PDB Chemical Component NDG

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for NDG

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
C1	C2	1.551	1.531
C1	O5	1.453	1.430
C1	O1	1.391	1.428
C1	H1	1.100	1.091
C2	C3	1.537	1.532
C2	N2	1.456	1.465
C2	H2	1.100	1.090
C3	C4	1.537	1.532
C3	O3	1.422	1.429
C3	H3	1.101	1.090
C4	C5	1.536	1.530
C4	O4	1.422	1.429
C4	H4	1.100	1.090
C5	C6	1.521	1.529
C5	O5	1.458	1.429
C5	H5	1.100	1.090
C6	O6	1.420	1.430
C6	H61	1.100	1.090
C6	H62	1.100	1.090
C7	C8	1.523	1.507
C7	O7	1.233	1.213
C7	N2	1.333	1.348
C8	H81	1.100	1.090
C8	H82	1.100	1.090
C8	H83	1.100	1.090
O3	HO3	0.950	0.967
O4	HO4	0.950	0.968
O6	HO6	0.949	0.967
N2	HN2	0.999	0.970
O1	HO1	0.950	0.967

Bond Angles for NDG

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C2	C1	O5	113.2	109.4
C2	C1	O1	111.3	109.5
C2	C1	H1	105.4	109.4
C1	C2	C3	111.9	109.1
C1	C2	N2	110.2	109.5
C1	C2	H2	107.4	109.5
O5	C1	O1	108.9	109.5
O5	C1	H1	108.0	109.5
C1	O5	C5	115.6	114.1
O1	C1	H1	110.0	109.5
C1	O1	HO1	109.5	114.0
C3	C2	N2	109.8	109.5
C3	C2	H2	107.8	109.5
C2	C3	C4	111.7	109.0
C2	C3	O3	109.3	109.5
C2	C3	H3	108.1	109.5
N2	C2	H2	109.7	109.6
C2	N2	C7	120.7	120.0
C2	N2	HN2	119.6	120.1
C4	C3	O3	109.4	109.6
C4	C3	H3	107.9	109.6
C3	C4	C5	111.4	109.2
C3	C4	O4	109.9	109.5
C3	C4	H4	107.9	109.5
O3	C3	H3	110.4	109.6
C3	O3	HO3	109.5	113.9
C5	C4	O4	109.6	109.5
C5	C4	H4	108.2	109.5
C4	C5	C6	114.3	109.5
C4	C5	O5	111.6	109.4
C4	C5	H5	104.0	109.5
O4	C4	H4	109.7	109.6
C4	O4	HO4	109.5	114.0
C6	C5	O5	107.6	109.5
C6	C5	H5	108.3	109.5
C5	C6	O6	111.2	109.5
C5	C6	H61	108.9	109.5
C5	C6	H62	108.5	109.5
O5	C5	H5	111.2	109.4
O6	C6	H61	108.9	109.4
O6	C6	H62	108.5	109.5
C6	O6	HO6	109.5	114.0
H61	C6	H62	110.9	109.5
C8	C7	O7	119.7	120.0
C8	C7	N2	117.4	120.0
C7	C8	H81	109.5	109.4
C7	C8	H82	109.5	109.5
C7	C8	H83	109.5	109.5
O7	C7	N2	122.8	120.0
C7	N2	HN2	119.6	120.0
H81	C8	H82	109.5	109.5
H81	C8	H83	109.4	109.5
H82	C8	H83	109.5	109.5

Torsion Angles for NDG

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
O5	C1	C2	O1	123.1	120.0
O5	C1	C2	H1	242.2	240.1
C2	C1	O5	C5	335.3	298.8
O1	C1	C2	H1	119.2	120.1
C2	C1	O1	HO1	221.2	180.0
C3	C2	C1	N2	237.6	240.1
C3	C2	C1	H2	118.2	119.9
C1	C2	C3	C4	332.9	303.0
C1	C2	C3	O3	211.7	183.1
C1	C2	C3	H3	91.5	62.9
N2	C2	C1	H2	240.6	239.8
C1	C2	N2	C7	180.0	85.1
C1	C2	N2	HN2	360.0	265.0
C2	C1	O5	O1	235.7	240.0
C2	C1	O5	H1	116.3	119.9
O5	C1	C2	C3	57.3	57.6
O5	C1	C2	N2	179.7	177.5
O5	C1	C2	H2	299.1	297.7
O1	C1	O5	H1	240.6	239.9
O5	C1	O1	HO1	95.8	60.1
C4	C5	O5	C1	326.6	61.1
C6	C5	O5	C1	92.7	181.2
C1	O5	C5	H5	211.0	301.2
C2	C1	O1	O5	125.5	120.0
C2	C1	O1	H1	243.6	240.0
O1	C1	C2	C3	294.2	297.6
O1	C1	C2	N2	56.6	57.5
O1	C1	C2	H2	176.0	177.7
O5	C1	O1	H1	118.1	120.0
O1	C1	O5	C5	99.7	58.8
C2	C1	H1	O5	238.8	240.1
C2	C1	H1	O1	120.0	120.1
H1	C1	C2	C3	175.1	177.6
H1	C1	C2	N2	297.5	297.4
H1	C1	C2	H2	56.9	57.7
O5	C1	H1	O1	241.3	239.9
H1	C1	O5	C5	219.0	178.9
H1	C1	O1	HO1	337.6	300.0
C3	C2	C1	O5	57.3	57.6
C3	C2	C1	O1	294.2	297.6
C3	C2	C1	H1	175.1	177.6
C1	C2	C3	N2	122.7	119.9
C1	C2	C3	H2	242.1	240.1
N2	C2	C3	H2	119.4	120.2
C3	C2	N2	C7	303.7	204.7
C3	C2	N2	HN2	123.7	24.7
C4	C3	C2	O3	121.3	119.9
C4	C3	C2	H3	241.4	240.1
C2	C3	C4	C5	331.3	57.0
C2	C3	C4	O4	93.0	176.9
C2	C3	C4	H4	212.6	297.0
O3	C3	C2	H3	120.2	120.2
C2	C3	O3	HO3	161.7	180.0
N2	C2	C1	O5	179.7	177.5
N2	C2	C1	O1	56.6	57.5
N2	C2	C1	H1	297.5	297.4
C1	C2	N2	C3	236.3	240.4
C1	C2	N2	H2	118.0	120.2
C3	C2	N2	H2	241.7	239.8
N2	C2	C3	C4	210.2	183.1
N2	C2	C3	O3	89.0	63.2
N2	C2	C3	H3	328.8	303.0
C8	C7	N2	C2	99.3	180.0
O7	C7	N2	C2	279.1	360.0
C7	N2	C2	HN2	180.0	180.0
H2	C2	C1	O5	299.1	297.7
H2	C2	C1	O1	176.0	177.7
H2	C2	C1	H1	56.9	57.7
C1	C2	H2	C3	120.8	119.7
C1	C2	H2	N2	240.3	239.8
C3	C2	H2	N2	119.5	120.2
H2	C2	C3	C4	90.8	62.9
H2	C2	C3	O3	329.6	303.0
H2	C2	C3	H3	209.4	182.8
H2	C2	N2	C7	62.0	324.9
H2	C2	N2	HN2	242.0	144.8
C4	C3	C2	N2	210.2	183.1
C4	C3	C2	H2	90.8	62.9
C2	C3	C4	O3	238.8	240.2
C2	C3	C4	H3	118.7	119.9
O3	C3	C4	H3	239.8	239.7
C4	C3	O3	HO3	39.0	60.4
C5	C4	C3	O4	238.3	240.1
C5	C4	C3	H4	118.7	120.0
C3	C4	C5	C6	300.3	182.4
C3	C4	C5	O5	62.6	302.4
C3	C4	C5	H5	182.5	62.3
O4	C4	C3	H4	240.4	239.9
C3	C4	O4	HO4	296.0	180.0
O3	C3	C2	N2	89.0	63.2
O3	C3	C2	H2	329.6	303.0
C2	C3	O3	C4	122.6	119.5
C2	C3	O3	H3	241.3	239.8
C4	C3	O3	H3	118.6	120.3
O3	C3	C4	C5	92.4	176.8
O3	C3	C4	O4	214.2	296.7
O3	C3	C4	H4	333.8	56.9
H3	C3	C2	N2	328.8	303.0
H3	C3	C2	H2	209.4	182.8
C2	C3	H3	C4	239.0	240.4
C2	C3	H3	O3	119.5	120.2
C4	C3	H3	O3	240.5	239.7
H3	C3	C4	C5	212.6	297.2
H3	C3	C4	O4	334.3	57.0
H3	C3	C4	H4	94.0	177.2
H3	C3	O3	HO3	280.4	300.1
C1	O5	C5	C4	326.6	61.1
C5	C4	C3	O3	92.4	176.8
C5	C4	C3	H3	212.6	297.2
C3	C4	C5	O4	121.9	119.9
C3	C4	C5	H4	241.5	240.1
O4	C4	C5	H4	119.6	120.2
C5	C4	O4	HO4	58.7	299.7
C6	C5	C4	O5	237.7	240.0
C6	C5	C4	H5	117.8	120.1
C4	C5	C6	O6	204.4	185.0
C4	C5	C6	H61	324.4	304.9
C4	C5	C6	H62	85.1	65.0
O5	C5	C4	H5	240.1	240.1
O4	C4	C3	O3	214.2	296.7
O4	C4	C3	H3	334.3	57.0
C3	C4	O4	C5	237.2	240.3
C3	C4	O4	H4	118.5	120.1
C5	C4	O4	H4	241.3	239.8
O4	C4	C5	C6	178.4	62.5
O4	C4	C5	O5	300.7	182.5
O4	C4	C5	H5	60.6	302.4
H4	C4	C3	O3	333.8	56.9
H4	C4	C3	H3	94.0	177.2
C3	C4	H4	C5	120.7	119.7
C3	C4	H4	O4	240.2	239.9
C5	C4	H4	O4	119.6	120.1
H4	C4	C5	C6	58.7	302.4
H4	C4	C5	O5	181.1	62.3
H4	C4	C5	H5	300.9	182.2
H4	C4	O4	HO4	177.4	59.9
C1	O5	C5	C6	92.7	181.2
C6	C5	C4	O4	178.4	62.5
C6	C5	C4	H4	58.7	302.4
C4	C5	C6	O5	124.5	120.0
C4	C5	C6	H5	244.7	239.9
O5	C5	C6	H5	120.2	120.0
O6	C6	C5	H61	240.0	240.1
O6	C6	C5	H62	119.3	120.0
C5	C6	O6	HO6	113.7	180.0
H61	C6	C5	H62	239.2	239.9
C5	O5	C1	O1	99.7	58.8
C5	O5	C1	H1	219.0	178.9
O5	C5	C4	O4	300.7	182.5
O5	C5	C4	H4	181.1	62.3
C4	C5	O5	C6	233.9	240.0
C4	C5	O5	H5	115.5	120.0
C6	C5	O5	H5	241.6	240.0
O5	C5	C6	O6	79.9	65.1
O5	C5	C6	H61	199.9	185.0
O5	C5	C6	H62	320.6	305.0
H5	C5	C4	O4	60.6	302.4
H5	C5	C4	H4	300.9	182.2
C4	C5	H5	C6	121.9	120.1
C4	C5	H5	O5	239.8	240.1
C6	C5	H5	O5	117.9	120.0
H5	C5	C6	O6	319.7	305.1
H5	C5	C6	H61	79.7	65.0
H5	C5	C6	H62	200.4	185.1
O6	C6	C5	O5	79.9	65.1
O6	C6	C5	H5	319.7	305.1
C5	C6	O6	H61	120.0	120.0
C5	C6	O6	H62	240.8	239.9
H61	C6	O6	H62	120.8	120.0
H61	C6	C5	O5	199.9	185.0
H61	C6	C5	H5	79.7	65.0
C5	C6	H61	O6	238.6	240.0
C5	C6	H61	H62	119.3	120.1
O6	C6	H61	H62	240.7	240.0
H61	C6	O6	HO6	353.8	60.1
H62	C6	C5	O5	320.6	305.0
H62	C6	C5	H5	200.4	185.1
C5	C6	H62	O6	120.9	120.0
C5	C6	H62	H61	240.5	240.0
O6	C6	H62	H61	119.5	119.9
H62	C6	O6	HO6	233.0	300.1
C2	N2	C7	C8	99.3	180.0
O7	C7	C8	N2	180.2	180.1
C8	C7	N2	HN2	279.3	0.1
H81	C8	C7	H82	240.0	240.0
H81	C8	C7	H83	120.0	120.0
H82	C8	C7	H83	240.0	240.0
C2	N2	C7	O7	279.1	360.0
C8	C7	O7	N2	179.8	179.9
O7	C7	C8	H81	254.0	90.0
O7	C7	C8	H82	14.0	210.0
O7	C7	C8	H83	134.0	330.1
O7	C7	N2	HN2	99.1	180.0
C7	N2	C2	H2	62.0	324.9
C2	N2	C7	HN2	180.0	180.0
C8	C7	N2	O7	180.2	180.1
N2	C7	C8	H81	73.8	270.0
N2	C7	C8	H82	193.8	29.9
N2	C7	C8	H83	313.8	150.0
H81	C8	C7	O7	254.0	90.0
H81	C8	C7	N2	73.8	270.0
C7	C8	H81	H82	120.0	120.0
C7	C8	H81	H83	240.0	240.0
H82	C8	H81	H83	120.0	120.0
H82	C8	C7	O7	14.0	210.0
H82	C8	C7	N2	193.8	29.9
C7	C8	H82	H81	240.0	240.0
C7	C8	H82	H83	120.0	120.1
H81	C8	H82	H83	240.0	240.0
H83	C8	C7	O7	134.0	330.1
H83	C8	C7	N2	313.8	150.0
C7	C8	H83	H81	120.0	120.0
C7	C8	H83	H82	240.0	239.9
H81	C8	H83	H82	120.0	120.0
HO3	O3	C3	H3	280.4	300.1
HO4	O4	C4	H4	177.4	59.9
HO6	O6	C6	H61	353.8	60.1
HO6	O6	C6	H62	233.0	300.1
HN2	N2	C2	H2	242.0	144.8
C2	N2	HN2	C7	180.0	180.0
HO1	O1	C1	H1	337.6	300.0