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Summary Geometry Related PDB entries

A1JBG

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	O2	sing	1.43Å	1.43Å
O2	C3	sing	1.36Å	1.39Å
C3	C8	doub	1.40Å	1.40Å	Aromatic
C3	C4	sing	1.39Å	1.39Å	Aromatic
C4	C5	doub	1.38Å	1.39Å	Aromatic
C5	C6	sing	1.38Å	1.39Å	Aromatic
C6	C7	doub	1.38Å	1.39Å	Aromatic
C7	C8	sing	1.40Å	1.39Å	Aromatic
C8	C9	sing	1.48Å	1.45Å
C9	S14	sing	1.77Å	1.72Å	Aromatic
C9	N10	doub	1.30Å	1.31Å	Aromatic
N10	N11	sing	1.26Å	1.37Å	Aromatic
N11	C12	doub	1.30Å	1.31Å	Aromatic
C12	N13	sing	1.39Å	1.35Å
C12	S14	sing	1.77Å	1.73Å	Aromatic
C1	H1	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
C1	H3	sing	1.09Å	1.10Å
N13	H4	sing	0.97Å	1.00Å
N13	H5	sing	0.97Å	1.00Å
C7	H6	sing	1.08Å	1.08Å
C4	H7	sing	1.08Å	1.08Å
C5	H8	sing	1.08Å	1.08Å
C6	H9	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	O2	C3	106.0°	117.0°
O2	C1	H1	109.5°	109.4°
O2	C1	H2	109.5°	109.4°
O2	C1	H3	109.5°	109.5°
O2	C3	C8	121.7°	120.2°
O2	C3	C4	117.3°	120.1°
C8	C3	C4	121.0°	119.7°
C3	C8	C7	119.5°	119.7°
C3	C8	C9	121.5°	120.1°
C3	C4	C5	118.9°	120.1°
C3	C4	H7	120.6°	120.0°
C4	C5	C6	120.4°	120.4°
C5	C4	H7	120.5°	119.9°
C4	C5	H8	119.8°	119.8°
C5	C6	C7	120.6°	120.3°
C6	C5	H8	119.8°	119.9°
C5	C6	H9	119.7°	119.9°
C6	C7	C8	119.5°	119.9°
C6	C7	H6	120.3°	120.0°
C7	C6	H9	119.7°	119.9°
C7	C8	C9	118.9°	120.1°
C8	C7	H6	120.2°	120.1°
C8	C9	S14	122.6°	126.1°
C8	C9	N10	122.5°	126.1°
S14	C9	N10	114.9°	107.8°
C9	S14	C12	86.9°	88.9°
C9	N10	N11	111.3°	117.7°
N10	N11	C12	113.4°	117.7°
N11	C12	N13	122.6°	126.1°
N11	C12	S14	113.5°	107.8°
N13	C12	S14	123.9°	126.1°
C12	N13	H4	109.5°	120.0°
C12	N13	H5	109.5°	120.0°
H1	C1	H2	109.4°	109.5°
H1	C1	H3	109.5°	109.5°
H2	C1	H3	109.5°	109.5°
H4	N13	H5	109.5°	119.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	O2	C3	C8	91.8°	180.0°
C1	O2	C3	C4	90.1°	0.3°
O2	C1	H1	H2	120.0°	119.9°
O2	C1	H1	H3	120.0°	120.0°
O2	C1	H2	H3	120.0°	120.0°
O2	C3	C8	C4	178.0°	179.8°
O2	C3	C4	C5	179.6°	179.7°
O2	C3	C8	C7	180.0°	179.7°
O2	C3	C8	C9	2.5°	0.2°
C3	O2	C1	H1	180.0°	60.0°
C3	O2	C1	H2	60.0°	60.0°
C3	O2	C1	H3	60.0°	180.0°
O2	C3	C4	H7	0.4°	0.2°
C8	C3	C4	C5	1.5°	0.0°
C3	C8	C7	C6	1.3°	0.0°
C3	C8	C7	C9	177.6°	179.9°
C3	C8	C9	S14	149.1°	180.0°
C3	C8	C9	N10	31.3°	0.4°
C3	C8	C7	H6	178.7°	179.9°
C8	C3	C4	H7	178.5°	180.0°
C3	C4	C5	H7	180.0°	180.0°
C3	C4	C5	C6	0.3°	0.0°
C4	C3	C8	C7	2.0°	0.0°
C4	C3	C8	C9	179.5°	180.0°
C3	C4	C5	H8	179.7°	179.9°
C4	C5	C6	H8	180.0°	179.9°
C4	C5	C6	C7	0.4°	0.0°
C4	C5	C6	H9	179.7°	180.0°
C5	C6	C7	H9	180.0°	179.9°
C5	C6	C7	C8	0.1°	0.0°
C5	C6	C7	H6	179.9°	179.9°
C6	C5	C4	H7	179.7°	180.0°
C6	C7	C8	H6	180.0°	180.0°
C6	C7	C8	C9	178.8°	180.0°
C7	C6	C5	H8	179.6°	179.9°
C7	C8	C9	S14	33.4°	0.1°
C7	C8	C9	N10	146.2°	179.7°
C8	C7	C6	H9	179.9°	180.0°
C8	C9	S14	N10	179.6°	179.7°
C8	C9	N10	N11	179.1°	179.9°
C8	C9	S14	C12	179.1°	180.0°
C9	C8	C7	H6	1.2°	0.0°
S14	C9	N10	N11	1.3°	0.2°
C9	S14	C12	N11	1.0°	0.3°
C9	S14	C12	N13	178.9°	180.0°
C9	N10	N11	C12	0.4°	0.0°
N10	C9	S14	C12	1.3°	0.3°
N10	N11	C12	N13	179.4°	180.0°
N10	N11	C12	S14	0.6°	0.2°
N11	C12	N13	S14	180.0°	179.7°
N11	C12	N13	H4	0.0°	179.6°
N11	C12	N13	H5	120.0°	0.3°
C12	N13	H4	H5	120.0°	179.9°
S14	C12	N13	H4	180.0°	0.1°
S14	C12	N13	H5	60.0°	180.0°
H1	C1	H2	H3	120.0°	120.1°
H6	C7	C6	H9	0.1°	0.0°
H7	C4	C5	H8	0.3°	0.1°
H8	C5	C6	H9	0.4°	0.1°

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PDB entries from 2026-07-01

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