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Summary Geometry Related PDB entries

I6D

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	C2	sing	1.51Å	1.51Å
C2	C9	doub	1.37Å	1.39Å	Aromatic
C2	C3	sing	1.38Å	1.39Å	Aromatic
C9	C8	sing	1.40Å	1.38Å	Aromatic
C3	C4	doub	1.38Å	1.38Å	Aromatic
C7	N3	sing	1.38Å	1.36Å	Aromatic
C7	N2	doub	1.30Å	1.30Å	Aromatic
C8	N3	sing	1.39Å	1.40Å	Aromatic
C8	C5	doub	1.39Å	1.41Å	Aromatic
N3	C6	sing	1.36Å	1.37Å	Aromatic
N2	N1	sing	1.29Å	1.41Å	Aromatic
C4	C5	sing	1.39Å	1.39Å	Aromatic
C5	S1	sing	1.77Å	1.76Å	Aromatic
C6	N1	doub	1.31Å	1.31Å	Aromatic
C6	S1	sing	1.77Å	1.73Å	Aromatic
C4	H1	sing	1.08Å	1.08Å
C7	H2	sing	1.08Å	1.08Å
C9	H3	sing	1.08Å	1.08Å
C3	H4	sing	1.08Å	1.08Å
C1	H5	sing	1.09Å	1.10Å
C1	H6	sing	1.09Å	1.10Å
C1	H7	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	C2	C9	120.0°	119.6°
C1	C2	C3	120.5°	119.5°
C2	C1	H5	109.5°	109.5°
C2	C1	H6	109.5°	109.5°
C2	C1	H7	109.5°	109.4°
C9	C2	C3	119.6°	120.9°
C2	C9	C8	119.5°	120.7°
C2	C9	H3	120.3°	119.7°
C2	C3	C4	121.7°	119.4°
C2	C3	H4	119.2°	120.3°
C9	C8	N3	128.9°	127.2°
C9	C8	C5	120.5°	117.7°
C8	C9	H3	120.3°	119.6°
C3	C4	C5	118.5°	119.9°
C3	C4	H1	120.7°	120.1°
C4	C3	H4	119.1°	120.2°
N3	C7	N2	109.4°	107.5°
C7	N3	C8	141.0°	138.5°
C7	N3	C6	106.2°	104.6°
N3	C7	H2	125.3°	126.2°
C7	N2	N1	108.1°	110.1°
N2	C7	H2	125.3°	126.3°
N3	C8	C5	110.6°	115.2°
C8	N3	C6	112.7°	116.9°
C8	C5	C4	120.2°	121.5°
C8	C5	S1	113.6°	106.3°
N3	C6	N1	109.8°	108.3°
N3	C6	S1	115.0°	106.8°
N2	N1	C6	106.5°	109.4°
C4	C5	S1	126.1°	132.2°
C5	C4	H1	120.7°	120.0°
C5	S1	C6	88.0°	94.8°
N1	C6	S1	135.2°	144.9°
H5	C1	H6	109.4°	109.4°
H5	C1	H7	109.4°	109.5°
H6	C1	H7	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	C2	C9	C3	179.3°	179.7°
C1	C2	C9	C8	179.8°	180.0°
C1	C2	C3	C4	180.0°	179.8°
C1	C2	C9	H3	0.2°	0.0°
C1	C2	C3	H4	0.0°	0.2°
C2	C1	H5	H6	120.0°	120.0°
C2	C1	H5	H7	120.0°	120.0°
C2	C1	H6	H7	120.0°	120.0°
C2	C9	C8	H3	180.0°	180.0°
C9	C2	C3	C4	0.7°	0.5°
C2	C9	C8	N3	178.2°	180.0°
C2	C9	C8	C5	0.5°	0.0°
C9	C2	C3	H4	179.3°	179.9°
C9	C2	C1	H5	90.3°	90.0°
C9	C2	C1	H6	149.6°	150.0°
C9	C2	C1	H7	29.6°	30.0°
C3	C2	C9	C8	0.9°	0.3°
C2	C3	C4	H4	180.0°	179.5°
C2	C3	C4	C5	0.1°	0.5°
C2	C3	C4	H1	179.9°	179.8°
C3	C2	C9	H3	179.1°	179.8°
C3	C2	C1	H5	90.4°	89.7°
C3	C2	C1	H6	29.6°	30.2°
C3	C2	C1	H7	149.6°	150.2°
C9	C8	N3	C7	3.5°	0.1°
C9	C8	N3	C5	178.8°	180.0°
C9	C8	N3	C6	179.0°	180.0°
C9	C8	C5	C4	0.1°	0.0°
C9	C8	C5	S1	178.4°	180.0°
C3	C4	C5	C8	0.3°	0.3°
C3	C4	C5	H1	180.0°	179.7°
C3	C4	C5	S1	178.4°	179.8°
N3	C7	N2	H2	180.0°	179.8°
C7	N3	C8	C6	175.6°	179.9°
C7	N3	C8	C5	175.3°	179.9°
N3	C7	N2	N1	0.8°	0.1°
C7	N3	C6	N1	1.7°	0.0°
C7	N3	C6	S1	179.4°	180.0°
N2	C7	N3	C8	176.2°	180.0°
N2	C7	N3	C6	0.5°	0.1°
C7	N2	N1	C6	1.9°	0.0°
N3	C8	C5	C4	179.0°	180.0°
N3	C8	C5	S1	2.6°	0.0°
C8	N3	C6	N1	178.8°	180.0°
C8	N3	C6	S1	2.4°	0.0°
C8	N3	C7	H2	3.8°	0.1°
N3	C8	C9	H3	1.8°	0.0°
C5	C8	N3	C6	0.2°	0.0°
C8	C5	C4	S1	178.1°	179.9°
C8	C5	S1	C6	3.3°	0.0°
C8	C5	C4	H1	179.7°	180.0°
C5	C8	C9	H3	179.5°	180.0°
N3	C6	N1	N2	2.1°	0.0°
N3	C6	S1	C5	3.2°	0.0°
N3	C6	N1	S1	178.6°	179.9°
C6	N3	C7	H2	179.6°	179.9°
N2	N1	C6	S1	179.3°	179.9°
N1	N2	C7	H2	179.2°	179.9°
C4	C5	S1	C6	178.5°	180.0°
C5	C4	C3	H4	179.9°	180.0°
C5	S1	C6	N1	178.3°	180.0°
S1	C5	C4	H1	1.6°	0.1°
H1	C4	C3	H4	0.1°	0.2°
H5	C1	H6	H7	119.9°	120.0°

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PDB entries from 2024-11-13

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