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Summary Geometry Related PDB entries

5Q8

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N2	C10	sing	1.38Å	1.32Å
C10	O	sing	1.35Å	1.41Å	Aromatic
C10	C8	doub	1.39Å	1.45Å	Aromatic
O	C7	sing	1.34Å	1.50Å	Aromatic
C4	C5	doub	1.38Å	1.38Å	Aromatic
C4	C3	sing	1.38Å	1.38Å	Aromatic
C5	C6	sing	1.38Å	1.39Å	Aromatic
C3	C2	doub	1.38Å	1.39Å	Aromatic
C8	C9	sing	1.43Å	1.48Å
C8	N	sing	1.36Å	1.33Å	Aromatic
C6	C1	doub	1.38Å	1.38Å	Aromatic
C7	C	sing	1.51Å	1.49Å
C7	N	doub	1.30Å	1.30Å	Aromatic
C2	C1	sing	1.38Å	1.39Å	Aromatic
C1	C	sing	1.51Å	1.51Å
C9	N1	trip	1.14Å	1.14Å
C4	H1	sing	1.08Å	1.08Å
C5	H2	sing	1.08Å	1.08Å
C6	H3	sing	1.08Å	1.08Å
N2	H4	sing	0.97Å	1.00Å
N2	H5	sing	0.97Å	1.00Å
C	H6	sing	1.09Å	1.10Å
C	H7	sing	1.09Å	1.10Å
C3	H8	sing	1.08Å	1.08Å
C2	H9	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N2	C10	O	121.1°	126.8°
N2	C10	C8	137.3°	126.7°
C10	N2	H4	109.5°	120.1°
C10	N2	H5	109.5°	120.0°
O	C10	C8	101.5°	106.5°
C10	O	C7	104.8°	108.3°
C10	C8	C9	128.2°	126.6°
C10	C8	N	116.4°	106.7°
O	C7	C	115.9°	125.1°
O	C7	N	112.4°	109.8°
C5	C4	C3	119.7°	120.0°
C4	C5	C6	120.2°	120.0°
C5	C4	H1	120.2°	120.0°
C4	C5	H2	119.9°	120.0°
C4	C3	C2	120.1°	120.0°
C3	C4	H1	120.1°	120.0°
C4	C3	H8	120.0°	120.0°
C5	C6	C1	120.8°	120.0°
C6	C5	H2	119.9°	120.0°
C5	C6	H3	119.6°	120.0°
C3	C2	C1	120.8°	120.0°
C2	C3	H8	119.9°	120.0°
C3	C2	H9	119.6°	120.0°
C9	C8	N	115.4°	126.7°
C8	C9	N1	179.6°	179.9°
C8	N	C7	104.8°	108.7°
C6	C1	C2	118.4°	120.0°
C6	C1	C	120.8°	120.0°
C1	C6	H3	119.6°	120.0°
C	C7	N	131.6°	125.1°
C7	C	C1	110.9°	109.5°
C7	C	H6	109.1°	109.5°
C7	C	H7	109.1°	109.5°
C2	C1	C	120.8°	120.0°
C1	C2	H9	119.6°	120.0°
C1	C	H6	109.1°	109.5°
C1	C	H7	109.1°	109.4°
H4	N2	H5	109.5°	119.9°
H6	C	H7	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N2	C10	O	C8	180.0°	179.8°
N2	C10	O	C7	179.4°	180.0°
N2	C10	C8	C9	0.1°	0.0°
N2	C10	C8	N	179.9°	179.8°
C10	N2	H4	H5	120.0°	180.0°
O	C10	C8	C9	179.8°	179.8°
O	C10	C8	N	0.2°	0.1°
C10	O	C7	C	178.6°	180.0°
C10	O	C7	N	1.3°	0.3°
O	C10	N2	H4	0.0°	0.1°
O	C10	N2	H5	120.0°	179.9°
C8	C10	O	C7	0.6°	0.2°
C10	C8	C9	N	180.0°	179.9°
C10	C8	N	C7	1.0°	0.1°
C10	C8	C9	N1	66.2°	171.7°
C8	C10	N2	H4	180.0°	179.9°
C8	C10	N2	H5	60.0°	0.2°
O	C7	N	C8	1.3°	0.3°
O	C7	C	N	176.7°	179.6°
O	C7	C	C1	58.3°	90.4°
O	C7	C	H6	178.5°	29.6°
O	C7	C	H7	61.9°	149.7°
C5	C4	C3	H1	180.0°	179.8°
C4	C5	C6	H2	180.0°	179.9°
C5	C4	C3	C2	0.4°	0.1°
C4	C5	C6	C1	0.3°	0.1°
C4	C5	C6	H3	179.7°	179.9°
C5	C4	C3	H8	179.6°	180.0°
C3	C4	C5	C6	0.1°	0.0°
C4	C3	C2	H8	180.0°	179.9°
C4	C3	C2	C1	0.6°	0.2°
C3	C4	C5	H2	179.9°	179.9°
C4	C3	C2	H9	179.4°	180.0°
C5	C6	C1	H3	180.0°	180.0°
C5	C6	C1	C2	0.0°	0.0°
C5	C6	C1	C	179.7°	180.0°
C6	C5	C4	H1	179.9°	179.8°
C3	C2	C1	C6	0.5°	0.2°
C3	C2	C1	H9	180.0°	179.8°
C3	C2	C1	C	179.9°	179.9°
C2	C3	C4	H1	179.6°	179.7°
C9	C8	N	C7	179.0°	180.0°
C8	N	C7	C	178.1°	179.9°
N	C8	C9	N1	113.8°	8.2°
C6	C1	C	C7	148.0°	90.0°
C6	C1	C2	C	179.7°	179.9°
C1	C6	C5	H2	179.7°	180.0°
C6	C1	C	H6	91.8°	30.0°
C6	C1	C	H7	27.8°	150.0°
C6	C1	C2	H9	179.6°	180.0°
C7	C	C1	C2	32.3°	89.9°
C7	C	C1	H6	120.2°	120.0°
C7	C	C1	H7	120.2°	120.0°
C7	C	H6	H7	119.3°	120.0°
N	C7	C	C1	118.4°	90.0°
N	C7	C	H6	1.8°	150.0°
N	C7	C	H7	121.3°	29.9°
C2	C1	C6	H3	180.0°	180.0°
C2	C1	C	H6	87.9°	150.1°
C2	C1	C	H7	152.5°	30.0°
C1	C2	C3	H8	179.4°	179.9°
C	C1	C6	H3	0.4°	0.0°
C1	C	H6	H7	119.3°	120.0°
C	C1	C2	H9	0.1°	0.1°
H1	C4	C5	H2	0.1°	0.3°
H1	C4	C3	H8	0.4°	0.2°
H2	C5	C6	H3	0.3°	0.0°
H8	C3	C2	H9	0.6°	0.1°

227111

PDB entries from 2024-11-06

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