RPD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O1P	P	doub	1.48Å	1.47Å
O2P	P	sing	1.61Å	1.50Å
O2P	HO2P	sing	0.97Å	0.95Å
O3P	P	sing	1.61Å	1.45Å
O3P	HO3P	sing	0.97Å	0.95Å
P	O5'	sing	1.61Å	1.63Å
O5'	C5'	sing	1.43Å	1.41Å
C5'	C4'	sing	1.53Å	1.52Å
C5'	H5'1	sing	1.09Å	1.12Å
C5'	H5'2	sing	1.09Å	1.12Å
C4'	O4'	sing	1.44Å	1.42Å
C4'	C3'	sing	1.55Å	1.51Å
C4'	H4	sing	1.09Å	1.11Å
O4'	C1'	sing	1.42Å	1.47Å
C3'	O3'	sing	1.43Å	1.44Å
C3'	C2'	sing	1.55Å	1.57Å
C3'	H3	sing	1.09Å	1.12Å
O3'	HO3'	sing	0.97Å	0.95Å
C2'	O2'	sing	1.43Å	1.44Å
C2'	C1'	sing	1.54Å	1.55Å
C2'	H2	sing	1.09Å	1.12Å
O2'	HO2'	sing	0.97Å	0.95Å
C1'	N1	sing	1.47Å	1.37Å
C1'	C4	sing	1.51Å	1.45Å
N1	C2	sing	1.35Å	1.38Å
N1	HN1	sing	0.97Å	1.02Å
C2	O2	doub	1.22Å	1.18Å
C2	N3	sing	1.34Å	1.37Å
N3	C4	sing	1.35Å	1.40Å
N3	C5A	sing	1.47Å	1.48Å
C4	O4	doub	1.21Å	1.24Å
C5A	C6A	sing	1.53Å	1.54Å
C5A	H51	sing	1.09Å	1.11Å
C5A	H52	sing	1.09Å	1.12Å
C6A	C7A	sing	1.53Å	1.55Å
C6A	H61	sing	1.09Å	1.11Å
C6A	H62	sing	1.09Å	1.11Å
C7A	C8A	sing	1.53Å	1.55Å
C7A	H71	sing	1.09Å	1.12Å
C7A	H72	sing	1.09Å	1.12Å
C8A	C9A	sing	1.51Å	1.53Å
C8A	NAA	sing	1.47Å	1.51Å
C8A	H81	sing	1.09Å	1.11Å
C9A	OJA	sing	1.34Å	1.35Å
C9A	OKA	doub	1.21Å	1.36Å
OJA	H91	sing	0.97Å	0.95Å
NAA	OAA	sing	1.46Å	1.46Å
NAA	CBA	sing	1.47Å	1.47Å
OAA	H10	sing	0.97Å	0.95Å
CBA	OBA	sing	1.43Å	1.42Å
CBA	H111	sing	1.09Å	1.11Å
CBA	H112	sing	1.09Å	1.12Å
OBA	H11	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O1P	P	O2P	109.0°	109.5°
O1P	P	O3P	109.7°	109.5°
O1P	P	O5'	109.0°	109.5°
P	O2P	HO2P	109.0°	106.8°
O2P	P	O3P	110.5°	109.4°
O2P	P	O5'	107.8°	109.5°
P	O3P	HO3P	109.8°	106.9°
O3P	P	O5'	110.8°	109.5°
P	O5'	C5'	124.2°	106.8°
O5'	C5'	C4'	110.9°	109.5°
O5'	C5'	H5'1	111.7°	109.5°
O5'	C5'	H5'2	111.7°	109.4°
C4'	C5'	H5'1	111.7°	109.5°
C4'	C5'	H5'2	111.7°	109.4°
C5'	C4'	O4'	110.2°	110.4°
C5'	C4'	C3'	114.0°	110.4°
C5'	C4'	H4	104.7°	110.2°
H5'1	C5'	H5'2	98.7°	109.5°
O4'	C4'	C3'	105.8°	105.2°
O4'	C4'	H4	113.1°	110.2°
C4'	O4'	C1'	114.6°	109.7°
C3'	C4'	H4	109.2°	110.3°
C4'	C3'	O3'	109.6°	111.1°
C4'	C3'	C2'	102.6°	101.0°
C4'	C3'	H3	113.9°	111.1°
O4'	C1'	C2'	102.3°	108.3°
O4'	C1'	N1	107.8°	111.5°
O4'	C1'	C4	117.2°	111.2°
O3'	C3'	C2'	110.0°	111.2°
O3'	C3'	H3	107.1°	111.0°
C3'	O3'	HO3'	109.6°	106.8°
C2'	C3'	H3	113.6°	111.1°
C3'	C2'	O2'	108.9°	110.9°
C3'	C2'	C1'	105.9°	102.0°
C3'	C2'	H2	112.2°	110.9°
O2'	C2'	C1'	109.8°	111.0°
O2'	C2'	H2	108.6°	110.8°
C2'	O2'	HO2'	108.9°	106.8°
C1'	C2'	H2	111.4°	110.9°
C2'	C1'	N1	107.6°	110.6°
C2'	C1'	C4	117.6°	110.8°
N1	C1'	C4	103.9°	104.3°
C1'	N1	C2	110.8°	106.3°
C1'	N1	HN1	111.7°	126.9°
C1'	C4	N3	109.9°	105.4°
C1'	C4	O4	129.1°	127.3°
C2	N1	HN1	111.7°	126.8°
N1	C2	O2	124.7°	123.8°
N1	C2	N3	109.6°	112.4°
O2	C2	N3	125.7°	123.8°
C2	N3	C4	105.8°	111.6°
C2	N3	C5A	126.1°	124.1°
C4	N3	C5A	128.0°	124.3°
N3	C4	O4	121.1°	127.3°
N3	C5A	C6A	110.3°	109.5°
N3	C5A	H51	111.9°	109.5°
N3	C5A	H52	111.9°	109.4°
C6A	C5A	H51	111.9°	109.6°
C6A	C5A	H52	111.9°	109.4°
C5A	C6A	C7A	111.3°	109.5°
C5A	C6A	H61	111.5°	109.5°
C5A	C6A	H62	111.5°	109.4°
H51	C5A	H52	98.5°	109.4°
C7A	C6A	H61	111.5°	109.6°
C7A	C6A	H62	111.5°	109.5°
C6A	C7A	C8A	108.8°	109.5°
C6A	C7A	H71	112.5°	109.5°
C6A	C7A	H72	112.5°	109.4°
H61	C6A	H62	98.9°	109.4°
C8A	C7A	H71	112.5°	109.5°
C8A	C7A	H72	112.5°	109.4°
C7A	C8A	C9A	111.7°	109.5°
C7A	C8A	NAA	113.1°	109.5°
C7A	C8A	H81	104.3°	109.4°
H71	C7A	H72	97.9°	109.4°
C9A	C8A	NAA	106.1°	109.5°
C9A	C8A	H81	111.5°	109.5°
C8A	C9A	OJA	121.0°	120.0°
C8A	C9A	OKA	118.6°	120.0°
NAA	C8A	H81	110.2°	109.4°
C8A	NAA	OAA	108.7°	106.7°
C8A	NAA	CBA	112.3°	106.7°
OJA	C9A	OKA	120.4°	119.9°
C9A	OJA	H91	121.0°	120.0°
OAA	NAA	CBA	109.4°	106.7°
NAA	OAA	H10	108.6°	106.8°
NAA	CBA	OBA	111.2°	109.5°
NAA	CBA	H111	111.6°	109.4°
NAA	CBA	H112	111.6°	109.5°
OBA	CBA	H111	111.6°	109.5°
OBA	CBA	H112	111.5°	109.5°
CBA	OBA	H11	111.2°	106.8°
H111	CBA	H112	98.8°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O1P	P	O2P	O3P	120.6°	120.0°
O1P	P	O2P	O5'	118.2°	120.0°
O1P	P	O2P	HO2P	180.0°	60.0°
O1P	P	O3P	O5'	120.4°	120.1°
O1P	P	O3P	HO3P	180.0°	180.0°
O1P	P	O5'	C5'	58.4°	60.0°
O2P	P	O3P	O5'	119.4°	120.0°
O2P	P	O3P	HO3P	59.8°	60.0°
O2P	P	O5'	C5'	59.8°	180.0°
HO2P	O2P	P	O3P	59.3°	60.0°
HO2P	O2P	P	O5'	61.9°	179.9°
O3P	P	O5'	C5'	179.2°	60.0°
HO3P	O3P	P	O5'	59.6°	59.9°
P	O5'	C5'	C4'	129.7°	179.9°
P	O5'	C5'	H5'1	105.1°	60.0°
P	O5'	C5'	H5'2	4.4°	60.0°
O5'	C5'	C4'	H5'1	125.2°	120.1°
O5'	C5'	C4'	H5'2	125.3°	119.9°
O5'	C5'	H5'1	H5'2	117.5°	120.0°
O5'	C5'	C4'	O4'	75.9°	61.4°
O5'	C5'	C4'	C3'	42.9°	177.3°
O5'	C5'	C4'	H4	162.2°	60.6°
C4'	C5'	H5'1	H5'2	117.6°	119.9°
C5'	C4'	O4'	C3'	123.7°	119.1°
C5'	C4'	O4'	H4	116.8°	122.0°
C5'	C4'	C3'	H4	116.7°	122.1°
C5'	C4'	O4'	C1'	103.6°	143.3°
C5'	C4'	C3'	O3'	150.7°	86.9°
C5'	C4'	C3'	C2'	92.5°	155.0°
C5'	C4'	C3'	H3	30.8°	37.2°
H5'1	C5'	C4'	O4'	158.9°	178.5°
H5'1	C5'	C4'	C3'	82.4°	62.7°
H5'1	C5'	C4'	H4	36.9°	59.5°
H5'2	C5'	C4'	O4'	49.4°	58.5°
H5'2	C5'	C4'	C3'	168.1°	57.4°
H5'2	C5'	C4'	H4	72.6°	179.5°
O4'	C4'	C3'	H4	122.1°	118.9°
O4'	C4'	C3'	O3'	88.1°	154.0°
O4'	C4'	C3'	C2'	28.8°	36.0°
O4'	C4'	C3'	H3	152.0°	81.9°
C4'	O4'	C1'	C2'	1.7°	1.8°
C4'	O4'	C1'	N1	111.5°	123.8°
C4'	O4'	C1'	C4	131.9°	120.1°
C3'	C4'	O4'	C1'	20.1°	24.2°
C4'	C3'	O3'	C2'	112.0°	111.7°
C4'	C3'	O3'	H3	124.1°	124.2°
C4'	C3'	C2'	H3	123.4°	117.9°
C4'	C3'	O3'	HO3'	180.0°	61.5°
C4'	C3'	C2'	O2'	146.0°	84.7°
C4'	C3'	C2'	C1'	28.0°	33.5°
C4'	C3'	C2'	H2	93.7°	151.8°
H4	C4'	O4'	C1'	139.6°	94.7°
H4	C4'	C3'	O3'	34.0°	35.1°
H4	C4'	C3'	C2'	150.8°	82.9°
H4	C4'	C3'	H3	85.9°	159.2°
O4'	C1'	C2'	C3'	16.6°	20.9°
O4'	C1'	C2'	O2'	134.1°	97.2°
O4'	C1'	C2'	N1	113.3°	122.6°
O4'	C1'	C2'	C4	130.0°	122.2°
O4'	C1'	C2'	H2	105.6°	139.1°
O4'	C1'	N1	C4	125.0°	120.2°
O4'	C1'	N1	C2	124.6°	120.3°
O4'	C1'	N1	HN1	110.1°	59.6°
O4'	C1'	C4	N3	118.2°	120.7°
O4'	C1'	C4	O4	61.7°	59.6°
O3'	C3'	C2'	H3	120.0°	124.1°
O3'	C3'	C2'	O2'	29.5°	33.3°
O3'	C3'	C2'	C1'	88.5°	151.5°
O3'	C3'	C2'	H2	149.7°	90.2°
C2'	C3'	O3'	HO3'	67.9°	173.2°
C3'	C2'	O2'	C1'	115.6°	112.7°
C3'	C2'	O2'	H2	122.5°	123.6°
C3'	C2'	C1'	H2	122.3°	118.2°
C3'	C2'	O2'	HO2'	180.0°	61.5°
C3'	C2'	C1'	N1	130.0°	101.6°
C3'	C2'	C1'	C4	113.3°	143.2°
H3	C3'	O3'	HO3'	55.9°	62.7°
H3	C3'	C2'	O2'	90.5°	157.4°
H3	C3'	C2'	C1'	151.5°	84.4°
H3	C3'	C2'	H2	29.7°	33.9°
O2'	C2'	C1'	H2	120.3°	123.6°
O2'	C2'	C1'	N1	112.5°	140.2°
O2'	C2'	C1'	C4	4.2°	25.0°
C1'	C2'	O2'	HO2'	64.4°	174.2°
C2'	C1'	N1	C4	125.4°	119.1°
C2'	C1'	N1	C2	125.8°	119.0°
C2'	C1'	N1	HN1	0.5°	61.1°
C2'	C1'	C4	N3	119.2°	118.8°
C2'	C1'	C4	O4	60.9°	60.9°
H2	C2'	O2'	HO2'	57.5°	62.1°
H2	C2'	C1'	N1	7.7°	16.6°
H2	C2'	C1'	C4	124.4°	98.6°
C1'	N1	C2	HN1	125.3°	180.0°
C1'	N1	C2	O2	179.8°	180.0°
C1'	N1	C2	N3	0.2°	0.0°
N1	C1'	C4	N3	0.5°	0.3°
N1	C1'	C4	O4	179.6°	180.0°
C4	C1'	N1	C2	0.4°	0.2°
C4	C1'	N1	HN1	124.9°	179.8°
C1'	C4	N3	C2	0.3°	0.3°
C1'	C4	N3	O4	180.0°	179.7°
C1'	C4	N3	C5A	179.9°	179.9°
N1	C2	O2	N3	179.9°	180.0°
N1	C2	N3	C4	0.1°	0.3°
N1	C2	N3	C5A	179.8°	180.0°
HN1	N1	C2	O2	54.8°	0.0°
HN1	N1	C2	N3	125.1°	180.0°
O2	C2	N3	C4	179.8°	179.7°
O2	C2	N3	C5A	0.1°	0.0°
C2	N3	C4	C5A	179.7°	179.8°
C2	N3	C4	O4	179.7°	179.9°
C2	N3	C5A	C6A	103.6°	90.1°
C2	N3	C5A	H51	131.1°	30.1°
C2	N3	C5A	H52	21.6°	150.0°
C4	N3	C5A	C6A	76.1°	90.2°
C4	N3	C5A	H51	49.2°	149.7°
C4	N3	C5A	H52	158.7°	29.7°
C5A	N3	C4	O4	0.1°	0.2°
N3	C5A	C6A	H51	125.3°	120.1°
N3	C5A	C6A	H52	125.3°	119.9°
N3	C5A	H51	H52	117.8°	119.9°
N3	C5A	C6A	C7A	51.9°	180.0°
N3	C5A	C6A	H61	73.4°	59.8°
N3	C5A	C6A	H62	177.1°	60.1°
C6A	C5A	H51	H52	117.8°	120.0°
C5A	C6A	C7A	H61	125.2°	120.1°
C5A	C6A	C7A	H62	125.2°	119.9°
C5A	C6A	H61	H62	117.4°	119.9°
C5A	C6A	C7A	C8A	178.0°	176.4°
C5A	C6A	C7A	H71	52.7°	63.5°
C5A	C6A	C7A	H72	56.8°	56.4°
H51	C5A	C6A	C7A	177.1°	59.9°
H51	C5A	C6A	H61	51.9°	180.0°
H51	C5A	C6A	H62	57.6°	60.1°
H52	C5A	C6A	C7A	73.4°	60.1°
H52	C5A	C6A	H61	161.4°	60.0°
H52	C5A	C6A	H62	51.9°	179.9°
C7A	C6A	H61	H62	117.4°	120.0°
C6A	C7A	C8A	H71	125.3°	120.1°
C6A	C7A	C8A	H72	125.3°	120.0°
C6A	C7A	H71	H72	118.4°	120.0°
C6A	C7A	C8A	C9A	150.9°	65.4°
C6A	C7A	C8A	NAA	89.4°	174.6°
C6A	C7A	C8A	H81	30.3°	54.6°
H61	C6A	C7A	C8A	56.8°	56.3°
H61	C6A	C7A	H71	177.9°	176.4°
H61	C6A	C7A	H72	68.5°	63.7°
H62	C6A	C7A	C8A	52.7°	63.7°
H62	C6A	C7A	H71	72.6°	56.4°
H62	C6A	C7A	H72	178.0°	176.3°
C8A	C7A	H71	H72	118.4°	119.9°
C7A	C8A	C9A	NAA	123.7°	120.1°
C7A	C8A	C9A	H81	116.3°	119.9°
C7A	C8A	NAA	H81	116.3°	119.9°
C7A	C8A	C9A	OJA	35.3°	97.1°
C7A	C8A	C9A	OKA	144.8°	82.9°
C7A	C8A	NAA	OAA	123.6°	47.7°
C7A	C8A	NAA	CBA	2.4°	66.1°
H71	C7A	C8A	C9A	83.8°	54.8°
H71	C7A	C8A	NAA	35.8°	65.3°
H71	C7A	C8A	H81	155.6°	174.7°
H72	C7A	C8A	C9A	25.6°	174.6°
H72	C7A	C8A	NAA	145.2°	54.6°
H72	C7A	C8A	H81	95.0°	65.4°
C9A	C8A	NAA	H81	120.9°	120.0°
C8A	C9A	OJA	OKA	179.8°	180.0°
C8A	C9A	OJA	H91	180.0°	180.0°
C9A	C8A	NAA	OAA	113.6°	72.3°
C9A	C8A	NAA	CBA	125.3°	173.9°
NAA	C8A	C9A	OJA	159.0°	23.0°
NAA	C8A	C9A	OKA	21.1°	157.0°
C8A	NAA	OAA	CBA	122.9°	113.8°
C8A	NAA	OAA	H10	180.0°	65.3°
C8A	NAA	CBA	OBA	180.0°	60.0°
C8A	NAA	CBA	H111	54.7°	180.0°
C8A	NAA	CBA	H112	54.7°	60.0°
H81	C8A	C9A	OJA	80.9°	143.0°
H81	C8A	C9A	OKA	98.9°	37.0°
H81	C8A	NAA	OAA	7.3°	167.6°
H81	C8A	NAA	CBA	113.9°	53.8°
OKA	C9A	OJA	H91	0.2°	0.0°
OAA	NAA	CBA	OBA	59.3°	173.8°
OAA	NAA	CBA	H111	66.0°	66.2°
OAA	NAA	CBA	H112	175.4°	53.8°
CBA	NAA	OAA	H10	57.1°	179.1°
NAA	CBA	OBA	H111	125.3°	120.0°
NAA	CBA	OBA	H112	125.3°	120.0°
NAA	CBA	H111	H112	117.5°	120.0°
NAA	CBA	OBA	H11	179.9°	180.0°
OBA	CBA	H111	H112	117.4°	120.0°
H111	CBA	OBA	H11	54.8°	60.0°
H112	CBA	OBA	H11	54.7°	60.0°

Definition date:	1999-07-08
Last modified:	2020-06-17
Release status:	REL
Processing site:	RCSB
Derived from:	1QF4