PDB Chemical Component YYJ

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 YYJ

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
C1	C2	1.553	1.530
C1	O1	1.469	1.429
C1	H11	1.100	1.091
C1	H12	1.100	1.089
C2	C3	1.509	1.540
C2	O2	1.446	1.429
C2	O5	1.454	1.438
C3	C4	1.496	1.548
C3	O3	1.398	1.430
C3	H3	1.100	1.090
C4	C5	1.498	1.550
C4	O4	1.423	1.429
C4	H4	1.100	1.090
C5	C6	1.544	1.530
C5	O5	1.450	1.444
C5	H5	1.100	1.090
C6	O6	1.462	1.430
C6	H61	1.100	1.090
C6	H62	1.100	1.090
O1	S1	1.464	1.521
O1S1	S1	1.442	1.522
O1S1	H1S1	0.950	0.967
O1S3	H1S3	0.950	0.967
O1S3	S3	1.444	1.522
O1S4	S4	1.457	1.521
O1S4	H1S4	0.950	0.967
O1S6	H1S6	0.950	0.966
O1S6	S6	1.432	1.523
O2	HO2	0.950	0.967
O2S1	S1	1.458	1.421
O2S3	S3	1.440	1.421
O2S4	S4	1.457	1.422
O2S6	S6	1.450	1.422
O3	S3	1.390	1.522
O3S1	S1	1.448	1.422
O3S3	S3	1.443	1.421
O3S4	S4	1.447	1.422
O3S6	S6	1.440	1.421
O4	S4	1.448	1.522
O6	S6	1.462	1.521

Bond Angles for YYJ

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C2	C1	O1	112.9	109.5
C2	C1	H11	108.6	109.5
C2	C1	H12	108.6	109.5
C1	C2	C3	108.7	109.9
C1	C2	O2	110.9	109.9
C1	C2	O5	109.6	109.9
O1	C1	H11	108.6	109.4
O1	C1	H12	108.6	109.5
C1	O1	S1	119.4	114.0
H11	C1	H12	109.5	109.4
C3	C2	O2	112.6	109.9
C3	C2	O5	104.1	107.3
C2	C3	C4	107.4	104.2
C2	C3	O3	109.3	110.5
C2	C3	H3	112.9	110.5
O2	C2	O5	110.7	110.0
C2	O2	HO2	109.5	114.0
C2	O5	C5	112.5	107.0
C4	C3	O3	98.1	110.4
C4	C3	H3	113.1	110.5
C3	C4	C5	108.1	102.1
C3	C4	O4	110.0	110.9
C3	C4	H4	106.9	111.0
O3	C3	H3	114.8	110.6
C3	O3	S3	116.0	113.9
C5	C4	O4	116.8	110.9
C5	C4	H4	106.9	110.9
C4	C5	C6	109.4	110.6
C4	C5	O5	104.6	103.5
C4	C5	H5	111.2	110.6
O4	C4	H4	107.8	110.8
C4	O4	S4	110.2	114.0
C6	C5	O5	109.0	110.6
C6	C5	H5	110.5	110.6
C5	C6	O6	114.6	109.5
C5	C6	H61	108.2	109.5
C5	C6	H62	108.2	109.5
O5	C5	H5	111.9	110.8
O6	C6	H61	108.2	109.4
O6	C6	H62	108.2	109.4
C6	O6	S6	123.8	114.0
H61	C6	H62	109.5	109.5
O1	S1	O1S1	108.5	107.2
O1	S1	O2S1	112.0	106.4
O1	S1	O3S1	108.2	106.4
S1	O1S1	H1S1	109.5	114.0
O1S1	S1	O2S1	106.8	106.4
O1S1	S1	O3S1	109.2	106.3
S3	O1S3	H1S3	109.5	114.0
O1S3	S3	O2S3	109.6	106.4
O1S3	S3	O3	107.8	107.2
O1S3	S3	O3S3	113.1	106.4
S4	O1S4	H1S4	109.5	114.1
O1S4	S4	O2S4	110.5	106.4
O1S4	S4	O3S4	106.3	106.4
O1S4	S4	O4	110.6	107.3
S6	O1S6	H1S6	109.5	114.0
O1S6	S6	O2S6	106.5	106.4
O1S6	S6	O3S6	107.8	106.4
O1S6	S6	O6	110.4	107.2
O2S1	S1	O3S1	112.0	123.1
O2S3	S3	O3	109.6	106.4
O2S3	S3	O3S3	107.4	123.2
O2S4	S4	O3S4	110.6	123.1
O2S4	S4	O4	109.4	106.4
O2S6	S6	O3S6	111.9	123.1
O2S6	S6	O6	108.1	106.4
O3	S3	O3S3	109.4	106.4
O3S4	S4	O4	109.4	106.4
O3S6	S6	O6	112.1	106.5

Torsion Angles for YYJ

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
O1	C1	C2	H11	239.5	240.0
O1	C1	C2	H12	120.5	120.0
C2	C1	O1	S1	264.6	180.0
H11	C1	C2	H12	241.0	240.0
C3	C2	C1	O2	235.7	238.9
C3	C2	C1	O5	113.2	117.8
C1	C2	C3	C4	230.8	242.6
C1	C2	C3	O3	125.3	124.0
C1	C2	C3	H3	356.2	1.3
O2	C2	C1	O5	237.5	238.9
C1	C2	O2	HO2	287.2	59.3
C1	C2	O5	C5	134.9	92.9
C2	C1	O1	H11	120.5	120.0
C2	C1	O1	H12	239.5	239.9
O1	C1	C2	C3	301.5	180.0
O1	C1	C2	O2	65.8	301.1
O1	C1	C2	O5	188.3	62.2
H11	C1	O1	H12	119.0	119.9
C1	O1	S1	O1S1	49.6	75.0
C1	O1	S1	O2S1	167.3	188.5
C1	O1	S1	O3S1	291.3	321.5
C2	C1	H11	O1	236.8	240.0
C2	C1	H11	H12	118.4	120.0
H11	C1	C2	C3	62.1	300.0
H11	C1	C2	O2	186.3	61.0
H11	C1	C2	O5	308.9	182.2
O1	C1	H11	H12	241.6	240.1
H11	C1	O1	S1	144.1	60.0
C2	C1	H12	O1	123.2	120.1
C2	C1	H12	H11	241.6	240.0
H12	C1	C2	C3	181.0	59.9
H12	C1	C2	O2	305.3	181.0
H12	C1	C2	O5	67.9	302.1
O1	C1	H12	H11	118.4	119.9
H12	C1	O1	S1	25.1	300.1
C3	C2	C1	O1	301.5	180.0
C3	C2	C1	H11	62.1	300.0
C3	C2	C1	H12	181.0	59.9
C1	C2	C3	O2	123.2	121.0
C1	C2	C3	O5	243.3	240.6
O2	C2	C3	O5	120.0	119.6
C3	C2	O2	HO2	49.2	180.3
C3	C2	O5	C5	18.8	333.5
C4	C3	C2	O3	105.5	118.6
C4	C3	C2	H3	234.6	241.3
C2	C3	C4	C5	2.7	20.9
C2	C3	C4	O4	131.2	139.1
C2	C3	C4	H4	247.9	262.7
O3	C3	C2	H3	129.1	122.7
C2	C3	O3	S3	272.6	263.5
O2	C2	C1	O1	65.8	301.1
O2	C2	C1	H11	186.3	61.0
O2	C2	C1	H12	305.3	181.0
C1	C2	O2	C3	238.0	239.0
C1	C2	O2	O5	121.9	121.1
C3	C2	O2	O5	243.9	242.1
O2	C2	C3	C4	107.6	121.6
O2	C2	C3	O3	2.1	3.0
O2	C2	C3	H3	233.0	240.3
O2	C2	O5	C5	257.5	213.9
O5	C2	C1	O1	188.3	62.2
O5	C2	C1	H11	308.9	182.2
O5	C2	C1	H12	67.9	302.1
C1	C2	O5	C3	116.1	119.4
C1	C2	O5	O2	237.4	238.9
C3	C2	O5	O2	121.3	119.5
O5	C2	C3	C4	347.5	2.0
O5	C2	C3	O3	242.0	243.4
O5	C2	C3	H3	112.9	120.7
O5	C2	O2	HO2	165.4	298.2
C4	C5	O5	C2	342.8	40.1
C6	C5	O5	C2	99.8	158.5
C2	O5	C5	H5	222.3	281.5
C4	C3	C2	O2	107.6	121.6
C4	C3	C2	O5	347.5	2.0
C2	C3	C4	O3	246.8	241.4
C2	C3	C4	H3	125.3	118.7
O3	C3	C4	H3	238.5	237.4
C4	C3	O3	S3	160.8	148.8
C5	C4	C3	O4	231.4	241.8
C5	C4	C3	H4	114.7	118.2
C3	C4	C5	C6	251.6	204.5
C3	C4	C5	O5	8.3	322.9
C3	C4	C5	H5	129.3	81.6
O4	C4	C3	H4	243.3	236.4
C3	C4	O4	S4	72.9	97.4
O3	C3	C2	O2	2.1	3.0
O3	C3	C2	O5	242.0	243.4
C2	C3	O3	C4	111.8	114.8
C2	C3	O3	H3	231.9	237.4
C4	C3	O3	H3	120.2	122.6
O3	C3	C4	C5	115.9	139.6
O3	C3	C4	O4	244.5	257.7
O3	C3	C4	H4	1.2	21.3
O1S3	S3	O3	C3	300.0	75.0
O2S3	S3	O3	C3	180.8	188.5
C3	O3	S3	O3S3	63.4	321.4
H3	C3	C2	O2	233.0	240.3
H3	C3	C2	O5	112.9	120.7
C2	C3	H3	C4	237.7	245.2
C2	C3	H3	O3	126.2	122.6
C4	C3	H3	O3	248.5	237.4
H3	C3	C4	C5	237.4	262.2
H3	C3	C4	O4	5.9	20.4
H3	C3	C4	H4	122.6	144.0
H3	C3	O3	S3	40.6	26.2
C2	O5	C5	C4	342.8	40.1
C5	C4	C3	O3	115.9	139.6
C5	C4	C3	H3	237.4	262.2
C3	C4	C5	O4	124.6	118.2
C3	C4	C5	H4	245.3	241.8
O4	C4	C5	H4	120.7	123.6
C5	C4	O4	S4	196.5	210.1
C6	C5	C4	O5	243.4	241.5
C6	C5	C4	H5	122.4	122.8
C4	C5	C6	O6	298.4	185.1
C4	C5	C6	H61	59.2	305.0
C4	C5	C6	H62	177.7	65.1
O5	C5	C4	H5	239.0	241.3
O4	C4	C3	O3	244.5	257.7
O4	C4	C3	H3	5.9	20.4
C3	C4	O4	C5	236.4	247.3
C3	C4	O4	H4	116.1	123.7
C5	C4	O4	H4	239.8	236.4
O4	C4	C5	C6	127.1	86.3
O4	C4	C5	O5	243.7	204.8
O4	C4	C5	H5	4.7	323.5
O1S4	S4	O4	C4	292.4	73.1
O2S4	S4	O4	C4	170.5	319.6
O3S4	S4	O4	C4	49.2	186.7
H4	C4	C3	O3	1.2	21.3
H4	C4	C3	H3	122.6	144.0
C3	C4	H4	C5	115.5	112.7
C3	C4	H4	O4	241.8	236.3
C5	C4	H4	O4	126.3	123.6
H4	C4	C5	C6	6.4	322.7
H4	C4	C5	O5	123.0	81.2
H4	C4	C5	H5	244.0	199.9
H4	C4	O4	S4	316.7	333.7
C2	O5	C5	C6	99.8	158.5
C6	C5	C4	O4	127.1	86.3
C6	C5	C4	H4	6.4	322.7
C4	C5	C6	O5	113.9	114.0
C4	C5	C6	H5	237.2	237.1
O5	C5	C6	H5	123.4	123.1
O6	C6	C5	H61	239.3	240.0
O6	C6	C5	H62	120.8	120.0
C5	C6	O6	S6	74.5	180.0
H61	C6	C5	H62	241.5	239.9
O5	C5	C4	O4	243.7	204.8
O5	C5	C4	H4	123.0	81.2
C4	C5	O5	C6	243.0	241.6
C4	C5	O5	H5	120.5	118.6
C6	C5	O5	H5	237.5	237.0
O5	C5	C6	O6	184.6	71.0
O5	C5	C6	H61	305.3	191.0
O5	C5	C6	H62	63.8	311.1
H5	C5	C4	O4	4.7	323.5
H5	C5	C4	H4	244.0	199.9
C4	C5	H5	C6	121.7	122.8
C4	C5	H5	O5	243.4	245.8
C6	C5	H5	O5	121.6	123.0
H5	C5	C6	O6	61.2	307.9
H5	C5	C6	H61	181.9	67.9
H5	C5	C6	H62	300.4	188.0
O6	C6	C5	O5	184.6	71.0
O6	C6	C5	H5	61.2	307.9
C5	C6	O6	H61	120.8	120.0
C5	C6	O6	H62	239.2	240.0
H61	C6	O6	H62	118.5	120.0
O1S6	S6	O6	C6	133.2	75.0
O2S6	S6	O6	C6	249.3	321.5
O3S6	S6	O6	C6	13.1	188.6
H61	C6	C5	O5	305.3	191.0
H61	C6	C5	H5	181.9	67.9
C5	C6	H61	O6	235.3	240.0
C5	C6	H61	H62	117.7	120.1
O6	C6	H61	H62	242.3	240.0
H61	C6	O6	S6	313.8	60.0
H62	C6	C5	O5	63.8	311.1
H62	C6	C5	H5	300.4	188.0
C5	C6	H62	O6	124.7	120.0
C5	C6	H62	H61	242.3	239.9
O6	C6	H62	H61	117.7	120.0
H62	C6	O6	S6	195.3	300.0
S1	O1	C1	H11	144.1	60.0
S1	O1	C1	H12	25.1	300.1
O1	S1	O1S1	H1S1	53.7	179.9
O1S1	S1	O1	O2S1	242.3	246.4
O1S1	S1	O1	O3S1	118.3	113.5
O2S1	S1	O1	O3S1	236.0	227.1
O1	S1	O1S1	O2S1	120.9	113.6
O1	S1	O1S1	O3S1	242.2	246.4
O2S1	S1	O1S1	O3S1	121.3	132.9
H1S1	O1S1	S1	O2S1	292.8	66.4
H1S1	O1S1	S1	O3S1	171.5	293.5
H1S3	O1S3	S3	O2S3	0.0	66.5
H1S3	O1S3	S3	O3	240.8	180.0
H1S3	O1S3	S3	O3S3	119.8	293.6
C3	O3	S3	O1S3	300.0	75.0
O2S3	S3	O1S3	O3	119.2	246.5
O2S3	S3	O1S3	O3S3	240.2	132.9
O3	S3	O1S3	O3S3	121.0	246.4
C4	O4	S4	O1S4	292.4	73.1
O2S4	S4	O1S4	O3S4	240.0	227.1
O2S4	S4	O1S4	O4	121.3	113.5
O3S4	S4	O1S4	O4	241.3	246.4
H1S4	O1S4	S4	O2S4	240.0	293.5
H1S4	O1S4	S4	O3S4	360.0	66.5
H1S4	O1S4	S4	O4	118.7	180.0
H1S6	O1S6	S6	O2S6	360.0	293.6
H1S6	O1S6	S6	O3S6	239.8	66.5
H1S6	O1S6	S6	O6	117.1	180.1
C6	O6	S6	O1S6	133.2	75.0
O2S6	S6	O1S6	O3S6	120.2	227.1
O2S6	S6	O1S6	O6	242.9	113.5
O3S6	S6	O1S6	O6	122.7	246.4
HO2	O2	C2	O5	165.4	298.2
O1	S1	O2S1	O1S1	241.4	245.9
O1	S1	O2S1	O3S1	121.9	123.0
O2S1	S1	O1S1	H1S1	292.8	66.4
O1S1	S1	O2S1	O3S1	240.5	237.1
C3	O3	S3	O2S3	180.8	188.5
O2S3	S3	O1S3	H1S3	0.0	66.5
O1S3	S3	O2S3	O3	241.9	114.1
O1S3	S3	O2S3	O3S3	123.2	237.0
O3	S3	O2S3	O3S3	241.3	123.0
C4	O4	S4	O2S4	170.5	319.6
O2S4	S4	O1S4	H1S4	240.0	293.5
O1S4	S4	O2S4	O3S4	117.4	123.0
O1S4	S4	O2S4	O4	237.9	245.8
O3S4	S4	O2S4	O4	120.5	122.9
C6	O6	S6	O2S6	249.3	321.5
O2S6	S6	O1S6	H1S6	360.0	293.6
O1S6	S6	O2S6	O3S6	242.5	122.9
O1S6	S6	O2S6	O6	118.6	245.9
O3S6	S6	O2S6	O6	236.1	123.0
S3	O3	C3	H3	40.6	26.2
O3	S3	O1S3	H1S3	240.8	180.0
O1S3	S3	O3	O2S3	119.2	246.5
O1S3	S3	O3	O3S3	236.7	113.6
O2S3	S3	O3	O3S3	117.4	227.1
O1	S1	O3S1	O1S1	117.9	114.1
O1	S1	O3S1	O2S1	236.0	237.0
O3S1	S1	O1S1	H1S1	171.5	293.5
O1S1	S1	O3S1	O2S1	118.1	122.9
O3S3	S3	O1S3	H1S3	119.8	293.6
O1S3	S3	O3S3	O2S3	239.0	122.9
O1S3	S3	O3S3	O3	120.2	245.9
O2S3	S3	O3S3	O3	241.2	122.9
C4	O4	S4	O3S4	49.2	186.7
O3S4	S4	O1S4	H1S4	360.0	66.5
O1S4	S4	O3S4	O2S4	240.1	237.0
O1S4	S4	O3S4	O4	119.5	114.2
O2S4	S4	O3S4	O4	239.5	237.1
C6	O6	S6	O3S6	13.1	188.6
O3S6	S6	O1S6	H1S6	239.8	66.5
O1S6	S6	O3S6	O2S6	116.7	237.1
O1S6	S6	O3S6	O6	238.3	114.1
O2S6	S6	O3S6	O6	121.6	237.0
S4	O4	C4	H4	316.7	333.7
O4	S4	O1S4	H1S4	118.7	180.0
O1S4	S4	O4	O2S4	121.9	113.6
O1S4	S4	O4	O3S4	243.2	246.4
O2S4	S4	O4	O3S4	121.2	132.9
S6	O6	C6	H61	313.8	60.0
S6	O6	C6	H62	195.3	300.0
O6	S6	O1S6	H1S6	117.1	180.1
O1S6	S6	O6	O2S6	243.9	113.5
O1S6	S6	O6	O3S6	120.2	246.4
O2S6	S6	O6	O3S6	236.3	132.9