Y5P

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
OP3	P	sing	1.61Å	1.61Å
P	O5'	sing	1.61Å	1.60Å
P	OP1	doub	1.48Å	1.49Å
P	OP2	sing	1.61Å	1.49Å
C5'	O5'	sing	1.43Å	1.42Å
C5'	C4'	sing	1.53Å	1.51Å
C4'	O4'	sing	1.44Å	1.46Å
C4'	C3'	sing	1.54Å	1.53Å
O4'	C1'	sing	1.44Å	1.41Å
C3'	O3'	sing	1.43Å	1.42Å
C3'	C2'	sing	1.55Å	1.52Å
C2'	O2'	sing	1.43Å	1.42Å
C2'	C1'	sing	1.55Å	1.52Å
C1'	N1	sing	1.46Å	1.48Å
N1	C2	sing	1.37Å	1.39Å
N1	C6	sing	1.39Å	1.38Å
C5	C6	doub	1.32Å	1.33Å
C2	N3	doub	1.29Å	1.37Å
N3	C4	sing	1.46Å	1.38Å
C4	C5	sing	1.50Å	1.43Å
OP3	HP3	sing	0.97Å	0.95Å
OP2	HP2	sing	0.97Å	0.95Å
C5'	HA1	sing	1.09Å	1.10Å
C5'	HB2	sing	1.09Å	1.10Å
C4'	HA	sing	1.09Å	1.10Å
C3'	HB	sing	1.09Å	1.10Å
C1'	HC	sing	1.09Å	1.10Å
C2'	H2'	sing	1.09Å	1.10Å
O2'	HD	sing	0.97Å	0.95Å
C2	H2	sing	1.08Å	1.08Å
C6	H6	sing	1.08Å	1.08Å
C4	H4	sing	1.09Å	1.10Å
O3'	H3'	sing	0.97Å	0.95Å
H5	C5	sing	1.08Å	1.08Å
C4	H4A	sing	1.09Å	1.10Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
OP3	P	O5'	103.7°	109.5°
OP3	P	OP1	108.0°	109.4°
OP3	P	OP2	108.8°	109.5°
P	OP3	HP3	109.5°	114.0°
O5'	P	OP1	106.0°	109.5°
O5'	P	OP2	110.7°	109.5°
P	O5'	C5'	121.8°	123.0°
OP1	P	OP2	118.5°	109.5°
P	OP2	HP2	109.5°	114.0°
O5'	C5'	C4'	111.6°	109.5°
O5'	C5'	HA1	108.9°	109.5°
O5'	C5'	HB2	108.9°	109.4°
C5'	C4'	O4'	109.2°	109.8°
C5'	C4'	C3'	115.2°	109.9°
C4'	C5'	HA1	108.9°	109.5°
C4'	C5'	HB2	109.0°	109.4°
C5'	C4'	HA	109.0°	109.9°
O4'	C4'	C3'	104.7°	107.2°
C4'	O4'	C1'	110.3°	107.0°
O4'	C4'	HA	109.8°	109.9°
C4'	C3'	O3'	113.1°	110.5°
C4'	C3'	C2'	103.2°	104.2°
C3'	C4'	HA	108.8°	110.0°
C4'	C3'	HB	108.1°	110.5°
O4'	C1'	C2'	107.4°	103.5°
O4'	C1'	N1	107.2°	110.6°
O4'	C1'	HC	111.0°	110.6°
O3'	C3'	C2'	114.3°	110.5°
O3'	C3'	HB	109.6°	110.4°
C3'	O3'	H3'	109.5°	114.0°
C3'	C2'	O2'	111.5°	110.9°
C3'	C2'	C1'	101.2°	102.1°
C2'	C3'	HB	108.1°	110.6°
C3'	C2'	H2'	111.1°	111.0°
O2'	C2'	C1'	108.7°	110.9°
O2'	C2'	H2'	112.7°	110.8°
C2'	O2'	HD	109.5°	113.9°
C2'	C1'	N1	112.1°	110.6°
C2'	C1'	HC	109.3°	110.6°
C1'	C2'	H2'	111.1°	110.9°
C1'	N1	C2	120.7°	120.3°
C1'	N1	C6	119.5°	120.3°
N1	C1'	HC	109.9°	110.7°
C2	N1	C6	119.8°	119.4°
N1	C2	N3	114.0°	121.2°
N1	C2	H2	123.0°	119.4°
N1	C6	C5	125.0°	119.6°
N1	C6	H6	117.5°	120.2°
C6	C5	C4	118.4°	121.2°
C5	C6	H6	117.5°	120.2°
C6	C5	H5	120.8°	119.4°
C2	N3	C4	128.6°	122.7°
N3	C2	H2	123.0°	119.4°
N3	C4	C5	114.2°	111.3°
N3	C4	H4	108.3°	109.1°
N3	C4	H4A	108.3°	109.1°
C5	C4	H4	108.3°	109.1°
C4	C5	H5	120.8°	119.4°
C5	C4	H4A	108.3°	109.1°
HA1	C5'	HB2	109.5°	109.5°
H4	C4	H4A	109.5°	109.1°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
OP3	P	O5'	OP1	113.7°	120.0°
OP3	P	O5'	OP2	116.5°	120.0°
OP3	P	OP1	OP2	124.3°	120.0°
OP3	P	O5'	C5'	121.9°	65.0°
OP3	P	OP2	HP2	123.9°	59.9°
O5'	P	OP1	OP2	125.1°	120.0°
P	O5'	C5'	C4'	118.1°	180.0°
O5'	P	OP3	HP3	112.2°	60.0°
O5'	P	OP2	HP2	122.8°	179.9°
P	O5'	C5'	HA1	2.2°	60.0°
P	O5'	C5'	HB2	121.5°	60.0°
OP1	P	O5'	C5'	124.5°	55.0°
OP1	P	OP3	HP3	0.0°	180.0°
OP1	P	OP2	HP2	0.0°	60.0°
OP2	P	O5'	C5'	5.3°	175.0°
OP2	P	OP3	HP3	129.9°	60.0°
O5'	C5'	C4'	HA1	120.3°	120.1°
O5'	C5'	C4'	HB2	120.3°	119.9°
O5'	C5'	C4'	O4'	49.6°	66.5°
O5'	C5'	C4'	C3'	167.1°	175.7°
O5'	C5'	HA1	HB2	119.0°	120.0°
O5'	C5'	C4'	HA	70.3°	54.5°
C5'	C4'	O4'	C3'	123.9°	119.4°
C5'	C4'	O4'	HA	119.4°	121.1°
C5'	C4'	C3'	HA	122.7°	121.2°
C5'	C4'	O4'	C1'	135.1°	145.9°
C5'	C4'	C3'	O3'	86.3°	119.9°
C5'	C4'	C3'	C2'	149.7°	121.4°
C4'	C5'	HA1	HB2	119.1°	120.0°
C5'	C4'	C3'	HB	35.3°	2.6°
O4'	C4'	C3'	HA	117.3°	119.5°
O4'	C4'	C3'	O3'	153.7°	120.7°
O4'	C4'	C3'	C2'	29.7°	2.1°
C4'	O4'	C1'	C2'	12.1°	40.1°
C4'	O4'	C1'	N1	108.6°	158.6°
O4'	C4'	C5'	HA1	70.7°	53.5°
O4'	C4'	C5'	HB2	169.9°	173.5°
O4'	C4'	C3'	HB	84.7°	116.8°
C4'	O4'	C1'	HC	131.4°	78.4°
C3'	C4'	O4'	C1'	11.2°	26.6°
C4'	C3'	O3'	C2'	117.7°	114.8°
C4'	C3'	O3'	HB	120.7°	122.5°
C4'	C3'	C2'	HB	114.4°	118.7°
C4'	C3'	C2'	O2'	79.7°	139.1°
C4'	C3'	C2'	C1'	35.7°	20.9°
C3'	C4'	C5'	HA1	46.8°	64.2°
C3'	C4'	C5'	HB2	72.6°	55.8°
C4'	C3'	C2'	H2'	153.7°	97.4°
C4'	C3'	O3'	H3'	180.0°	180.0°
O4'	C1'	C2'	C3'	30.0°	37.0°
O4'	C1'	C2'	O2'	87.4°	155.3°
O4'	C1'	C2'	N1	117.5°	118.5°
O4'	C1'	C2'	HC	120.4°	118.5°
O4'	C1'	N1	HC	120.7°	123.0°
O4'	C1'	N1	C2	176.3°	53.5°
O4'	C1'	N1	C6	3.8°	126.7°
C1'	O4'	C4'	HA	105.4°	93.0°
O4'	C1'	C2'	H2'	148.0°	81.2°
O3'	C3'	C2'	HB	122.3°	122.6°
O3'	C3'	C2'	O2'	43.5°	20.4°
O3'	C3'	C2'	C1'	159.0°	97.8°
O3'	C3'	C4'	HA	36.4°	1.2°
O3'	C3'	C2'	H2'	83.0°	144.0°
C3'	C2'	O2'	C1'	110.7°	112.7°
C3'	C2'	O2'	H2'	125.7°	123.7°
C3'	C2'	C1'	H2'	118.0°	118.3°
C3'	C2'	C1'	N1	87.5°	155.5°
C2'	C3'	C4'	HA	87.6°	117.5°
C3'	C2'	C1'	HC	150.5°	81.5°
C3'	C2'	O2'	HD	180.0°	61.4°
C2'	C3'	O3'	H3'	62.3°	65.2°
O2'	C2'	C1'	H2'	124.5°	123.5°
O2'	C2'	C1'	N1	155.1°	86.3°
O2'	C2'	C3'	HB	165.9°	102.2°
O2'	C2'	C1'	HC	33.0°	36.7°
C2'	C1'	N1	HC	121.7°	122.9°
C2'	C1'	N1	C2	58.7°	60.6°
C2'	C1'	N1	C6	121.4°	119.2°
C1'	C2'	C3'	HB	78.7°	139.6°
C1'	C2'	O2'	HD	69.3°	174.1°
C1'	N1	C2	C6	179.8°	179.8°
C1'	N1	C6	C5	179.8°	162.4°
C1'	N1	C2	N3	179.9°	162.3°
N1	C1'	C2'	H2'	30.5°	37.3°
C1'	N1	C2	H2	0.0°	17.7°
C1'	N1	C6	H6	0.2°	17.3°
C2	N1	C6	C5	0.0°	17.8°
N1	C2	N3	H2	180.0°	180.0°
N1	C2	N3	C4	0.3°	0.4°
C2	N1	C1'	HC	63.0°	176.5°
C2	N1	C6	H6	180.0°	162.5°
N1	C6	C5	H6	180.0°	179.7°
C6	N1	C2	N3	0.2°	17.9°
N1	C6	C5	C4	0.2°	0.2°
C6	N1	C1'	HC	116.8°	3.7°
C6	N1	C2	H2	179.8°	162.1°
N1	C6	C5	H5	179.8°	179.9°
C6	C5	C4	N3	0.1°	15.8°
C6	C5	C4	H5	180.0°	179.7°
C6	C5	C4	H4	120.5°	104.6°
C6	C5	C4	H4A	120.8°	136.3°
C2	N3	C4	C5	0.2°	16.4°
C2	N3	C4	H4	120.9°	104.1°
C2	N3	C4	H4A	120.6°	136.8°
N3	C4	C5	H4	120.7°	120.4°
N3	C4	C5	H4A	120.7°	120.5°
C4	N3	C2	H2	179.7°	179.6°
N3	C4	H4	H4A	117.8°	119.1°
N3	C4	C5	H5	179.9°	163.9°
C4	C5	C6	H6	179.8°	179.9°
C5	C4	H4	H4A	117.9°	119.1°
HA1	C5'	C4'	HA	169.4°	174.6°
HB2	C5'	C4'	HA	50.0°	65.4°
HA	C4'	C3'	HB	158.0°	123.7°
HB	C3'	C2'	H2'	39.3°	21.4°
HB	C3'	O3'	H3'	59.2°	57.5°
HC	C1'	C2'	H2'	91.5°	160.3°
H2'	C2'	O2'	HD	54.3°	62.3°
H6	C6	C5	H5	0.2°	0.4°
H4	C4	C5	H5	59.5°	75.7°
H5	C5	C4	H4A	59.2°	43.4°

Release date:	2014-10-08
Definition date:	2014-09-25
Last modified:	2020-06-17
Release status:	REL
Processing site:	EBI
Derived from:	4V19