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Summary Geometry Related PDB entries

XYD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	doub	1.39Å	1.57Å	Aromatic
C1	C6	sing	1.39Å	1.54Å	Aromatic
C1	N	sing	1.40Å	1.35Å
C2	C3	sing	1.38Å	1.57Å	Aromatic
C2	C9	sing	1.51Å	1.53Å
C3	C4	doub	1.38Å	1.53Å	Aromatic
C3	H3	sing	1.08Å	1.10Å
C4	C5	sing	1.38Å	1.54Å	Aromatic
C4	H4	sing	1.08Å	1.10Å
C5	C6	doub	1.38Å	1.54Å	Aromatic
C5	C8	sing	1.51Å	1.52Å
C6	H6	sing	1.08Å	1.10Å
N	H1N	sing	0.97Å	1.02Å
N	H2N	sing	0.97Å	1.02Å
C8	H81	sing	1.09Å	1.12Å
C8	H82	sing	1.09Å	1.12Å
C8	H83	sing	1.09Å	1.11Å
C9	H91	sing	1.09Å	1.11Å
C9	H92	sing	1.09Å	1.12Å
C9	H93	sing	1.09Å	1.11Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	C1	C6	121.9°	119.9°
C2	C1	N	122.6°	120.1°
C1	C2	C3	116.8°	119.9°
C1	C2	C9	123.3°	120.0°
C6	C1	N	115.5°	120.0°
C1	C6	C5	118.6°	119.9°
C1	C6	H6	120.6°	120.0°
C1	N	H1N	122.6°	120.0°
C1	N	H2N	107.6°	119.9°
C3	C2	C9	119.9°	120.1°
C2	C3	C4	122.3°	120.1°
C2	C3	H3	119.9°	119.9°
C2	C9	H91	123.4°	109.4°
C2	C9	H92	107.3°	109.5°
C2	C9	H93	107.3°	109.5°
C4	C3	H3	117.8°	120.0°
C3	C4	C5	118.7°	120.1°
C3	C4	H4	120.4°	119.9°
C5	C4	H4	120.8°	120.0°
C4	C5	C6	121.7°	120.1°
C4	C5	C8	117.0°	119.9°
C6	C5	C8	121.3°	120.0°
C5	C6	H6	120.8°	120.1°
C5	C8	H81	117.0°	109.5°
C5	C8	H82	109.5°	109.5°
C5	C8	H83	109.5°	109.5°
H1N	N	H2N	107.5°	120.1°
H81	C8	H82	109.4°	109.4°
H81	C8	H83	109.5°	109.5°
H82	C8	H83	100.7°	109.5°
H91	C9	H92	107.3°	109.5°
H91	C9	H93	107.4°	109.4°
H92	C9	H93	102.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	C1	C6	N	179.8°	179.9°
C1	C2	C3	C9	179.4°	180.0°
C1	C2	C3	C4	0.2°	0.0°
C1	C2	C3	H3	179.8°	180.0°
C2	C1	C6	C5	0.6°	0.4°
C2	C1	C6	H6	179.4°	180.0°
C2	C1	N	H1N	180.0°	180.0°
C2	C1	N	H2N	54.7°	0.0°
C1	C2	C9	H91	180.0°	90.0°
C1	C2	C9	H92	54.7°	30.0°
C1	C2	C9	H93	54.7°	150.1°
C6	C1	C2	C3	0.3°	0.2°
C6	C1	C2	C9	179.1°	179.8°
C1	C6	C5	C4	1.6°	0.4°
C1	C6	C5	H6	180.0°	179.6°
C1	C6	C5	C8	179.2°	179.8°
C6	C1	N	H1N	0.3°	0.1°
C6	C1	N	H2N	125.5°	179.8°
N	C1	C2	C3	180.0°	180.0°
N	C1	C2	C9	0.7°	0.0°
N	C1	C6	C5	179.2°	179.8°
N	C1	C6	H6	0.8°	0.1°
C1	N	H1N	H2N	125.3°	180.0°
C2	C3	C4	H3	180.0°	180.0°
C2	C3	C4	C5	0.8°	0.0°
C2	C3	C4	H4	179.2°	180.0°
C3	C2	C9	H91	0.7°	90.0°
C3	C2	C9	H92	125.9°	150.0°
C3	C2	C9	H93	124.7°	29.9°
C9	C2	C3	C4	179.2°	180.0°
C9	C2	C3	H3	0.8°	0.0°
C2	C9	H91	H92	125.3°	120.0°
C2	C9	H91	H93	125.3°	120.0°
C2	C9	H92	H93	112.7°	120.1°
C3	C4	C5	H4	180.0°	180.0°
C3	C4	C5	C6	1.7°	0.2°
C3	C4	C5	C8	179.1°	180.0°
H3	C3	C4	C5	179.2°	180.0°
H3	C3	C4	H4	0.8°	0.0°
C4	C5	C6	C8	179.1°	179.9°
C4	C5	C6	H6	178.4°	180.0°
C4	C5	C8	H81	180.0°	90.0°
C4	C5	C8	H82	54.8°	150.1°
C4	C5	C8	H83	54.7°	30.0°
H4	C4	C5	C6	178.3°	179.8°
H4	C4	C5	C8	0.9°	0.0°
C6	C5	C8	H81	0.8°	90.2°
C6	C5	C8	H82	124.4°	29.7°
C6	C5	C8	H83	126.1°	149.8°
C8	C5	C6	H6	0.8°	0.1°
C5	C8	H81	H82	125.2°	120.0°
C5	C8	H81	H83	125.3°	120.0°
C5	C8	H82	H83	115.3°	120.1°
H81	C8	H82	H83	115.2°	120.0°
H91	C9	H92	H93	112.8°	120.0°

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PDB entries from 2026-02-04

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