4	90.0°	180.0°
N3	C5	C6	H6	90.0°	180.0°
C5	C6	C7	H6	90.0°	179.3°
C7	C6	C5	H5	90.0°	179.8°
HN1	N1	C2	H2	90.0°	0.0°
H5	C5	C6	H6	90.0°	0.5°

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PDB entries from 2026-01-14

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