A1IT3

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C5	C6	doub	1.35Å	1.39Å
C5	C4	sing	1.42Å	1.40Å
C6	N1	sing	1.37Å	1.36Å
O4	C4	doub	1.22Å	1.25Å
C4	N3	sing	1.35Å	1.34Å
N1	C1'	sing	1.46Å	1.45Å
N1	C2	sing	1.35Å	1.40Å
C1'	O4'	sing	1.44Å	1.44Å
C1'	C2'	sing	1.54Å	1.56Å
O4'	C4'	sing	1.44Å	1.46Å
N3	C2	sing	1.35Å	1.34Å
S2'	C2'	sing	1.81Å	1.77Å
C2	O2	doub	1.22Å	1.27Å
O3'	C3'	sing	1.43Å	1.44Å
C2'	C3'	sing	1.55Å	1.54Å
C4'	C3'	sing	1.54Å	1.54Å
C4'	C5'	sing	1.53Å	1.51Å
C5'	O5'	sing	1.43Å	1.45Å
O5'	P	sing	1.61Å	1.63Å
O3P	P	doub	1.48Å	1.50Å
P	O2P	sing	1.61Å	1.50Å
P	O1P	sing	1.61Å	1.49Å
C5	H5	sing	1.08Å	1.08Å
C6	H6	sing	1.08Å	1.08Å
C1'	H1'	sing	1.09Å	1.10Å
C2'	H2'	sing	1.09Å	1.10Å
C3'	H3'	sing	1.09Å	1.10Å
C4'	H4'	sing	1.09Å	1.10Å
C5'	H5'2	sing	1.09Å	1.10Å
C5'	H5'1	sing	1.09Å	1.10Å
N3	HN3	sing	0.97Å	1.00Å
O1P	H1	sing	0.97Å	0.95Å
O2P	H2	sing	0.97Å	0.95Å
O3'	HO3'	sing	0.97Å	0.95Å
S2'	HO2'	sing	1.34Å	1.30Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C6	C5	C4	119.7°	119.2°
C5	C6	N1	118.0°	119.6°
C6	C5	H5	120.2°	120.4°
C5	C6	H6	121.0°	120.1°
C5	C4	O4	122.0°	120.4°
C5	C4	N3	120.9°	119.4°
C4	C5	H5	120.2°	120.4°
C6	N1	C1'	118.1°	119.7°
C6	N1	C2	121.0°	120.6°
N1	C6	H6	121.0°	120.2°
O4	C4	N3	117.1°	120.3°
C4	N3	C2	120.1°	120.3°
C4	N3	HN3	120.0°	119.9°
C1'	N1	C2	120.8°	119.7°
N1	C1'	O4'	110.3°	110.3°
N1	C1'	C2'	111.4°	110.4°
N1	C1'	H1'	109.7°	110.3°
N1	C2	N3	120.3°	120.9°
N1	C2	O2	122.2°	119.5°
O4'	C1'	C2'	107.3°	104.8°
C1'	O4'	C4'	109.1°	105.3°
O4'	C1'	H1'	109.8°	110.3°
C1'	C2'	S2'	111.5°	110.5°
C1'	C2'	C3'	100.8°	104.1°
C2'	C1'	H1'	108.2°	110.4°
C1'	C2'	H2'	110.3°	110.5°
O4'	C4'	C3'	107.3°	104.9°
O4'	C4'	C5'	109.1°	110.4°
O4'	C4'	H4'	108.7°	110.4°
N3	C2	O2	117.5°	119.6°
C2	N3	HN3	120.0°	119.8°
S2'	C2'	C3'	115.7°	110.5°
S2'	C2'	H2'	107.8°	110.5°
C2'	S2'	HO2'	102.0°	103.0°
O3'	C3'	C2'	110.0°	110.5°
O3'	C3'	C4'	112.5°	110.7°
O3'	C3'	H3'	110.9°	110.5°
C3'	O3'	HO3'	109.5°	114.0°
C2'	C3'	C4'	104.2°	104.0°
C3'	C2'	H2'	110.6°	110.5°
C2'	C3'	H3'	109.5°	110.5°
C3'	C4'	C5'	115.7°	110.4°
C4'	C3'	H3'	109.5°	110.5°
C3'	C4'	H4'	107.8°	110.4°
C4'	C5'	O5'	110.1°	109.5°
C5'	C4'	H4'	108.0°	110.3°
C4'	C5'	H5'2	109.3°	109.5°
C4'	C5'	H5'1	109.3°	109.5°
C5'	O5'	P	121.8°	123.0°
O5'	C5'	H5'2	109.3°	109.4°
O5'	C5'	H5'1	109.3°	109.5°
O5'	P	O3P	108.1°	109.5°
O5'	P	O2P	108.8°	109.5°
O5'	P	O1P	103.3°	109.5°
O3P	P	O2P	110.3°	109.5°
O3P	P	O1P	114.2°	109.5°
O2P	P	O1P	111.8°	109.4°
P	O2P	H2	109.5°	114.0°
P	O1P	H1	109.5°	114.1°
H5'2	C5'	H5'1	109.5°	109.4°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C6	C5	C4	H5	180.0°	180.0°
C5	C6	N1	H6	180.0°	179.9°
C6	C5	C4	O4	178.0°	179.7°
C6	C5	C4	N3	0.3°	0.0°
C5	C6	N1	C1'	178.6°	180.0°
C5	C6	N1	C2	1.5°	0.1°
C4	C5	C6	N1	0.5°	0.0°
C5	C4	O4	N3	178.4°	179.6°
C5	C4	N3	C2	1.0°	0.1°
C4	C5	C6	H6	179.5°	179.9°
C5	C4	N3	HN3	178.9°	180.0°
C6	N1	C1'	C2	179.8°	180.0°
C6	N1	C1'	O4'	121.9°	126.5°
C6	N1	C1'	C2'	119.1°	118.1°
C6	N1	C2	N3	2.3°	0.0°
C6	N1	C2	O2	179.1°	180.0°
N1	C6	C5	H5	179.5°	180.0°
C6	N1	C1'	H1'	0.7°	4.2°
O4	C4	N3	C2	177.4°	179.7°
O4	C4	C5	H5	2.0°	0.3°
O4	C4	N3	HN3	2.7°	0.3°
C4	N3	C2	N1	2.0°	0.1°
C4	N3	C2	HN3	180.0°	180.0°
C4	N3	C2	O2	179.0°	180.0°
N3	C4	C5	H5	179.7°	180.0°
N1	C1'	O4'	C2'	121.5°	118.9°
N1	C1'	O4'	H1'	121.1°	122.2°
N1	C1'	C2'	H1'	120.7°	122.3°
N1	C1'	O4'	C4'	138.8°	159.3°
C1'	N1	C2	N3	177.9°	180.0°
N1	C1'	C2'	S2'	84.9°	98.5°
C1'	N1	C2	O2	1.0°	0.0°
N1	C1'	C2'	C3'	151.7°	142.8°
C1'	N1	C6	H6	1.4°	0.1°
N1	C1'	C2'	H2'	34.8°	24.1°
C2	N1	C1'	O4'	58.0°	53.6°
C2	N1	C1'	C2'	61.1°	61.8°
N1	C2	N3	O2	177.0°	180.0°
C2	N1	C6	H6	178.5°	180.0°
C2	N1	C1'	H1'	179.1°	175.8°
N1	C2	N3	HN3	178.0°	180.0°
O4'	C1'	C2'	H1'	118.5°	118.8°
O4'	C1'	C2'	S2'	154.3°	142.6°
O4'	C1'	C2'	C3'	30.9°	24.0°
C1'	O4'	C4'	C3'	3.9°	40.4°
C1'	O4'	C4'	C5'	122.2°	159.3°
O4'	C1'	C2'	H2'	86.0°	94.7°
C1'	O4'	C4'	H4'	120.2°	78.4°
C2'	C1'	O4'	C4'	17.3°	40.4°
C1'	C2'	S2'	C3'	114.4°	114.7°
C1'	C2'	S2'	H2'	121.2°	122.6°
C1'	C2'	C3'	O3'	88.8°	118.8°
C1'	C2'	C3'	H2'	116.6°	118.6°
C1'	C2'	C3'	C4'	32.0°	0.0°
C1'	C2'	C3'	H3'	149.0°	118.6°
C1'	C2'	S2'	HO2'	180.0°	180.0°
O4'	C4'	C3'	O3'	95.6°	142.6°
O4'	C4'	C3'	C2'	23.6°	23.9°
O4'	C4'	C3'	C5'	122.0°	118.9°
O4'	C4'	C3'	H4'	117.0°	118.9°
O4'	C4'	C5'	H4'	118.0°	122.3°
O4'	C4'	C5'	O5'	178.0°	69.6°
C4'	O4'	C1'	H1'	100.1°	78.5°
O4'	C4'	C3'	H3'	140.6°	94.7°
O4'	C4'	C5'	H5'2	61.9°	170.4°
O4'	C4'	C5'	H5'1	57.9°	50.4°
S2'	C2'	C3'	O3'	31.6°	0.1°
S2'	C2'	C3'	H2'	123.0°	122.7°
S2'	C2'	C3'	C4'	152.4°	118.7°
S2'	C2'	C1'	H1'	35.8°	23.8°
S2'	C2'	C3'	H3'	90.6°	122.7°
O2	C2	N3	HN3	1.0°	0.0°
O3'	C3'	C2'	C4'	120.8°	118.8°
O3'	C3'	C2'	H3'	122.2°	122.6°
O3'	C3'	C4'	H3'	123.8°	122.7°
O3'	C3'	C4'	C5'	142.4°	98.4°
O3'	C3'	C2'	H2'	154.6°	122.6°
O3'	C3'	C4'	H4'	21.4°	23.7°
C2'	C3'	C4'	H3'	117.0°	118.6°
C2'	C3'	C4'	C5'	98.4°	142.8°
C3'	C2'	C1'	H1'	87.6°	94.9°
C2'	C3'	C4'	H4'	140.5°	95.0°
C2'	C3'	O3'	HO3'	180.0°	61.4°
C3'	C2'	S2'	HO2'	65.6°	65.3°
C3'	C4'	C5'	H4'	120.9°	122.2°
C3'	C4'	C5'	O5'	60.9°	174.9°
C4'	C3'	C2'	H2'	84.6°	118.6°
C3'	C4'	C5'	H5'2	59.2°	54.9°
C3'	C4'	C5'	H5'1	179.0°	65.0°
C4'	C3'	O3'	HO3'	64.4°	176.2°
C4'	C5'	O5'	H5'2	120.1°	120.1°
C4'	C5'	O5'	H5'1	120.1°	120.0°
C4'	C5'	O5'	P	170.6°	180.0°
C5'	C4'	C3'	H3'	18.6°	24.2°
C4'	C5'	H5'2	H5'1	119.7°	120.0°
C5'	O5'	P	O3P	56.0°	55.0°
C5'	O5'	P	O2P	63.8°	65.0°
C5'	O5'	P	O1P	177.3°	175.0°
O5'	C5'	C4'	H4'	59.9°	52.7°
O5'	C5'	H5'2	H5'1	119.7°	119.9°
O5'	P	O3P	O2P	118.9°	120.0°
O5'	P	O3P	O1P	114.3°	120.0°
O5'	P	O2P	O1P	113.4°	120.0°
P	O5'	C5'	H5'2	69.3°	60.0°
P	O5'	C5'	H5'1	50.5°	59.9°
O5'	P	O1P	H1	117.1°	180.0°
O5'	P	O2P	H2	118.4°	60.0°
O3P	P	O2P	O1P	128.2°	120.0°
O3P	P	O1P	H1	0.0°	60.0°
O3P	P	O2P	H2	0.0°	180.0°
O2P	P	O1P	H1	126.1°	60.0°
O1P	P	O2P	H2	128.2°	60.0°
H5	C5	C6	H6	0.5°	0.1°
H1'	C1'	C2'	H2'	155.5°	146.4°
H2'	C2'	C3'	H3'	32.4°	0.0°
H2'	C2'	S2'	HO2'	58.9°	57.3°
H3'	C3'	C4'	H4'	102.4°	146.4°
H3'	C3'	O3'	HO3'	58.7°	61.1°
H4'	C4'	C5'	H5'2	180.0°	67.3°
H4'	C4'	C5'	H5'1	60.2°	172.8°

Release date:	2025-10-22
Definition date:	2024-11-13
Last modified:	2025-10-17
Release status:	REL
Processing site:	PDBE
Derived from:	9HDY