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Summary Geometry Related PDB entries

JYX

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C7	N4	doub	1.32Å	1.34Å	Aromatic
C7	C6	sing	1.39Å	1.39Å	Aromatic
N4	C8	sing	1.32Å	1.32Å	Aromatic
C6	C5	doub	1.38Å	1.39Å	Aromatic
C8	C4	doub	1.41Å	1.38Å	Aromatic
C8	N1	sing	1.38Å	1.38Å	Aromatic
C5	C4	sing	1.40Å	1.39Å	Aromatic
C2	N1	sing	1.46Å	1.47Å
C2	C1	sing	1.53Å	1.50Å
C4	N3	sing	1.36Å	1.39Å	Aromatic
N1	C3	sing	1.37Å	1.38Å	Aromatic
N3	C3	doub	1.31Å	1.32Å	Aromatic
C3	N2	sing	1.38Å	1.33Å
C1	H1	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
C1	H3	sing	1.09Å	1.10Å
C2	H4	sing	1.09Å	1.10Å
C2	H5	sing	1.09Å	1.10Å
N2	H6	sing	0.97Å	1.00Å
N2	H7	sing	0.97Å	1.00Å
C5	H8	sing	1.08Å	1.08Å
C6	H9	sing	1.08Å	1.08Å
C7	H10	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N4	C7	C6	123.9°	121.4°
C7	N4	C8	114.1°	121.6°
N4	C7	H10	118.1°	119.4°
C7	C6	C5	120.5°	119.5°
C7	C6	H9	119.8°	120.3°
C6	C7	H10	118.0°	119.2°
N4	C8	C4	127.2°	120.4°
N4	C8	N1	126.8°	133.6°
C6	C5	C4	116.0°	118.2°
C6	C5	H8	122.0°	120.9°
C5	C6	H9	119.8°	120.3°
C4	C8	N1	106.0°	105.9°
C8	C4	C5	118.3°	119.0°
C8	C4	N3	110.3°	107.3°
C8	N1	C2	125.2°	126.3°
C8	N1	C3	106.2°	107.4°
C5	C4	N3	131.4°	133.7°
C4	C5	H8	122.0°	121.0°
N1	C2	C1	112.0°	109.5°
C2	N1	C3	128.6°	126.3°
N1	C2	H4	108.9°	109.5°
N1	C2	H5	108.9°	109.5°
C2	C1	H1	109.5°	109.5°
C2	C1	H2	109.5°	109.5°
C2	C1	H3	109.5°	109.5°
C1	C2	H4	108.8°	109.5°
C1	C2	H5	108.8°	109.5°
C4	N3	C3	104.5°	109.4°
N1	C3	N3	112.9°	109.9°
N1	C3	N2	123.1°	125.0°
N3	C3	N2	124.0°	125.1°
C3	N2	H6	109.5°	120.0°
C3	N2	H7	109.5°	120.0°
H1	C1	H2	109.5°	109.4°
H1	C1	H3	109.5°	109.5°
H2	C1	H3	109.5°	109.5°
H4	C2	H5	109.4°	109.4°
H6	N2	H7	109.5°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N4	C7	C6	H10	180.0°	179.7°
N4	C7	C6	C5	0.1°	0.0°
C7	N4	C8	C4	0.3°	0.6°
C7	N4	C8	N1	180.0°	179.7°
N4	C7	C6	H9	179.9°	180.0°
C6	C7	N4	C8	0.4°	0.3°
C7	C6	C5	H9	180.0°	180.0°
C7	C6	C5	C4	0.3°	0.0°
C7	C6	C5	H8	179.7°	180.0°
N4	C8	C4	N1	179.7°	179.3°
N4	C8	C4	C5	0.1°	0.5°
N4	C8	N1	C2	1.1°	0.7°
N4	C8	C4	N3	179.6°	179.7°
N4	C8	N1	C3	179.3°	179.5°
C8	N4	C7	H10	179.7°	180.0°
C6	C5	C4	C8	0.4°	0.2°
C6	C5	C4	H8	180.0°	180.0°
C6	C5	C4	N3	179.8°	180.0°
C5	C6	C7	H10	179.9°	179.7°
C8	C4	C5	N3	179.4°	179.8°
C4	C8	N1	C2	179.2°	179.8°
C4	C8	N1	C3	0.5°	0.3°
C8	C4	N3	C3	0.3°	0.2°
C8	C4	C5	H8	179.6°	179.7°
N1	C8	C4	C5	179.7°	179.8°
C8	N1	C2	C3	179.6°	179.8°
C8	N1	C2	C1	76.3°	90.2°
N1	C8	C4	N3	0.1°	0.4°
C8	N1	C3	N3	0.7°	0.2°
C8	N1	C3	N2	179.3°	179.8°
C8	N1	C2	H4	44.1°	149.7°
C8	N1	C2	H5	163.3°	29.8°
C5	C4	N3	C3	179.2°	180.0°
C4	C5	C6	H9	179.7°	180.0°
N1	C2	C1	H4	120.4°	120.1°
N1	C2	C1	H5	120.4°	120.0°
C2	N1	C3	N3	179.0°	180.0°
C2	N1	C3	N2	0.3°	0.0°
N1	C2	C1	H1	180.0°	180.0°
N1	C2	C1	H2	60.0°	60.0°
N1	C2	C1	H3	60.0°	60.0°
N1	C2	H4	H5	118.9°	120.0°
C1	C2	N1	C3	104.1°	90.0°
C2	C1	H1	H2	120.0°	120.0°
C2	C1	H1	H3	120.0°	120.1°
C2	C1	H2	H3	120.0°	120.0°
C1	C2	H4	H5	118.8°	119.9°
C4	N3	C3	N1	0.6°	0.0°
C4	N3	C3	N2	179.2°	180.0°
N3	C4	C5	H8	0.2°	0.0°
N1	C3	N3	N2	178.6°	180.0°
C3	N1	C2	H4	135.5°	30.0°
C3	N1	C2	H5	16.3°	150.0°
N1	C3	N2	H6	178.5°	0.0°
N1	C3	N2	H7	61.5°	179.9°
N3	C3	N2	H6	0.0°	179.9°
N3	C3	N2	H7	120.0°	0.0°
C3	N2	H6	H7	120.0°	179.9°
H1	C1	H2	H3	120.0°	119.9°
H1	C1	C2	H4	59.6°	59.9°
H1	C1	C2	H5	59.6°	60.0°
H2	C1	C2	H4	179.6°	60.1°
H2	C1	C2	H5	60.4°	180.0°
H3	C1	C2	H4	60.4°	179.9°
H3	C1	C2	H5	179.6°	60.0°
H8	C5	C6	H9	0.3°	0.0°
H9	C6	C7	H10	0.1°	0.3°

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PDB entries from 2024-08-07

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