DPB

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C11	C12	doub	1.38Å	1.36Å	Aromatic
C11	C10	sing	1.38Å	1.53Å	Aromatic
C11	H11	sing	1.08Å	1.10Å
C12	C7	sing	1.38Å	1.47Å	Aromatic
C12	H12	sing	1.08Å	1.10Å
C7	C8	doub	1.38Å	1.46Å	Aromatic
C7	C6'	sing	1.51Å	1.56Å
C8	C9	sing	1.38Å	1.41Å	Aromatic
C8	H8	sing	1.08Å	1.10Å
C9	C10	doub	1.38Å	1.44Å	Aromatic
C9	H9	sing	1.08Å	1.10Å
C10	H10	sing	1.08Å	1.10Å
C2	N1	sing	1.34Å	1.39Å
C2	N3	sing	1.35Å	1.36Å
C2	O2	doub	1.22Å	1.24Å
N1	C6	sing	1.37Å	1.43Å
N1	C1'	sing	1.47Å	1.46Å
C6	C5	doub	1.35Å	1.41Å
C6	H6	sing	1.08Å	1.10Å
C5	C4	sing	1.41Å	1.46Å
C5	C5M	sing	1.51Å	1.65Å
C4	N3	sing	1.35Å	1.31Å
C4	O4	doub	1.22Å	1.27Å
N3	H3	sing	0.97Å	1.02Å
C5M	H71	sing	1.09Å	1.11Å
C5M	H72	sing	1.09Å	1.11Å
C5M	H73	sing	1.09Å	1.12Å
C1'	O4'	sing	1.43Å	1.48Å
C1'	C2'	sing	1.54Å	1.42Å
C1'	H1'	sing	1.09Å	1.11Å
O4'	C4'	sing	1.44Å	1.48Å
C4'	C3'	sing	1.53Å	1.19Å
C4'	C5'	sing	1.53Å	1.42Å
C4'	H4'	sing	1.10Å	1.11Å
C3'	C2'	sing	1.54Å	1.42Å
C3'	O3'	sing	1.39Å	1.48Å
C3'	H3'	sing	1.11Å	1.11Å
C2'	H2'	sing	1.09Å	1.11Å
C2'	H2''	sing	1.10Å	1.12Å
C5'	O5'	sing	1.42Å	1.35Å
C5'	H5'	sing	1.08Å	1.12Å
C5'	H5''	sing	1.10Å	1.11Å
O5'	C6'	sing	1.42Å	1.44Å
C6'	O3'	sing	1.40Å	1.61Å
C6'	P	sing	1.84Å	1.96Å
P	OP2	sing	1.61Å	1.59Å
P	OP1	doub	1.48Å	1.47Å
P	OP3	sing	1.61Å	1.53Å
OP2	HOP2	sing	0.97Å	0.95Å
OP3	HOP3	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C12	C11	C10	125.0°	120.0°
C12	C11	H11	110.9°	119.9°
C11	C12	C7	116.9°	120.0°
C11	C12	H12	117.9°	120.0°
C10	C11	H11	124.1°	120.1°
C11	C10	C9	114.0°	120.0°
C11	C10	H10	125.6°	120.0°
C7	C12	H12	125.3°	120.0°
C12	C7	C8	122.6°	120.0°
C12	C7	C6'	119.7°	120.0°
C8	C7	C6'	117.8°	119.9°
C7	C8	C9	117.6°	120.0°
C7	C8	H8	122.5°	120.0°
C7	C6'	O5'	100.4°	110.0°
C7	C6'	O3'	135.5°	110.7°
C7	C6'	P	106.4°	107.0°
C9	C8	H8	119.9°	120.0°
C8	C9	C10	124.0°	120.0°
C8	C9	H9	117.0°	120.0°
C10	C9	H9	119.1°	120.0°
C9	C10	H10	120.4°	120.0°
N1	C2	N3	118.8°	121.0°
N1	C2	O2	125.0°	119.5°
C2	N1	C6	125.2°	120.6°
C2	N1	C1'	115.9°	119.8°
N3	C2	O2	116.3°	119.6°
C2	N3	C4	121.1°	120.2°
C2	N3	H3	121.5°	119.9°
C6	N1	C1'	118.9°	119.6°
N1	C6	C5	112.9°	119.6°
N1	C6	H6	124.2°	120.2°
N1	C1'	O4'	124.9°	110.6°
N1	C1'	C2'	117.6°	110.1°
N1	C1'	H1'	87.5°	109.0°
C5	C6	H6	122.9°	120.2°
C6	C5	C4	120.4°	119.1°
C6	C5	C5M	116.3°	120.4°
C4	C5	C5M	123.3°	120.4°
C5	C4	N3	121.7°	119.4°
C5	C4	O4	117.9°	120.3°
C5	C5M	H71	109.7°	109.5°
C5	C5M	H72	116.3°	109.5°
C5	C5M	H73	109.7°	109.5°
N3	C4	O4	120.4°	120.3°
C4	N3	H3	117.4°	119.9°
H71	C5M	H72	109.7°	109.5°
H71	C5M	H73	100.5°	109.5°
H72	C5M	H73	109.8°	109.4°
O4'	C1'	C2'	98.1°	108.1°
O4'	C1'	H1'	110.9°	109.7°
C1'	O4'	C4'	99.4°	109.8°
C2'	C1'	H1'	119.4°	109.4°
C1'	C2'	C3'	121.6°	104.5°
C1'	C2'	H2'	107.9°	111.0°
C1'	C2'	H2''	107.9°	110.0°
O4'	C4'	C3'	126.5°	105.9°
O4'	C4'	C5'	82.3°	108.0°
O4'	C4'	H4'	127.5°	111.0°
C3'	C4'	C5'	130.3°	110.3°
C3'	C4'	H4'	74.2°	111.1°
C4'	C3'	C2'	94.2°	104.9°
C4'	C3'	O3'	108.6°	115.8°
C4'	C3'	H3'	119.0°	107.3°
C5'	C4'	H4'	123.4°	110.3°
C4'	C5'	O5'	101.8°	109.9°
C4'	C5'	H5'	115.2°	110.5°
C4'	C5'	H5''	115.1°	108.0°
C2'	C3'	O3'	108.9°	114.0°
C2'	C3'	H3'	118.8°	107.0°
C3'	C2'	H2'	107.9°	111.9°
C3'	C2'	H2''	107.9°	110.0°
O3'	C3'	H3'	106.6°	107.4°
C3'	O3'	C6'	127.9°	119.2°
H2'	C2'	H2''	102.0°	109.3°
O5'	C5'	H5'	115.1°	112.5°
O5'	C5'	H5''	115.2°	108.4°
C5'	O5'	C6'	116.4°	110.9°
H5'	C5'	H5''	95.3°	107.4°
O5'	C6'	O3'	87.9°	113.7°
O5'	C6'	P	111.3°	107.4°
O3'	C6'	P	111.0°	107.9°
C6'	P	OP2	93.4°	109.4°
C6'	P	OP1	112.0°	109.5°
C6'	P	OP3	112.1°	109.5°
OP2	P	OP1	108.2°	109.4°
OP2	P	OP3	109.5°	109.5°
P	OP2	HOP2	93.4°	106.8°
OP1	P	OP3	118.6°	109.5°
P	OP3	HOP3	112.1°	106.8°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C12	C11	C10	H11	180.0°	179.9°
C11	C12	C7	H12	180.0°	179.6°
C11	C12	C7	C8	0.5°	0.5°
C11	C12	C7	C6'	179.1°	179.8°
C12	C11	C10	C9	0.2°	0.1°
C12	C11	C10	H10	179.8°	179.8°
C10	C11	C12	C7	0.1°	0.4°
C10	C11	C12	H12	179.9°	180.0°
C11	C10	C9	C8	0.2°	0.0°
C11	C10	C9	H10	180.0°	180.0°
C11	C10	C9	H9	179.8°	180.0°
H11	C11	C12	C7	179.9°	179.7°
H11	C11	C12	H12	0.1°	0.1°
H11	C11	C10	C9	179.8°	180.0°
H11	C11	C10	H10	0.2°	0.1°
C12	C7	C8	C6'	179.7°	179.7°
C12	C7	C8	C9	0.5°	0.3°
C12	C7	C8	H8	179.5°	179.7°
C12	C7	C6'	O5'	34.8°	3.0°
C12	C7	C6'	O3'	132.4°	129.5°
C12	C7	C6'	P	81.2°	113.2°
H12	C12	C7	C8	179.5°	180.0°
H12	C12	C7	C6'	0.9°	0.2°
C7	C8	C9	H8	180.0°	180.0°
C7	C8	C9	C10	0.2°	0.0°
C7	C8	C9	H9	179.8°	180.0°
C8	C7	C6'	O5'	145.5°	177.3°
C8	C7	C6'	O3'	47.9°	50.8°
C8	C7	C6'	P	98.4°	66.5°
C6'	C7	C8	C9	179.1°	180.0°
C6'	C7	C8	H8	0.9°	0.0°
C7	C6'	O3'	C3'	132.7°	81.9°
C7	C6'	O5'	C5'	152.4°	66.6°
C7	C6'	O5'	O3'	135.9°	124.8°
C7	C6'	O5'	P	112.3°	116.0°
C7	C6'	O3'	P	145.3°	116.7°
C7	C6'	P	OP2	68.6°	175.9°
C7	C6'	P	OP1	42.6°	64.1°
C7	C6'	P	OP3	178.7°	55.9°
C8	C9	C10	H9	180.0°	180.0°
C8	C9	C10	H10	179.8°	180.0°
H8	C8	C9	C10	179.9°	180.0°
H8	C8	C9	H9	0.1°	0.0°
H9	C9	C10	H10	0.2°	0.0°
N1	C2	N3	O2	179.9°	180.0°
C2	N1	C6	C1'	179.0°	180.0°
C2	N1	C6	C5	0.0°	0.1°
C2	N1	C6	H6	180.0°	180.0°
N1	C2	N3	C4	0.4°	0.2°
N1	C2	N3	H3	179.6°	180.0°
C2	N1	C1'	O4'	157.9°	178.6°
C2	N1	C1'	C2'	78.2°	59.2°
C2	N1	C1'	H1'	43.9°	60.7°
N3	C2	N1	C6	0.2°	0.0°
N3	C2	N1	C1'	179.2°	180.0°
C2	N3	C4	C5	0.4°	0.4°
C2	N3	C4	H3	180.0°	179.8°
C2	N3	C4	O4	179.4°	180.0°
O2	C2	N1	C6	179.7°	179.9°
O2	C2	N1	C1'	0.7°	0.0°
O2	C2	N3	C4	179.5°	179.7°
O2	C2	N3	H3	0.5°	0.0°
N1	C6	C5	H6	180.0°	179.9°
N1	C6	C5	C4	0.0°	0.3°
N1	C6	C5	C5M	179.5°	180.0°
C6	N1	C1'	O4'	21.2°	1.4°
C6	N1	C1'	C2'	102.7°	120.7°
C6	N1	C1'	H1'	135.2°	119.3°
C1'	N1	C6	C5	179.0°	180.0°
C1'	N1	C6	H6	1.0°	0.1°
N1	C1'	O4'	C2'	132.0°	120.5°
N1	C1'	O4'	H1'	102.1°	120.3°
N1	C1'	C2'	H1'	103.8°	119.7°
N1	C1'	O4'	C4'	134.1°	103.9°
N1	C1'	C2'	C3'	140.7°	120.6°
N1	C1'	C2'	H2'	94.0°	0.2°
N1	C1'	C2'	H2''	15.5°	121.3°
C6	C5	C4	C5M	179.5°	179.8°
C6	C5	C4	N3	0.2°	0.5°
C6	C5	C4	O4	179.6°	180.0°
C6	C5	C5M	H71	54.7°	90.0°
C6	C5	C5M	H72	180.0°	150.0°
C6	C5	C5M	H73	54.7°	30.0°
H6	C6	C5	C4	180.0°	179.8°
H6	C6	C5	C5M	0.5°	0.1°
C5	C4	N3	O4	179.8°	179.5°
C5	C4	N3	H3	179.6°	179.8°
C4	C5	C5M	H71	124.8°	90.2°
C4	C5	C5M	H72	0.4°	29.8°
C4	C5	C5M	H73	125.7°	149.7°
C5M	C5	C4	N3	179.7°	179.8°
C5M	C5	C4	O4	0.1°	0.2°
C5	C5M	H71	H72	128.9°	120.0°
C5	C5M	H71	H73	115.5°	120.0°
C5	C5M	H72	H73	125.3°	120.0°
O4	C4	N3	H3	0.6°	0.3°
H71	C5M	H72	H73	109.5°	120.0°
O4'	C1'	C2'	H1'	119.6°	119.4°
C1'	O4'	C4'	C3'	0.2°	26.1°
C1'	O4'	C4'	C5'	135.2°	92.1°
C1'	O4'	C4'	H4'	98.2°	146.9°
O4'	C1'	C2'	C3'	4.2°	0.2°
O4'	C1'	C2'	H2'	129.5°	121.1°
O4'	C1'	C2'	H2''	121.1°	117.8°
C2'	C1'	O4'	C4'	2.1°	16.6°
C1'	C2'	C3'	C4'	4.1°	14.8°
C1'	C2'	C3'	H2'	125.3°	120.2°
C1'	C2'	C3'	H2''	125.3°	118.0°
C1'	C2'	C3'	O3'	115.4°	142.5°
C1'	C2'	C3'	H3'	122.4°	98.9°
C1'	C2'	H2'	H2''	113.5°	121.5°
H1'	C1'	O4'	C4'	123.7°	135.8°
H1'	C1'	C2'	C3'	115.4°	119.7°
H1'	C1'	C2'	H2'	9.9°	119.5°
H1'	C1'	C2'	H2''	119.3°	1.6°
O4'	C4'	C3'	C5'	114.1°	116.7°
O4'	C4'	C3'	H4'	125.2°	120.7°
O4'	C4'	C5'	H4'	130.3°	121.5°
O4'	C4'	C3'	C2'	2.3°	24.9°
O4'	C4'	C3'	O3'	113.9°	151.5°
O4'	C4'	C3'	H3'	124.0°	88.6°
O4'	C4'	C5'	O5'	99.8°	165.6°
O4'	C4'	C5'	H5'	25.5°	40.8°
O4'	C4'	C5'	H5''	134.9°	76.4°
C3'	C4'	C5'	H4'	97.5°	123.1°
C4'	C3'	C2'	O3'	111.3°	127.7°
C4'	C3'	C2'	H3'	126.5°	113.7°
C4'	C3'	O3'	H3'	129.4°	119.8°
C4'	C3'	C2'	H2'	129.4°	105.4°
C4'	C3'	C2'	H2''	121.1°	132.8°
C3'	C4'	C5'	O5'	32.5°	50.2°
C3'	C4'	C5'	H5'	157.7°	74.6°
C3'	C4'	C5'	H5''	92.8°	168.3°
C4'	C3'	O3'	C6'	0.7°	31.7°
C5'	C4'	C3'	C2'	111.8°	91.8°
C5'	C4'	C3'	O3'	0.3°	34.8°
C5'	C4'	C3'	H3'	121.8°	154.7°
C4'	C5'	O5'	H5'	125.3°	123.6°
C4'	C5'	O5'	H5''	125.3°	117.8°
C4'	C5'	H5'	H5''	121.0°	117.5°
C4'	C5'	O5'	C6'	79.5°	62.6°
H4'	C4'	C3'	C2'	127.6°	145.5°
H4'	C4'	C3'	O3'	120.9°	87.9°
H4'	C4'	C3'	H3'	1.2°	32.0°
H4'	C4'	C5'	O5'	129.9°	72.9°
H4'	C4'	C5'	H5'	104.8°	162.3°
H4'	C4'	C5'	H5''	4.6°	45.1°
C2'	C3'	O3'	H3'	129.3°	118.3°
C3'	C2'	H2'	H2''	113.4°	122.1°
C2'	C3'	O3'	C6'	102.1°	90.1°
O3'	C3'	C2'	H2'	119.3°	22.3°
O3'	C3'	C2'	H2''	9.9°	99.5°
C3'	O3'	C6'	O5'	30.1°	42.5°
C3'	O3'	C6'	P	82.0°	161.4°
H3'	C3'	C2'	H2'	2.9°	140.9°
H3'	C3'	C2'	H2''	112.3°	19.1°
H3'	C3'	O3'	C6'	128.7°	151.6°
O5'	C5'	H5'	H5''	121.0°	119.2°
C5'	O5'	C6'	O3'	71.7°	58.2°
C5'	O5'	C6'	P	40.1°	177.4°
H5'	C5'	O5'	C6'	155.2°	61.0°
H5''	C5'	O5'	C6'	45.8°	179.6°
O5'	C6'	O3'	P	112.1°	118.9°
O5'	C6'	P	OP2	177.0°	58.0°
O5'	C6'	P	OP1	65.8°	177.9°
O5'	C6'	P	OP3	70.3°	62.1°
O3'	C6'	P	OP2	86.8°	64.9°
O3'	C6'	P	OP1	162.0°	55.0°
O3'	C6'	P	OP3	25.9°	175.0°
C6'	P	OP2	OP1	114.5°	119.9°
C6'	P	OP2	OP3	114.9°	120.1°
C6'	P	OP1	OP3	133.0°	120.0°
C6'	P	OP2	HOP2	180.0°	60.1°
C6'	P	OP3	HOP3	180.0°	180.0°
OP2	P	OP1	OP3	125.4°	120.0°
OP2	P	OP3	HOP3	77.7°	60.0°
OP1	P	OP2	HOP2	65.5°	180.0°
OP1	P	OP3	HOP3	47.1°	60.0°
OP3	P	OP2	HOP2	65.1°	60.0°

Definition date:	2003-09-17
Last modified:	2020-06-17
Release status:	REL
Processing site:	RCSB