PRD_900078

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
P	OP3	doub	1.48Å	1.52Å
P	OP1	sing	1.61Å	1.51Å
P	O1'	sing	1.61Å	1.64Å
P	OP2	sing	1.61Å	1.52Å
C1	O1	sing	1.43Å	1.45Å
C1	C2	sing	1.53Å	1.53Å
C1	O5	sing	1.43Å	1.44Å
O1	C4'	sing	1.43Å	1.44Å
C2	O2	sing	1.43Å	1.44Å
C2	C3	sing	1.53Å	1.52Å
C3	O3	sing	1.43Å	1.43Å
C3	C4	sing	1.53Å	1.54Å
C4	O4	sing	1.43Å	1.40Å
C4	C5	sing	1.53Å	1.52Å
C5	O5	sing	1.43Å	1.43Å
C5	C6	sing	1.53Å	1.49Å
C6	O6	sing	1.43Å	1.41Å
C1'	C2'	sing	1.53Å	1.55Å
C1'	O1'	sing	1.43Å	1.47Å
C1'	O5'	sing	1.43Å	1.44Å
C2'	O2'	sing	1.43Å	1.45Å
C2'	C3'	sing	1.53Å	1.55Å
C3'	O3'	sing	1.43Å	1.45Å
C3'	C4'	sing	1.53Å	1.57Å
C4'	C5'	sing	1.53Å	1.57Å
C5'	O5'	sing	1.43Å	1.45Å
C5'	C6'	sing	1.53Å	1.53Å
C6'	O6'	sing	1.43Å	1.44Å
C1	H1	sing	1.09Å	1.10Å
C2	H2	sing	1.09Å	1.10Å
O2	HO2	sing	0.97Å	0.95Å
C3	H3	sing	1.09Å	1.10Å
O3	HO3	sing	0.97Å	0.95Å
C4	H4	sing	1.09Å	1.10Å
O4	HO4	sing	0.97Å	0.95Å
C5	H5	sing	1.09Å	1.10Å
C6	H6A	sing	1.09Å	1.10Å
C6	H6	sing	1.09Å	1.10Å
O6	HO6	sing	0.97Å	0.95Å
C1'	H1'	sing	1.09Å	1.10Å
C2'	H2'	sing	1.09Å	1.10Å
O2'	HO2'	sing	0.97Å	0.95Å
C3'	H3'	sing	1.09Å	1.10Å
O3'	HO3'	sing	0.97Å	0.95Å
C4'	H4'	sing	1.09Å	1.10Å
C5'	H5'	sing	1.09Å	1.10Å
C6'	H6'	sing	1.09Å	1.10Å
C6'	H6'A	sing	1.09Å	1.10Å
O6'	HO6'	sing	0.97Å	0.95Å
OP1	HOP1	sing	0.97Å	0.95Å
OP2	HOP2	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
OP3	P	OP1	113.0°	109.5°
OP3	P	O1'	112.0°	109.5°
OP3	P	OP2	108.7°	109.5°
OP1	P	O1'	100.0°	109.4°
OP1	P	OP2	115.2°	109.4°
P	OP1	HOP1	109.5°	114.0°
O1'	P	OP2	107.5°	109.5°
P	O1'	C1'	121.8°	123.0°
P	OP2	HOP2	109.5°	114.0°
O1	C1	C2	112.2°	109.5°
O1	C1	O5	111.4°	109.5°
C1	O1	C4'	110.4°	114.0°
O1	C1	H1	107.1°	109.5°
C2	C1	O5	112.4°	109.4°
C1	C2	O2	109.2°	109.5°
C1	C2	C3	113.8°	109.2°
C2	C1	H1	106.1°	109.5°
C1	C2	H2	107.9°	109.5°
C1	O5	C5	114.9°	114.1°
O5	C1	H1	107.2°	109.5°
O1	C4'	C3'	111.8°	109.5°
O1	C4'	C5'	106.3°	109.5°
O1	C4'	H4'	108.3°	109.5°
O2	C2	C3	108.6°	109.5°
O2	C2	H2	109.1°	109.5°
C2	O2	HO2	109.5°	114.0°
C2	C3	O3	106.5°	109.5°
C2	C3	C4	109.3°	109.0°
C3	C2	H2	108.1°	109.6°
C2	C3	H3	108.7°	109.5°
O3	C3	C4	113.8°	109.6°
O3	C3	H3	110.0°	109.6°
C3	O3	HO3	109.5°	114.0°
C3	C4	O4	112.6°	109.5°
C3	C4	C5	107.8°	109.2°
C4	C3	H3	108.5°	109.6°
C3	C4	H4	108.7°	109.5°
O4	C4	C5	108.0°	109.5°
O4	C4	H4	110.6°	109.5°
C4	O4	HO4	109.5°	114.1°
C4	C5	O5	109.7°	109.4°
C4	C5	C6	111.7°	109.5°
C5	C4	H4	109.0°	109.6°
C4	C5	H5	109.3°	109.5°
O5	C5	C6	106.0°	109.4°
O5	C5	H5	110.4°	109.5°
C5	C6	O6	105.5°	109.5°
C6	C5	H5	109.6°	109.5°
C5	C6	H6A	110.5°	109.4°
C5	C6	H6	110.4°	109.5°
O6	C6	H6A	110.4°	109.5°
O6	C6	H6	110.4°	109.5°
C6	O6	HO6	109.5°	114.0°
C2'	C1'	O1'	117.2°	109.5°
C2'	C1'	O5'	100.7°	109.4°
C1'	C2'	O2'	116.0°	109.5°
C1'	C2'	C3'	106.5°	109.1°
C2'	C1'	H1'	108.5°	109.4°
C1'	C2'	H2'	105.3°	109.5°
O1'	C1'	O5'	110.5°	109.5°
O1'	C1'	H1'	109.5°	109.5°
C1'	O5'	C5'	112.4°	114.1°
O5'	C1'	H1'	110.0°	109.5°
O2'	C2'	C3'	116.3°	109.5°
O2'	C2'	H2'	106.4°	109.5°
C2'	O2'	HO2'	109.5°	114.0°
C2'	C3'	O3'	109.0°	109.5°
C2'	C3'	C4'	106.6°	109.0°
C3'	C2'	H2'	105.3°	109.6°
C2'	C3'	H3'	108.3°	109.6°
O3'	C3'	C4'	115.0°	109.5°
O3'	C3'	H3'	109.6°	109.5°
C3'	O3'	HO3'	109.5°	114.0°
C3'	C4'	C5'	116.5°	109.2°
C4'	C3'	H3'	108.1°	109.6°
C3'	C4'	H4'	106.8°	109.5°
C4'	C5'	O5'	112.4°	109.4°
C4'	C5'	C6'	117.1°	109.5°
C5'	C4'	H4'	106.8°	109.6°
C4'	C5'	H5'	106.5°	109.5°
O5'	C5'	C6'	105.7°	109.5°
O5'	C5'	H5'	107.9°	109.5°
C5'	C6'	O6'	111.4°	109.5°
C6'	C5'	H5'	106.9°	109.5°
C5'	C6'	H6'	109.0°	109.5°
C5'	C6'	H6'A	109.0°	109.5°
O6'	C6'	H6'	109.0°	109.5°
O6'	C6'	H6'A	109.0°	109.5°
C6'	O6'	HO6'	109.5°	114.0°
H6A	C6	H6	109.5°	109.4°
H6'	C6'	H6'A	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
OP3	P	OP1	O1'	119.3°	120.0°
OP3	P	OP1	OP2	125.8°	120.0°
OP3	P	O1'	OP2	119.4°	120.1°
OP3	P	O1'	C1'	178.8°	54.9°
OP3	P	OP1	HOP1	0.0°	180.0°
OP3	P	OP2	HOP2	0.0°	59.9°
OP1	P	O1'	OP2	120.6°	119.9°
OP1	P	O1'	C1'	58.8°	65.1°
OP1	P	OP2	HOP2	128.0°	60.1°
P	O1'	C1'	C2'	178.9°	150.0°
P	O1'	C1'	O5'	64.4°	90.0°
P	O1'	C1'	H1'	56.9°	30.1°
O1'	P	OP1	HOP1	119.3°	59.9°
O1'	P	OP2	HOP2	121.5°	180.0°
OP2	P	O1'	C1'	61.8°	175.0°
OP2	P	OP1	HOP1	125.8°	60.0°
O1	C1	C2	O5	126.6°	119.9°
O1	C1	C2	H1	116.6°	120.1°
O1	C1	O5	H1	116.8°	120.1°
O1	C1	C2	O2	39.2°	57.6°
O1	C1	C2	C3	82.4°	62.3°
O1	C1	O5	C5	77.2°	58.8°
C1	O1	C4'	C3'	92.4°	85.2°
C1	O1	C4'	C5'	139.4°	155.1°
O1	C1	C2	H2	157.7°	177.7°
C1	O1	C4'	H4'	25.0°	34.9°
C2	C1	O5	H1	116.2°	120.0°
C2	C1	O1	C4'	166.0°	167.6°
C1	C2	O2	C3	124.7°	119.7°
C1	C2	O2	H2	117.7°	120.1°
C1	C2	C3	H2	119.9°	120.0°
C1	C2	C3	O3	172.7°	176.9°
C1	C2	C3	C4	49.4°	57.0°
C2	C1	O5	C5	49.8°	61.2°
C1	C2	O2	HO2	180.0°	60.0°
C1	C2	C3	H3	68.8°	62.9°
O5	C1	O1	C4'	66.9°	72.5°
O5	C1	C2	O2	165.7°	177.5°
O5	C1	C2	C3	44.2°	57.6°
C1	O5	C5	C4	60.7°	61.2°
C1	O5	C5	C6	178.6°	178.9°
O5	C1	C2	H2	75.7°	62.4°
C1	O5	C5	H5	59.9°	58.9°
O1	C4'	C3'	C2'	159.9°	176.9°
O1	C4'	C3'	O3'	79.2°	63.2°
O1	C4'	C3'	C5'	122.5°	119.9°
O1	C4'	C3'	H4'	118.3°	120.1°
O1	C4'	C5'	H4'	115.5°	120.2°
O1	C4'	C5'	O5'	157.0°	177.5°
O1	C4'	C5'	C6'	80.4°	62.5°
C4'	O1	C1	H1	50.0°	47.5°
O1	C4'	C3'	H3'	43.6°	56.9°
O1	C4'	C5'	H5'	39.1°	57.5°
O2	C2	C3	H2	118.3°	120.1°
O2	C2	C3	O3	65.4°	63.3°
O2	C2	C3	C4	171.3°	176.9°
O2	C2	C1	H1	77.4°	62.5°
O2	C2	C3	H3	53.1°	57.0°
C2	C3	O3	C4	120.5°	119.5°
C2	C3	O3	H3	117.6°	120.2°
C2	C3	C4	H3	118.4°	119.8°
C2	C3	C4	O4	177.2°	176.9°
C2	C3	C4	C5	58.2°	57.0°
C3	C2	C1	H1	161.0°	177.6°
C3	C2	O2	HO2	55.4°	179.7°
C2	C3	O3	HO3	180.0°	60.0°
C2	C3	C4	H4	59.9°	63.0°
O3	C3	C4	H3	122.7°	120.3°
O3	C3	C4	O4	63.9°	63.3°
O3	C3	C4	C5	177.1°	176.8°
O3	C3	C2	H2	52.9°	56.9°
O3	C3	C4	H4	59.0°	56.9°
C3	C4	O4	C5	118.9°	119.7°
C3	C4	O4	H4	121.9°	120.1°
C3	C4	C5	H4	117.9°	119.9°
C3	C4	C5	O5	63.7°	57.6°
C3	C4	C5	C6	179.1°	177.6°
C4	C3	C2	H2	70.4°	63.0°
C4	C3	O3	HO3	59.5°	179.6°
C3	C4	O4	HO4	180.0°	60.0°
C3	C4	C5	H5	57.5°	62.3°
O4	C4	C5	H4	120.2°	120.2°
O4	C4	C5	O5	174.4°	177.5°
O4	C4	C5	C6	57.2°	62.5°
O4	C4	C3	H3	58.9°	57.0°
O4	C4	C5	H5	64.4°	57.6°
C4	C5	O5	C6	120.8°	119.9°
C4	C5	O5	H5	120.5°	120.0°
C4	C5	C6	H5	121.3°	120.1°
C4	C5	C6	O6	46.7°	175.0°
C5	C4	C3	H3	60.2°	62.9°
C5	C4	O4	HO4	61.1°	179.7°
C4	C5	C6	H6A	166.0°	55.0°
C4	C5	C6	H6	72.7°	64.9°
O5	C5	C6	H5	119.2°	120.0°
O5	C5	C6	O6	72.8°	65.1°
C5	O5	C1	H1	166.0°	178.9°
O5	C5	C4	H4	54.2°	62.3°
O5	C5	C6	H6A	46.5°	174.9°
O5	C5	C6	H6	167.9°	55.0°
C5	C6	O6	H6A	119.4°	119.9°
C5	C6	O6	H6	119.3°	120.0°
C6	C5	C4	H4	63.1°	57.6°
C5	C6	H6A	H6	121.8°	120.0°
C5	C6	O6	HO6	180.0°	180.0°
O6	C6	C5	H5	168.0°	54.9°
O6	C6	H6A	H6	121.8°	120.1°
C2'	C1'	O1'	O5'	114.6°	120.0°
C2'	C1'	O1'	H1'	124.1°	120.0°
C2'	C1'	O5'	H1'	114.4°	119.9°
C1'	C2'	O2'	C3'	126.4°	119.6°
C1'	C2'	O2'	H2'	116.7°	120.2°
C1'	C2'	C3'	H2'	111.5°	119.9°
C1'	C2'	C3'	O3'	174.6°	176.8°
C1'	C2'	C3'	C4'	60.7°	57.0°
C2'	C1'	O5'	C5'	74.3°	61.2°
C1'	C2'	O2'	HO2'	180.0°	60.1°
C1'	C2'	C3'	H3'	55.4°	63.0°
O1'	C1'	O5'	H1'	121.0°	120.1°
O1'	C1'	C2'	O2'	90.8°	57.5°
O1'	C1'	C2'	C3'	40.4°	62.4°
O1'	C1'	O5'	C5'	50.3°	58.8°
O1'	C1'	C2'	H2'	151.9°	177.6°
O5'	C1'	C2'	O2'	149.3°	177.5°
O5'	C1'	C2'	C3'	79.5°	57.6°
C1'	O5'	C5'	C4'	51.3°	61.2°
C1'	O5'	C5'	C6'	179.8°	178.8°
O5'	C1'	C2'	H2'	32.0°	62.3°
C1'	O5'	C5'	H5'	65.8°	58.8°
O2'	C2'	C3'	H2'	117.5°	120.2°
O2'	C2'	C3'	O3'	43.6°	63.3°
O2'	C2'	C3'	C4'	168.3°	176.9°
O2'	C2'	C1'	H1'	33.8°	62.5°
O2'	C2'	C3'	H3'	75.6°	56.9°
C2'	C3'	O3'	C4'	119.6°	119.6°
C2'	C3'	O3'	H3'	118.4°	120.2°
C2'	C3'	C4'	H3'	116.3°	120.0°
C2'	C3'	C4'	C5'	37.3°	57.0°
C3'	C2'	C1'	H1'	165.0°	177.6°
C3'	C2'	O2'	HO2'	53.6°	179.7°
C2'	C3'	O3'	HO3'	180.0°	60.1°
C2'	C3'	C4'	H4'	81.8°	63.0°
O3'	C3'	C4'	H3'	122.8°	120.2°
O3'	C3'	C4'	C5'	158.2°	176.9°
O3'	C3'	C2'	H2'	73.9°	56.9°
O3'	C3'	C4'	H4'	39.1°	56.9°
C3'	C4'	C5'	H4'	119.2°	119.9°
C3'	C4'	C5'	O5'	31.7°	57.6°
C3'	C4'	C5'	C6'	154.3°	177.6°
C4'	C3'	C2'	H2'	50.8°	63.0°
C4'	C3'	O3'	HO3'	60.4°	179.6°
C3'	C4'	C5'	H5'	86.3°	62.4°
C4'	C5'	O5'	C6'	128.9°	120.0°
C4'	C5'	O5'	H5'	117.1°	120.0°
C4'	C5'	C6'	H5'	119.2°	120.0°
C4'	C5'	C6'	O6'	43.9°	175.9°
C5'	C4'	C3'	H3'	78.9°	63.0°
C4'	C5'	C6'	H6'	164.2°	55.9°
C4'	C5'	C6'	H6'A	76.4°	64.1°
O5'	C5'	C6'	H5'	114.7°	120.0°
O5'	C5'	C6'	O6'	82.2°	64.1°
C5'	O5'	C1'	H1'	171.3°	178.9°
O5'	C5'	C4'	H4'	87.5°	62.3°
O5'	C5'	C6'	H6'	38.1°	175.9°
O5'	C5'	C6'	H6'A	157.6°	55.9°
C5'	C6'	O6'	H6'	120.3°	120.0°
C5'	C6'	O6'	H6'A	120.3°	120.0°
C6'	C5'	C4'	H4'	35.1°	57.7°
C5'	C6'	H6'	H6'A	119.2°	120.0°
C5'	C6'	O6'	HO6'	180.0°	180.0°
O6'	C6'	C5'	H5'	163.1°	55.9°
O6'	C6'	H6'	H6'A	119.1°	120.0°
H1	C1	C2	H2	41.1°	57.6°
H2	C2	O2	HO2	62.2°	60.1°
H2	C2	C3	H3	171.3°	177.1°
H3	C3	O3	HO3	62.4°	60.2°
H3	C3	C4	H4	178.2°	177.2°
H4	C4	O4	HO4	58.2°	60.1°
H4	C4	C5	H5	175.4°	177.7°
H5	C5	C6	H6A	72.7°	65.1°
H5	C5	C6	H6	48.7°	175.0°
H6A	C6	O6	HO6	60.6°	60.0°
H6	C6	O6	HO6	60.7°	60.0°
H1'	C1'	C2'	H2'	83.4°	57.6°
H2'	C2'	O2'	HO2'	63.3°	60.1°
H2'	C2'	C3'	H3'	167.0°	177.1°
H3'	C3'	O3'	HO3'	61.6°	60.2°
H3'	C3'	C4'	H4'	161.9°	177.0°
H4'	C4'	C5'	H5'	154.5°	177.7°
H5'	C5'	C6'	H6'	76.6°	64.1°
H5'	C5'	C6'	H6'A	42.8°	175.9°
H6'	C6'	O6'	HO6'	59.7°	60.0°
H6'A	C6'	O6'	HO6'	59.7°	60.0°

Release date:	2020-07-29
Last modified:	2020-07-29
Processing site:	RCSB