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Summary Geometry Related PDB entries

S9J

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
N1	N	sing	1.37Å	1.41Å
N	C8	sing	1.35Å	1.40Å
C8	O2	doub	1.21Å	1.22Å
C8	C7	sing	1.51Å	1.52Å
C7	O1	sing	1.43Å	1.42Å
C	O	sing	1.43Å	1.43Å
O1	C6	sing	1.36Å	1.38Å
O	C1	sing	1.36Å	1.38Å
C6	C1	doub	1.39Å	1.41Å	Aromatic
C6	C5	sing	1.39Å	1.40Å	Aromatic
C1	C2	sing	1.38Å	1.41Å	Aromatic
C5	C4	doub	1.38Å	1.39Å	Aromatic
C2	C3	doub	1.38Å	1.40Å	Aromatic
C4	C3	sing	1.38Å	1.39Å	Aromatic
N1	H1	sing	1.01Å	1.00Å
N1	H2	sing	1.01Å	1.00Å
C4	H3	sing	1.08Å	1.08Å
C5	H4	sing	1.08Å	1.08Å
C7	H5	sing	1.09Å	1.10Å
C7	H6	sing	1.09Å	1.10Å
N	H7	sing	0.97Å	1.00Å
C	H8	sing	1.09Å	1.10Å
C	H9	sing	1.09Å	1.10Å
C	H10	sing	1.09Å	1.10Å
C2	H11	sing	1.08Å	1.08Å
C3	H12	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
N1	N	C8	124.9°	120.0°
N	N1	H1	109.5°	111.0°
N	N1	H2	109.4°	111.0°
N1	N	H7	117.5°	120.0°
N	C8	O2	121.5°	120.0°
N	C8	C7	120.2°	120.0°
C8	N	H7	117.6°	120.0°
O2	C8	C7	118.4°	120.0°
C8	C7	O1	108.2°	109.5°
C8	C7	H5	109.8°	109.5°
C8	C7	H6	109.8°	109.4°
C7	O1	C6	113.9°	117.0°
O1	C7	H5	109.8°	109.5°
O1	C7	H6	109.8°	109.5°
C	O	C1	122.1°	117.0°
O	C	H8	109.5°	109.5°
O	C	H9	109.5°	109.5°
O	C	H10	109.5°	109.5°
O1	C6	C1	118.8°	120.1°
O1	C6	C5	120.1°	120.0°
O	C1	C6	117.9°	120.0°
O	C1	C2	123.3°	120.1°
C1	C6	C5	121.0°	119.9°
C6	C1	C2	118.8°	119.9°
C6	C5	C4	119.2°	120.0°
C6	C5	H4	120.4°	120.0°
C1	C2	C3	119.7°	120.0°
C1	C2	H11	120.1°	120.1°
C5	C4	C3	120.5°	120.1°
C5	C4	H3	119.8°	119.9°
C4	C5	H4	120.4°	120.0°
C2	C3	C4	120.8°	120.2°
C3	C2	H11	120.1°	120.0°
C2	C3	H12	119.6°	119.9°
C3	C4	H3	119.7°	120.0°
C4	C3	H12	119.6°	119.9°
H1	N1	H2	109.5°	111.0°
H5	C7	H6	109.5°	109.5°
H8	C	H9	109.5°	109.5°
H8	C	H10	109.5°	109.4°
H9	C	H10	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
N1	N	C8	H7	180.0°	180.0°
N1	N	C8	O2	0.3°	0.1°
N1	N	C8	C7	180.0°	180.0°
N	N1	H1	H2	120.0°	123.9°
N	C8	O2	C7	179.7°	179.9°
N	C8	C7	O1	65.9°	180.0°
C8	N	N1	H1	180.0°	56.1°
C8	N	N1	H2	60.0°	179.9°
N	C8	C7	H5	174.3°	59.9°
N	C8	C7	H6	53.9°	60.0°
O2	C8	C7	O1	114.3°	0.1°
O2	C8	C7	H5	5.5°	120.0°
O2	C8	C7	H6	125.9°	120.1°
O2	C8	N	H7	179.7°	180.0°
C8	C7	O1	H5	119.8°	120.0°
C8	C7	O1	H6	119.8°	120.0°
C8	C7	O1	C6	171.1°	180.0°
C8	C7	H5	H6	120.6°	119.9°
C7	C8	N	H7	0.0°	0.0°
C7	O1	C6	C1	119.5°	180.0°
C7	O1	C6	C5	63.3°	0.0°
O1	C7	H5	H6	120.6°	120.0°
C	O	C1	C6	168.3°	180.0°
C	O	C1	C2	11.9°	0.0°
O	C	H8	H9	120.0°	120.1°
O	C	H8	H10	120.0°	120.0°
O	C	H9	H10	120.0°	120.0°
O1	C6	C1	O	3.5°	0.0°
O1	C6	C1	C5	177.2°	180.0°
O1	C6	C1	C2	176.3°	180.0°
O1	C6	C5	C4	176.2°	180.0°
O1	C6	C5	H4	3.8°	0.0°
C6	O1	C7	H5	51.3°	60.0°
C6	O1	C7	H6	69.0°	60.0°
O	C1	C6	C2	179.8°	179.9°
O	C1	C6	C5	179.3°	179.9°
O	C1	C2	C3	179.9°	180.0°
C1	O	C	H8	180.0°	180.0°
C1	O	C	H9	60.0°	60.0°
C1	O	C	H10	60.0°	60.0°
O	C1	C2	H11	0.1°	0.1°
C1	C6	C5	C4	0.9°	0.0°
C6	C1	C2	C3	0.3°	0.0°
C1	C6	C5	H4	179.1°	180.0°
C6	C1	C2	H11	179.7°	180.0°
C5	C6	C1	C2	0.9°	0.0°
C6	C5	C4	H4	180.0°	179.9°
C6	C5	C4	C3	0.3°	0.0°
C6	C5	C4	H3	179.7°	179.7°
C1	C2	C3	H11	180.0°	179.9°
C1	C2	C3	C4	0.3°	0.0°
C1	C2	C3	H12	179.7°	179.7°
C5	C4	C3	C2	0.3°	0.0°
C5	C4	C3	H3	180.0°	179.7°
C5	C4	C3	H12	179.7°	179.7°
C2	C3	C4	H12	180.0°	179.7°
C2	C3	C4	H3	179.7°	179.7°
C3	C4	C5	H4	179.7°	180.0°
C4	C3	C2	H11	179.7°	180.0°
H1	N1	N	H7	0.0°	123.9°
H2	N1	N	H7	120.0°	0.0°
H3	C4	C5	H4	0.3°	0.4°
H3	C4	C3	H12	0.3°	0.0°
H8	C	H9	H10	120.0°	120.0°
H11	C2	C3	H12	0.3°	0.3°

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PDB entries from 2024-07-31

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