DDY

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C4	C5	sing	1.41Å	1.40Å
C4	N4	sing	1.38Å	1.33Å
C4	N3	doub	1.33Å	1.41Å
PB	O3B	doub	1.48Å	1.60Å
PB	O1B	sing	1.61Å	1.48Å
PB	O2B	sing	1.61Å	1.47Å
PB	O3A	sing	1.61Å	1.63Å
PA	O3A	sing	1.61Å	1.62Å
PA	O1A	doub	1.48Å	1.47Å
PA	O2A	sing	1.61Å	1.48Å
PA	O5'	sing	1.61Å	1.61Å
C2	O2	doub	1.22Å	1.23Å
C2	N1	sing	1.35Å	1.42Å
C2	N3	sing	1.33Å	1.40Å
C5	C6	doub	1.35Å	1.40Å
C5	H5	sing	1.08Å	1.08Å
O1B	H1B	sing	0.97Å	0.95Å
O2B	H2B	sing	0.97Å	0.95Å
O2A	H2A	sing	0.97Å	0.95Å
O5'	C5'	sing	1.43Å	1.43Å
C5'	C4'	sing	1.53Å	1.53Å
C5'	H5'1	sing	1.09Å	1.10Å
C5'	H5'2	sing	1.09Å	1.10Å
C4'	O4'	sing	1.44Å	1.46Å
C4'	C3'	sing	1.55Å	1.33Å
C4'	H4'	sing	1.09Å	1.10Å
O4'	C1'	sing	1.44Å	1.45Å
C3'	C2'	sing	1.55Å	1.32Å
C3'	H3'1	sing	1.09Å	1.10Å
C3'	H3'2	sing	1.09Å	1.10Å
C2'	C1'	sing	1.54Å	1.33Å
C2'	H2'1	sing	1.09Å	1.10Å
C2'	H2'2	sing	1.09Å	1.10Å
C1'	N1	sing	1.46Å	1.50Å
C1'	H1'	sing	1.09Å	1.10Å
N1	C6	sing	1.36Å	1.42Å
C6	H6	sing	1.08Å	1.08Å
N4	HN41	sing	0.97Å	1.00Å
N4	HN42	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C5	C4	N4	120.1°	120.2°
C5	C4	N3	120.4°	119.6°
C4	C5	C6	119.7°	119.0°
C4	C5	H5	120.1°	120.5°
N4	C4	N3	119.5°	120.2°
C4	N4	HN41	120.0°	120.0°
C4	N4	HN42	120.0°	120.0°
C4	N3	C2	120.4°	120.7°
O3B	PB	O1B	107.2°	109.5°
O3B	PB	O2B	108.8°	109.5°
O3B	PB	O3A	104.2°	109.5°
O1B	PB	O2B	117.8°	109.5°
O1B	PB	O3A	110.8°	109.5°
PB	O1B	H1B	109.5°	114.0°
O2B	PB	O3A	107.2°	109.5°
PB	O2B	H2B	109.5°	114.0°
PB	O3A	PA	125.6°	134.0°
O3A	PA	O1A	111.7°	109.5°
O3A	PA	O2A	107.9°	109.4°
O3A	PA	O5'	100.4°	109.5°
O1A	PA	O2A	117.6°	109.4°
O1A	PA	O5'	109.6°	109.5°
O2A	PA	O5'	108.2°	109.5°
PA	O2A	H2A	109.5°	114.0°
PA	O5'	C5'	122.5°	123.0°
O2	C2	N1	120.5°	119.4°
O2	C2	N3	119.9°	119.4°
N1	C2	N3	119.6°	121.1°
C2	N1	C1'	120.0°	119.9°
C2	N1	C6	119.5°	120.3°
C6	C5	H5	120.1°	120.5°
C5	C6	N1	120.4°	119.2°
C5	C6	H6	119.8°	120.4°
O5'	C5'	C4'	108.8°	109.4°
O5'	C5'	H5'1	109.7°	109.5°
O5'	C5'	H5'2	109.7°	109.5°
C4'	C5'	H5'1	109.7°	109.5°
C4'	C5'	H5'2	109.7°	109.4°
C5'	C4'	O4'	111.6°	110.6°
C5'	C4'	C3'	109.0°	110.6°
C5'	C4'	H4'	106.6°	110.6°
H5'1	C5'	H5'2	109.3°	109.5°
O4'	C4'	C3'	103.3°	103.5°
O4'	C4'	H4'	112.0°	110.6°
C4'	O4'	C1'	104.6°	107.0°
C3'	C4'	H4'	114.4°	110.7°
C4'	C3'	C2'	111.9°	102.1°
C4'	C3'	H3'1	108.7°	110.9°
C4'	C3'	H3'2	108.7°	110.9°
O4'	C1'	C2'	103.8°	107.3°
O4'	C1'	N1	113.4°	109.9°
O4'	C1'	H1'	112.5°	109.9°
C2'	C3'	H3'1	108.6°	110.9°
C2'	C3'	H3'2	108.7°	110.8°
C3'	C2'	C1'	111.5°	104.2°
C3'	C2'	H2'1	108.8°	110.5°
C3'	C2'	H2'2	108.8°	110.5°
H3'1	C3'	H3'2	110.3°	110.8°
C1'	C2'	H2'1	108.8°	110.5°
C1'	C2'	H2'2	108.8°	110.5°
C2'	C1'	N1	114.3°	109.9°
C2'	C1'	H1'	111.5°	109.9°
H2'1	C2'	H2'2	110.1°	110.6°
N1	C1'	H1'	101.6°	110.0°
C1'	N1	C6	120.4°	119.8°
N1	C6	H6	119.8°	120.4°
HN41	N4	HN42	120.0°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C5	C4	N4	N3	179.3°	179.7°
C5	C4	N3	C2	0.2°	0.0°
C4	C5	C6	H5	180.0°	180.0°
C4	C5	C6	N1	0.2°	0.0°
C4	C5	C6	H6	179.9°	180.0°
C5	C4	N4	HN41	179.3°	0.0°
C5	C4	N4	HN42	0.8°	180.0°
N4	C4	N3	C2	179.1°	179.7°
N4	C4	C5	C6	179.0°	180.0°
N4	C4	C5	H5	1.0°	0.0°
C4	N4	HN41	HN42	180.0°	180.0°
C4	N3	C2	O2	179.0°	179.8°
C4	N3	C2	N1	0.3°	0.6°
N3	C4	C5	C6	0.2°	0.3°
N3	C4	C5	H5	179.8°	179.7°
N3	C4	N4	HN41	0.0°	179.7°
N3	C4	N4	HN42	180.0°	0.3°
O3B	PB	O1B	O2B	123.0°	120.0°
O3B	PB	O1B	O3A	113.1°	120.0°
O3B	PB	O2B	O3A	112.2°	120.0°
O3B	PB	O3A	PA	47.8°	40.0°
O3B	PB	O1B	H1B	0.0°	60.0°
O3B	PB	O2B	H2B	0.0°	180.0°
O1B	PB	O2B	O3A	125.7°	120.0°
O1B	PB	O3A	PA	67.1°	159.9°
O1B	PB	O2B	H2B	122.2°	60.0°
O2B	PB	O3A	PA	163.1°	80.1°
O2B	PB	O1B	H1B	123.0°	60.0°
PB	O3A	PA	O1A	43.2°	44.9°
PB	O3A	PA	O2A	87.6°	75.0°
PB	O3A	PA	O5'	159.3°	165.0°
O3A	PB	O1B	H1B	113.1°	180.0°
O3A	PB	O2B	H2B	112.2°	60.0°
O3A	PA	O1A	O2A	125.6°	120.0°
O3A	PA	O1A	O5'	110.3°	120.0°
O3A	PA	O2A	O5'	107.7°	120.0°
O3A	PA	O2A	H2A	127.4°	60.0°
O3A	PA	O5'	C5'	121.7°	175.1°
O1A	PA	O2A	O5'	124.8°	120.0°
O1A	PA	O2A	H2A	0.0°	180.0°
O1A	PA	O5'	C5'	4.0°	55.0°
O2A	PA	O5'	C5'	125.4°	65.0°
O5'	PA	O2A	H2A	124.8°	60.0°
PA	O5'	C5'	C4'	160.8°	180.0°
PA	O5'	C5'	H5'1	40.8°	60.0°
PA	O5'	C5'	H5'2	79.2°	60.1°
O2	C2	N1	N3	179.3°	179.2°
O2	C2	N1	C1'	5.7°	0.0°
O2	C2	N1	C6	178.6°	179.9°
C2	N1	C6	C5	0.6°	0.6°
C2	N1	C1'	O4'	158.4°	53.5°
C2	N1	C1'	C2'	82.8°	64.3°
C2	N1	C1'	C6	175.6°	180.0°
C2	N1	C1'	H1'	37.4°	174.6°
C2	N1	C6	H6	179.4°	179.4°
N3	C2	N1	C1'	175.0°	179.2°
N3	C2	N1	C6	0.7°	0.9°
C5	C6	N1	C1'	175.1°	179.5°
C5	C6	N1	H6	180.0°	179.9°
H5	C5	C6	N1	179.8°	180.0°
H5	C5	C6	H6	0.1°	0.0°
O5'	C5'	C4'	H5'1	120.0°	120.1°
O5'	C5'	C4'	H5'2	120.0°	120.0°
O5'	C5'	H5'1	H5'2	120.3°	120.0°
O5'	C5'	C4'	O4'	57.9°	66.5°
O5'	C5'	C4'	C3'	55.6°	179.5°
O5'	C5'	C4'	H4'	179.5°	56.4°
C4'	C5'	H5'1	H5'2	120.2°	119.9°
C5'	C4'	O4'	C3'	117.0°	118.5°
C5'	C4'	O4'	H4'	119.4°	122.9°
C5'	C4'	C3'	H4'	119.2°	123.0°
C5'	C4'	O4'	C1'	137.4°	158.6°
C5'	C4'	C3'	C2'	131.5°	155.5°
C5'	C4'	C3'	H3'1	11.5°	37.3°
C5'	C4'	C3'	H3'2	108.5°	86.3°
H5'1	C5'	C4'	O4'	177.9°	53.6°
H5'1	C5'	C4'	C3'	64.4°	60.5°
H5'1	C5'	C4'	H4'	59.5°	176.5°
H5'2	C5'	C4'	O4'	62.1°	173.5°
H5'2	C5'	C4'	C3'	175.6°	59.5°
H5'2	C5'	C4'	H4'	60.5°	63.6°
O4'	C4'	C3'	H4'	122.0°	118.5°
O4'	C4'	C3'	C2'	12.8°	37.0°
O4'	C4'	C3'	H3'1	107.2°	81.2°
O4'	C4'	C3'	H3'2	132.8°	155.2°
C4'	O4'	C1'	C2'	21.0°	26.5°
C4'	O4'	C1'	N1	145.6°	145.9°
C4'	O4'	C1'	H1'	99.7°	92.9°
C3'	C4'	O4'	C1'	20.4°	40.1°
C4'	C3'	C2'	H3'1	120.0°	118.3°
C4'	C3'	C2'	H3'2	120.0°	118.2°
C4'	C3'	H3'1	H3'2	119.0°	123.7°
C4'	C3'	C2'	C1'	0.9°	20.9°
C4'	C3'	C2'	H2'1	119.2°	139.6°
C4'	C3'	C2'	H2'2	120.9°	97.7°
H4'	C4'	O4'	C1'	103.2°	78.5°
H4'	C4'	C3'	C2'	109.2°	81.5°
H4'	C4'	C3'	H3'1	130.8°	160.3°
H4'	C4'	C3'	H3'2	10.8°	36.6°
O4'	C1'	C2'	C3'	14.1°	2.0°
O4'	C1'	C2'	N1	124.0°	119.4°
O4'	C1'	C2'	H1'	121.4°	119.4°
O4'	C1'	C2'	H2'1	105.9°	116.6°
O4'	C1'	C2'	H2'2	134.1°	120.7°
O4'	C1'	N1	H1'	121.0°	121.1°
O4'	C1'	N1	C6	17.2°	126.4°
C2'	C3'	H3'1	H3'2	119.0°	123.6°
C3'	C2'	C1'	H2'1	120.0°	118.7°
C3'	C2'	C1'	H2'2	120.0°	118.7°
C3'	C2'	H2'1	H2'2	119.2°	122.7°
C3'	C2'	C1'	N1	138.1°	121.4°
C3'	C2'	C1'	H1'	107.3°	117.4°
H3'1	C3'	C2'	C1'	120.9°	97.4°
H3'1	C3'	C2'	H2'1	0.8°	21.3°
H3'1	C3'	C2'	H2'2	119.1°	144.0°
H3'2	C3'	C2'	C1'	119.1°	139.1°
H3'2	C3'	C2'	H2'1	120.8°	102.3°
H3'2	C3'	C2'	H2'2	0.9°	20.4°
C1'	C2'	H2'1	H2'2	119.1°	122.6°
C2'	C1'	N1	H1'	120.3°	121.1°
C2'	C1'	N1	C6	101.5°	115.8°
H2'1	C2'	C1'	N1	18.1°	2.8°
H2'1	C2'	C1'	H1'	132.7°	123.9°
H2'2	C2'	C1'	N1	101.8°	119.9°
H2'2	C2'	C1'	H1'	12.7°	1.3°
C1'	N1	C6	H6	4.9°	0.6°
H1'	C1'	N1	C6	138.2°	5.4°

Definition date:	2004-04-19
Last modified:	2020-06-17
Release status:	REL
Processing site:	RCSB
Derived from:	1S9F