8N9

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
CM4	C4	sing	1.51Å	1.42Å
C4	C5	doub	1.32Å	1.44Å
C4	N3	sing	1.37Å	1.45Å
C6	C5	sing	1.51Å	1.56Å
C6	C7	sing	1.53Å	1.48Å
C7'	N3	sing	1.47Å	1.44Å
C7'	C5'	sing	1.51Å	1.54Å
C6'	C5'	doub	1.38Å	1.36Å	Aromatic
C6'	N1'	sing	1.33Å	1.33Å	Aromatic
C5	S1	sing	1.78Å	1.69Å
N3	C2	sing	1.40Å	1.57Å
OB1	PB	doub	1.48Å	1.57Å
O7	C7	sing	1.43Å	1.45Å
O7	PA1	sing	1.61Å	1.62Å
C5'	C4'	sing	1.40Å	1.41Å	Aromatic
N1'	C2'	doub	1.32Å	1.32Å	Aromatic
OA2	PA1	sing	1.61Å	1.47Å
O8	C8	sing	1.36Å	1.41Å
C2	S1	sing	1.78Å	1.70Å
C2	C8	doub	1.34Å	1.42Å
PA1	OA3	sing	1.61Å	1.61Å
PA1	OA1	doub	1.48Å	1.49Å
C8	C9	sing	1.51Å	1.51Å
PB	OA3	sing	1.61Å	1.58Å
PB	OB3	sing	1.61Å	1.46Å
PB	OB2	sing	1.61Å	1.45Å
C2'	CM2	sing	1.51Å	1.52Å
C2'	N3'	sing	1.32Å	1.31Å	Aromatic
C4'	N3'	doub	1.33Å	1.35Å	Aromatic
C4'	N4'	sing	1.38Å	1.41Å
C9	O9	sing	1.43Å	1.40Å
C6'	H1	sing	1.08Å	1.08Å
C9	H2	sing	1.09Å	1.10Å
C9	H3	sing	1.09Å	1.10Å
CM2	H5	sing	1.09Å	1.10Å
CM2	H6	sing	1.09Å	1.10Å
CM2	H7	sing	1.09Å	1.10Å
C7'	H8	sing	1.09Å	1.10Å
C7'	H9	sing	1.09Å	1.10Å
C7	H10	sing	1.09Å	1.10Å
C7	H11	sing	1.09Å	1.10Å
C6	H12	sing	1.09Å	1.10Å
C6	H13	sing	1.09Å	1.10Å
CM4	H15	sing	1.09Å	1.10Å
CM4	H16	sing	1.09Å	1.10Å
CM4	H17	sing	1.09Å	1.10Å
N4'	H20	sing	0.97Å	1.00Å
N4'	H21	sing	0.97Å	1.00Å
O9	H23	sing	0.97Å	0.95Å
O8	H24	sing	0.97Å	0.95Å
OB2	H25	sing	0.97Å	0.95Å
OB3	H26	sing	0.97Å	0.95Å
OA2	H4	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
CM4	C4	C5	128.3°	120.4°
CM4	C4	N3	119.6°	120.4°
C4	CM4	H15	109.5°	109.5°
C4	CM4	H16	109.5°	109.5°
C4	CM4	H17	109.4°	109.5°
C5	C4	N3	105.1°	119.2°
C4	C5	C6	118.3°	127.6°
C4	C5	S1	115.2°	104.8°
C4	N3	C7'	121.5°	121.7°
C4	N3	C2	111.9°	116.6°
C5	C6	C7	117.4°	109.4°
C6	C5	S1	121.2°	127.6°
C5	C6	H12	107.4°	109.5°
C5	C6	H13	107.5°	109.5°
C6	C7	O7	104.8°	109.4°
C6	C7	H10	110.6°	109.5°
C6	C7	H11	110.6°	109.5°
C7	C6	H12	107.5°	109.5°
C7	C6	H13	107.4°	109.4°
N3	C7'	C5'	115.0°	109.5°
C7'	N3	C2	121.3°	121.7°
N3	C7'	H8	108.1°	109.5°
N3	C7'	H9	108.1°	109.4°
C7'	C5'	C6'	120.1°	120.9°
C7'	C5'	C4'	124.0°	120.8°
C5'	C7'	H8	108.1°	109.5°
C5'	C7'	H9	108.1°	109.5°
C5'	C6'	N1'	120.6°	119.2°
C6'	C5'	C4'	115.7°	118.3°
C5'	C6'	H1	119.7°	120.4°
C6'	N1'	C2'	120.0°	121.0°
N1'	C6'	H1	119.7°	120.4°
C5	S1	C2	94.9°	96.0°
N3	C2	S1	106.5°	103.4°
N3	C2	C8	117.9°	128.3°
OB1	PB	OA3	104.7°	109.5°
OB1	PB	OB3	107.2°	109.5°
OB1	PB	OB2	104.8°	109.5°
C7	O7	PA1	108.6°	123.0°
O7	C7	H10	110.6°	109.4°
O7	C7	H11	110.6°	109.5°
O7	PA1	OA2	106.9°	109.5°
O7	PA1	OA3	102.6°	109.5°
O7	PA1	OA1	113.0°	109.5°
C5'	C4'	N3'	123.2°	118.9°
C5'	C4'	N4'	122.8°	120.5°
N1'	C2'	CM2	116.2°	119.1°
N1'	C2'	N3'	124.8°	121.9°
OA2	PA1	OA3	111.0°	109.5°
OA2	PA1	OA1	116.3°	109.5°
PA1	OA2	H4	109.5°	114.0°
O8	C8	C2	126.7°	120.0°
O8	C8	C9	115.0°	120.0°
C8	O8	H24	109.5°	114.0°
S1	C2	C8	124.8°	128.3°
C2	C8	C9	118.3°	120.0°
OA3	PA1	OA1	106.3°	109.5°
PA1	OA3	PB	130.5°	134.0°
C8	C9	O9	85.9°	109.5°
C8	C9	H2	115.0°	109.5°
C8	C9	H3	115.0°	109.5°
OA3	PB	OB3	113.1°	109.4°
OA3	PB	OB2	105.6°	109.5°
OB3	PB	OB2	120.1°	109.4°
PB	OB3	H26	109.5°	114.0°
PB	OB2	H25	109.5°	114.0°
CM2	C2'	N3'	118.9°	119.1°
C2'	CM2	H5	109.5°	109.5°
C2'	CM2	H6	109.4°	109.5°
C2'	CM2	H7	109.4°	109.5°
C2'	N3'	C4'	115.6°	120.7°
N3'	C4'	N4'	114.0°	120.5°
C4'	N4'	H20	109.5°	120.0°
C4'	N4'	H21	109.5°	120.0°
O9	C9	H2	115.0°	109.5°
O9	C9	H3	115.0°	109.5°
C9	O9	H23	109.5°	114.0°
H2	C9	H3	109.4°	109.4°
H5	CM2	H6	109.5°	109.5°
H5	CM2	H7	109.5°	109.4°
H6	CM2	H7	109.5°	109.5°
H8	C7'	H9	109.5°	109.5°
H10	C7	H11	109.4°	109.5°
H12	C6	H13	109.5°	109.5°
H15	CM4	H16	109.5°	109.5°
H15	CM4	H17	109.5°	109.5°
H16	CM4	H17	109.5°	109.4°
H20	N4'	H21	109.4°	120.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
CM4	C4	C5	N3	149.8°	180.0°
CM4	C4	C5	C6	30.9°	0.0°
CM4	C4	N3	C7'	26.3°	0.0°
CM4	C4	C5	S1	174.5°	179.7°
CM4	C4	N3	C2	179.2°	180.0°
C4	CM4	H15	H16	120.0°	120.0°
C4	CM4	H15	H17	120.0°	120.0°
C4	CM4	H16	H17	120.0°	120.0°
C4	C5	C6	S1	153.0°	179.6°
C4	C5	C6	C7	103.5°	95.3°
C5	C4	N3	C7'	179.3°	180.0°
C5	C4	N3	C2	26.3°	0.0°
C4	C5	S1	C2	13.0°	0.3°
C4	C5	C6	H12	135.3°	24.7°
C4	C5	C6	H13	17.6°	144.7°
C5	C4	CM4	H15	180.0°	5.5°
C5	C4	CM4	H16	60.0°	114.6°
C5	C4	CM4	H17	60.0°	125.5°
N3	C4	C5	C6	179.4°	180.0°
C4	N3	C7'	C2	152.1°	180.0°
C4	N3	C7'	C5'	67.8°	69.6°
N3	C4	C5	S1	24.8°	0.3°
C4	N3	C2	S1	18.2°	0.2°
C4	N3	C2	C8	164.3°	179.9°
C4	N3	C7'	H8	53.0°	50.4°
C4	N3	C7'	H9	171.4°	170.4°
N3	C4	CM4	H15	34.0°	174.5°
N3	C4	CM4	H16	154.0°	65.4°
N3	C4	CM4	H17	86.0°	54.5°
C5	C6	C7	H12	121.1°	120.0°
C5	C6	C7	H13	121.1°	120.0°
C5	C6	C7	O7	169.1°	180.0°
C6	C5	S1	C2	166.8°	179.9°
C5	C6	C7	H10	71.6°	60.1°
C5	C6	C7	H11	49.8°	60.0°
C5	C6	H12	H13	116.4°	120.0°
C7	C6	C5	S1	49.5°	85.0°
C6	C7	O7	H10	119.3°	120.0°
C6	C7	O7	H11	119.3°	120.0°
C6	C7	O7	PA1	160.9°	180.0°
C6	C7	H10	H11	122.1°	120.1°
C7	C6	H12	H13	116.4°	120.0°
N3	C7'	C5'	H8	120.8°	120.0°
N3	C7'	C5'	H9	120.8°	120.0°
N3	C7'	C5'	C6'	118.3°	107.8°
N3	C7'	C5'	C4'	68.2°	72.2°
C7'	N3	C2	S1	172.7°	179.8°
C7'	N3	C2	C8	41.2°	0.1°
N3	C7'	H8	H9	117.5°	120.0°
C7'	C5'	C6'	C4'	174.0°	180.0°
C7'	C5'	C6'	N1'	177.0°	180.0°
C5'	C7'	N3	C2	84.3°	110.4°
C7'	C5'	C4'	N3'	176.7°	180.0°
C7'	C5'	C4'	N4'	4.0°	0.4°
C7'	C5'	C6'	H1	3.0°	0.0°
C5'	C7'	H8	H9	117.4°	120.0°
C5'	C6'	N1'	H1	180.0°	180.0°
C5'	C6'	N1'	C2'	3.8°	0.0°
C6'	C5'	C4'	N3'	2.9°	0.0°
C6'	C5'	C4'	N4'	177.7°	179.7°
C6'	C5'	C7'	H8	2.5°	12.2°
C6'	C5'	C7'	H9	120.8°	132.2°
N1'	C6'	C5'	C4'	3.0°	0.0°
C6'	N1'	C2'	CM2	177.4°	180.0°
C6'	N1'	C2'	N3'	4.6°	0.1°
C5	S1	C2	N3	3.0°	0.3°
C5	S1	C2	C8	146.1°	180.0°
S1	C5	C6	H12	71.7°	155.0°
S1	C5	C6	H13	170.6°	34.9°
N3	C2	C8	O8	12.4°	7.8°
N3	C2	S1	C8	143.1°	179.7°
N3	C2	C8	C9	166.8°	172.2°
C2	N3	C7'	H8	154.9°	129.6°
C2	N3	C7'	H9	36.5°	9.6°
OB1	PB	OA3	PA1	61.7°	40.0°
OB1	PB	OA3	OB3	116.3°	120.0°
OB1	PB	OA3	OB2	110.4°	120.1°
OB1	PB	OB3	OB2	119.3°	120.1°
OB1	PB	OB2	H25	0.0°	180.0°
OB1	PB	OB3	H26	0.0°	60.0°
C7	O7	PA1	OA2	164.2°	65.0°
C7	O7	PA1	OA3	79.0°	175.0°
C7	O7	PA1	OA1	35.0°	55.0°
O7	C7	H10	H11	122.1°	120.0°
O7	C7	C6	H12	47.9°	60.0°
O7	C7	C6	H13	69.8°	60.0°
O7	PA1	OA2	OA3	111.1°	120.0°
O7	PA1	OA2	OA1	127.3°	120.0°
O7	PA1	OA3	OA1	118.9°	120.0°
O7	PA1	OA3	PB	98.5°	160.0°
PA1	O7	C7	H10	79.8°	60.0°
PA1	O7	C7	H11	41.7°	60.0°
O7	PA1	OA2	H4	127.3°	60.0°
C5'	C4'	N3'	C2'	3.4°	0.0°
C5'	C4'	N3'	N4'	179.4°	179.6°
C4'	C5'	C6'	H1	177.0°	180.0°
C4'	C5'	C7'	H8	171.0°	167.8°
C4'	C5'	C7'	H9	52.7°	47.8°
C5'	C4'	N4'	H20	179.4°	172.3°
C5'	C4'	N4'	H21	60.6°	7.6°
N1'	C2'	CM2	N3'	178.2°	179.9°
N1'	C2'	N3'	C4'	4.2°	0.0°
C2'	N1'	C6'	H1	176.2°	180.0°
N1'	C2'	CM2	H5	0.0°	90.0°
N1'	C2'	CM2	H6	120.0°	150.0°
N1'	C2'	CM2	H7	120.0°	29.9°
OA2	PA1	OA3	OA1	127.3°	120.0°
OA2	PA1	OA3	PB	15.3°	80.0°
O8	C8	C2	S1	151.7°	172.6°
O8	C8	C2	C9	179.1°	180.0°
O8	C8	C9	O9	95.4°	65.0°
O8	C8	C9	H2	20.4°	55.0°
O8	C8	C9	H3	148.9°	174.9°
S1	C2	C8	C9	27.4°	7.4°
C2	C8	C9	O9	85.4°	115.0°
C2	C8	C9	H2	158.8°	125.0°
C2	C8	C9	H3	30.4°	5.0°
C2	C8	O8	H24	180.0°	175.0°
PA1	OA3	PB	OB3	54.6°	160.0°
PA1	OA3	PB	OB2	172.1°	80.1°
OA3	PA1	OA2	H4	121.6°	60.0°
OA1	PA1	OA3	PB	142.6°	40.0°
OA1	PA1	OA2	H4	0.0°	180.0°
C8	C9	O9	H2	115.7°	120.0°
C8	C9	O9	H3	115.7°	120.0°
C8	C9	H2	H3	131.2°	120.0°
C8	C9	O9	H23	180.0°	180.0°
C9	C8	O8	H24	0.8°	5.0°
OA3	PB	OB3	OB2	125.9°	120.0°
OA3	PB	OB2	H25	110.3°	60.0°
OA3	PB	OB3	H26	114.8°	180.0°
OB3	PB	OB2	H25	120.4°	60.0°
OB2	PB	OB3	H26	119.3°	60.0°
CM2	C2'	N3'	C4'	177.8°	180.0°
C2'	CM2	H5	H6	120.0°	120.0°
C2'	CM2	H5	H7	120.0°	120.0°
C2'	CM2	H6	H7	119.9°	120.0°
C2'	N3'	C4'	N4'	177.2°	179.7°
N3'	C2'	CM2	H5	178.2°	90.1°
N3'	C2'	CM2	H6	61.8°	29.9°
N3'	C2'	CM2	H7	58.2°	150.0°
N3'	C4'	N4'	H20	0.0°	8.1°
N3'	C4'	N4'	H21	120.0°	172.1°
C4'	N4'	H20	H21	120.0°	179.9°
O9	C9	H2	H3	131.3°	120.0°
H2	C9	O9	H23	64.3°	60.0°
H3	C9	O9	H23	64.2°	60.0°
H5	CM2	H6	H7	120.0°	120.0°
H10	C7	C6	H12	167.2°	59.9°
H10	C7	C6	H13	49.5°	180.0°
H11	C7	C6	H12	71.4°	180.0°
H11	C7	C6	H13	170.9°	59.9°
H15	CM4	H16	H17	120.0°	120.0°

Release date:	2018-06-27
Definition date:	2017-08-09
Last modified:	2021-03-13
Release status:	REL
Processing site:	PDBJ
Derived from:	5XU9