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Summary Geometry Related PDB entries

JMJ

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
S07	C06	sing	1.76Å	1.84Å	Aromatic
S07	C03	sing	1.76Å	1.92Å	Aromatic
N08	C06	sing	1.39Å	1.42Å
N08	C09	sing	1.35Å	1.45Å
C06	N05	doub	1.30Å	1.33Å	Aromatic
S02	C03	sing	1.76Å	2.03Å
S02	C01	sing	1.81Å	1.79Å
C03	N04	doub	1.30Å	1.33Å	Aromatic
C12	C11	doub	1.36Å	1.38Å	Aromatic
C12	C13	sing	1.40Å	1.47Å	Aromatic
C09	C11	sing	1.47Å	1.47Å
C09	O10	doub	1.22Å	1.23Å
C11	O15	sing	1.35Å	1.41Å	Aromatic
C13	C14	doub	1.35Å	1.39Å	Aromatic
N05	N04	sing	1.38Å	1.26Å	Aromatic
O15	C14	sing	1.34Å	1.38Å	Aromatic
C13	H131	sing	1.08Å	1.08Å
C01	H013	sing	1.09Å	1.10Å
C01	H011	sing	1.09Å	1.10Å
C01	H012	sing	1.09Å	1.10Å
N08	H081	sing	0.97Å	1.00Å
C12	H121	sing	1.08Å	1.08Å
C14	H141	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C06	S07	C03	89.8°	90.4°
S07	C06	N08	132.9°	125.4°
S07	C06	N05	103.8°	109.3°
S07	C03	S02	131.3°	125.4°
S07	C03	N04	103.0°	109.1°
C06	N08	C09	121.1°	120.0°
N08	C06	N05	123.3°	125.3°
C06	N08	H081	119.5°	120.0°
N08	C09	C11	138.0°	120.0°
N08	C09	O10	111.0°	120.0°
C09	N08	H081	119.5°	120.0°
C06	N05	N04	123.2°	115.6°
C03	S02	C01	104.2°	103.0°
S02	C03	N04	125.7°	125.5°
S02	C01	H013	109.5°	109.5°
S02	C01	H011	109.5°	109.5°
S02	C01	H012	109.5°	109.4°
C03	N04	N05	120.1°	115.7°
C11	C12	C13	108.7°	106.7°
C12	C11	C09	133.0°	126.0°
C12	C11	O15	105.6°	108.0°
C11	C12	H121	125.7°	126.6°
C12	C13	C14	106.7°	107.1°
C12	C13	H131	126.7°	126.5°
C13	C12	H121	125.6°	126.6°
C11	C09	O10	110.7°	120.0°
C09	C11	O15	121.2°	126.0°
C11	O15	C14	111.9°	109.4°
C13	C14	O15	107.0°	108.8°
C14	C13	H131	126.7°	126.4°
C13	C14	H141	126.5°	125.7°
O15	C14	H141	126.5°	125.6°
H013	C01	H011	109.5°	109.5°
H013	C01	H012	109.5°	109.5°
H011	C01	H012	109.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
S07	C06	N08	N05	179.7°	179.7°
S07	C06	N08	C09	147.7°	179.7°
C06	S07	C03	S02	179.3°	179.9°
C06	S07	C03	N04	0.0°	0.3°
S07	C06	N05	N04	3.3°	0.3°
S07	C06	N08	H081	32.3°	0.3°
C03	S07	C06	N08	178.3°	179.9°
C03	S07	C06	N05	1.5°	0.3°
S07	C03	S02	N04	179.2°	179.8°
S07	C03	S02	C01	147.8°	179.7°
S07	C03	N04	N05	1.9°	0.2°
C06	N08	C09	H081	180.0°	180.0°
C06	N08	C09	C11	175.6°	180.0°
C06	N08	C09	O10	1.8°	0.0°
N08	C06	N05	N04	176.5°	180.0°
C09	N08	C06	N05	32.1°	0.0°
N08	C09	C11	C12	2.7°	179.5°
N08	C09	C11	O10	173.8°	180.0°
N08	C09	C11	O15	171.5°	0.0°
C06	N05	N04	C03	3.8°	0.0°
N05	C06	N08	H081	147.9°	180.0°
S02	C03	N04	N05	178.7°	180.0°
C03	S02	C01	H013	180.0°	180.0°
C03	S02	C01	H011	60.0°	60.0°
C03	S02	C01	H012	60.0°	60.0°
C01	S02	C03	N04	31.4°	0.0°
S02	C01	H013	H011	120.0°	120.0°
S02	C01	H013	H012	120.0°	119.9°
S02	C01	H011	H012	120.0°	120.0°
C11	C12	C13	H121	180.0°	180.0°
C12	C11	C09	O15	174.1°	179.5°
C12	C11	C09	O10	176.5°	0.5°
C11	C12	C13	C14	0.1°	0.0°
C12	C11	O15	C14	2.1°	0.4°
C11	C12	C13	H131	179.8°	179.6°
C13	C12	C11	C09	176.1°	179.8°
C13	C12	C11	O15	1.3°	0.3°
C12	C13	C14	H131	180.0°	179.7°
C12	C13	C14	O15	1.1°	0.2°
C12	C13	C14	H141	178.9°	179.8°
C09	C11	O15	C14	177.6°	180.0°
C11	C09	N08	H081	4.4°	0.0°
C09	C11	C12	H121	3.9°	0.2°
O10	C09	C11	O15	2.4°	180.0°
O10	C09	N08	H081	178.2°	180.0°
C11	O15	C14	C13	2.0°	0.4°
O15	C11	C12	H121	178.7°	179.8°
C11	O15	C14	H141	178.0°	179.6°
C13	C14	O15	H141	180.0°	180.0°
C14	C13	C12	H121	179.8°	180.0°
O15	C14	C13	H131	178.9°	179.9°
H131	C13	C12	H121	0.2°	0.3°
H131	C13	C14	H141	1.1°	0.1°
H013	C01	H011	H012	120.0°	120.0°

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PDB entries from 2026-01-21

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