5MD

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O5'	C5'	sing	1.43Å	1.46Å
O5'	H5'	sing	0.97Å	0.95Å
C5'	C4'	sing	1.53Å	1.54Å
C5'	H5'1	sing	1.09Å	1.11Å
C5'	H5'2	sing	1.09Å	1.12Å
C4'	O4'	sing	1.44Å	1.41Å
C4'	C3'	sing	1.54Å	1.49Å
C4'	H4'	sing	1.09Å	1.12Å
O4'	C1'	sing	1.44Å	1.45Å
C1'	C1	sing	1.51Å	1.54Å
C1'	C2'	sing	1.55Å	1.51Å
C1'	H1'	sing	1.09Å	1.11Å
C1	C6	doub	1.35Å	1.36Å
C1	C2	sing	1.41Å	1.48Å
C6	N5	sing	1.37Å	1.37Å
C6	H6	sing	1.08Å	1.10Å
C2	O2	doub	1.22Å	1.22Å
C2	N3	sing	1.35Å	1.37Å
N3	C4	sing	1.35Å	1.36Å
N3	HN3	sing	0.97Å	1.02Å
C4	O4	doub	1.22Å	1.20Å
C4	N5	sing	1.34Å	1.38Å
N5	C5	sing	1.47Å	1.46Å
C5	H51	sing	1.09Å	1.11Å
C5	H52	sing	1.09Å	1.12Å
C5	H53	sing	1.09Å	1.12Å
C3'	O3'	sing	1.43Å	1.41Å
C3'	C2'	sing	1.55Å	1.50Å
C3'	H3'	sing	1.09Å	1.12Å
O3'	H3'A	sing	0.97Å	0.95Å
C2'	H2'1	sing	1.09Å	1.12Å
C2'	H2'2	sing	1.09Å	1.11Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C5'	O5'	H5'	109.5°	106.7°
O5'	C5'	C4'	109.4°	109.5°
O5'	C5'	H5'1	112.3°	109.5°
O5'	C5'	H5'2	112.2°	109.4°
C4'	C5'	H5'1	112.2°	109.5°
C4'	C5'	H5'2	112.2°	109.5°
C5'	C4'	O4'	108.0°	110.1°
C5'	C4'	C3'	115.9°	109.9°
C5'	C4'	H4'	104.8°	109.8°
H5'1	C5'	H5'2	98.2°	109.5°
O4'	C4'	C3'	104.9°	107.4°
O4'	C4'	H4'	115.8°	109.7°
C4'	O4'	C1'	112.1°	106.9°
C3'	C4'	H4'	107.9°	109.8°
C4'	C3'	O3'	109.6°	110.7°
C4'	C3'	C2'	103.4°	104.2°
C4'	C3'	H3'	112.0°	110.4°
O4'	C1'	C1	116.9°	110.6°
O4'	C1'	C2'	100.9°	103.6°
O4'	C1'	H1'	112.0°	110.6°
C1	C1'	C2'	113.7°	110.6°
C1	C1'	H1'	98.8°	110.6°
C1'	C1	C6	119.2°	120.4°
C1'	C1	C2	121.0°	120.4°
C2'	C1'	H1'	115.3°	110.6°
C1'	C2'	C3'	109.8°	102.1°
C1'	C2'	H2'1	112.1°	110.9°
C1'	C2'	H2'2	112.1°	110.9°
C6	C1	C2	119.7°	119.1°
C1	C6	N5	122.0°	119.6°
C1	C6	H6	118.4°	120.2°
C1	C2	O2	130.0°	120.3°
C1	C2	N3	113.3°	119.4°
N5	C6	H6	119.6°	120.2°
C6	N5	C4	120.6°	120.7°
C6	N5	C5	118.3°	119.6°
O2	C2	N3	116.4°	120.3°
C2	N3	C4	127.4°	120.3°
C2	N3	HN3	116.4°	119.8°
C4	N3	HN3	116.2°	119.9°
N3	C4	O4	117.5°	119.5°
N3	C4	N5	117.0°	120.9°
O4	C4	N5	124.8°	119.6°
C4	N5	C5	121.1°	119.7°
N5	C5	H51	118.3°	109.4°
N5	C5	H52	109.0°	109.5°
N5	C5	H53	109.0°	109.5°
H51	C5	H52	109.1°	109.4°
H51	C5	H53	109.0°	109.4°
H52	C5	H53	101.0°	109.5°
O3'	C3'	C2'	105.3°	110.5°
O3'	C3'	H3'	110.2°	110.5°
C3'	O3'	H3'A	109.7°	106.9°
C2'	C3'	H3'	115.9°	110.4°
C3'	C2'	H2'1	112.1°	110.9°
C3'	C2'	H2'2	112.1°	110.9°
H2'1	C2'	H2'2	98.3°	110.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O5'	C5'	C4'	H5'1	125.3°	120.0°
O5'	C5'	C4'	H5'2	125.2°	120.0°
O5'	C5'	H5'1	H5'2	118.2°	120.0°
O5'	C5'	C4'	O4'	50.7°	61.9°
O5'	C5'	C4'	C3'	167.9°	180.0°
O5'	C5'	C4'	H4'	73.4°	59.0°
H5'	O5'	C5'	C4'	180.0°	180.0°
H5'	O5'	C5'	H5'1	54.8°	60.0°
H5'	O5'	C5'	H5'2	54.7°	60.0°
C4'	C5'	H5'1	H5'2	118.1°	120.0°
C5'	C4'	O4'	C3'	124.1°	119.7°
C5'	C4'	O4'	H4'	117.1°	121.0°
C5'	C4'	C3'	H4'	117.1°	121.0°
C5'	C4'	O4'	C1'	91.9°	145.9°
C5'	C4'	C3'	O3'	153.8°	119.6°
C5'	C4'	C3'	C2'	94.3°	121.6°
C5'	C4'	C3'	H3'	31.1°	3.0°
H5'1	C5'	C4'	O4'	74.6°	178.1°
H5'1	C5'	C4'	C3'	42.6°	60.0°
H5'1	C5'	C4'	H4'	161.3°	61.0°
H5'2	C5'	C4'	O4'	175.9°	58.0°
H5'2	C5'	C4'	C3'	66.9°	60.0°
H5'2	C5'	C4'	H4'	51.9°	179.0°
O4'	C4'	C3'	H4'	124.0°	119.2°
C4'	O4'	C1'	C1	99.4°	158.4°
C4'	O4'	C1'	C2'	24.5°	39.8°
C4'	O4'	C1'	H1'	147.6°	78.8°
O4'	C4'	C3'	O3'	87.3°	120.6°
O4'	C4'	C3'	C2'	24.6°	1.8°
O4'	C4'	C3'	H3'	150.1°	116.8°
C3'	C4'	O4'	C1'	32.2°	26.2°
C4'	C3'	C2'	C1'	10.4°	20.9°
C4'	C3'	O3'	C2'	110.6°	114.9°
C4'	C3'	O3'	H3'	123.7°	122.6°
C4'	C3'	C2'	H3'	122.9°	118.6°
C4'	C3'	O3'	H3'A	180.0°	176.3°
C4'	C3'	C2'	H2'1	135.7°	139.1°
C4'	C3'	C2'	H2'2	114.9°	97.2°
H4'	C4'	O4'	C1'	151.0°	93.1°
H4'	C4'	C3'	O3'	36.7°	1.3°
H4'	C4'	C3'	C2'	148.6°	117.4°
H4'	C4'	C3'	H3'	85.9°	124.0°
O4'	C1'	C1	C2'	117.1°	114.2°
O4'	C1'	C1	H1'	120.2°	122.9°
O4'	C1'	C2'	H1'	120.9°	118.6°
O4'	C1'	C1	C6	0.7°	123.6°
O4'	C1'	C1	C2	176.9°	56.5°
O4'	C1'	C2'	C3'	7.3°	36.9°
O4'	C1'	C2'	H2'1	117.9°	155.2°
O4'	C1'	C2'	H2'2	132.5°	81.3°
C1	C1'	C2'	H1'	113.1°	122.9°
C1'	C1	C6	C2	177.6°	179.9°
C1'	C1	C6	N5	177.3°	180.0°
C1'	C1	C6	H6	2.7°	0.1°
C1'	C1	C2	O2	9.4°	0.1°
C1'	C1	C2	N3	177.3°	179.9°
C1	C1'	C2'	C3'	118.8°	155.5°
C1	C1'	C2'	H2'1	116.0°	86.3°
C1	C1'	C2'	H2'2	6.5°	37.3°
C2'	C1'	C1	C6	117.8°	122.1°
C2'	C1'	C1	C2	59.8°	57.8°
C1'	C2'	C3'	O3'	104.6°	97.9°
C1'	C2'	C3'	H2'1	125.2°	118.2°
C1'	C2'	C3'	H2'2	125.3°	118.2°
C1'	C2'	C3'	H3'	133.4°	139.5°
C1'	C2'	H2'1	H2'2	118.1°	123.6°
H1'	C1'	C1	C6	119.5°	0.8°
H1'	C1'	C1	C2	62.9°	179.3°
H1'	C1'	C2'	C3'	128.1°	81.6°
H1'	C1'	C2'	H2'1	2.9°	36.6°
H1'	C1'	C2'	H2'2	106.6°	160.2°
C1	C6	N5	H6	180.0°	179.9°
C6	C1	C2	O2	173.0°	179.9°
C6	C1	C2	N3	0.3°	0.0°
C1	C6	N5	C4	0.0°	0.3°
C1	C6	N5	C5	178.5°	180.0°
C2	C1	C6	N5	0.4°	0.1°
C2	C1	C6	H6	179.6°	180.0°
C1	C2	O2	N3	173.2°	180.0°
C1	C2	N3	C4	0.0°	0.3°
C1	C2	N3	HN3	180.0°	180.0°
C6	N5	C4	N3	0.3°	0.5°
C6	N5	C4	O4	169.9°	180.0°
C6	N5	C4	C5	178.4°	179.7°
C6	N5	C5	H51	180.0°	180.0°
C6	N5	C5	H52	54.7°	60.1°
C6	N5	C5	H53	54.7°	60.1°
H6	C6	N5	C4	180.0°	179.8°
H6	C6	N5	C5	1.6°	0.1°
O2	C2	N3	C4	174.4°	179.7°
O2	C2	N3	HN3	5.6°	0.0°
C2	N3	C4	HN3	180.0°	179.8°
C2	N3	C4	O4	170.6°	180.0°
C2	N3	C4	N5	0.4°	0.5°
N3	C4	O4	N5	170.2°	179.5°
N3	C4	N5	C5	178.0°	179.8°
HN3	N3	C4	O4	9.4°	0.2°
HN3	N3	C4	N5	179.7°	179.7°
O4	C4	N5	C5	11.7°	0.2°
C4	N5	C5	H51	1.6°	0.3°
C4	N5	C5	H52	123.7°	119.7°
C4	N5	C5	H53	126.9°	120.2°
N5	C5	H51	H52	125.3°	120.0°
N5	C5	H51	H53	125.3°	120.0°
N5	C5	H52	H53	114.7°	120.1°
H51	C5	H52	H53	114.8°	119.9°
O3'	C3'	C2'	H3'	122.1°	122.5°
O3'	C3'	C2'	H2'1	20.6°	20.2°
O3'	C3'	C2'	H2'2	130.1°	143.9°
C2'	C3'	O3'	H3'A	69.4°	61.4°
C3'	C2'	H2'1	H2'2	118.0°	123.7°
H3'	C3'	O3'	H3'A	56.3°	61.1°
H3'	C3'	C2'	H2'1	101.4°	102.3°
H3'	C3'	C2'	H2'2	8.0°	21.4°

Definition date:	2000-07-26
Last modified:	2020-06-17
Release status:	REL
Processing site:	RCSB
Derived from:	1F8Y