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Summary Geometry Related PDB entries

A1JLJ

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1	C1	doub	1.21Å	1.18Å
O2	C1	sing	1.35Å	1.35Å
C1	C2	sing	1.48Å	1.49Å
C2	C12	doub	1.39Å	1.41Å	Aromatic
C2	N1	sing	1.33Å	1.37Å	Aromatic
C12	C5	sing	1.40Å	1.40Å	Aromatic
C11	C10	doub	1.38Å	1.38Å	Aromatic
C11	C6	sing	1.39Å	1.39Å	Aromatic
C10	C9	sing	1.39Å	1.36Å	Aromatic
N1	C3	doub	1.31Å	1.36Å	Aromatic
C5	C6	sing	1.48Å	1.49Å
C5	C4	doub	1.40Å	1.41Å	Aromatic
C6	C7	doub	1.39Å	1.40Å	Aromatic
C9	F1	sing	1.35Å	1.33Å
C9	C8	doub	1.39Å	1.41Å	Aromatic
C3	C4	sing	1.38Å	1.40Å	Aromatic
C7	C8	sing	1.38Å	1.41Å	Aromatic
O2	H1	sing	0.97Å	0.95Å
C7	H4	sing	1.08Å	1.08Å
C4	H3	sing	1.08Å	1.08Å
C12	H8	sing	1.08Å	1.08Å
C3	H2	sing	1.08Å	1.08Å
C10	H6	sing	1.08Å	1.08Å
C11	H7	sing	1.08Å	1.08Å
C8	H5	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1	C1	O2	124.5°	120.1°
O1	C1	C2	117.5°	119.9°
O2	C1	C2	118.0°	120.0°
C1	O2	H1	109.5°	117.0°
C1	C2	C12	118.8°	119.7°
C1	C2	N1	117.6°	119.7°
C12	C2	N1	123.6°	120.6°
C2	C12	C5	118.8°	119.0°
C2	C12	H8	120.6°	120.5°
C2	N1	C3	117.0°	121.9°
C12	C5	C6	120.7°	120.9°
C12	C5	C4	117.9°	118.2°
C5	C12	H8	120.6°	120.6°
C10	C11	C6	121.2°	119.9°
C11	C10	C9	120.7°	120.1°
C11	C10	H6	119.7°	119.9°
C10	C11	H7	119.4°	120.1°
C11	C6	C5	119.8°	120.1°
C11	C6	C7	118.5°	119.8°
C6	C11	H7	119.4°	120.0°
C10	C9	F1	117.2°	119.9°
C10	C9	C8	120.6°	120.2°
C9	C10	H6	119.6°	119.9°
N1	C3	C4	122.6°	121.1°
N1	C3	H2	118.7°	119.5°
C6	C5	C4	121.4°	120.9°
C5	C6	C7	121.6°	120.1°
C5	C4	C3	120.1°	119.2°
C5	C4	H3	119.9°	120.4°
C6	C7	C8	120.4°	119.9°
C6	C7	H4	119.8°	120.0°
F1	C9	C8	122.1°	119.9°
C9	C8	C7	118.6°	120.0°
C9	C8	H5	120.7°	120.0°
C3	C4	H3	119.9°	120.4°
C4	C3	H2	118.7°	119.5°
C8	C7	H4	119.8°	120.0°
C7	C8	H5	120.7°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1	C1	O2	C2	179.4°	180.0°
O1	C1	C2	C12	13.1°	0.0°
O1	C1	C2	N1	167.7°	180.0°
O1	C1	O2	H1	0.0°	0.0°
O2	C1	C2	C12	166.4°	180.0°
O2	C1	C2	N1	12.9°	0.0°
C1	C2	C12	N1	179.2°	180.0°
C1	C2	C12	C5	178.2°	180.0°
C1	C2	N1	C3	179.3°	179.8°
C2	C1	O2	H1	179.4°	180.0°
C1	C2	C12	H8	1.8°	0.0°
C2	C12	C5	H8	180.0°	180.0°
C12	C2	N1	C3	0.1°	0.3°
C2	C12	C5	C6	179.2°	180.0°
C2	C12	C5	C4	1.6°	0.3°
N1	C2	C12	C5	1.1°	0.0°
C2	N1	C3	C4	0.6°	0.2°
N1	C2	C12	H8	179.0°	180.0°
C2	N1	C3	H2	179.4°	179.7°
C12	C5	C6	C11	21.4°	0.2°
C12	C5	C6	C4	179.2°	179.7°
C12	C5	C6	C7	160.7°	179.7°
C12	C5	C4	C3	1.2°	0.3°
C12	C5	C4	H3	178.9°	179.7°
C10	C11	C6	H7	180.0°	180.0°
C11	C10	C9	H6	180.0°	180.0°
C10	C11	C6	C5	179.9°	179.9°
C10	C11	C6	C7	2.2°	0.0°
C11	C10	C9	F1	179.0°	180.0°
C11	C10	C9	C8	0.2°	0.6°
C6	C11	C10	C9	1.5°	0.3°
C11	C6	C5	C7	177.8°	179.9°
C11	C6	C5	C4	159.4°	180.0°
C11	C6	C7	C8	1.7°	0.1°
C11	C6	C7	H4	178.3°	179.7°
C6	C11	C10	H6	178.5°	179.7°
C10	C9	F1	C8	179.2°	179.4°
C10	C9	C8	C7	0.2°	0.5°
C9	C10	C11	H7	178.5°	179.7°
C10	C9	C8	H5	179.8°	179.4°
N1	C3	C4	C5	0.0°	0.1°
N1	C3	C4	H2	180.0°	179.9°
N1	C3	C4	H3	180.0°	180.0°
C6	C5	C4	C3	179.6°	180.0°
C5	C6	C7	C8	179.6°	180.0°
C5	C6	C7	H4	0.4°	0.2°
C6	C5	C4	H3	0.3°	0.0°
C6	C5	C12	H8	0.8°	0.0°
C5	C6	C11	H7	0.1°	0.0°
C4	C5	C6	C7	18.5°	0.0°
C5	C4	C3	H3	180.0°	179.9°
C4	C5	C12	H8	178.4°	179.7°
C5	C4	C3	H2	180.0°	180.0°
C6	C7	C8	C9	0.5°	0.2°
C6	C7	C8	H4	180.0°	179.8°
C7	C6	C11	H7	177.8°	179.9°
C6	C7	C8	H5	179.5°	179.7°
F1	C9	C8	C7	179.4°	180.0°
F1	C9	C10	H6	1.0°	0.0°
F1	C9	C8	H5	0.6°	0.0°
C9	C8	C7	H5	180.0°	179.9°
C9	C8	C7	H4	179.5°	180.0°
C8	C9	C10	H6	179.8°	179.4°
H4	C7	C8	H5	0.5°	0.1°
H3	C4	C3	H2	0.0°	0.0°
H6	C10	C11	H7	1.5°	0.3°

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PDB entries from 2026-07-01

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