PDB Chemical Component RUB

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 RUB

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
C1	C2	1.533	1.507
C1	O1	1.454	1.429
C1	H11	1.115	1.089
C1	H12	1.115	1.090
C2	C3	1.582	1.505
C2	O2	1.248	1.208
C3	C4	1.529	1.529
C3	O3	1.383	1.429
C3	H3	1.116	1.090
C4	C5	1.541	1.530
C4	O4	1.389	1.428
C4	H4	1.115	1.090
C5	O5	1.438	1.428
C5	H51	1.115	1.090
C5	H52	1.115	1.090
O1	P1	1.605	1.609
O3	HO3	0.950	0.966
O4	HO4	0.950	0.966
O5	P2	1.638	1.610
P1	O1P	1.462	1.481
P1	O2P	1.605	1.610
P1	O3P	1.460	1.609
P2	O4P	1.511	1.481
P2	O5P	1.586	1.610
P2	O6P	1.489	1.609
O2P	HOP2	0.950	0.967
O3P	HOP3	0.950	0.967
O5P	HOP5	0.949	0.968
O6P	HOP6	0.949	0.966

Bond Angles for RUB

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C2	C1	O1	119.7	109.5
C2	C1	H11	108.6	109.4
C2	C1	H12	108.5	109.5
C1	C2	C3	115.8	120.1
C1	C2	O2	121.5	119.9
O1	C1	H11	108.5	109.5
O1	C1	H12	108.5	109.5
C1	O1	P1	120.4	106.8
H11	C1	H12	101.4	109.5
C3	C2	O2	122.6	120.0
C2	C3	C4	114.6	109.5
C2	C3	O3	109.3	109.5
C2	C3	H3	105.5	109.5
C4	C3	O3	107.5	109.5
C4	C3	H3	107.4	109.4
C3	C4	C5	112.9	109.5
C3	C4	O4	109.9	109.5
C3	C4	H4	106.4	109.5
O3	C3	H3	112.8	109.5
C3	O3	HO3	109.3	106.8
C5	C4	O4	108.4	109.5
C5	C4	H4	108.1	109.4
C4	C5	O5	118.9	109.5
C4	C5	H51	108.8	109.5
C4	C5	H52	108.8	109.5
O4	C4	H4	111.1	109.4
C4	O4	HO4	109.9	106.9
O5	C5	H51	108.8	109.4
O5	C5	H52	108.8	109.5
C5	O5	P2	122.3	106.9
H51	C5	H52	101.2	109.4
O1	P1	O1P	108.7	109.5
O1	P1	O2P	101.8	109.5
O1	P1	O3P	108.9	109.5
O5	P2	O4P	107.5	109.4
O5	P2	O5P	103.0	109.5
O5	P2	O6P	108.6	109.5
O1P	P1	O2P	108.1	109.4
O1P	P1	O3P	119.7	109.4
O2P	P1	O3P	108.2	109.5
P1	O2P	HOP2	101.9	106.8
P1	O3P	HOP3	108.8	106.7
O4P	P2	O5P	108.9	109.5
O4P	P2	O6P	120.2	109.4
O5P	P2	O6P	107.4	109.5
P2	O5P	HOP5	103.0	106.8
P2	O6P	HOP6	108.6	106.8

Torsion Angles for RUB

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
O1	C1	C2	H11	234.7	240.0
O1	C1	C2	H12	125.3	120.0
C2	C1	O1	P1	177.6	180.0
H11	C1	C2	H12	250.5	240.1
C3	C2	C1	O2	177.2	180.0
C1	C2	C3	C4	68.9	90.0
C1	C2	C3	O3	189.5	210.0
C1	C2	C3	H3	311.1	330.0
C2	C1	O1	H11	125.3	120.0
C2	C1	O1	H12	234.7	240.0
O1	C1	C2	C3	169.2	180.0
O1	C1	C2	O2	352.0	0.0
H11	C1	O1	H12	109.4	120.0
C1	O1	P1	O1P	187.2	60.0
C1	O1	P1	O2P	73.2	180.0
C1	O1	P1	O3P	319.1	300.1
C2	C1	H11	O1	228.4	240.0
C2	C1	H11	H12	114.2	119.9
H11	C1	C2	C3	294.5	300.0
H11	C1	C2	O2	117.3	120.0
O1	C1	H11	H12	245.8	240.0
H11	C1	O1	P1	52.3	60.0
C2	C1	H12	O1	131.6	120.1
C2	C1	H12	H11	245.8	240.1
H12	C1	C2	C3	43.9	59.9
H12	C1	C2	O2	226.8	240.0
O1	C1	H12	H11	114.2	120.0
H12	C1	O1	P1	302.9	300.0
C3	C2	C1	O1	169.2	180.0
C3	C2	C1	H11	294.5	300.0
C3	C2	C1	H12	43.9	59.9
C1	C2	C3	O2	182.9	180.0
C4	C3	C2	O3	239.4	240.0
C4	C3	C2	H3	117.8	120.0
C2	C3	C4	C5	176.3	180.0
C2	C3	C4	O4	297.4	300.0
C2	C3	C4	H4	57.8	60.0
O3	C3	C2	H3	238.4	240.0
C2	C3	O3	HO3	180.0	300.0
O2	C2	C1	O1	352.0	0.0
O2	C2	C1	H11	117.3	120.0
O2	C2	C1	H12	226.8	240.0
C1	C2	O2	C3	177.0	180.0
O2	C2	C3	C4	246.0	270.0
O2	C2	C3	O3	6.6	30.0
O2	C2	C3	H3	128.2	150.0
C4	C3	C2	O2	246.0	270.0
C2	C3	C4	O3	121.6	120.0
C2	C3	C4	H3	243.2	240.0
O3	C3	C4	H3	121.6	120.0
C4	C3	O3	HO3	304.8	60.0
C5	C4	C3	O4	238.9	240.0
C5	C4	C3	H4	118.4	120.0
C3	C4	C5	O5	197.9	180.0
C3	C4	C5	H51	323.2	300.1
C3	C4	C5	H52	72.6	60.0
O4	C4	C3	H4	239.5	240.0
C3	C4	O4	HO4	180.0	300.0
O3	C3	C2	O2	6.6	30.0
C2	C3	O3	C4	235.1	240.0
C2	C3	O3	H3	117.0	120.0
C4	C3	O3	H3	241.9	240.1
O3	C3	C4	C5	54.7	60.0
O3	C3	C4	O4	175.8	180.0
O3	C3	C4	H4	296.2	300.0
H3	C3	C2	O2	128.2	150.0
C2	C3	H3	C4	122.6	120.0
C2	C3	H3	O3	240.8	240.0
C4	C3	H3	O3	118.2	120.0
H3	C3	C4	C5	293.1	300.0
H3	C3	C4	O4	54.2	60.0
H3	C3	C4	H4	174.6	180.0
H3	C3	O3	HO3	63.0	180.0
C5	C4	C3	O3	54.7	60.0
C5	C4	C3	H3	293.1	300.0
C3	C4	C5	O4	122.0	120.0
C3	C4	C5	H4	242.5	240.0
O4	C4	C5	H4	120.6	119.9
C5	C4	O4	HO4	303.8	60.0
O5	C5	C4	H51	234.7	240.0
O5	C5	C4	H52	125.3	120.0
C4	C5	O5	P2	210.8	180.0
H51	C5	C4	H52	250.6	240.1
O4	C4	C3	O3	175.8	180.0
O4	C4	C3	H3	54.2	60.0
C3	C4	O4	C5	236.2	239.9
C3	C4	O4	H4	117.6	120.0
C5	C4	O4	H4	241.3	240.1
O4	C4	C5	O5	75.9	60.0
O4	C4	C5	H51	201.2	180.0
O4	C4	C5	H52	310.6	299.9
H4	C4	C3	O3	296.2	300.0
H4	C4	C3	H3	174.6	180.0
C3	C4	H4	C5	121.5	120.0
C3	C4	H4	O4	240.3	240.0
C5	C4	H4	O4	118.8	120.0
H4	C4	C5	O5	315.4	300.1
H4	C4	C5	H51	80.6	60.1
H4	C4	C5	H52	190.1	180.0
H4	C4	O4	HO4	62.5	179.9
O5	C5	C4	O4	75.9	60.0
O5	C5	C4	H4	315.4	300.1
C4	C5	O5	H51	125.3	120.1
C4	C5	O5	H52	234.7	240.0
H51	C5	O5	H52	109.4	119.9
C5	O5	P2	O4P	165.4	60.0
C5	O5	P2	O5P	50.5	180.0
C5	O5	P2	O6P	296.9	300.0
H51	C5	C4	O4	201.2	180.0
H51	C5	C4	H4	80.6	60.1
C4	C5	H51	O5	229.1	239.9
C4	C5	H51	H52	114.5	120.0
O5	C5	H51	H52	245.5	240.1
H51	C5	O5	P2	85.5	59.9
H52	C5	C4	O4	310.6	299.9
H52	C5	C4	H4	190.1	180.0
C4	C5	H52	O5	130.9	120.1
C4	C5	H52	H51	245.5	240.0
O5	C5	H52	H51	114.5	119.9
H52	C5	O5	P2	336.1	300.0
P1	O1	C1	H11	52.3	60.0
P1	O1	C1	H12	302.9	300.0
O1P	P1	O1	O2P	114.0	240.1
O1P	P1	O1	O3P	228.1	120.0
O2P	P1	O1	O3P	114.1	239.9
O1	P1	O2P	HOP2	180.0	180.1
O1	P1	O3P	HOP3	179.9	299.9
HO3	O3	C3	H3	63.0	180.0
HO4	O4	C4	H4	62.5	179.9
P2	O5	C5	H51	85.5	59.9
P2	O5	C5	H52	336.1	300.0
O4P	P2	O5	O5P	114.9	240.0
O4P	P2	O5	O6P	228.5	120.0
O5P	P2	O5	O6P	113.6	239.9
O5	P2	O5P	HOP5	180.0	180.0
O5	P2	O6P	HOP6	180.0	300.0
O1	P1	O1P	O2P	250.2	120.0
O1	P1	O1P	O3P	125.8	240.0
O2P	P1	O1P	O3P	235.6	120.0
O1P	P1	O2P	HOP2	65.6	300.0
O1P	P1	O3P	HOP3	305.7	180.0
O1	P1	O2P	O1P	114.4	240.0
O1	P1	O2P	O3P	245.4	120.1
O1P	P1	O2P	O3P	131.0	240.0
O2P	P1	O3P	HOP3	70.1	60.0
O1	P1	O3P	O1P	234.3	120.0
O1	P1	O3P	O2P	109.9	239.9
O1P	P1	O3P	O2P	235.6	119.9
O3P	P1	O2P	HOP2	294.6	60.0
O5	P2	O4P	O5P	249.1	120.0
O5	P2	O4P	O6P	124.8	240.0
O5P	P2	O4P	O6P	235.7	120.0
O4P	P2	O5P	HOP5	66.1	300.0
O4P	P2	O6P	HOP6	304.3	180.0
O5	P2	O5P	O4P	113.9	240.0
O5	P2	O5P	O6P	245.5	120.1
O4P	P2	O5P	O6P	131.6	240.0
O5P	P2	O6P	HOP6	69.3	60.1
O5	P2	O6P	O4P	235.7	119.9
O5	P2	O6P	O5P	110.7	239.9
O4P	P2	O6P	O5P	235.0	120.0
O6P	P2	O5P	HOP5	294.5	60.0
HOP2	O2P	P1	O3P	294.6	60.0
HOP5	O5P	P2	O6P	294.5	60.0