D3N

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O3'	C3'	sing	1.43Å	1.48Å
C2'	C3'	sing	1.55Å	1.53Å
C2'	C1'	sing	1.54Å	1.50Å
C3'	C4'	sing	1.55Å	1.50Å
C1'	N1	sing	1.46Å	1.44Å
C1'	O4'	sing	1.44Å	1.42Å
O2	C2	doub	1.22Å	1.24Å
N1	C2	sing	1.35Å	1.35Å
N1	C6	sing	1.39Å	1.41Å
C2	N3	sing	1.35Å	1.36Å
C7	C6	doub	1.38Å	1.35Å	Aromatic
C7	C8	sing	1.39Å	1.41Å	Aromatic
C6	C5	sing	1.41Å	1.41Å	Aromatic
C4'	O4'	sing	1.44Å	1.40Å
C4'	C5'	sing	1.53Å	1.51Å
C8	C9	doub	1.36Å	1.36Å	Aromatic
N3	C4	sing	1.39Å	1.41Å
C5	C4	doub	1.41Å	1.38Å	Aromatic
C5	C10	sing	1.41Å	1.41Å	Aromatic
C4	C13	sing	1.38Å	1.40Å	Aromatic
C9	C10	sing	1.41Å	1.37Å	Aromatic
C10	C11	doub	1.41Å	1.41Å	Aromatic
C13	C12	doub	1.39Å	1.40Å	Aromatic
C5'	O5'	sing	1.43Å	1.39Å
C11	C12	sing	1.36Å	1.37Å	Aromatic
O5'	P	sing	1.61Å	1.61Å
O2P	P	doub	1.48Å	1.46Å
P	O1P	sing	1.61Å	1.50Å
O1P	H1	sing	0.97Å	0.95Å
C5'	H3	sing	1.09Å	1.10Å
C5'	H4	sing	1.09Å	1.10Å
C4'	H5	sing	1.09Å	1.10Å
C3'	H6	sing	1.09Å	1.10Å
O3'	H7	sing	0.97Å	0.95Å
C2'	H8	sing	1.09Å	1.10Å
C2'	H9	sing	1.09Å	1.10Å
C1'	H10	sing	1.09Å	1.10Å
N3	H11	sing	0.97Å	1.00Å
C7	H12	sing	1.08Å	1.08Å
C8	H13	sing	1.08Å	1.08Å
C9	H14	sing	1.08Å	1.08Å
C11	H15	sing	1.08Å	1.08Å
C12	H16	sing	1.08Å	1.08Å
C13	H17	sing	1.08Å	1.08Å
P	OP3	sing	1.61Å	15.80Å
OP3	H2	sing	0.97Å	0.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O3'	C3'	C2'	113.8°	110.9°
O3'	C3'	C4'	103.3°	110.9°
O3'	C3'	H6	112.0°	110.8°
C3'	O3'	H7	109.5°	114.0°
C3'	C2'	C1'	105.4°	104.2°
C2'	C3'	C4'	104.1°	102.1°
C2'	C3'	H6	111.3°	110.9°
C3'	C2'	H8	110.5°	110.5°
C3'	C2'	H9	110.5°	110.4°
C2'	C1'	N1	120.6°	109.9°
C2'	C1'	O4'	107.9°	107.3°
C1'	C2'	H8	110.5°	110.5°
C1'	C2'	H9	110.5°	110.5°
C2'	C1'	H10	107.6°	109.9°
C3'	C4'	O4'	108.2°	103.5°
C3'	C4'	C5'	111.2°	110.6°
C3'	C4'	H5	109.8°	110.8°
C4'	C3'	H6	111.8°	110.9°
N1	C1'	O4'	103.4°	109.9°
C1'	N1	C2	119.2°	119.8°
C1'	N1	C6	116.8°	119.9°
N1	C1'	H10	108.3°	109.8°
C1'	O4'	C4'	109.7°	106.9°
O4'	C1'	H10	108.6°	110.1°
O2	C2	N1	122.8°	118.8°
O2	C2	N3	120.1°	118.8°
C2	N1	C6	123.8°	120.4°
N1	C2	N3	117.1°	122.4°
N1	C6	C7	124.2°	122.1°
N1	C6	C5	117.2°	118.7°
C2	N3	C4	123.8°	120.4°
C2	N3	H11	118.1°	119.8°
C6	C7	C8	119.6°	120.4°
C7	C6	C5	118.6°	119.2°
C6	C7	H12	120.2°	119.9°
C7	C8	C9	123.0°	121.5°
C8	C7	H12	120.2°	119.8°
C7	C8	H13	118.5°	119.3°
C6	C5	C4	120.5°	119.6°
C6	C5	C10	120.9°	120.2°
O4'	C4'	C5'	106.9°	110.6°
O4'	C4'	H5	111.2°	110.6°
C4'	C5'	O5'	111.9°	109.5°
C4'	C5'	H3	108.9°	109.5°
C4'	C5'	H4	108.8°	109.4°
C5'	C4'	H5	109.5°	110.5°
C8	C9	C10	118.4°	119.9°
C9	C8	H13	118.5°	119.3°
C8	C9	H14	120.8°	120.1°
N3	C4	C5	117.6°	118.6°
N3	C4	C13	120.2°	122.2°
C4	N3	H11	118.1°	119.8°
C4	C5	C10	118.6°	120.2°
C5	C4	C13	122.2°	119.1°
C5	C10	C9	119.6°	118.9°
C5	C10	C11	118.9°	118.9°
C4	C13	C12	119.1°	120.4°
C4	C13	H17	120.5°	119.8°
C9	C10	C11	121.5°	122.2°
C10	C9	H14	120.8°	120.0°
C10	C11	C12	121.9°	119.8°
C10	C11	H15	119.1°	120.1°
C13	C12	C11	119.3°	121.5°
C13	C12	H16	120.3°	119.3°
C12	C13	H17	120.5°	119.8°
C5'	O5'	P	117.9°	123.0°
O5'	C5'	H3	108.8°	109.5°
O5'	C5'	H4	108.9°	109.4°
C12	C11	H15	119.1°	120.1°
C11	C12	H16	120.4°	119.2°
O5'	P	O2P	113.6°	109.5°
O5'	P	O1P	106.4°	109.5°
O5'	P	OP3	29.7°	109.5°
O2P	P	O1P	117.1°	109.5°
O2P	P	OP3	134.5°	109.5°
P	O1P	H1	109.5°	113.9°
O1P	P	OP3	77.3°	109.5°
H3	C5'	H4	109.5°	109.5°
H8	C2'	H9	109.5°	110.5°
P	OP3	H2	90.0°	113.9°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O3'	C3'	C2'	C4'	111.7°	118.2°
O3'	C3'	C2'	H6	127.7°	123.6°
O3'	C3'	C2'	C1'	122.7°	139.1°
O3'	C3'	C4'	H6	120.6°	123.6°
O3'	C3'	C4'	O4'	139.4°	155.2°
O3'	C3'	C4'	C5'	103.5°	86.3°
O3'	C3'	C4'	H5	17.9°	36.6°
O3'	C3'	C2'	H8	117.9°	102.2°
O3'	C3'	C2'	H9	3.4°	20.4°
C3'	C2'	C1'	H8	119.4°	118.7°
C3'	C2'	C1'	H9	119.3°	118.6°
C2'	C3'	C4'	H6	120.3°	118.2°
C3'	C2'	C1'	N1	119.8°	121.5°
C3'	C2'	C1'	O4'	1.5°	2.1°
C2'	C3'	C4'	O4'	20.2°	37.0°
C2'	C3'	C4'	C5'	137.4°	155.5°
C2'	C3'	C4'	H5	101.2°	81.6°
C2'	C3'	O3'	H7	180.0°	67.3°
C3'	C2'	H8	H9	121.8°	122.6°
C3'	C2'	C1'	H10	115.5°	117.6°
C1'	C2'	C3'	C4'	11.0°	20.8°
C2'	C1'	N1	O4'	120.5°	117.8°
C2'	C1'	N1	H10	124.4°	121.0°
C2'	C1'	O4'	H10	116.3°	119.5°
C2'	C1'	N1	C2	50.3°	68.3°
C2'	C1'	N1	C6	134.2°	111.4°
C2'	C1'	O4'	C4'	14.7°	26.5°
C1'	C2'	C3'	H6	109.6°	97.3°
C1'	C2'	H8	H9	121.9°	122.6°
C3'	C4'	O4'	C1'	22.3°	40.1°
C3'	C4'	O4'	C5'	119.8°	118.5°
C3'	C4'	O4'	H5	120.6°	118.7°
C3'	C4'	C5'	H5	121.5°	123.1°
C3'	C4'	C5'	O5'	153.6°	179.4°
C3'	C4'	C5'	H3	33.3°	60.5°
C3'	C4'	C5'	H4	86.0°	59.5°
C4'	C3'	O3'	H7	67.8°	180.0°
C4'	C3'	C2'	H8	130.4°	139.6°
C4'	C3'	C2'	H9	108.4°	97.8°
N1	C1'	O4'	H10	114.9°	121.1°
C1'	N1	C2	O2	4.4°	0.0°
C1'	N1	C2	C6	175.1°	179.7°
C1'	N1	C2	N3	175.9°	180.0°
C1'	N1	C6	C7	5.0°	0.0°
C1'	N1	C6	C5	175.3°	179.8°
N1	C1'	O4'	C4'	143.5°	146.0°
N1	C1'	C2'	H8	0.4°	2.8°
N1	C1'	C2'	H9	120.9°	119.9°
O4'	C1'	N1	C2	70.2°	49.5°
O4'	C1'	N1	C6	105.3°	130.8°
C1'	O4'	C4'	C5'	142.1°	158.6°
C1'	O4'	C4'	H5	98.3°	78.6°
O4'	C1'	C2'	H8	117.8°	116.6°
O4'	C1'	C2'	H9	120.9°	120.7°
O2	C2	N1	N3	179.7°	179.9°
O2	C2	N1	C6	179.5°	179.7°
O2	C2	N3	C4	178.6°	180.0°
O2	C2	N3	H11	1.3°	0.0°
C2	N1	C6	C7	179.7°	179.7°
C2	N1	C6	C5	0.0°	0.5°
N1	C2	N3	C4	1.7°	0.1°
C2	N1	C1'	H10	174.6°	170.7°
N1	C2	N3	H11	178.3°	180.0°
C6	N1	C2	N3	0.8°	0.2°
N1	C6	C7	C5	179.7°	179.7°
N1	C6	C7	C8	178.8°	180.0°
N1	C6	C5	C4	0.1°	0.5°
N1	C6	C5	C10	179.4°	179.7°
C6	N1	C1'	H10	9.9°	9.6°
N1	C6	C7	H12	1.3°	0.0°
C2	N3	C4	H11	180.0°	180.0°
C2	N3	C4	C5	1.8°	0.1°
C2	N3	C4	C13	179.2°	179.9°
C6	C7	C8	H12	180.0°	180.0°
C6	C7	C8	C9	0.1°	0.0°
C7	C6	C5	C4	179.8°	179.7°
C7	C6	C5	C10	0.3°	0.1°
C6	C7	C8	H13	179.9°	180.0°
C8	C7	C6	C5	0.9°	0.2°
C7	C8	C9	H13	180.0°	180.0°
C7	C8	C9	C10	1.4°	0.6°
C7	C8	C9	H14	178.5°	180.0°
C6	C5	C4	N3	0.9°	0.2°
C6	C5	C4	C10	179.5°	179.8°
C6	C5	C4	C13	179.9°	179.8°
C6	C5	C10	C9	1.2°	0.6°
C6	C5	C10	C11	178.7°	179.8°
C5	C6	C7	H12	179.0°	179.7°
O4'	C4'	C5'	H5	120.6°	122.8°
O4'	C4'	C5'	O5'	88.4°	66.5°
O4'	C4'	C5'	H3	151.2°	53.6°
O4'	C4'	C5'	H4	31.9°	173.6°
O4'	C4'	C3'	H6	100.0°	81.2°
C4'	O4'	C1'	H10	101.6°	93.0°
C4'	C5'	O5'	H3	120.4°	120.0°
C4'	C5'	O5'	H4	120.3°	120.0°
C4'	C5'	O5'	P	150.7°	180.0°
C4'	C5'	H3	H4	118.9°	120.0°
C5'	C4'	C3'	H6	17.1°	37.3°
C8	C9	C10	C5	2.0°	0.9°
C8	C9	C10	H14	180.0°	179.5°
C8	C9	C10	C11	177.8°	180.0°
C9	C8	C7	H12	179.9°	180.0°
N3	C4	C5	C13	179.0°	180.0°
N3	C4	C5	C10	178.6°	180.0°
N3	C4	C13	C12	179.8°	180.0°
N3	C4	C13	H17	0.2°	0.0°
C4	C5	C10	C9	178.3°	179.2°
C4	C5	C10	C11	1.9°	0.0°
C5	C4	C13	C12	0.8°	0.0°
C5	C4	N3	H11	178.3°	180.0°
C5	C4	C13	H17	179.2°	180.0°
C10	C5	C4	C13	0.4°	0.0°
C5	C10	C9	C11	179.8°	179.1°
C5	C10	C11	C12	2.1°	0.0°
C5	C10	C9	H14	178.0°	179.7°
C5	C10	C11	H15	177.9°	180.0°
C4	C13	C12	H17	180.0°	180.0°
C4	C13	C12	C11	0.6°	0.0°
C13	C4	N3	H11	0.8°	0.0°
C4	C13	C12	H16	179.4°	179.9°
C9	C10	C11	C12	178.0°	179.1°
C10	C9	C8	H13	178.6°	179.4°
C9	C10	C11	H15	2.0°	0.9°
C10	C11	C12	C13	0.9°	0.0°
C10	C11	C12	H15	180.0°	180.0°
C11	C10	C9	H14	2.2°	0.6°
C10	C11	C12	H16	179.1°	180.0°
C13	C12	C11	H16	180.0°	179.9°
C13	C12	C11	H15	179.1°	180.0°
C5'	O5'	P	O2P	79.2°	55.0°
C5'	O5'	P	O1P	51.0°	65.0°
O5'	C5'	H3	H4	118.9°	120.0°
O5'	C5'	C4'	H5	32.1°	56.4°
C5'	O5'	P	OP3	62.1°	175.0°
C11	C12	C13	H17	179.4°	180.0°
O5'	P	O2P	O1P	124.7°	120.1°
O5'	P	O2P	OP3	25.7°	120.0°
O5'	P	O1P	OP3	5.6°	120.0°
O5'	P	O1P	H1	128.2°	60.0°
P	O5'	C5'	H3	30.3°	60.0°
P	O5'	C5'	H4	89.0°	60.0°
O5'	P	OP3	H2	90.0°	179.9°
O2P	P	O1P	OP3	133.8°	120.0°
O2P	P	O1P	H1	0.0°	180.0°
O2P	P	OP3	H2	90.0°	60.0°
O1P	P	OP3	H2	90.0°	60.0°
H1	O1P	P	OP3	133.8°	60.0°
H3	C5'	C4'	H5	88.2°	176.4°
H4	C5'	C4'	H5	152.5°	63.6°
H5	C4'	C3'	H6	138.5°	160.3°
H6	C3'	O3'	H7	52.6°	56.3°
H6	C3'	C2'	H8	9.8°	21.4°
H6	C3'	C2'	H9	131.1°	144.0°
H8	C2'	C1'	H10	125.1°	123.7°
H9	C2'	C1'	H10	3.8°	1.1°
H12	C7	C8	H13	0.1°	0.0°
H13	C8	C9	H14	1.5°	0.0°
H15	C11	C12	H16	0.9°	0.1°
H16	C12	C13	H17	0.6°	0.0°

Release date:	2013-06-12
Definition date:	2012-11-02
Last modified:	2013-06-07
Release status:	REL
Processing site:	RCSB
Derived from:	4HQI