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Summary Geometry Related PDB entries

RYD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O	C5	sing	1.43Å	1.35Å
C5	C4	sing	1.51Å	1.49Å
C4	C6	doub	1.36Å	1.40Å	Aromatic
C4	C3	sing	1.39Å	1.36Å	Aromatic
C6	C7	sing	1.40Å	1.42Å	Aromatic
C3	C2	doub	1.37Å	1.37Å	Aromatic
C7	N1	sing	1.35Å	1.35Å	Aromatic
C7	C1	doub	1.41Å	1.40Å	Aromatic
C2	C1	sing	1.39Å	1.38Å	Aromatic
N1	N2	doub	1.29Å	1.32Å	Aromatic
C1	N	sing	1.37Å	1.41Å	Aromatic
N2	N	sing	1.40Å	1.38Å	Aromatic
N	C	sing	1.46Å	1.43Å
C5	H1	sing	1.09Å	1.10Å
C5	H2	sing	1.09Å	1.10Å
C6	H3	sing	1.08Å	1.08Å
O	H4	sing	0.97Å	0.95Å
C3	H5	sing	1.08Å	1.08Å
C2	H6	sing	1.08Å	1.08Å
C	H7	sing	1.09Å	1.10Å
C	H8	sing	1.09Å	1.10Å
C	H9	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O	C5	C4	97.9°	109.5°
O	C5	H1	112.3°	109.5°
O	C5	H2	112.3°	109.5°
C5	O	H4	109.5°	114.0°
C5	C4	C6	122.4°	119.6°
C5	C4	C3	116.2°	119.6°
C4	C5	H1	112.3°	109.4°
C4	C5	H2	112.3°	109.5°
C6	C4	C3	121.2°	120.8°
C4	C6	C7	116.6°	119.8°
C4	C6	H3	121.7°	120.1°
C4	C3	C2	121.8°	120.5°
C4	C3	H5	119.1°	119.7°
C6	C7	N1	131.2°	133.2°
C6	C7	C1	121.1°	119.1°
C7	C6	H3	121.7°	120.1°
C3	C2	C1	119.7°	119.8°
C2	C3	H5	119.1°	119.7°
C3	C2	H6	120.2°	120.1°
N1	C7	C1	107.5°	107.7°
C7	N1	N2	110.8°	110.3°
C7	C1	C2	119.4°	119.9°
C7	C1	N	105.8°	106.1°
C2	C1	N	134.7°	134.0°
C1	C2	H6	120.2°	120.1°
N1	N2	N	108.7°	109.5°
C1	N	N2	107.2°	106.4°
C1	N	C	127.6°	126.8°
N2	N	C	125.0°	126.8°
N	C	H7	109.5°	109.5°
N	C	H8	109.4°	109.4°
N	C	H9	109.5°	109.4°
H1	C5	H2	109.4°	109.5°
H7	C	H8	109.5°	109.5°
H7	C	H9	109.5°	109.5°
H8	C	H9	109.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O	C5	C4	H1	118.1°	120.0°
O	C5	C4	H2	118.1°	120.1°
O	C5	C4	C6	68.1°	90.0°
O	C5	C4	C3	116.9°	89.9°
O	C5	H1	H2	125.4°	120.0°
C5	C4	C6	C3	174.7°	179.9°
C5	C4	C6	C7	171.2°	180.0°
C5	C4	C3	C2	171.1°	180.0°
C4	C5	H1	H2	125.4°	120.0°
C5	C4	C6	H3	8.8°	0.0°
C4	C5	O	H4	180.0°	180.0°
C5	C4	C3	H5	8.9°	0.1°
C4	C6	C7	H3	180.0°	179.9°
C6	C4	C3	C2	4.0°	0.1°
C4	C6	C7	N1	175.4°	180.0°
C4	C6	C7	C1	0.6°	0.1°
C6	C4	C5	H1	173.8°	150.0°
C6	C4	C5	H2	50.0°	30.1°
C6	C4	C3	H5	176.0°	180.0°
C3	C4	C6	C7	3.5°	0.1°
C4	C3	C2	H5	180.0°	179.9°
C4	C3	C2	C1	1.2°	0.0°
C3	C4	C5	H1	1.1°	30.1°
C3	C4	C5	H2	125.0°	150.1°
C3	C4	C6	H3	176.5°	179.9°
C4	C3	C2	H6	178.7°	180.0°
C6	C7	N1	C1	176.4°	179.9°
C6	C7	C1	C2	2.0°	0.0°
C6	C7	N1	N2	174.6°	180.0°
C6	C7	C1	N	175.1°	180.0°
C3	C2	C1	C7	1.7°	0.0°
C3	C2	C1	H6	180.0°	180.0°
C3	C2	C1	N	174.4°	180.0°
N1	C7	C1	C2	178.8°	179.9°
N1	C7	C1	N	1.7°	0.0°
C7	N1	N2	N	1.1°	0.0°
N1	C7	C6	H3	4.6°	0.1°
C7	C1	C2	N	176.1°	180.0°
C1	C7	N1	N2	1.8°	0.0°
C7	C1	N	N2	1.0°	0.0°
C7	C1	N	C	173.6°	180.0°
C1	C7	C6	H3	179.4°	180.0°
C7	C1	C2	H6	178.3°	180.0°
C2	C1	N	N2	177.5°	179.9°
C2	C1	N	C	2.8°	0.0°
C1	C2	C3	H5	178.7°	180.0°
N1	N2	N	C1	0.0°	0.0°
N1	N2	N	C	174.9°	180.0°
C1	N	N2	C	174.9°	180.0°
N	C1	C2	H6	5.6°	0.0°
C1	N	C	H7	173.8°	90.0°
C1	N	C	H8	66.2°	150.0°
C1	N	C	H9	53.7°	30.0°
N2	N	C	H7	0.0°	90.0°
N2	N	C	H8	120.0°	30.0°
N2	N	C	H9	120.0°	150.0°
N	C	H7	H8	120.0°	120.0°
N	C	H7	H9	120.0°	120.0°
N	C	H8	H9	120.0°	119.9°
H1	C5	O	H4	61.9°	60.0°
H2	C5	O	H4	61.9°	60.0°
H5	C3	C2	H6	1.3°	0.1°
H7	C	H8	H9	120.0°	120.1°

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