JKM

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O20	P	sing	1.65Å	1.70Å
O3P	P	doub	1.48Å	1.50Å
P	O2P	sing	1.61Å	1.61Å
P	O2'	sing	1.64Å	1.74Å
C1'	N1	sing	1.47Å	1.52Å
C2	N1	sing	1.35Å	1.50Å
N1	C6	sing	1.37Å	1.42Å
O2	C2	doub	1.22Å	1.20Å
C2	N3	sing	1.35Å	1.42Å
N3	C4	sing	1.35Å	1.35Å
C4	C5	sing	1.42Å	1.44Å
C4	O4	doub	1.22Å	1.34Å
C6	C5	doub	1.35Å	1.36Å
C5	H5	sing	1.08Å	1.08Å
C6	H6	sing	1.08Å	1.08Å
O4'	C1'	sing	1.46Å	1.45Å
C2'	C1'	sing	1.52Å	1.53Å
C1'	H1'	sing	1.09Å	1.10Å
C3'	C2'	sing	1.57Å	1.58Å
C2'	O2'	sing	1.41Å	1.38Å
C2'	H2'	sing	1.09Å	1.10Å
O20	C3'	sing	1.41Å	1.40Å
O2P	HO2P	sing	0.97Å	0.95Å
C4'	C3'	sing	1.51Å	1.54Å
C3'	H3'	sing	1.09Å	1.10Å
C4'	C5'	sing	1.53Å	1.55Å
C4'	O4'	sing	1.45Å	1.43Å
C4'	H4'	sing	1.09Å	1.10Å
O5'	C5'	sing	1.43Å	1.41Å
C5'	H5'	sing	1.09Å	1.10Å
C5'	H5'A	sing	1.09Å	1.10Å
O5'	HO5'	sing	0.97Å	0.95Å
N3	HN3	sing	0.97Å	1.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O20	P	O3P	120.6°	110.7°
O20	P	O2P	104.1°	110.7°
O20	P	O2'	90.9°	103.1°
P	O20	C3'	110.2°	99.4°
O3P	P	O2P	113.8°	110.6°
O3P	P	O2'	117.9°	110.7°
O2P	P	O2'	106.4°	110.7°
P	O2P	HO2P	109.5°	113.9°
P	O2'	C2'	105.5°	101.8°
C1'	N1	C2	131.0°	119.7°
C1'	N1	C6	111.0°	119.7°
N1	C1'	O4'	115.5°	110.6°
N1	C1'	C2'	121.8°	110.6°
N1	C1'	H1'	104.8°	110.6°
C2	N1	C6	118.0°	120.6°
N1	C2	O2	122.0°	119.6°
N1	C2	N3	117.6°	120.9°
N1	C6	C5	123.5°	119.7°
N1	C6	H6	118.3°	120.2°
O2	C2	N3	120.3°	119.5°
C2	N3	C4	119.2°	120.2°
C2	N3	HN3	120.4°	119.9°
N3	C4	C5	125.4°	119.4°
N3	C4	O4	121.7°	120.3°
C4	N3	HN3	120.4°	119.9°
C5	C4	O4	112.9°	120.3°
C4	C5	C6	116.3°	119.1°
C4	C5	H5	121.8°	120.4°
C6	C5	H5	121.9°	120.5°
C5	C6	H6	118.3°	120.1°
O4'	C1'	C2'	103.1°	103.2°
O4'	C1'	H1'	105.5°	110.9°
C1'	O4'	C4'	110.6°	109.3°
C2'	C1'	H1'	104.7°	110.7°
C1'	C2'	C3'	96.2°	99.0°
C1'	C2'	O2'	127.3°	124.4°
C1'	C2'	H2'	109.8°	109.6°
C3'	C2'	O2'	98.7°	104.0°
C3'	C2'	H2'	109.2°	108.6°
C2'	C3'	O20	102.9°	102.4°
C2'	C3'	C4'	103.4°	100.1°
C2'	C3'	H3'	106.4°	109.9°
O2'	C2'	H2'	112.1°	109.7°
O20	C3'	C4'	127.0°	123.9°
O20	C3'	H3'	108.6°	110.0°
C4'	C3'	H3'	106.9°	109.2°
C3'	C4'	C5'	105.1°	110.2°
C3'	C4'	O4'	104.0°	105.7°
C3'	C4'	H4'	111.4°	110.2°
C5'	C4'	O4'	111.6°	110.2°
C5'	C4'	H4'	111.2°	110.2°
C4'	C5'	O5'	109.1°	109.5°
C4'	C5'	H5'	109.6°	109.4°
C4'	C5'	H5'A	109.6°	109.5°
O4'	C4'	H4'	113.1°	110.2°
O5'	C5'	H5'	109.6°	109.5°
O5'	C5'	H5'A	109.6°	109.5°
C5'	O5'	HO5'	109.5°	114.0°
H5'	C5'	H5'A	109.4°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O20	P	O3P	O2P	124.8°	123.1°
O20	P	O3P	O2'	109.5°	113.7°
O20	P	O2P	O2'	95.2°	113.7°
P	O20	C3'	C2'	31.9°	46.2°
O20	P	O2'	C2'	33.6°	9.1°
O20	P	O2P	HO2P	133.2°	66.3°
P	O20	C3'	C4'	150.0°	157.6°
P	O20	C3'	H3'	80.5°	70.6°
O3P	P	O2P	O2'	131.6°	123.1°
O3P	P	O2'	C2'	92.2°	109.3°
O3P	P	O20	C3'	125.7°	143.0°
O3P	P	O2P	HO2P	0.0°	56.9°
O2P	P	O2'	C2'	138.6°	127.6°
O2P	P	O20	C3'	105.0°	93.9°
P	O2'	C2'	C1'	158.4°	148.0°
P	O2'	C2'	C3'	53.7°	36.5°
P	O2'	C2'	H2'	61.2°	79.5°
O2'	P	O20	C3'	2.2°	24.5°
O2'	P	O2P	HO2P	131.6°	180.0°
C1'	N1	C2	C6	179.1°	179.8°
C1'	N1	C2	O2	1.2°	0.2°
C1'	N1	C2	N3	178.3°	179.7°
C1'	N1	C6	C5	179.8°	179.8°
C1'	N1	C6	H6	0.2°	0.2°
N1	C1'	O4'	C2'	135.3°	118.4°
N1	C1'	O4'	H1'	115.2°	123.1°
N1	C1'	C2'	H1'	118.2°	123.0°
N1	C1'	C2'	C3'	176.8°	161.3°
N1	C1'	C2'	O2'	77.3°	84.8°
N1	C1'	C2'	H2'	63.8°	47.8°
N1	C1'	O4'	C4'	169.1°	143.2°
N1	C2	O2	N3	179.5°	179.9°
N1	C2	N3	C4	1.2°	0.1°
C2	N1	C6	C5	0.9°	0.0°
C2	N1	C6	H6	179.1°	180.0°
C2	N1	C1'	O4'	81.2°	175.8°
C2	N1	C1'	C2'	45.0°	62.1°
C2	N1	C1'	H1'	163.2°	60.9°
N1	C2	N3	HN3	178.8°	180.0°
C6	N1	C2	O2	179.7°	180.0°
C6	N1	C2	N3	0.8°	0.1°
N1	C6	C5	C4	2.0°	0.0°
N1	C6	C5	H6	180.0°	180.0°
N1	C6	C5	H5	178.0°	180.0°
C6	N1	C1'	O4'	98.0°	4.0°
C6	N1	C1'	C2'	135.8°	117.6°
C6	N1	C1'	H1'	17.6°	119.3°
O2	C2	N3	C4	179.2°	180.0°
O2	C2	N3	HN3	0.7°	0.1°
C2	N3	C4	HN3	180.0°	179.9°
C2	N3	C4	C5	0.0°	0.1°
C2	N3	C4	O4	179.8°	180.0°
N3	C4	C5	O4	179.8°	179.9°
N3	C4	C5	C6	1.6°	0.0°
N3	C4	C5	H5	178.4°	179.9°
C4	C5	C6	H5	180.0°	179.9°
C4	C5	C6	H6	178.0°	179.9°
C5	C4	N3	HN3	180.0°	179.9°
O4	C4	C5	C6	178.6°	179.9°
O4	C4	C5	H5	1.4°	0.0°
O4	C4	N3	HN3	0.2°	0.1°
H5	C5	C6	H6	2.0°	0.0°
O4'	C1'	C2'	H1'	110.2°	118.7°
O4'	C1'	C2'	C3'	45.2°	43.0°
O4'	C1'	C2'	O2'	151.1°	156.9°
O4'	C1'	C2'	H2'	67.9°	70.5°
C1'	O4'	C4'	C3'	5.3°	5.2°
C1'	O4'	C4'	C5'	107.4°	124.3°
C1'	O4'	C4'	H4'	126.3°	113.9°
C1'	C2'	C3'	O2'	129.3°	128.9°
C1'	C2'	C3'	H2'	113.5°	114.3°
C1'	C2'	O2'	H2'	140.3°	132.6°
C1'	C2'	C3'	O20	175.6°	173.6°
C1'	C2'	C3'	C4'	42.1°	45.3°
C1'	C2'	C3'	H3'	70.3°	69.5°
C2'	C1'	O4'	C4'	33.8°	24.8°
H1'	C1'	C2'	C3'	65.0°	75.7°
H1'	C1'	C2'	O2'	40.9°	38.2°
H1'	C1'	C2'	H2'	178.0°	170.8°
H1'	C1'	O4'	C4'	75.7°	93.7°
C3'	C2'	O2'	H2'	114.9°	116.0°
C2'	C3'	O20	C4'	118.1°	111.4°
C2'	C3'	O20	H3'	112.4°	116.8°
C2'	C3'	C4'	H3'	112.0°	115.4°
C2'	C3'	C4'	C5'	141.6°	150.7°
C2'	C3'	C4'	O4'	24.2°	31.6°
C2'	C3'	C4'	H4'	97.9°	87.5°
O2'	C2'	C3'	O20	55.1°	57.4°
O2'	C2'	C3'	C4'	171.4°	174.3°
O2'	C2'	C3'	H3'	59.0°	59.4°
H2'	C2'	C3'	O20	62.1°	59.3°
H2'	C2'	C3'	C4'	71.4°	69.0°
H2'	C2'	C3'	H3'	176.2°	176.1°
O20	C3'	C4'	H3'	130.2°	132.1°
O20	C3'	C4'	C5'	100.6°	96.8°
O20	C3'	C4'	O4'	142.0°	144.2°
O20	C3'	C4'	H4'	20.0°	25.0°
C3'	C4'	C5'	O4'	112.1°	116.3°
C3'	C4'	C5'	H4'	120.7°	121.9°
C3'	C4'	O4'	H4'	121.0°	119.1°
C3'	C4'	C5'	O5'	75.1°	175.0°
C3'	C4'	C5'	H5'	44.8°	55.0°
C3'	C4'	C5'	H5'A	164.9°	65.0°
H3'	C3'	C4'	C5'	29.6°	35.3°
H3'	C3'	C4'	O4'	87.8°	83.7°
H3'	C3'	C4'	H4'	150.1°	157.1°
C5'	C4'	O4'	H4'	126.3°	121.8°
C4'	C5'	O5'	H5'	119.9°	120.0°
C4'	C5'	O5'	H5'A	120.0°	120.0°
C4'	C5'	H5'	H5'A	120.2°	120.0°
C4'	C5'	O5'	HO5'	180.0°	180.0°
O4'	C4'	C5'	O5'	172.8°	68.7°
O4'	C4'	C5'	H5'	67.2°	171.3°
O4'	C4'	C5'	H5'A	52.9°	51.3°
H4'	C4'	C5'	O5'	45.5°	53.2°
H4'	C4'	C5'	H5'	165.5°	66.9°
H4'	C4'	C5'	H5'A	74.4°	173.2°
O5'	C5'	H5'	H5'A	120.2°	120.0°
H5'	C5'	O5'	HO5'	60.1°	60.0°
H5'A	C5'	O5'	HO5'	60.0°	60.0°

Definition date:	2012-02-24
Last modified:	2020-06-17
Release status:	REL
Processing site:	RCSB
Derived from:	4DVL