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Summary Geometry Related PDB entries

A1JDK

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C9	doub	1.38Å	1.39Å	Aromatic
C1	C2	sing	1.38Å	1.40Å	Aromatic
C9	C8	sing	1.38Å	1.38Å	Aromatic
C2	C3	doub	1.38Å	1.39Å	Aromatic
C8	C4	doub	1.39Å	1.40Å	Aromatic
C3	C4	sing	1.39Å	1.40Å	Aromatic
C4	N1	sing	1.40Å	1.42Å
N1	N2	sing	1.40Å	1.25Å
N2	C5	sing	1.39Å	1.46Å
N4	C5	doub	1.31Å	1.36Å	Aromatic
N4	C7	sing	1.34Å	1.35Å	Aromatic
C5	N3	sing	1.36Å	1.32Å	Aromatic
C7	C6	doub	1.34Å	1.32Å	Aromatic
N3	C6	sing	1.38Å	1.37Å	Aromatic
N1	H1	sing	0.97Å	1.00Å
N3	H2	sing	0.97Å	1.00Å
C6	H3	sing	1.08Å	1.08Å
C7	H4	sing	1.08Å	1.08Å
C8	H5	sing	1.08Å	1.08Å
C1	H6	sing	1.08Å	1.08Å
C2	H7	sing	1.08Å	1.08Å
C3	H8	sing	1.08Å	1.08Å
N2	H9	sing	0.97Å	1.00Å
C9	H11	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C9	C1	C2	120.3°	120.1°
C1	C9	C8	119.9°	120.1°
C9	C1	H6	119.8°	120.0°
C1	C9	H11	120.0°	119.9°
C1	C2	C3	120.5°	120.0°
C2	C1	H6	119.9°	119.9°
C1	C2	H7	119.7°	120.0°
C9	C8	C4	119.7°	119.9°
C9	C8	H5	120.2°	120.1°
C8	C9	H11	120.0°	119.9°
C2	C3	C4	118.7°	119.9°
C3	C2	H7	119.7°	120.0°
C2	C3	H8	120.7°	120.0°
C8	C4	C3	120.9°	119.9°
C8	C4	N1	115.9°	120.1°
C4	C8	H5	120.2°	120.0°
C3	C4	N1	123.2°	120.1°
C4	C3	H8	120.7°	120.1°
C4	N1	N2	119.8°	120.0°
C4	N1	H1	106.8°	120.0°
N1	N2	C5	104.0°	120.0°
N2	N1	H1	106.8°	120.0°
N1	N2	H9	110.8°	120.0°
N2	C5	N4	126.5°	125.8°
N2	C5	N3	124.2°	125.8°
C5	N2	H9	110.8°	120.0°
C5	N4	C7	108.3°	109.3°
N4	C5	N3	109.2°	108.4°
N4	C7	C6	106.4°	108.3°
N4	C7	H4	126.8°	125.9°
C5	N3	C6	105.5°	107.0°
C5	N3	H2	127.3°	126.5°
C7	C6	N3	110.6°	107.0°
C7	C6	H3	124.7°	126.5°
C6	C7	H4	126.8°	125.8°
C6	N3	H2	127.3°	126.6°
N3	C6	H3	124.7°	126.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C9	C1	C2	H6	180.0°	179.8°
C1	C9	C8	H11	180.0°	179.6°
C9	C1	C2	C3	0.2°	0.2°
C1	C9	C8	C4	0.1°	0.0°
C1	C9	C8	H5	180.0°	180.0°
C9	C1	C2	H7	179.8°	180.0°
C2	C1	C9	C8	0.2°	0.3°
C1	C2	C3	H7	180.0°	179.7°
C1	C2	C3	C4	0.1°	0.0°
C1	C2	C3	H8	179.8°	180.0°
C2	C1	C9	H11	179.8°	179.9°
C9	C8	C4	H5	180.0°	179.9°
C9	C8	C4	C3	0.0°	0.2°
C9	C8	C4	N1	179.4°	180.0°
C8	C9	C1	H6	179.9°	179.9°
C2	C3	C4	C8	0.0°	0.3°
C2	C3	C4	H8	180.0°	180.0°
C2	C3	C4	N1	179.3°	180.0°
C3	C2	C1	H6	179.8°	180.0°
C8	C4	C3	N1	179.3°	179.7°
C8	C4	N1	N2	179.4°	180.0°
C8	C4	N1	H1	58.0°	0.2°
C8	C4	C3	H8	179.9°	179.8°
C4	C8	C9	H11	179.9°	179.7°
C3	C4	N1	N2	0.1°	0.3°
C3	C4	N1	H1	121.4°	179.5°
C3	C4	C8	H5	180.0°	179.7°
C4	C3	C2	H7	179.9°	179.7°
C4	N1	N2	H1	121.4°	179.8°
C4	N1	N2	C5	179.9°	179.8°
N1	C4	C8	H5	0.6°	0.0°
N1	C4	C3	H8	0.7°	0.0°
C4	N1	N2	H9	61.0°	0.3°
N1	N2	C5	H9	119.1°	180.0°
N1	N2	C5	N4	0.3°	0.0°
N1	N2	C5	N3	179.7°	180.0°
N2	C5	N4	N3	180.0°	180.0°
N2	C5	N4	C7	180.0°	179.7°
N2	C5	N3	C6	180.0°	180.0°
C5	N2	N1	H1	58.4°	0.1°
N2	C5	N3	H2	0.0°	0.3°
C5	N4	C7	C6	0.0°	0.4°
N4	C5	N3	C6	0.0°	0.0°
N4	C5	N3	H2	180.0°	179.7°
C5	N4	C7	H4	180.0°	180.0°
N4	C5	N2	H9	119.4°	180.0°
C7	N4	C5	N3	0.0°	0.2°
N4	C7	C6	H4	180.0°	179.6°
N4	C7	C6	N3	0.0°	0.4°
N4	C7	C6	H3	180.0°	179.6°
C5	N3	C6	C7	0.0°	0.3°
C5	N3	C6	H2	180.0°	179.7°
C5	N3	C6	H3	180.0°	179.7°
N3	C5	N2	H9	60.6°	0.0°
C7	C6	N3	H3	180.0°	180.0°
C7	C6	N3	H2	180.0°	180.0°
N3	C6	C7	H4	180.0°	180.0°
H1	N1	N2	H9	177.6°	179.9°
H2	N3	C6	H3	0.0°	0.0°
H3	C6	C7	H4	0.0°	0.0°
H5	C8	C9	H11	0.0°	0.4°
H6	C1	C2	H7	0.2°	0.2°
H6	C1	C9	H11	0.1°	0.3°
H7	C2	C3	H8	0.2°	0.3°

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PDB entries from 2026-06-17

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