D4M

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
OP2	P	sing	1.61Å	1.55Å
OP2	HOP2	sing	0.97Å	0.95Å
P	OP1	doub	1.48Å	1.60Å
P	OP3	sing	1.61Å	1.54Å
P	O5'	sing	1.61Å	1.63Å
OP3	HOP3	sing	0.97Å	0.95Å
O5'	C5'	sing	1.43Å	1.46Å
C5'	C4'	sing	1.53Å	1.52Å
C5'	H5'	sing	1.09Å	1.12Å
C5'	H5''	sing	1.09Å	1.11Å
C4'	O4'	sing	1.44Å	1.49Å
C4'	C3'	sing	1.51Å	1.52Å
C4'	H4'	sing	1.09Å	1.11Å
O4'	C1'	sing	1.44Å	1.47Å
C3'	C2'	doub	1.31Å	1.33Å
C3'	H3'	sing	1.08Å	1.10Å
C2'	C1'	sing	1.51Å	1.54Å
C2'	H2'	sing	1.08Å	1.10Å
C1'	N1	sing	1.47Å	1.49Å
C1'	H1'	sing	1.09Å	1.12Å
N1	C6	sing	1.37Å	1.42Å
N1	C2	sing	1.35Å	1.43Å
C6	C5	doub	1.35Å	1.39Å
C6	H6	sing	1.08Å	1.10Å
C5	C5M	sing	1.51Å	1.53Å
C5	C4	sing	1.42Å	1.42Å
C5M	H71	sing	1.09Å	1.12Å
C5M	H72	sing	1.09Å	1.11Å
C5M	H73	sing	1.09Å	1.11Å
C4	O4	doub	1.22Å	1.25Å
C4	N3	sing	1.35Å	1.37Å
N3	C2	sing	1.35Å	1.38Å
N3	H3	sing	0.97Å	1.02Å
C2	O2	doub	1.22Å	1.23Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
P	OP2	HOP2	106.9°	106.8°
OP2	P	OP1	106.9°	109.4°
OP2	P	OP3	117.7°	109.5°
OP2	P	O5'	104.5°	109.5°
OP1	P	OP3	106.5°	109.5°
OP1	P	O5'	110.7°	109.5°
OP3	P	O5'	110.4°	109.5°
P	OP3	HOP3	117.7°	106.7°
P	O5'	C5'	118.9°	106.8°
O5'	C5'	C4'	104.5°	109.4°
O5'	C5'	H5'	114.1°	109.5°
O5'	C5'	H5''	114.1°	109.5°
C4'	C5'	H5'	114.1°	109.4°
C4'	C5'	H5''	114.1°	109.4°
C5'	C4'	O4'	105.9°	110.2°
C5'	C4'	C3'	110.6°	110.3°
C5'	C4'	H4'	110.6°	110.1°
H5'	C5'	H5''	96.3°	109.5°
O4'	C4'	C3'	108.1°	105.7°
O4'	C4'	H4'	113.0°	110.2°
C4'	O4'	C1'	105.8°	103.7°
C3'	C4'	H4'	108.6°	110.2°
C4'	C3'	C2'	108.2°	108.4°
C4'	C3'	H3'	131.3°	125.8°
O4'	C1'	C2'	106.1°	105.8°
O4'	C1'	N1	110.6°	110.2°
O4'	C1'	H1'	111.9°	110.2°
C2'	C3'	H3'	120.5°	125.8°
C3'	C2'	C1'	111.1°	108.3°
C3'	C2'	H2'	118.3°	125.8°
C1'	C2'	H2'	130.6°	125.9°
C2'	C1'	N1	112.2°	110.2°
C2'	C1'	H1'	110.3°	110.2°
N1	C1'	H1'	105.7°	110.2°
C1'	N1	C6	121.0°	119.7°
C1'	N1	C2	120.9°	119.7°
C6	N1	C2	118.1°	120.6°
N1	C6	C5	120.4°	119.7°
N1	C6	H6	120.7°	120.2°
N1	C2	N3	119.5°	120.9°
N1	C2	O2	123.4°	119.6°
C5	C6	H6	118.9°	120.2°
C6	C5	C5M	118.3°	120.5°
C6	C5	C4	120.6°	119.2°
C5M	C5	C4	121.0°	120.4°
C5	C5M	H71	118.3°	109.5°
C5	C5M	H72	109.0°	109.5°
C5	C5M	H73	109.0°	109.5°
C5	C4	O4	125.3°	120.4°
C5	C4	N3	118.3°	119.3°
H71	C5M	H72	108.9°	109.5°
H71	C5M	H73	109.0°	109.4°
H72	C5M	H73	101.1°	109.5°
O4	C4	N3	116.4°	120.3°
C4	N3	C2	123.1°	120.3°
C4	N3	H3	118.2°	119.8°
C2	N3	H3	118.7°	119.9°
N3	C2	O2	117.1°	119.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
OP2	P	OP1	OP3	126.6°	120.0°
OP2	P	OP1	O5'	113.3°	120.0°
OP2	P	OP3	O5'	119.9°	120.0°
OP2	P	OP3	HOP3	180.0°	60.0°
OP2	P	O5'	C5'	152.3°	65.0°
HOP2	OP2	P	OP1	180.0°	180.0°
HOP2	OP2	P	OP3	60.4°	60.0°
HOP2	OP2	P	O5'	62.6°	60.0°
OP1	P	OP3	O5'	120.2°	120.0°
OP1	P	OP3	HOP3	60.1°	60.0°
OP1	P	O5'	C5'	92.9°	55.0°
OP3	P	O5'	C5'	24.8°	175.0°
O5'	P	OP3	HOP3	60.1°	180.0°
P	O5'	C5'	C4'	141.6°	180.0°
P	O5'	C5'	H5'	93.1°	60.0°
P	O5'	C5'	H5''	16.4°	60.1°
O5'	C5'	C4'	H5'	125.3°	120.0°
O5'	C5'	C4'	H5''	125.3°	120.0°
O5'	C5'	H5'	H5''	120.0°	120.0°
O5'	C5'	C4'	O4'	68.6°	66.5°
O5'	C5'	C4'	C3'	174.5°	177.2°
O5'	C5'	C4'	H4'	54.2°	55.3°
C4'	C5'	H5'	H5''	120.0°	120.0°
C5'	C4'	O4'	C3'	118.6°	119.1°
C5'	C4'	O4'	H4'	121.3°	121.7°
C5'	C4'	C3'	H4'	121.6°	121.8°
C5'	C4'	O4'	C1'	127.5°	146.4°
C5'	C4'	C3'	C2'	122.0°	136.5°
C5'	C4'	C3'	H3'	57.9°	43.5°
H5'	C5'	C4'	O4'	56.6°	173.5°
H5'	C5'	C4'	C3'	60.2°	57.2°
H5'	C5'	C4'	H4'	179.4°	64.7°
H5''	C5'	C4'	O4'	166.1°	53.5°
H5''	C5'	C4'	C3'	49.2°	62.8°
H5''	C5'	C4'	H4'	71.1°	175.3°
O4'	C4'	C3'	H4'	122.9°	119.1°
O4'	C4'	C3'	C2'	6.5°	17.4°
O4'	C4'	C3'	H3'	173.4°	162.5°
C4'	O4'	C1'	C2'	7.9°	27.3°
C4'	O4'	C1'	N1	129.8°	146.3°
C4'	O4'	C1'	H1'	112.5°	91.8°
C3'	C4'	O4'	C1'	8.9°	27.3°
C4'	C3'	C2'	H3'	180.0°	180.0°
C4'	C3'	C2'	C1'	1.4°	0.1°
C4'	C3'	C2'	H2'	178.6°	180.0°
H4'	C4'	O4'	C1'	111.3°	91.8°
H4'	C4'	C3'	C2'	116.4°	101.7°
H4'	C4'	C3'	H3'	63.6°	78.3°
O4'	C1'	C2'	C3'	4.2°	17.3°
O4'	C1'	C2'	N1	120.9°	119.1°
O4'	C1'	C2'	H1'	121.4°	119.1°
O4'	C1'	C2'	H2'	175.8°	162.6°
O4'	C1'	N1	H1'	121.4°	121.8°
O4'	C1'	N1	C6	64.2°	127.5°
O4'	C1'	N1	C2	116.7°	52.5°
C3'	C2'	C1'	H2'	180.0°	179.9°
C3'	C2'	C1'	N1	125.1°	136.4°
C3'	C2'	C1'	H1'	117.3°	101.8°
H3'	C3'	C2'	C1'	178.5°	179.9°
H3'	C3'	C2'	H2'	1.4°	0.0°
C2'	C1'	N1	H1'	120.3°	121.8°
C2'	C1'	N1	C6	54.1°	116.1°
C2'	C1'	N1	C2	125.1°	63.9°
H2'	C2'	C1'	N1	54.9°	43.6°
H2'	C2'	C1'	H1'	62.8°	78.3°
C1'	N1	C6	C2	179.2°	180.0°
C1'	N1	C6	C5	179.8°	180.0°
C1'	N1	C6	H6	0.2°	0.0°
C1'	N1	C2	N3	179.0°	180.0°
C1'	N1	C2	O2	0.3°	0.0°
H1'	C1'	N1	C6	174.4°	5.7°
H1'	C1'	N1	C2	4.7°	174.3°
N1	C6	C5	H6	180.0°	179.9°
N1	C6	C5	C5M	177.7°	180.0°
N1	C6	C5	C4	1.1°	0.3°
C6	N1	C2	N3	0.2°	0.0°
C6	N1	C2	O2	178.9°	180.0°
C2	N1	C6	C5	1.1°	0.0°
C2	N1	C6	H6	178.9°	180.0°
N1	C2	N3	C4	1.4°	0.2°
N1	C2	N3	O2	178.8°	180.0°
N1	C2	N3	H3	178.6°	179.9°
C6	C5	C5M	C4	178.8°	179.7°
C6	C5	C5M	H71	180.0°	90.0°
C6	C5	C5M	H72	54.8°	150.0°
C6	C5	C5M	H73	54.7°	29.9°
C6	C5	C4	O4	178.8°	179.9°
C6	C5	C4	N3	0.0°	0.5°
H6	C6	C5	C5M	2.4°	0.1°
H6	C6	C5	C4	178.9°	179.8°
C5	C5M	H71	H72	125.2°	120.0°
C5	C5M	H71	H73	125.3°	120.0°
C5	C5M	H72	H73	114.8°	120.0°
C5M	C5	C4	O4	0.1°	0.2°
C5M	C5	C4	N3	178.8°	179.8°
C4	C5	C5M	H71	1.2°	90.3°
C4	C5	C5M	H72	124.0°	29.7°
C4	C5	C5M	H73	126.5°	149.8°
C5	C4	O4	N3	178.9°	179.6°
C5	C4	N3	C2	1.3°	0.5°
C5	C4	N3	H3	178.7°	179.8°
H71	C5M	H72	H73	114.8°	120.0°
O4	C4	N3	C2	177.6°	179.9°
O4	C4	N3	H3	2.4°	0.2°
C4	N3	C2	H3	180.0°	179.7°
C4	N3	C2	O2	179.8°	179.8°
H3	N3	C2	O2	0.2°	0.1°

Definition date:	2005-05-10
Last modified:	2020-05-27
Release status:	REL
Processing site:	RCSB
Derived from:	1Z4Q