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Summary Geometry Related PDB entries

Y6S

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
I13	C01	sing	2.09Å	2.11Å
C01	C06	doub	1.39Å	1.48Å	Aromatic
C01	C02	sing	1.38Å	1.51Å	Aromatic
C06	C05	sing	1.36Å	1.51Å	Aromatic
C02	C03	doub	1.39Å	1.58Å	Aromatic
C05	C04	doub	1.40Å	1.58Å	Aromatic
C03	C04	sing	1.41Å	1.39Å	Aromatic
C03	N07	sing	1.37Å	1.37Å	Aromatic
O11	C10	doub	1.22Å	1.26Å
C04	C09	sing	1.42Å	1.37Å	Aromatic
N07	C08	sing	1.38Å	1.37Å	Aromatic
C09	C08	doub	1.36Å	1.39Å	Aromatic
C08	C10	sing	1.47Å	1.53Å
C10	O12	sing	1.35Å	1.26Å
C02	H1	sing	1.08Å	1.08Å
C05	H2	sing	1.08Å	1.08Å
C06	H3	sing	1.08Å	1.08Å
C09	H4	sing	1.08Å	1.08Å
N07	H5	sing	0.97Å	1.00Å
O12	H6	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
I13	C01	C06	120.1°	119.7°
I13	C01	C02	120.2°	119.7°
C06	C01	C02	119.7°	120.6°
C01	C06	C05	119.3°	120.6°
C01	C06	H3	120.4°	119.8°
C01	C02	C03	120.2°	119.8°
C01	C02	H1	119.9°	120.1°
C06	C05	C04	120.9°	119.8°
C06	C05	H2	119.6°	120.1°
C05	C06	H3	120.4°	119.6°
C02	C03	C04	120.6°	119.5°
C02	C03	N07	131.8°	133.2°
C03	C02	H1	119.9°	120.1°
C05	C04	C03	119.4°	119.7°
C05	C04	C09	132.2°	133.3°
C04	C05	H2	119.6°	120.1°
C04	C03	N07	107.6°	107.4°
C03	C04	C09	108.4°	107.0°
C03	N07	C08	108.4°	108.8°
C03	N07	H5	125.8°	125.6°
O11	C10	C08	120.4°	120.0°
O11	C10	O12	120.7°	120.0°
C04	C09	C08	107.8°	107.7°
C04	C09	H4	126.1°	126.2°
N07	C08	C09	107.9°	109.1°
N07	C08	C10	126.6°	125.4°
C08	N07	H5	125.8°	125.6°
C09	C08	C10	125.6°	125.4°
C08	C09	H4	126.1°	126.1°
C08	C10	O12	118.9°	120.0°
C10	O12	H6	109.5°	117.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
I13	C01	C06	C02	179.9°	179.7°
I13	C01	C06	C05	180.0°	179.7°
I13	C01	C02	C03	180.0°	179.7°
I13	C01	C02	H1	0.0°	0.3°
I13	C01	C06	H3	0.0°	0.3°
C01	C06	C05	H3	180.0°	180.0°
C06	C01	C02	C03	0.2°	0.0°
C01	C06	C05	C04	0.1°	0.0°
C06	C01	C02	H1	179.8°	180.0°
C01	C06	C05	H2	179.9°	180.0°
C02	C01	C06	C05	0.2°	0.0°
C01	C02	C03	H1	180.0°	180.0°
C01	C02	C03	C04	0.1°	0.0°
C01	C02	C03	N07	180.0°	180.0°
C02	C01	C06	H3	179.9°	180.0°
C06	C05	C04	H2	180.0°	180.0°
C06	C05	C04	C03	0.0°	0.0°
C06	C05	C04	C09	179.9°	180.0°
C02	C03	C04	C05	0.0°	0.0°
C02	C03	C04	N07	180.0°	180.0°
C02	C03	C04	C09	179.9°	180.0°
C02	C03	N07	C08	179.8°	180.0°
C02	C03	N07	H5	0.2°	0.1°
C05	C04	C03	C09	179.9°	180.0°
C05	C04	C03	N07	180.0°	180.0°
C05	C04	C09	C08	179.8°	180.0°
C04	C05	C06	H3	179.9°	180.0°
C05	C04	C09	H4	0.2°	0.0°
C04	C03	N07	C08	0.2°	0.0°
C03	C04	C09	C08	0.3°	0.0°
C04	C03	C02	H1	179.9°	180.0°
C03	C04	C05	H2	180.0°	180.0°
C03	C04	C09	H4	179.7°	180.0°
C04	C03	N07	H5	179.8°	179.9°
N07	C03	C04	C09	0.0°	0.0°
C03	N07	C08	H5	180.0°	179.9°
C03	N07	C08	C09	0.4°	0.0°
C03	N07	C08	C10	179.7°	180.0°
N07	C03	C02	H1	0.0°	0.1°
O11	C10	C08	N07	42.9°	179.7°
O11	C10	C08	C09	137.9°	0.3°
O11	C10	C08	O12	179.4°	179.7°
O11	C10	O12	H6	0.0°	0.3°
C04	C09	C08	N07	0.4°	0.0°
C04	C09	C08	H4	180.0°	180.0°
C04	C09	C08	C10	179.7°	180.0°
C09	C04	C05	H2	0.1°	0.0°
N07	C08	C09	C10	179.3°	180.0°
N07	C08	C10	O12	137.7°	0.0°
N07	C08	C09	H4	179.6°	180.0°
C09	C08	C10	O12	41.5°	180.0°
C09	C08	N07	H5	179.6°	179.9°
C10	C08	C09	H4	0.3°	0.0°
C10	C08	N07	H5	0.4°	0.1°
C08	C10	O12	H6	179.4°	180.0°
H2	C05	C06	H3	0.1°	0.0°

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PDB entries from 2024-07-10

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