PDB Chemical Component UPC

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 UPC

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
C1'	N1	1.468	1.465
N1	C6	1.354	1.368
N1	C2	1.411	1.346
O2	C2	1.361	1.215
C2	N3	1.346	1.346
N3	C4	1.353	1.348
C5	C4	1.398	1.416
C4	O4	1.353	1.218
C6	C5	1.389	1.351
C5	H5	1.081	1.080
C6	H6	1.080	1.080
O2A	PA	1.512	1.480
PA	C3A	1.720	1.823
PA	O5'	1.626	1.609
PA	O1A	1.495	1.610
O2B	PB	1.502	1.479
O3B	PB	1.604	1.610
PB	O1B	1.509	1.610
PB	C3A	1.736	1.823
O2G	PG	1.511	1.481
O1G	PG	1.510	1.610
PG	O3B	1.622	1.609
PG	O3G	1.823	1.610
O4'	C1'	1.428	1.438
C2'	C1'	1.533	1.541
C1'	H1'	1.100	1.090
O1A	HO1A	0.950	0.967
O1B	HO1B	0.950	0.967
O1G	HO1G	0.950	0.967
C3'	C2'	1.513	1.548
C2'	H2'	1.100	1.090
C2'	H2'A	1.100	1.090
O3'	C3'	1.433	1.428
C4'	C3'	1.523	1.550
C3'	H3'	1.100	1.091
O3'	HO3'	0.950	0.967
C3A	H3A	1.100	1.090
C3A	H3AA	1.100	1.090
O3G	HO3G	0.950	0.967
C5'	C4'	1.524	1.530
C4'	O4'	1.437	1.446
C4'	H4'	1.100	1.089
C5'	O5'	1.418	1.429
C5'	H5'	1.099	1.090
C5'	H5'A	1.100	1.090
N3	HN3	1.000	0.970

Bond Angles for UPC

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C2	N1	C6	119.9	120.6
N1	C6	C5	120.0	119.7
N1	C6	H6	120.0	120.2
N1	C2	N3	120.1	120.9
O2	C2	N3	119.9	119.5
C2	N3	C4	120.2	120.3
C2	N3	HN3	119.9	119.9
N3	C4	O4	118.5	120.3
C4	N3	HN3	119.9	119.9
C6	C5	H5	120.7	120.4
O2A	PA	C3A	107.8	109.5
O2A	PA	O5'	110.8	109.5
C3A	PA	O5'	102.5	109.5
O1A	PA	C3A	113.4	109.5
PA	C3A	PB	119.7	109.5
PA	C3A	H3A	106.2	109.5
PA	C3A	H3AA	106.2	109.5
O1A	PA	O5'	105.3	109.5
PA	O5'	C5'	124.0	123.0
PA	O1A	HO1A	109.5	114.0
O2B	PB	C3A	111.5	109.5
O1B	PB	C3A	109.7	109.5
PB	O1B	HO1B	109.5	114.0
PB	C3A	H3A	106.2	109.5
PB	C3A	H3AA	106.2	109.5
O2G	PG	O3B	102.9	109.5
O2G	PG	O3G	107.2	109.5
O1G	PG	O3B	107.8	109.5
O1G	PG	O3G	111.9	109.5
O3B	PG	O3G	110.2	109.5
PG	O3G	HO3G	109.5	114.0
O4'	C1'	H1'	108.1	109.9
C2'	C1'	H1'	115.3	109.9
C3'	C2'	H2'	111.7	110.5
C3'	C2'	H2'A	111.6	110.6
H2'	C2'	H2'A	107.2	110.5
O3'	C3'	H3'	102.2	110.8
C4'	C3'	H3'	112.1	110.9
H3A	C3A	H3AA	112.5	109.4
C5'	C4'	H4'	104.5	110.7
O4'	C4'	H4'	114.3	110.5
O5'	C5'	H5'	109.1	109.4
O5'	C5'	H5'A	109.1	109.5
H5'	C5'	H5'A	109.9	109.4

Torsion Angles for UPC

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
C1'	N1	C6	H6	358.6	0.3
C6	N1	C2	N3	359.8	360.0
N1	C6	C5	H5	180.0	180.0
C2	N1	C6	C5	359.9	360.0
C2	N1	C6	H6	179.9	180.0
O2	C2	N1	N3	180.0	180.0
N1	C2	N3	C4	0.5	0.1
N1	C2	N3	HN3	180.5	179.9
O2	C2	N1	C6	179.8	180.0
N1	C2	O2	N3	180.0	180.0
O2	C2	N3	C4	180.6	180.0
O2	C2	N3	HN3	0.6	359.9
N3	C2	N1	C6	359.8	360.0
C2	N3	C4	O4	179.4	180.0
C4	N3	C2	HN3	180.0	180.1
C2	N3	C4	HN3	180.0	179.9
N1	C6	C5	C4	0.1	0.0
C5	C4	N3	HN3	179.4	180.1
O4	C4	N3	HN3	359.4	0.1
N1	C6	C5	H6	180.0	180.0
N1	C6	H6	C5	180.0	180.0
H6	C6	C5	H5	0.1	0.0
C3A	PA	O2A	O5'	248.6	240.0
O1A	PA	O2A	C3A	231.5	240.0
O2A	PA	C3A	PB	51.2	300.0
O2A	PA	C3A	H3A	171.2	60.0
O2A	PA	C3A	H3AA	291.2	179.9
O1A	PA	O2A	O5'	120.1	120.0
O2A	PA	O5'	C5'	344.4	55.0
O2A	PA	O1A	HO1A	0.0	180.0
O2A	PA	C3A	O5'	116.9	120.0
O1A	PA	C3A	O5'	247.0	240.0
C3A	PA	O5'	C5'	99.2	175.0
C3A	PA	O1A	HO1A	234.3	60.0
O2B	PB	C3A	PA	342.2	300.0
O1B	PB	C3A	PA	111.8	60.0
PB	C3A	PA	H3A	240.0	240.0
PB	C3A	PA	H3AA	120.0	120.0
H3A	C3A	PA	H3AA	240.0	240.1
O2A	PA	O5'	C3A	245.2	240.0
O1A	PA	O5'	C3A	118.9	120.0
O5'	PA	C3A	PB	294.3	180.0
O5'	PA	C3A	H3A	54.3	300.0
O5'	PA	C3A	H3AA	174.3	60.0
O5'	PA	O1A	HO1A	123.0	300.0
PA	O5'	C5'	H5'	88.3	60.0
PA	O5'	C5'	H5'A	328.3	300.1
O2A	PA	O1A	C3A	125.7	120.0
O2A	PA	O1A	O5'	237.0	240.0
C3A	PA	O1A	O5'	111.3	120.0
O1A	PA	C3A	PB	181.3	60.0
O1A	PA	C3A	H3A	301.3	180.0
O1A	PA	C3A	H3AA	61.3	299.9
O1A	PA	O5'	C5'	218.1	295.0
PA	C3A	PB	O2B	342.2	300.0
O1B	PB	O2B	C3A	233.6	240.0
O2B	PB	O1B	HO1B	360.0	180.0
O2B	PB	C3A	H3A	222.2	180.0
O2B	PB	C3A	H3AA	102.2	60.0
O3B	PB	O1B	HO1B	119.4	300.0
O3B	PB	C3A	H3A	106.6	60.0
O3B	PB	C3A	H3AA	346.7	300.0
PA	C3A	PB	O1B	111.8	60.0
O2B	PB	O1B	C3A	127.3	120.0
O1B	PB	C3A	H3A	351.8	300.0
O1B	PB	C3A	H3AA	231.8	180.0
PB	C3A	PA	O5'	294.3	180.0
PA	C3A	PB	H3A	120.0	120.0
PA	C3A	PB	H3AA	240.0	240.0
C3A	PB	O1B	HO1B	232.7	60.0
H3A	C3A	PB	H3AA	120.0	120.0
O1G	PG	O2G	O3B	117.7	120.0
O1G	PG	O2G	O3G	233.8	240.0
O3B	PG	O2G	O3G	116.2	120.0
O2G	PG	O3G	HO3G	0.0	300.1
O2G	PG	O1G	O3B	245.1	240.0
O2G	PG	O1G	O3G	123.8	120.0
O3B	PG	O1G	O3G	238.7	240.0
O1G	PG	O3G	HO3G	128.8	60.0
O2G	PG	O3B	O3G	246.0	240.0
O1G	PG	O3B	O3G	122.4	120.0
O3B	PG	O3G	HO3G	248.8	180.0
O2G	PG	O3G	O3B	111.3	120.0
O1G	PG	O3G	O3B	240.1	240.0
C2'	C1'	O4'	H1'	235.8	240.4
O4'	C1'	C2'	H1'	119.7	119.5
HO1A	O1A	PA	C3A	234.3	60.0
HO1A	O1A	PA	O5'	123.0	300.0
HO1B	O1B	PB	C3A	232.7	60.0
HO1G	O1G	PG	O3B	114.9	300.0
HO1G	O1G	PG	O3G	236.2	60.0
C3'	C2'	C1'	H1'	216.9	242.5
H2'	C2'	C3'	H2'A	120.0	122.6
H2'	C2'	C1'	H1'	336.9	1.1
C3'	C2'	H2'	H2'A	237.4	237.3
H2'A	C2'	C1'	H1'	96.9	123.6
C3'	C2'	H2'A	H2'	122.6	122.7
O3'	C3'	C2'	H2'	38.1	20.5
O3'	C3'	C2'	H2'A	278.1	257.8
C4'	C3'	O3'	H3'	238.4	236.3
C4'	C3'	C2'	H2'	275.5	262.2
C4'	C3'	C2'	H2'A	155.5	139.6
O3'	C3'	C4'	H3'	116.0	123.6
H3'	C3'	C2'	H2'	154.1	144.0
H3'	C3'	C2'	H2'A	34.1	21.4
HO3'	O3'	C3'	H3'	56.3	297.9
H3A	C3A	PA	O5'	54.3	300.0
PA	C3A	H3A	PB	231.6	240.0
PA	C3A	H3A	H3AA	115.8	120.0
PB	C3A	H3A	H3AA	244.2	240.0
H3AA	C3A	PA	O5'	174.3	60.0
PA	C3A	H3AA	PB	128.4	120.0
PA	C3A	H3AA	H3A	244.2	240.0
PB	C3A	H3AA	H3A	115.8	120.0
PA	O5'	C5'	C4'	208.3	180.0
C5'	C4'	C3'	H3'	327.4	322.7
O4'	C4'	C5'	H4'	122.9	122.8
C4'	O4'	C1'	H1'	125.0	93.2
O4'	C4'	C3'	H3'	87.8	81.2
C5'	C4'	O4'	H4'	243.2	237.1
H4'	C4'	C3'	H3'	210.7	199.7
O5'	C5'	C4'	H4'	170.5	308.1
H5'	C5'	O5'	H5'A	120.0	119.9
H5'	C5'	C4'	H4'	290.5	68.0
O5'	C5'	H5'	H5'A	240.5	240.0
H5'A	C5'	C4'	H4'	50.5	188.0
O5'	C5'	H5'A	H5'	119.5	120.0
C2	N3	HN3	C4	180.0	180.1
HN3	N3	C4	O4	359.4	0.1