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Summary Geometry Related PDB entries

NO9

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O5	C5	doub	1.22Å	1.25Å
C5	O4	sing	1.35Å	1.26Å
C5	C2	sing	1.47Å	1.43Å
C7	C4	sing	1.51Å	1.51Å
O3	S	doub	1.42Å	1.44Å
C2	C4	doub	1.36Å	1.48Å	Aromatic
C2	C1	sing	1.47Å	1.47Å	Aromatic
C4	O1	sing	1.34Å	1.39Å	Aromatic
C1	S	sing	1.76Å	1.69Å
C1	C3	doub	1.34Å	1.47Å	Aromatic
S	N1	sing	1.66Å	1.62Å
S	O2	doub	1.42Å	1.46Å
O1	C3	sing	1.34Å	1.40Å	Aromatic
C3	C6	sing	1.51Å	1.51Å
O4	H1	sing	0.97Å	0.95Å
C7	H2	sing	1.09Å	1.10Å
C7	H3	sing	1.09Å	1.10Å
C7	H4	sing	1.09Å	1.10Å
C6	H5	sing	1.09Å	1.10Å
C6	H6	sing	1.09Å	1.10Å
C6	H7	sing	1.09Å	1.10Å
N1	H8	sing	0.97Å	1.00Å
N1	H9	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O5	C5	O4	120.2°	120.0°
O5	C5	C2	125.1°	120.0°
O4	C5	C2	114.7°	120.0°
C5	O4	H1	109.5°	117.0°
C5	C2	C4	128.1°	127.2°
C5	C2	C1	123.9°	127.1°
C7	C4	C2	133.4°	125.8°
C7	C4	O1	117.5°	125.8°
C4	C7	H2	109.5°	109.5°
C4	C7	H3	109.5°	109.5°
C4	C7	H4	109.5°	109.4°
O3	S	C1	107.8°	106.4°
O3	S	N1	113.8°	106.4°
O3	S	O2	108.1°	123.1°
C4	C2	C1	106.2°	105.6°
C2	C4	O1	109.0°	108.4°
C2	C1	S	123.3°	127.1°
C2	C1	C3	105.4°	105.9°
C4	O1	C3	109.4°	110.9°
S	C1	C3	130.1°	127.0°
C1	S	N1	114.0°	107.2°
C1	S	O2	106.9°	106.4°
C1	C3	O1	109.3°	109.1°
C1	C3	C6	134.1°	125.4°
N1	S	O2	105.8°	106.4°
S	N1	H8	109.5°	120.0°
S	N1	H9	109.5°	120.0°
O1	C3	C6	116.6°	125.4°
C3	C6	H5	109.5°	109.5°
C3	C6	H6	109.5°	109.5°
C3	C6	H7	109.5°	109.5°
H2	C7	H3	109.4°	109.5°
H2	C7	H4	109.5°	109.5°
H3	C7	H4	109.5°	109.5°
H5	C6	H6	109.5°	109.5°
H5	C6	H7	109.4°	109.5°
H6	C6	H7	109.5°	109.5°
H8	N1	H9	109.4°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O5	C5	O4	C2	178.9°	180.0°
O5	C5	C2	C4	66.7°	90.1°
O5	C5	C2	C1	130.6°	90.3°
O5	C5	O4	H1	0.0°	0.0°
O4	C5	C2	C4	114.4°	89.9°
O4	C5	C2	C1	48.2°	89.7°
C5	C2	C4	C7	12.0°	0.0°
C5	C2	C4	C1	165.1°	179.7°
C5	C2	C4	O1	172.5°	180.0°
C5	C2	C1	S	17.1°	0.0°
C5	C2	C1	C3	173.9°	179.8°
C2	C5	O4	H1	178.9°	180.0°
C7	C4	C2	O1	175.5°	180.0°
C7	C4	C2	C1	177.0°	179.7°
C7	C4	O1	C3	179.9°	180.0°
C4	C7	H2	H3	120.0°	120.0°
C4	C7	H2	H4	120.0°	119.9°
C4	C7	H3	H4	120.0°	119.9°
O3	S	C1	C2	49.2°	23.6°
O3	S	C1	N1	127.4°	113.6°
O3	S	C1	O2	116.0°	132.9°
O3	S	C1	C3	117.0°	156.6°
O3	S	N1	O2	118.6°	132.9°
O3	S	N1	H8	180.0°	96.5°
O3	S	N1	H9	60.0°	83.6°
C4	C2	C1	S	177.1°	179.7°
C4	C2	C1	C3	8.0°	0.5°
C2	C4	O1	C3	3.7°	0.0°
C2	C4	C7	H2	175.2°	90.0°
C2	C4	C7	H3	55.2°	150.0°
C2	C4	C7	H4	64.8°	30.0°
C1	C2	C4	O1	7.5°	0.3°
C2	C1	S	C3	166.2°	179.8°
C2	C1	S	N1	78.2°	90.0°
C2	C1	S	O2	165.2°	156.5°
C2	C1	C3	O1	6.1°	0.5°
C2	C1	C3	C6	175.8°	179.8°
C4	O1	C3	C1	1.5°	0.3°
C4	O1	C3	C6	180.0°	180.0°
O1	C4	C7	H2	0.0°	90.0°
O1	C4	C7	H3	120.0°	30.0°
O1	C4	C7	H4	120.0°	150.0°
C1	S	N1	O2	117.2°	113.5°
S	C1	C3	O1	174.1°	179.7°
S	C1	C3	C6	7.8°	0.0°
C1	S	N1	H8	55.7°	150.0°
C1	S	N1	H9	64.2°	30.0°
C3	C1	S	N1	115.6°	89.8°
C3	C1	S	O2	0.9°	23.7°
C1	C3	O1	C6	178.5°	179.7°
C1	C3	C6	H5	178.0°	179.7°
C1	C3	C6	H6	58.0°	59.6°
C1	C3	C6	H7	62.0°	60.3°
S	N1	H8	H9	120.0°	180.0°
O2	S	N1	H8	61.5°	36.4°
O2	S	N1	H9	178.6°	143.5°
O1	C3	C6	H5	0.0°	0.0°
O1	C3	C6	H6	120.0°	120.0°
O1	C3	C6	H7	120.0°	120.0°
C3	C6	H5	H6	120.0°	120.0°
C3	C6	H5	H7	120.0°	120.0°
C3	C6	H6	H7	120.0°	120.0°
H2	C7	H3	H4	120.0°	120.0°
H5	C6	H6	H7	120.0°	120.0°

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PDB entries from 2024-07-17

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