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Summary Geometry Related PDB entries

A1AXD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	sing	1.51Å	1.51Å
C2	C3	doub	1.38Å	1.39Å	Aromatic
C2	C8	sing	1.38Å	1.39Å	Aromatic
C3	C4	sing	1.38Å	1.38Å	Aromatic
C4	C5	doub	1.40Å	1.39Å	Aromatic
C5	C6	sing	1.48Å	1.49Å
C5	C7	sing	1.40Å	1.39Å	Aromatic
C6	N1	sing	1.35Å	1.33Å
C6	O1	doub	1.22Å	1.24Å
C7	C8	doub	1.38Å	1.39Å	Aromatic
C8	C9	sing	1.51Å	1.51Å
C1	H12	sing	1.09Å	1.10Å
C1	H11	sing	1.09Å	1.10Å
C1	H13	sing	1.09Å	1.10Å
C3	H3	sing	1.08Å	1.08Å
C4	H4	sing	1.08Å	1.08Å
C7	H7	sing	1.08Å	1.08Å
C9	H92	sing	1.09Å	1.10Å
C9	H91	sing	1.09Å	1.10Å
C9	H93	sing	1.09Å	1.10Å
N1	HN11	sing	0.97Å	1.00Å
N1	HN12	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	C2	C3	120.4°	119.9°
C1	C2	C8	120.4°	119.9°
C2	C1	H12	109.5°	109.5°
C2	C1	H11	109.5°	109.5°
C2	C1	H13	109.5°	109.5°
C3	C2	C8	119.2°	120.3°
C2	C3	C4	121.3°	120.2°
C2	C3	H3	119.4°	119.9°
C2	C8	C7	119.3°	120.2°
C2	C8	C9	120.8°	119.9°
C3	C4	C5	119.9°	119.8°
C4	C3	H3	119.3°	119.9°
C3	C4	H4	120.0°	120.1°
C4	C5	C6	123.1°	120.2°
C4	C5	C7	118.9°	119.7°
C5	C4	H4	120.1°	120.0°
C6	C5	C7	117.9°	120.2°
C5	C6	N1	118.1°	120.0°
C5	C6	O1	119.7°	120.0°
C5	C7	C8	121.4°	119.8°
C5	C7	H7	119.3°	120.0°
N1	C6	O1	122.2°	120.0°
C6	N1	HN11	120.0°	119.9°
C6	N1	HN12	120.0°	120.1°
C7	C8	C9	119.9°	119.9°
C8	C7	H7	119.3°	120.1°
C8	C9	H92	109.5°	109.5°
C8	C9	H91	109.5°	109.5°
C8	C9	H93	109.4°	109.4°
H12	C1	H11	109.5°	109.4°
H12	C1	H13	109.5°	109.5°
H11	C1	H13	109.5°	109.4°
H92	C9	H91	109.5°	109.5°
H92	C9	H93	109.5°	109.4°
H91	C9	H93	109.4°	109.4°
HN11	N1	HN12	120.0°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	C2	C3	C8	179.7°	179.7°
C1	C2	C3	C4	179.9°	180.0°
C1	C2	C8	C7	180.0°	179.7°
C1	C2	C8	C9	0.2°	0.1°
C2	C1	H12	H11	120.0°	120.0°
C2	C1	H12	H13	120.0°	120.1°
C2	C1	H11	H13	120.0°	120.0°
C1	C2	C3	H3	0.1°	0.0°
C2	C3	C4	H3	180.0°	180.0°
C2	C3	C4	C5	0.4°	0.0°
C3	C2	C8	C7	0.2°	0.6°
C3	C2	C8	C9	180.0°	179.8°
C3	C2	C1	H12	89.9°	90.0°
C3	C2	C1	H11	150.1°	150.0°
C3	C2	C1	H13	30.2°	30.0°
C2	C3	C4	H4	179.6°	180.0°
C8	C2	C3	C4	0.4°	0.3°
C2	C8	C7	C5	0.1°	0.6°
C2	C8	C7	C9	179.8°	179.6°
C8	C2	C1	H12	89.9°	90.3°
C8	C2	C1	H11	30.1°	29.7°
C8	C2	C1	H13	150.1°	149.7°
C8	C2	C3	H3	179.6°	179.7°
C2	C8	C7	H7	179.9°	179.7°
C2	C8	C9	H92	90.1°	89.9°
C2	C8	C9	H91	149.9°	150.0°
C2	C8	C9	H93	29.9°	30.0°
C3	C4	C5	H4	180.0°	180.0°
C3	C4	C5	C6	179.9°	180.0°
C3	C4	C5	C7	0.3°	0.0°
C4	C5	C6	C7	179.8°	180.0°
C4	C5	C6	N1	61.6°	0.0°
C4	C5	C6	O1	119.0°	180.0°
C4	C5	C7	C8	0.1°	0.3°
C5	C4	C3	H3	179.6°	180.0°
C4	C5	C7	H7	179.9°	180.0°
C5	C6	N1	O1	179.4°	180.0°
C6	C5	C7	C8	180.0°	179.7°
C6	C5	C4	H4	0.1°	0.0°
C6	C5	C7	H7	0.1°	0.0°
C5	C6	N1	HN11	179.4°	0.0°
C5	C6	N1	HN12	0.6°	180.0°
C7	C5	C6	N1	118.2°	180.0°
C7	C5	C6	O1	61.2°	0.0°
C5	C7	C8	H7	180.0°	179.6°
C5	C7	C8	C9	179.9°	179.8°
C7	C5	C4	H4	179.8°	180.0°
C6	N1	HN11	HN12	180.0°	179.9°
O1	C6	N1	HN11	0.0°	180.0°
O1	C6	N1	HN12	180.0°	0.0°
C7	C8	C9	H92	90.1°	89.7°
C7	C8	C9	H91	29.9°	30.4°
C7	C8	C9	H93	149.9°	150.3°
C9	C8	C7	H7	0.1°	0.1°
C8	C9	H92	H91	120.0°	120.1°
C8	C9	H92	H93	120.0°	120.0°
C8	C9	H91	H93	119.9°	119.9°
H12	C1	H11	H13	120.0°	120.0°
H3	C3	C4	H4	0.4°	0.0°
H92	C9	H91	H93	120.0°	119.9°

250059

PDB entries from 2026-03-04

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