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Summary Geometry Related PDB entries

2JE

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N3	C2	sing	1.36Å	1.37Å	Aromatic
N3	C4	sing	1.36Å	1.36Å	Aromatic
C2	N4	doub	1.30Å	1.37Å	Aromatic
C4	C5	doub	1.36Å	1.47Å	Aromatic
N4	C5	sing	1.36Å	1.36Å	Aromatic
C5	C22	sing	1.47Å	1.50Å
C22	O6	doub	1.22Å	1.24Å
C22	S1	sing	1.76Å	1.80Å
S1	C11	sing	1.81Å	1.84Å
C11	C12	sing	1.53Å	1.55Å
C12	N1	sing	1.47Å	1.45Å
C4	H1	sing	1.08Å	1.08Å
N3	H2	sing	0.97Å	1.00Å
C2	H3	sing	1.08Å	1.08Å
C11	H5	sing	1.09Å	1.10Å
C11	H6	sing	1.09Å	1.10Å
C12	H7	sing	1.09Å	1.10Å
C12	H8	sing	1.09Å	1.10Å
N1	H9	sing	1.01Å	1.00Å
N1	H4	sing	1.01Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C2	N3	C4	108.5°	107.6°
N3	C2	N4	110.2°	109.0°
C2	N3	H2	125.7°	126.2°
N3	C2	H3	124.9°	125.4°
N3	C4	C5	106.3°	106.8°
N3	C4	H1	126.8°	126.6°
C4	N3	H2	125.7°	126.2°
C2	N4	C5	108.2°	109.0°
N4	C2	H3	124.9°	125.6°
C4	C5	N4	106.8°	107.6°
C4	C5	C22	132.4°	126.2°
C5	C4	H1	126.8°	126.6°
N4	C5	C22	120.8°	126.2°
C5	C22	O6	120.5°	120.0°
C5	C22	S1	118.4°	120.0°
O6	C22	S1	121.2°	120.0°
C22	S1	C11	96.9°	100.0°
S1	C11	C12	115.4°	109.5°
S1	C11	H5	108.0°	109.4°
S1	C11	H6	107.9°	109.5°
C11	C12	N1	110.3°	109.5°
C12	C11	H5	107.9°	109.5°
C12	C11	H6	108.0°	109.5°
C11	C12	H7	109.3°	109.4°
C11	C12	H8	109.3°	109.5°
N1	C12	H7	109.2°	109.5°
N1	C12	H8	109.2°	109.5°
C12	N1	H9	109.5°	111.0°
C12	N1	H4	109.5°	111.0°
H5	C11	H6	109.5°	109.5°
H7	C12	H8	109.5°	109.5°
H9	N1	H4	109.5°	111.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C2	N3	C4	H2	180.0°	180.0°
N3	C2	N4	H3	180.0°	180.0°
C2	N3	C4	C5	0.2°	0.0°
N3	C2	N4	C5	0.3°	0.0°
C2	N3	C4	H1	179.8°	179.7°
C4	N3	C2	N4	0.3°	0.0°
N3	C4	C5	H1	180.0°	179.7°
N3	C4	C5	N4	0.1°	0.0°
N3	C4	C5	C22	179.8°	179.8°
C4	N3	C2	H3	179.7°	180.0°
C2	N4	C5	C4	0.1°	0.0°
C2	N4	C5	C22	180.0°	179.8°
N4	C2	N3	H2	179.6°	180.0°
C4	C5	N4	C22	179.9°	179.8°
C4	C5	C22	O6	0.0°	0.0°
C4	C5	C22	S1	179.3°	180.0°
C5	C4	N3	H2	179.7°	180.0°
N4	C5	C22	O6	179.9°	179.7°
N4	C5	C22	S1	0.7°	0.3°
N4	C5	C4	H1	179.9°	179.7°
C5	N4	C2	H3	179.7°	180.0°
C5	C22	O6	S1	179.3°	180.0°
C5	C22	S1	C11	179.9°	180.0°
C22	C5	C4	H1	0.2°	0.0°
O6	C22	S1	C11	0.6°	0.0°
C22	S1	C11	C12	103.8°	180.0°
C22	S1	C11	H5	17.1°	60.0°
C22	S1	C11	H6	135.4°	60.0°
S1	C11	C12	H5	120.9°	120.0°
S1	C11	C12	H6	120.8°	120.0°
S1	C11	C12	N1	120.9°	180.0°
S1	C11	H5	H6	117.3°	120.0°
S1	C11	C12	H7	0.8°	60.0°
S1	C11	C12	H8	118.9°	60.0°
C11	C12	N1	H7	120.1°	120.0°
C11	C12	N1	H8	120.1°	120.0°
C12	C11	H5	H6	117.3°	120.0°
C11	C12	H7	H8	119.6°	120.0°
C11	C12	N1	H9	180.0°	180.0°
C11	C12	N1	H4	60.0°	56.1°
N1	C12	C11	H5	118.2°	60.1°
N1	C12	C11	H6	0.1°	60.0°
N1	C12	H7	H8	119.6°	120.1°
C12	N1	H9	H4	120.0°	124.0°
H1	C4	N3	H2	0.3°	0.3°
H2	N3	C2	H3	0.4°	0.0°
H5	C11	C12	H7	121.7°	179.9°
H5	C11	C12	H8	2.0°	60.0°
H6	C11	C12	H7	120.0°	60.1°
H6	C11	C12	H8	120.2°	180.0°
H7	C12	N1	H9	59.9°	60.0°
H7	C12	N1	H4	179.9°	176.1°
H8	C12	N1	H9	59.9°	60.0°
H8	C12	N1	H4	60.2°	63.9°

224572

PDB entries from 2024-09-04

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