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Summary Geometry Related PDB entries

WDN

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
S	C8	sing	1.70Å	1.68Å	Aromatic
S	C7	sing	1.75Å	1.70Å	Aromatic
C8	C5	doub	1.36Å	1.35Å	Aromatic
O2	C4	doub	1.22Å	1.22Å
C7	C6	doub	1.33Å	1.36Å	Aromatic
C5	C4	sing	1.47Å	1.46Å
C5	C6	sing	1.44Å	1.43Å	Aromatic
C4	N	sing	1.35Å	1.39Å
N	C1	sing	1.46Å	1.45Å
N	C	sing	1.46Å	1.47Å
C1	C2	sing	1.51Å	1.51Å
C3	O1	sing	1.45Å	1.40Å
C2	O1	sing	1.34Å	1.33Å
C2	O	doub	1.21Å	1.21Å
C7	H1	sing	1.08Å	1.08Å
C8	H2	sing	1.08Å	1.08Å
C1	H3	sing	1.09Å	1.10Å
C1	H4	sing	1.09Å	1.10Å
C6	H5	sing	1.08Å	1.08Å
C3	H6	sing	1.09Å	1.10Å
C3	H7	sing	1.09Å	1.10Å
C3	H8	sing	1.09Å	1.10Å
C	H9	sing	1.09Å	1.10Å
C	H10	sing	1.09Å	1.10Å
C	H11	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C8	S	C7	92.9°	92.4°
S	C8	C5	111.3°	110.8°
S	C8	H2	124.3°	124.6°
S	C7	C6	111.7°	110.6°
S	C7	H1	124.1°	124.7°
C8	C5	C4	123.6°	123.4°
C8	C5	C6	113.0°	113.1°
C5	C8	H2	124.3°	124.6°
O2	C4	C5	122.4°	120.0°
O2	C4	N	120.8°	120.0°
C7	C6	C5	111.1°	113.0°
C6	C7	H1	124.2°	124.6°
C7	C6	H5	124.4°	123.5°
C4	C5	C6	123.5°	123.4°
C5	C4	N	116.8°	120.0°
C5	C6	H5	124.4°	123.5°
C4	N	C1	119.0°	120.0°
C4	N	C	121.2°	120.0°
C1	N	C	117.9°	120.0°
N	C1	C2	108.1°	109.5°
N	C1	H3	109.8°	109.5°
N	C1	H4	109.8°	109.4°
N	C	H9	109.5°	109.5°
N	C	H10	109.4°	109.5°
N	C	H11	109.5°	109.5°
C1	C2	O1	122.8°	120.1°
C1	C2	O	123.3°	120.0°
C2	C1	H3	109.8°	109.5°
C2	C1	H4	109.8°	109.5°
C3	O1	C2	117.6°	117.1°
O1	C3	H6	109.5°	109.5°
O1	C3	H7	109.5°	109.5°
O1	C3	H8	109.5°	109.4°
O1	C2	O	113.9°	120.0°
H3	C1	H4	109.4°	109.5°
H6	C3	H7	109.5°	109.5°
H6	C3	H8	109.4°	109.5°
H7	C3	H8	109.5°	109.4°
H9	C	H10	109.5°	109.4°
H9	C	H11	109.4°	109.5°
H10	C	H11	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
S	C8	C5	H2	180.0°	179.5°
C8	S	C7	C6	0.0°	0.0°
S	C8	C5	C4	179.5°	179.5°
S	C8	C5	C6	0.1°	0.4°
C8	S	C7	H1	180.0°	179.7°
C7	S	C8	C5	0.1°	0.3°
S	C7	C6	H1	180.0°	179.7°
S	C7	C6	C5	0.1°	0.3°
C7	S	C8	H2	179.9°	179.8°
S	C7	C6	H5	180.0°	179.7°
C8	C5	C4	O2	47.8°	33.6°
C8	C5	C6	C7	0.1°	0.5°
C8	C5	C4	C6	179.5°	180.0°
C8	C5	C4	N	131.8°	146.5°
C8	C5	C6	H5	179.9°	179.5°
O2	C4	C5	N	179.6°	179.9°
O2	C4	C5	C6	131.7°	146.4°
O2	C4	N	C1	16.2°	4.3°
O2	C4	N	C	179.5°	175.8°
C7	C6	C5	C4	179.5°	179.5°
C7	C6	C5	H5	180.0°	180.0°
C5	C4	N	C1	164.1°	175.8°
C5	C4	N	C	0.2°	4.1°
C4	C5	C8	H2	0.5°	0.0°
C4	C5	C6	H5	0.5°	0.5°
C6	C5	C4	N	48.6°	33.5°
C5	C6	C7	H1	180.0°	179.9°
C6	C5	C8	H2	179.9°	180.0°
C4	N	C1	C	164.8°	179.9°
C4	N	C1	C2	103.7°	90.0°
C4	N	C1	H3	16.1°	30.0°
C4	N	C1	H4	136.5°	150.0°
C4	N	C	H9	180.0°	84.2°
C4	N	C	H10	60.0°	155.8°
C4	N	C	H11	60.0°	35.8°
N	C1	C2	H3	119.8°	120.0°
N	C1	C2	H4	119.8°	120.0°
N	C1	C2	O1	162.5°	180.0°
N	C1	C2	O	18.1°	0.0°
N	C1	H3	H4	120.6°	120.0°
C1	N	C	H9	15.5°	95.9°
C1	N	C	H10	135.5°	24.1°
C1	N	C	H11	104.5°	144.1°
C	N	C1	C2	61.1°	89.9°
C	N	C1	H3	179.1°	150.1°
C	N	C1	H4	58.7°	30.0°
N	C	H9	H10	120.0°	120.0°
N	C	H9	H11	120.0°	120.1°
N	C	H10	H11	120.0°	120.1°
C1	C2	O1	C3	0.2°	180.0°
C1	C2	O1	O	179.4°	180.0°
C2	C1	H3	H4	120.6°	120.0°
C3	O1	C2	O	179.2°	0.1°
O1	C3	H6	H7	120.0°	120.0°
O1	C3	H6	H8	120.0°	120.0°
O1	C3	H7	H8	120.0°	120.0°
O1	C2	C1	H3	42.7°	60.0°
O1	C2	C1	H4	77.7°	60.0°
C2	O1	C3	H6	180.0°	180.0°
C2	O1	C3	H7	60.0°	60.0°
C2	O1	C3	H8	60.0°	60.0°
O	C2	C1	H3	137.9°	120.0°
O	C2	C1	H4	101.7°	120.0°
H1	C7	C6	H5	0.0°	0.0°
H6	C3	H7	H8	120.0°	120.0°
H9	C	H10	H11	120.0°	120.0°

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PDB entries from 2024-08-07

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