XPB

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
O3'	C3'	sing	1.43Å	1.43Å
C3'	C4'	sing	1.55Å	1.53Å
C3'	C2'	sing	1.55Å	1.52Å
C4'	C5'	sing	1.53Å	1.51Å
C4'	O4'	sing	1.44Å	1.45Å
C5'	O5'	sing	1.43Å	1.44Å
C2'	C1'	sing	1.54Å	1.52Å
O4'	C1'	sing	1.44Å	1.42Å
OP1	P	doub	1.48Å	1.48Å
C1'	N9	sing	1.46Å	1.46Å
O5'	P	sing	1.61Å	1.60Å
P	OP2	sing	1.61Å	1.48Å
N9	C4	sing	1.37Å	1.38Å	Aromatic
N9	C8	sing	1.36Å	1.38Å	Aromatic
N3	C4	sing	1.33Å	1.33Å	Aromatic
N3	C2	doub	1.32Å	1.35Å	Aromatic
N2	C2	sing	1.39Å	1.37Å
C4	C5	doub	1.41Å	1.41Å	Aromatic
C8	N7	doub	1.30Å	1.31Å	Aromatic
C2	N1	sing	1.33Å	1.35Å	Aromatic
C5	N7	sing	1.36Å	1.39Å	Aromatic
C5	C6	sing	1.40Å	1.41Å	Aromatic
N1	C6	doub	1.33Å	1.33Å	Aromatic
C6	O6	sing	1.35Å	1.34Å
O6	C10	sing	1.43Å	1.44Å
C10	C11	sing	1.53Å	1.52Å
C11	C12	sing	1.53Å	1.53Å
O13	C13	doub	1.21Å	1.22Å
C12	C13	sing	1.51Å	1.52Å
C13	C14	sing	1.47Å	1.50Å
C14	C15	doub	1.40Å	1.40Å	Aromatic
C14	C18	sing	1.40Å	1.40Å	Aromatic
C15	C16	sing	1.38Å	1.39Å	Aromatic
C18	N1'	doub	1.32Å	1.34Å	Aromatic
C16	C17	doub	1.38Å	1.40Å	Aromatic
N1'	C17	sing	1.32Å	1.34Å	Aromatic
C8	H8	sing	1.08Å	1.08Å
N2	H22	sing	0.97Å	1.00Å
N2	H21	sing	0.97Å	1.00Å
C10	H10	sing	1.09Å	1.10Å
C10	H7	sing	1.09Å	1.10Å
C11	H11	sing	1.09Å	1.10Å
C11	H9	sing	1.09Å	1.10Å
C12	H12	sing	1.09Å	1.10Å
C12	H13	sing	1.09Å	1.10Å
C15	H15	sing	1.08Å	1.08Å
OP2	H2	sing	0.97Å	0.95Å
C5'	H5'	sing	1.09Å	1.10Å
C5'	H5''	sing	1.09Å	1.10Å
C4'	H4'	sing	1.09Å	1.10Å
C3'	H3'	sing	1.09Å	1.10Å
O3'	H3	sing	0.97Å	0.95Å
C2'	H2''	sing	1.09Å	1.10Å
C2'	H2'	sing	1.09Å	1.10Å
C1'	H1'	sing	1.09Å	1.10Å
C16	H16	sing	1.08Å	1.08Å
C17	H17	sing	1.08Å	1.08Å
C18	H18	sing	1.08Å	1.08Å
P	OP3	sing	1.61Å	17.16Å
OP3	H1	sing	0.97Å	0.00Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
O3'	C3'	C4'	107.9°	110.9°
O3'	C3'	C2'	107.8°	111.0°
O3'	C3'	H3'	112.1°	110.8°
C3'	O3'	H3	109.5°	114.0°
C4'	C3'	C2'	107.5°	102.1°
C3'	C4'	C5'	115.8°	110.6°
C3'	C4'	O4'	104.4°	103.5°
C3'	C4'	H4'	108.6°	110.7°
C4'	C3'	H3'	110.7°	110.9°
C3'	C2'	C1'	102.3°	104.2°
C2'	C3'	H3'	110.7°	110.9°
C3'	C2'	H2''	111.2°	110.5°
C3'	C2'	H2'	111.3°	110.4°
C5'	C4'	O4'	109.4°	110.6°
C4'	C5'	O5'	110.0°	109.4°
C4'	C5'	H5'	109.4°	109.5°
C4'	C5'	H5''	109.3°	109.5°
C5'	C4'	H4'	108.8°	110.6°
C4'	O4'	C1'	110.8°	107.0°
O4'	C4'	H4'	109.6°	110.7°
C5'	O5'	P	121.2°	123.0°
O5'	C5'	H5'	109.3°	109.5°
O5'	C5'	H5''	109.3°	109.4°
C2'	C1'	O4'	105.9°	107.3°
C2'	C1'	N9	112.8°	109.9°
C1'	C2'	H2''	111.2°	110.5°
C1'	C2'	H2'	111.2°	110.5°
C2'	C1'	H1'	109.3°	109.9°
O4'	C1'	N9	107.8°	109.9°
O4'	C1'	H1'	110.8°	109.9°
OP1	P	O5'	113.3°	109.5°
OP1	P	OP2	109.3°	109.5°
OP1	P	OP3	171.4°	109.5°
C1'	N9	C4	125.0°	126.3°
C1'	N9	C8	128.1°	126.3°
N9	C1'	H1'	110.2°	110.0°
O5'	P	OP2	113.2°	109.5°
O5'	P	OP3	72.7°	109.4°
P	OP2	H2	109.5°	114.0°
OP2	P	OP3	72.3°	109.5°
C4	N9	C8	106.9°	107.4°
N9	C4	N3	127.4°	134.8°
N9	C4	C5	104.7°	106.1°
N9	C8	N7	113.4°	110.0°
N9	C8	H8	123.3°	125.0°
C4	N3	C2	111.2°	120.5°
N3	C4	C5	127.9°	119.1°
N3	C2	N2	116.7°	118.9°
N3	C2	N1	127.7°	122.3°
N2	C2	N1	115.6°	118.8°
C2	N2	H22	109.5°	120.0°
C2	N2	H21	109.5°	120.0°
C4	C5	N7	110.6°	107.1°
C4	C5	C6	114.4°	118.4°
C8	N7	C5	104.5°	109.5°
N7	C8	H8	123.3°	125.1°
C2	N1	C6	119.1°	121.2°
N7	C5	C6	135.0°	134.6°
C5	C6	N1	119.7°	118.6°
C5	C6	O6	126.2°	120.7°
N1	C6	O6	114.0°	120.7°
C6	O6	C10	119.7°	117.0°
O6	C10	C11	106.8°	109.5°
O6	C10	H10	110.1°	109.4°
O6	C10	H7	110.1°	109.6°
C10	C11	C12	111.3°	109.5°
C11	C10	H10	110.1°	109.4°
C11	C10	H7	110.2°	109.5°
C10	C11	H11	109.0°	109.4°
C10	C11	H9	109.0°	109.5°
C11	C12	C13	113.0°	109.5°
C12	C11	H11	109.0°	109.4°
C12	C11	H9	109.0°	109.5°
C11	C12	H12	108.6°	109.5°
C11	C12	H13	108.6°	109.5°
O13	C13	C12	121.2°	120.0°
O13	C13	C14	120.1°	120.0°
C12	C13	C14	118.7°	120.0°
C13	C12	H12	108.6°	109.5°
C13	C12	H13	108.6°	109.5°
C13	C14	C15	118.8°	120.6°
C13	C14	C18	123.7°	120.6°
C15	C14	C18	117.5°	118.8°
C14	C15	C16	119.1°	118.3°
C14	C15	H15	120.5°	120.9°
C14	C18	N1'	124.1°	120.6°
C14	C18	H18	117.9°	119.7°
C15	C16	C17	118.4°	119.3°
C16	C15	H15	120.5°	120.9°
C15	C16	H16	120.8°	120.3°
C18	N1'	C17	117.1°	121.9°
N1'	C18	H18	117.9°	119.7°
C16	C17	N1'	123.7°	121.1°
C17	C16	H16	120.8°	120.3°
C16	C17	H17	118.1°	119.5°
N1'	C17	H17	118.1°	119.4°
H22	N2	H21	109.5°	120.0°
H10	C10	H7	109.5°	109.4°
H11	C11	H9	109.5°	109.5°
H12	C12	H13	109.5°	109.4°
H5'	C5'	H5''	109.4°	109.5°
H2''	C2'	H2'	109.5°	110.6°
P	OP3	H1	90.0°	114.0°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
O3'	C3'	C4'	C2'	116.0°	118.3°
O3'	C3'	C4'	H3'	123.0°	123.6°
O3'	C3'	C2'	H3'	123.0°	123.6°
O3'	C3'	C4'	C5'	128.1°	86.2°
O3'	C3'	C4'	O4'	111.6°	155.3°
O3'	C3'	C2'	C1'	95.4°	139.1°
O3'	C3'	C4'	H4'	5.3°	36.7°
O3'	C3'	C2'	H2''	145.8°	102.2°
O3'	C3'	C2'	H2'	23.5°	20.5°
C4'	C3'	C2'	H3'	121.0°	118.2°
C3'	C4'	C5'	O4'	117.6°	114.0°
C3'	C4'	C5'	H4'	122.7°	123.0°
C3'	C4'	O4'	H4'	116.2°	118.7°
C3'	C4'	C5'	O5'	55.4°	179.5°
C4'	C3'	C2'	C1'	20.7°	20.9°
C3'	C4'	O4'	C1'	15.4°	40.1°
C3'	C4'	C5'	H5'	175.5°	60.5°
C3'	C4'	C5'	H5''	64.7°	59.5°
C4'	C3'	O3'	H3	180.0°	180.0°
C4'	C3'	C2'	H2''	98.2°	139.5°
C4'	C3'	C2'	H2'	139.5°	97.8°
C2'	C3'	C4'	C5'	115.9°	155.5°
C2'	C3'	C4'	O4'	4.5°	37.0°
C3'	C2'	C1'	H2''	118.8°	118.7°
C3'	C2'	C1'	H2'	118.9°	118.6°
C3'	C2'	C1'	O4'	29.9°	2.1°
C3'	C2'	C1'	N9	147.6°	121.5°
C2'	C3'	C4'	H4'	121.3°	81.6°
C2'	C3'	O3'	H3	64.2°	67.2°
C3'	C2'	H2''	H2'	123.4°	122.6°
C3'	C2'	C1'	H1'	89.4°	117.4°
C5'	C4'	O4'	H4'	119.3°	122.9°
C4'	C5'	O5'	H5'	120.1°	120.0°
C4'	C5'	O5'	H5''	120.1°	120.0°
C5'	C4'	O4'	C1'	139.9°	158.6°
C4'	C5'	O5'	P	165.8°	180.0°
C4'	C5'	H5'	H5''	119.8°	120.1°
C5'	C4'	C3'	H3'	5.1°	37.3°
O4'	C4'	C5'	O5'	62.2°	66.5°
C4'	O4'	C1'	C2'	29.3°	26.6°
C4'	O4'	C1'	N9	150.2°	146.0°
O4'	C4'	C5'	H5'	57.9°	53.5°
O4'	C4'	C5'	H5''	177.7°	173.6°
O4'	C4'	C3'	H3'	125.5°	81.1°
C4'	O4'	C1'	H1'	89.1°	92.9°
C5'	O5'	P	OP1	70.3°	55.0°
C5'	O5'	P	OP2	164.4°	65.0°
O5'	C5'	H5'	H5''	119.7°	120.0°
O5'	C5'	C4'	H4'	178.1°	56.4°
C5'	O5'	P	OP3	103.1°	175.0°
C2'	C1'	O4'	N9	120.9°	119.4°
C2'	C1'	O4'	H1'	118.4°	119.5°
C2'	C1'	N9	H1'	122.5°	121.1°
C2'	C1'	N9	C4	125.0°	85.7°
C2'	C1'	N9	C8	54.8°	94.3°
C1'	C2'	C3'	H3'	141.6°	97.3°
C1'	C2'	H2''	H2'	123.3°	122.7°
O4'	C1'	N9	H1'	121.0°	121.1°
O4'	C1'	N9	C4	118.5°	156.5°
O4'	C1'	N9	C8	61.7°	23.5°
C1'	O4'	C4'	H4'	100.8°	78.6°
O4'	C1'	C2'	H2''	88.9°	116.6°
O4'	C1'	C2'	H2'	148.8°	120.7°
OP1	P	O5'	OP2	125.3°	120.0°
OP1	P	O5'	OP3	173.5°	120.0°
OP1	P	OP2	OP3	171.1°	120.0°
OP1	P	OP2	H2	0.0°	180.0°
OP1	P	OP3	H1	90.0°	60.0°
C1'	N9	C4	C8	179.8°	180.0°
C1'	N9	C4	N3	0.1°	0.3°
C1'	N9	C4	C5	179.7°	180.0°
C1'	N9	C8	N7	179.7°	179.8°
C1'	N9	C8	H8	0.3°	0.1°
N9	C1'	C2'	H2''	28.8°	2.8°
N9	C1'	C2'	H2'	93.6°	119.9°
O5'	P	OP2	OP3	61.6°	120.0°
O5'	P	OP2	H2	127.4°	60.0°
P	O5'	C5'	H5'	45.7°	60.0°
P	O5'	C5'	H5''	74.1°	60.0°
O5'	P	OP3	H1	90.0°	180.0°
OP2	P	OP3	H1	90.0°	60.0°
N9	C4	N3	C5	179.8°	179.7°
N9	C4	N3	C2	179.8°	179.8°
C4	N9	C8	N7	0.1°	0.2°
N9	C4	C5	N7	0.0°	0.2°
N9	C4	C5	C6	179.6°	179.8°
C4	N9	C8	H8	180.0°	179.9°
C4	N9	C1'	H1'	2.5°	35.4°
C8	N9	C4	N3	179.9°	179.7°
C8	N9	C4	C5	0.1°	0.0°
N9	C8	N7	H8	180.0°	179.7°
N9	C8	N7	C5	0.0°	0.3°
C8	N9	C1'	H1'	177.2°	144.6°
C4	N3	C2	N2	177.4°	180.0°
C4	N3	C2	N1	1.0°	0.1°
N3	C4	C5	N7	179.9°	179.9°
N3	C4	C5	C6	0.2°	0.1°
N3	C2	N2	N1	178.6°	180.0°
C2	N3	C4	C5	0.4°	0.1°
N3	C2	N1	C6	1.0°	0.0°
N3	C2	N2	H22	0.0°	0.0°
N3	C2	N2	H21	120.0°	180.0°
N2	C2	N1	C6	177.5°	179.9°
C2	N2	H22	H21	120.0°	180.0°
C4	C5	N7	C8	0.0°	0.3°
C4	C5	N7	C6	179.5°	180.0°
C4	C5	C6	N1	0.3°	0.0°
C4	C5	C6	O6	179.3°	180.0°
C8	N7	C5	C6	179.5°	179.7°
C2	N1	C6	C5	0.2°	0.1°
C2	N1	C6	O6	179.8°	180.0°
N1	C2	N2	H22	178.6°	180.0°
N1	C2	N2	H21	58.6°	0.0°
N7	C5	C6	N1	179.8°	180.0°
N7	C5	C6	O6	0.3°	0.0°
C5	N7	C8	H8	180.0°	180.0°
C5	C6	N1	O6	179.6°	180.0°
C5	C6	O6	C10	87.7°	180.0°
N1	C6	O6	C10	92.8°	0.1°
C6	O6	C10	C11	98.9°	180.0°
C6	O6	C10	H10	20.7°	60.1°
C6	O6	C10	H7	141.5°	59.9°
O6	C10	C11	H10	119.6°	120.0°
O6	C10	C11	H7	119.6°	120.1°
O6	C10	C11	C12	130.1°	180.0°
O6	C10	H10	H7	121.2°	120.1°
O6	C10	C11	H11	9.8°	60.0°
O6	C10	C11	H9	109.6°	59.9°
C10	C11	C12	H11	120.3°	120.0°
C10	C11	C12	H9	120.3°	120.1°
C10	C11	C12	C13	158.9°	180.0°
C11	C10	H10	H7	121.3°	120.0°
C10	C11	H11	H9	119.2°	120.0°
C10	C11	C12	H12	80.6°	60.0°
C10	C11	C12	H13	38.4°	59.9°
C11	C12	C13	O13	0.4°	0.0°
C11	C12	C13	H12	120.5°	120.0°
C11	C12	C13	H13	120.5°	120.0°
C11	C12	C13	C14	179.5°	180.0°
C12	C11	C10	H10	110.3°	60.0°
C12	C11	C10	H7	10.5°	59.9°
C12	C11	H11	H9	119.2°	120.0°
C11	C12	H12	H13	118.4°	119.9°
O13	C13	C12	C14	179.9°	180.0°
O13	C13	C14	C15	1.2°	0.0°
O13	C13	C14	C18	178.8°	179.7°
O13	C13	C12	H12	121.0°	120.0°
O13	C13	C12	H13	120.1°	120.0°
C12	C13	C14	C15	178.9°	180.0°
C12	C13	C14	C18	1.1°	0.3°
C13	C12	C11	H11	38.6°	60.0°
C13	C12	C11	H9	80.8°	60.0°
C13	C12	H12	H13	118.4°	120.0°
C13	C14	C15	C18	180.0°	179.7°
C13	C14	C15	C16	179.9°	180.0°
C13	C14	C18	N1'	180.0°	179.8°
C14	C13	C12	H12	59.0°	60.0°
C14	C13	C12	H13	60.0°	60.0°
C13	C14	C15	H15	0.0°	0.1°
C13	C14	C18	H18	0.0°	0.0°
C14	C15	C16	H15	180.0°	179.9°
C15	C14	C18	N1'	0.0°	0.5°
C14	C15	C16	C17	0.0°	0.1°
C14	C15	C16	H16	180.0°	180.0°
C15	C14	C18	H18	180.0°	179.7°
C18	C14	C15	C16	0.0°	0.3°
C14	C18	N1'	H18	180.0°	179.8°
C14	C18	N1'	C17	0.0°	0.5°
C18	C14	C15	H15	180.0°	179.8°
C15	C16	C17	H16	180.0°	179.9°
C15	C16	C17	N1'	0.0°	0.1°
C15	C16	C17	H17	180.0°	180.0°
C18	N1'	C17	C16	0.0°	0.3°
C18	N1'	C17	H17	180.0°	179.7°
C16	C17	N1'	H17	180.0°	180.0°
C17	C16	C15	H15	180.0°	180.0°
N1'	C17	C16	H16	180.0°	180.0°
C17	N1'	C18	H18	180.0°	179.7°
H10	C10	C11	H11	129.4°	NaN°
H10	C10	C11	H9	9.9°	60.0°
H7	C10	C11	H11	109.8°	60.0°
H7	C10	C11	H9	130.8°	180.0°
H11	C11	C12	H12	159.2°	180.0°
H11	C11	C12	H13	81.9°	60.0°
H9	C11	C12	H12	39.7°	60.1°
H9	C11	C12	H13	158.7°	180.0°
H15	C15	C16	H16	0.0°	0.1°
H2	OP2	P	OP3	171.1°	59.9°
H5'	C5'	C4'	H4'	61.8°	176.4°
H5''	C5'	C4'	H4'	58.0°	63.5°
H4'	C4'	C3'	H3'	117.7°	160.3°
H3'	C3'	O3'	H3	57.9°	56.4°
H3'	C3'	C2'	H2''	22.8°	21.4°
H3'	C3'	C2'	H2'	99.5°	144.1°
H2''	C2'	C1'	H1'	151.7°	123.9°
H2'	C2'	C1'	H1'	29.4°	1.2°
H16	C16	C17	H17	0.0°	0.0°

Release date:	2014-08-06
Definition date:	2014-07-30
Last modified:	2014-08-01
Release status:	REL
Processing site:	RCSB
Derived from:	1PYJ