PDB Chemical Component KDO

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 KDO

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
C1	O1A	1.247	1.208
C1	O1B	1.247	1.342
C1	C2	1.518	1.507
O1B	HO1B	0.950	0.967
C2	O2	1.382	1.429
C2	C3	1.533	1.529
C2	O6	1.439	1.426
O2	HO2	0.949	0.967
C3	C4	1.533	1.532
C3	H31	1.115	1.090
C3	H32	1.115	1.090
C4	O4	1.445	1.429
C4	C5	1.537	1.532
C4	H4	1.114	1.091
O4	HO4	0.949	0.966
C5	O5	1.459	1.429
C5	C6	1.531	1.529
C5	H5	1.115	1.090
O5	HO5	0.950	0.967
C6	O6	1.451	1.425
C6	C7	1.521	1.529
C6	H6	1.115	1.091
C7	O7	1.417	1.428
C7	C8	1.532	1.530
C7	H7	1.116	1.090
O7	HO7	0.950	0.967
C8	O8	1.417	1.429
C8	H81	1.115	1.090
C8	H82	1.116	1.089
O8	HO8	0.950	0.966

Bond Angles for KDO

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
O1A	C1	O1B	122.7	120.0
O1A	C1	C2	118.8	120.0
O1B	C1	C2	118.6	120.0
C1	O1B	HO1B	122.7	120.1
C1	C2	O2	109.9	109.4
C1	C2	C3	109.1	109.4
C1	C2	O6	108.0	109.4
O2	C2	C3	109.8	109.4
O2	C2	O6	109.0	109.4
C2	O2	HO2	109.9	106.9
C3	C2	O6	111.1	109.8
C2	C3	C4	110.9	109.0
C2	C3	H31	111.7	109.5
C2	C3	H32	111.7	109.5
C2	O6	C6	112.8	107.6
C4	C3	H31	111.7	109.6
C4	C3	H32	111.7	109.6
C3	C4	O4	110.0	109.6
C3	C4	C5	108.8	108.6
C3	C4	H4	109.9	109.6
H31	C3	H32	98.6	109.6
O4	C4	C5	110.6	109.8
O4	C4	H4	108.1	109.6
C4	O4	HO4	110.1	106.8
C5	C4	H4	109.4	109.6
C4	C5	O5	109.8	109.5
C4	C5	C6	105.6	109.0
C4	C5	H5	112.2	109.6
O5	C5	C6	110.7	109.7
O5	C5	H5	107.2	109.5
C5	O5	HO5	109.8	106.8
C6	C5	H5	111.4	109.5
C5	C6	O6	109.8	109.8
C5	C6	C7	111.6	109.4
C5	C6	H6	108.3	109.4
O6	C6	C7	111.1	109.4
O6	C6	H6	108.9	109.4
C7	C6	H6	107.0	109.4
C6	C7	O7	108.6	109.5
C6	C7	C8	111.5	109.5
C6	C7	H7	108.7	109.4
O7	C7	C8	109.6	109.5
O7	C7	H7	110.7	109.5
C7	O7	HO7	108.6	106.8
C8	C7	H7	107.8	109.4
C7	C8	O8	109.5	109.5
C7	C8	H81	112.2	109.4
C7	C8	H82	112.2	109.5
O8	C8	H81	112.2	109.4
O8	C8	H82	112.2	109.5
C8	O8	HO8	109.5	106.8
H81	C8	H82	98.2	109.4

Torsion Angles for KDO

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
O1B	C1	O1A	C2	179.5	180.1
O1A	C1	O1B	HO1B	180.0	359.9
O1A	C1	C2	O2	125.0	119.9
O1A	C1	C2	C3	245.4	239.7
O1A	C1	C2	O6	6.2	0.1
O1A	C1	O1B	C2	180.5	179.9
O1B	C1	C2	O2	305.5	299.8
O1B	C1	C2	C3	65.8	59.6
O1B	C1	C2	O6	186.7	180.0
O1A	C1	C2	O1B	179.5	180.1
C2	C1	O1B	HO1B	359.5	180.0
O2	C2	C1	C3	239.6	240.2
O2	C2	C1	O6	118.7	119.8
C1	C2	O2	HO2	180.0	300.1
C3	C2	C1	O6	239.1	239.7
C1	C2	C3	C4	171.0	181.3
C1	C2	C3	H31	296.3	301.2
C1	C2	C3	H32	45.7	61.4
C1	C2	O6	C6	184.9	172.3
HO1B	O1B	C1	C2	359.5	180.0
C1	C2	O2	C3	120.0	119.8
C1	C2	O2	O6	241.8	240.2
C3	C2	O2	O6	121.9	120.4
O2	C2	C3	C4	291.4	301.1
O2	C2	C3	H31	56.7	61.0
O2	C2	C3	H32	166.1	181.2
O2	C2	O6	C6	65.6	52.6
C1	C2	C3	O2	239.5	240.2
C1	C2	C3	O6	119.0	120.1
O2	C2	C3	O6	239.4	239.9
C3	C2	O2	HO2	60.0	180.3
C3	C2	O6	C6	304.6	292.4
C4	C3	C2	H31	234.7	240.1
C4	C3	C2	H32	125.3	119.9
C2	C3	C4	O4	182.3	186.4
C2	C3	C4	C5	303.6	306.3
C2	C3	C4	H4	63.3	66.0
H31	C3	C2	H32	250.6	239.8
C1	C2	O6	O2	119.3	119.8
C1	C2	O6	C3	240.4	239.9
O2	C2	O6	C3	121.0	120.1
O6	C2	O2	HO2	298.1	59.9
O6	C2	C3	C4	52.0	61.3
O6	C2	C3	H31	177.3	181.1
O6	C2	C3	H32	286.7	301.4
C5	C6	O6	C2	63.1	67.6
C2	O6	C6	C7	187.1	187.7
C2	O6	C6	H6	304.6	307.5
HO2	O2	C2	C3	60.0	180.3
HO2	O2	C2	O6	298.1	59.9
C4	C3	C2	O6	52.0	61.3
C2	C3	C4	H31	125.3	119.9
C2	C3	C4	H32	234.7	240.1
H31	C3	C4	H32	109.4	120.3
O4	C4	C3	C5	238.7	240.1
O4	C4	C3	H4	119.0	120.3
C3	C4	O4	HO4	180.0	300.0
C5	C4	C3	H4	240.3	240.3
C3	C4	C5	O5	302.0	293.7
C3	C4	C5	C6	61.3	53.8
C3	C4	C5	H5	182.8	173.6
H31	C3	C2	O6	177.3	181.1
C2	C3	H31	C4	235.2	240.4
C2	C3	H31	H32	117.5	120.2
C4	C3	H31	H32	242.4	239.7
H31	C3	C4	O4	57.0	66.5
H31	C3	C4	C5	178.3	186.4
H31	C3	C4	H4	298.1	306.1
H32	C3	C2	O6	286.7	301.4
C2	C3	H32	C4	124.8	119.6
C2	C3	H32	H31	242.5	239.8
C4	C3	H32	H31	117.6	120.3
H32	C3	C4	O4	307.6	306.2
H32	C3	C4	C5	68.9	66.1
H32	C3	C4	H4	188.6	185.9
O4	C4	C3	H31	57.0	66.5
O4	C4	C3	H32	307.6	306.2
C3	C4	O4	C5	120.2	119.2
C3	C4	O4	H4	239.9	239.6
C5	C4	O4	H4	119.7	120.4
O4	C4	C5	O5	62.9	53.6
O4	C4	C5	C6	182.3	173.6
O4	C4	C5	H5	303.8	293.4
C5	C4	C3	H31	178.3	186.4
C5	C4	C3	H32	68.9	66.1
C3	C4	C5	O4	239.1	240.1
C3	C4	C5	H4	120.1	119.8
O4	C4	C5	H4	241.0	239.6
C5	C4	O4	HO4	59.8	180.8
O5	C5	C4	C6	240.7	240.0
O5	C5	C4	H5	119.2	120.1
C4	C5	O5	HO5	180.0	300.0
C6	C5	C4	H5	238.5	240.2
C4	C5	C6	O6	295.5	298.7
C4	C5	C6	C7	171.9	178.5
C4	C5	C6	H6	54.4	58.7
H4	C4	C3	H31	298.1	306.1
H4	C4	C3	H32	188.6	185.9
C3	C4	H4	O4	120.1	120.4
C3	C4	H4	C5	240.6	240.9
O4	C4	H4	C5	120.5	120.5
H4	C4	O4	HO4	300.1	60.4
H4	C4	C5	O5	181.9	174.0
H4	C4	C5	C6	301.3	294.0
H4	C4	C5	H5	62.8	53.8
HO4	O4	C4	C5	59.8	180.8
HO4	O4	C4	H4	300.1	60.4
O5	C5	C4	H4	181.9	174.0
C4	C5	O5	C6	116.2	119.6
C4	C5	O5	H5	237.8	239.8
C6	C5	O5	H5	121.7	120.2
O5	C5	C6	O6	54.3	58.6
O5	C5	C6	C7	290.7	298.5
O5	C5	C6	H6	173.1	178.7
C2	O6	C6	C5	63.1	67.6
C6	C5	C4	H4	301.3	294.0
C4	C5	C6	O5	241.2	240.1
C4	C5	C6	H5	122.0	119.9
O5	C5	C6	H5	240.8	239.8
C6	C5	O5	HO5	63.8	180.3
O6	C6	C5	C7	123.6	120.1
O6	C6	C5	H6	241.2	239.9
C7	C6	C5	H6	117.6	119.8
C5	C6	C7	O7	288.8	300.2
C5	C6	C7	C8	168.0	180.1
C5	C6	C7	H7	49.3	60.2
H5	C5	C4	H4	62.8	53.8
C4	C5	H5	O5	120.7	120.2
C4	C5	H5	C6	241.9	240.4
O5	C5	H5	C6	121.2	120.3
H5	C5	O5	HO5	302.1	60.2
H5	C5	C6	O6	173.5	178.8
H5	C5	C6	C7	49.9	58.7
H5	C5	C6	H6	292.4	298.9
HO5	O5	C5	C6	63.8	180.3
HO5	O5	C5	H5	302.1	60.2
O6	C6	C5	H5	173.5	178.8
C5	C6	O6	C7	236.1	239.9
C5	C6	O6	H6	118.5	120.0
C7	C6	O6	H6	242.4	240.2
O6	C6	C7	O7	165.9	179.9
O6	C6	C7	C8	45.1	59.8
O6	C6	C7	H7	286.5	299.9
C7	C6	C5	H5	49.9	58.7
C5	C6	C7	O6	122.9	120.3
C5	C6	C7	H6	241.6	240.2
O6	C6	C7	H6	118.8	119.9
O7	C7	C6	C8	120.8	120.1
O7	C7	C6	H7	239.4	240.0
C6	C7	O7	HO7	180.0	300.0
C8	C7	C6	H7	118.7	119.9
C6	C7	C8	O8	73.1	180.0
C6	C7	C8	H81	198.5	60.1
C6	C7	C8	H82	307.8	300.1
H6	C6	C5	H5	292.4	298.9
C5	C6	H6	O6	240.6	239.7
C5	C6	H6	C7	120.5	119.8
O6	C6	H6	C7	239.9	240.1
H6	C6	C7	O7	47.1	60.0
H6	C6	C7	C8	286.4	299.9
H6	C6	C7	H7	167.7	180.0
O7	C7	C6	H6	47.1	60.0
C6	C7	O7	C8	238.0	239.9
C6	C7	O7	H7	119.3	120.0
C8	C7	O7	H7	241.3	240.1
O7	C7	C8	O8	312.9	59.9
O7	C7	C8	H81	78.2	299.9
O7	C7	C8	H82	187.6	180.0
C8	C7	C6	H6	286.4	299.9
C6	C7	C8	O7	120.2	120.1
C6	C7	C8	H7	240.8	240.1
O7	C7	C8	H7	120.6	119.9
C8	C7	O7	HO7	302.0	60.1
O8	C8	C7	H81	234.7	120.0
O8	C8	C7	H82	125.3	239.9
C7	C8	O8	HO8	180.0	180.0
H81	C8	C7	H82	250.6	119.9
H7	C7	C6	H6	167.7	180.0
C6	C7	H7	O7	240.8	239.9
C6	C7	H7	C8	121.0	120.0
O7	C7	H7	C8	240.2	240.0
H7	C7	O7	HO7	60.7	180.0
H7	C7	C8	O8	192.4	299.9
H7	C7	C8	H81	317.7	180.0
H7	C7	C8	H82	67.1	60.0
HO7	O7	C7	C8	302.0	60.1
HO7	O7	C7	H7	60.7	180.0
O8	C8	C7	H7	192.4	299.9
C7	C8	O8	H81	125.3	240.0
C7	C8	O8	H82	234.7	120.1
H81	C8	O8	H82	109.4	240.1
H81	C8	C7	H7	317.7	180.0
C7	C8	H81	O8	236.1	120.0
C7	C8	H81	H82	118.1	240.0
O8	C8	H81	H82	241.9	120.0
H81	C8	O8	HO8	54.7	299.9
H82	C8	C7	H7	67.1	60.0
C7	C8	H82	O8	123.8	239.9
C7	C8	H82	H81	241.9	120.0
O8	C8	H82	H81	118.1	240.1
H82	C8	O8	HO8	305.3	59.9
HO8	O8	C8	H81	54.7	299.9
HO8	O8	C8	H82	305.3	59.9