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Summary Geometry Related PDB entries

D9Z

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O2	S1	doub	1.42Å	1.43Å
S1	O1	doub	1.42Å	1.43Å
S1	N3	sing	1.66Å	1.59Å
S1	C8	sing	1.76Å	1.65Å
C8	S2	sing	1.71Å	1.71Å	Aromatic
C8	N2	doub	1.29Å	1.35Å	Aromatic
S2	C7	sing	1.76Å	1.73Å	Aromatic
N2	N1	sing	1.26Å	1.37Å	Aromatic
N1	C7	doub	1.31Å	1.34Å	Aromatic
C7	C1	sing	1.48Å	1.40Å	Aromatic
C1	C6	doub	1.39Å	1.39Å	Aromatic
C1	C2	sing	1.40Å	1.36Å	Aromatic
C6	C5	sing	1.38Å	1.41Å	Aromatic
C2	C3	doub	1.38Å	1.38Å	Aromatic
C2	CL1	sing	1.74Å	1.70Å
C3	C4	sing	1.38Å	1.40Å	Aromatic
C4	C5	doub	1.38Å	1.38Å	Aromatic
N3	HN3	sing	0.97Å	1.00Å
N3	HN3A	sing	0.97Å	1.00Å
C6	H6	sing	1.08Å	1.08Å
C3	H3	sing	1.08Å	1.08Å
C4	H4	sing	1.08Å	1.08Å
C5	H5	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O2	S1	O1	113.8°	123.2°
O2	S1	N3	110.7°	106.4°
O2	S1	C8	105.2°	106.4°
O1	S1	N3	109.5°	106.4°
O1	S1	C8	104.3°	106.4°
N3	S1	C8	113.2°	107.2°
S1	N3	HN3	109.5°	120.0°
S1	N3	HN3A	109.4°	120.0°
S1	C8	S2	130.9°	125.5°
S1	C8	N2	115.7°	125.5°
S2	C8	N2	113.3°	108.9°
C8	S2	C7	90.0°	89.4°
C8	N2	N1	110.7°	117.9°
S2	C7	N1	109.9°	107.5°
S2	C7	C1	129.0°	126.2°
N2	N1	C7	116.0°	116.3°
N1	C7	C1	121.1°	126.2°
C7	C1	C6	121.0°	120.1°
C7	C1	C2	119.3°	120.1°
C6	C1	C2	119.7°	119.7°
C1	C6	C5	118.3°	119.9°
C1	C6	H6	120.9°	120.1°
C1	C2	C3	123.8°	119.8°
C1	C2	CL1	132.1°	120.1°
C6	C5	C4	120.5°	120.2°
C5	C6	H6	120.8°	120.0°
C6	C5	H5	119.7°	120.0°
C3	C2	CL1	104.1°	120.1°
C2	C3	C4	116.7°	120.2°
C2	C3	H3	121.6°	119.9°
C3	C4	C5	120.9°	120.3°
C4	C3	H3	121.7°	119.9°
C3	C4	H4	119.6°	119.9°
C5	C4	H4	119.5°	119.9°
C4	C5	H5	119.7°	119.9°
HN3	N3	HN3A	109.5°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O2	S1	O1	N3	124.5°	123.0°
O2	S1	O1	C8	114.0°	122.9°
O2	S1	N3	C8	117.8°	113.5°
O2	S1	C8	S2	6.7°	66.5°
O2	S1	C8	N2	177.2°	113.9°
O2	S1	N3	HN3	76.8°	113.5°
O2	S1	N3	HN3A	163.2°	66.5°
O1	S1	N3	C8	115.9°	113.5°
O1	S1	C8	S2	126.7°	66.4°
O1	S1	C8	N2	57.2°	113.2°
O1	S1	N3	HN3	156.9°	113.5°
O1	S1	N3	HN3A	36.9°	66.4°
N3	S1	C8	S2	114.3°	180.0°
N3	S1	C8	N2	61.8°	0.4°
S1	N3	HN3	HN3A	120.0°	180.0°
S1	C8	S2	N2	176.2°	179.7°
S1	C8	S2	C7	173.8°	180.0°
S1	C8	N2	N1	173.8°	180.0°
C8	S1	N3	HN3	41.0°	0.0°
C8	S1	N3	HN3A	79.0°	180.0°
S2	C8	N2	N1	3.0°	0.3°
C8	S2	C7	N1	1.0°	0.2°
C8	S2	C7	C1	179.0°	180.0°
N2	C8	S2	C7	2.4°	0.3°
C8	N2	N1	C7	2.3°	0.1°
S2	C7	N1	N2	0.5°	0.1°
S2	C7	N1	C1	178.2°	179.8°
S2	C7	C1	C6	178.9°	180.0°
S2	C7	C1	C2	0.4°	0.3°
N2	N1	C7	C1	177.7°	179.9°
N1	C7	C1	C6	1.0°	0.2°
N1	C7	C1	C2	178.2°	180.0°
C7	C1	C6	C2	179.2°	179.7°
C7	C1	C6	C5	179.7°	180.0°
C7	C1	C2	C3	178.6°	180.0°
C7	C1	C2	CL1	0.8°	0.0°
C7	C1	C6	H6	0.3°	0.1°
C1	C6	C5	H6	180.0°	179.9°
C6	C1	C2	C3	2.1°	0.3°
C6	C1	C2	CL1	178.4°	179.7°
C1	C6	C5	C4	0.4°	0.0°
C1	C6	C5	H5	179.6°	180.0°
C2	C1	C6	C5	1.1°	0.3°
C1	C2	C3	CL1	179.6°	180.0°
C1	C2	C3	C4	1.5°	0.0°
C2	C1	C6	H6	178.9°	179.8°
C1	C2	C3	H3	178.4°	180.0°
C6	C5	C4	C3	0.9°	0.2°
C6	C5	C4	H5	180.0°	180.0°
C6	C5	C4	H4	179.1°	180.0°
C2	C3	C4	H3	180.0°	179.9°
C2	C3	C4	C5	0.0°	0.2°
C2	C3	C4	H4	180.0°	180.0°
CL1	C2	C3	C4	178.9°	180.0°
CL1	C2	C3	H3	1.1°	0.0°
C3	C4	C5	H4	180.0°	179.8°
C3	C4	C5	H5	179.0°	179.8°
C4	C5	C6	H6	179.6°	180.0°
C5	C4	C3	H3	180.0°	179.7°
H6	C6	C5	H5	0.4°	0.0°
H3	C3	C4	H4	0.0°	0.1°
H4	C4	C5	H5	1.0°	0.1°

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PDB entries from 2024-10-09

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