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Summary Geometry Related PDB entries

JYR

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C10	O4	sing	1.43Å	1.43Å
C1	C2	doub	1.36Å	1.39Å	Aromatic
C1	C6	sing	1.39Å	1.38Å	Aromatic
C1	N1	sing	1.48Å	1.33Å
C2	C3	sing	1.41Å	1.33Å	Aromatic
C3	C4	doub	1.40Å	1.34Å	Aromatic
C3	C7	sing	1.45Å	1.35Å	Aromatic
C4	C5	sing	1.40Å	1.33Å	Aromatic
C4	S1	sing	1.76Å	1.61Å	Aromatic
C5	C6	doub	1.37Å	1.38Å	Aromatic
C7	C8	doub	1.35Å	1.33Å	Aromatic
C7	O3	sing	1.36Å	1.36Å
C8	C9	sing	1.42Å	1.33Å
C8	S1	sing	1.75Å	1.53Å	Aromatic
C9	O4	sing	1.35Å	1.35Å
C9	O5	doub	1.22Å	1.23Å
N1	O1	sing	1.22Å	1.39Å
N1	O2	doub	1.22Å	1.37Å
C10	H1	sing	1.09Å	1.10Å
C10	H2	sing	1.09Å	1.10Å
C10	H3	sing	1.09Å	1.10Å
C2	H4	sing	1.08Å	1.08Å
C5	H6	sing	1.08Å	1.08Å
C6	H7	sing	1.08Å	1.08Å
O3	H9	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C10	O4	C9	107.3°	117.0°
O4	C10	H1	109.5°	109.5°
O4	C10	H2	109.5°	109.5°
O4	C10	H3	109.5°	109.5°
C2	C1	C6	119.2°	120.5°
C2	C1	N1	121.4°	119.7°
C1	C2	C3	121.4°	120.5°
C1	C2	H4	119.3°	119.7°
C6	C1	N1	119.4°	119.7°
C1	C6	C5	117.5°	120.3°
C1	C6	H7	121.3°	119.9°
C1	N1	O1	118.5°	120.0°
C1	N1	O2	119.4°	120.0°
C2	C3	C4	118.6°	118.8°
C2	C3	C7	128.6°	129.0°
C3	C2	H4	119.3°	119.7°
C4	C3	C7	112.8°	112.1°
C3	C4	C5	122.5°	119.6°
C3	C4	S1	106.6°	110.2°
C3	C7	C8	112.5°	114.2°
C3	C7	O3	123.8°	122.9°
C5	C4	S1	130.9°	130.2°
C4	C5	C6	120.7°	120.3°
C4	C5	H6	119.6°	119.8°
C4	S1	C8	98.4°	92.4°
C6	C5	H6	119.7°	119.9°
C5	C6	H7	121.3°	119.9°
C8	C7	O3	123.8°	122.9°
C7	C8	C9	127.5°	124.5°
C7	C8	S1	109.6°	111.1°
C7	O3	H9	109.5°	114.0°
C9	C8	S1	122.8°	124.5°
C8	C9	O4	115.8°	120.0°
C8	C9	O5	120.5°	120.0°
O4	C9	O5	123.8°	120.0°
O1	N1	O2	122.0°	120.0°
H1	C10	H2	109.5°	109.5°
H1	C10	H3	109.5°	109.4°
H2	C10	H3	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C10	O4	C9	C8	176.5°	180.0°
C10	O4	C9	O5	4.0°	0.0°
O4	C10	H1	H2	120.0°	120.0°
O4	C10	H1	H3	120.0°	120.0°
O4	C10	H2	H3	120.0°	120.0°
C2	C1	C6	N1	179.8°	179.8°
C1	C2	C3	H4	180.0°	179.9°
C1	C2	C3	C4	0.3°	0.0°
C1	C2	C3	C7	179.8°	179.9°
C2	C1	C6	C5	0.6°	0.1°
C2	C1	N1	O1	179.7°	0.0°
C2	C1	N1	O2	0.0°	180.0°
C2	C1	C6	H7	179.4°	180.0°
C6	C1	C2	C3	0.1°	0.1°
C1	C6	C5	C4	1.1°	0.0°
C1	C6	C5	H7	180.0°	179.9°
C6	C1	N1	O1	0.1°	179.7°
C6	C1	N1	O2	179.8°	0.2°
C6	C1	C2	H4	180.0°	180.0°
C1	C6	C5	H6	178.9°	179.9°
N1	C1	C2	C3	179.7°	179.7°
N1	C1	C6	C5	179.6°	179.7°
C1	N1	O1	O2	179.7°	180.0°
N1	C1	C2	H4	0.2°	0.2°
N1	C1	C6	H7	0.4°	0.2°
C2	C3	C4	C7	179.6°	180.0°
C2	C3	C4	C5	0.2°	0.0°
C2	C3	C4	S1	179.8°	180.0°
C2	C3	C7	C8	179.3°	180.0°
C2	C3	C7	O3	0.4°	0.1°
C3	C4	C5	S1	179.9°	179.9°
C3	C4	C5	C6	0.9°	0.0°
C4	C3	C7	C8	1.1°	0.0°
C4	C3	C7	O3	179.9°	180.0°
C3	C4	S1	C8	0.0°	0.0°
C4	C3	C2	H4	179.7°	180.0°
C3	C4	C5	H6	179.1°	179.9°
C7	C3	C4	C5	179.4°	180.0°
C7	C3	C4	S1	0.6°	0.0°
C3	C7	C8	O3	178.9°	179.9°
C3	C7	C8	C9	178.3°	180.0°
C3	C7	C8	S1	1.1°	0.0°
C7	C3	C2	H4	0.2°	0.0°
C3	C7	O3	H9	180.0°	90.0°
C4	C5	C6	H6	180.0°	179.9°
C5	C4	S1	C8	179.9°	180.0°
C4	C5	C6	H7	178.9°	179.9°
S1	C4	C5	C6	179.0°	180.0°
C4	S1	C8	C7	0.6°	0.0°
C4	S1	C8	C9	178.0°	180.0°
S1	C4	C5	H6	1.0°	0.1°
C7	C8	C9	S1	176.9°	180.0°
C7	C8	C9	O4	1.1°	180.0°
C7	C8	C9	O5	178.4°	0.0°
C8	C7	O3	H9	1.2°	90.1°
O3	C7	C8	C9	2.7°	0.1°
O3	C7	C8	S1	180.0°	179.9°
C8	C9	O4	O5	179.5°	179.9°
S1	C8	C9	O4	175.8°	0.0°
S1	C8	C9	O5	4.7°	180.0°
C9	O4	C10	H1	180.0°	180.0°
C9	O4	C10	H2	60.0°	60.0°
C9	O4	C10	H3	60.0°	60.0°
H1	C10	H2	H3	120.0°	119.9°
H6	C5	C6	H7	1.1°	0.1°

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PDB entries from 2024-07-10

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