PRD_900087

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
P	OP2	doub	1.48Å	1.50Å
P	C	sing	1.82Å	1.83Å
P	OP1	sing	1.61Å	1.55Å
P	OP3	sing	1.61Å	1.57Å
O3	C3	sing	1.43Å	1.41Å
C3	C4	sing	1.53Å	1.48Å
C3	C2	sing	1.53Å	1.47Å
C2	O2	sing	1.43Å	1.43Å
C2	C1	sing	1.53Å	1.52Å
C1	O5	sing	1.43Å	1.46Å
C1	O4'	sing	1.43Å	1.42Å
O5	C5	sing	1.43Å	1.46Å
C5	C4	sing	1.53Å	1.52Å
C5	C6	sing	1.53Å	1.52Å
C4	O4	sing	1.43Å	1.41Å
C6	O6	sing	1.43Å	1.41Å
O4'	C4'	sing	1.43Å	1.43Å
C4'	C5'	sing	1.53Å	1.52Å
C4'	C3'	sing	1.53Å	1.49Å
C3'	O3'	sing	1.43Å	1.41Å
C3'	C2'	sing	1.53Å	1.44Å
C2'	O2'	sing	1.43Å	1.44Å
C2'	C1'	sing	1.53Å	1.50Å
C1'	O5'	sing	1.43Å	1.46Å
C1'	C	sing	1.53Å	1.53Å
O5'	C5'	sing	1.43Å	1.42Å
C5'	C6'	sing	1.53Å	1.52Å
C6'	O6'	sing	1.43Å	1.40Å
O3	H1	sing	0.97Å	0.95Å
C3	H2	sing	1.09Å	1.10Å
C2	H3	sing	1.09Å	1.10Å
C1	H4	sing	1.09Å	1.10Å
C5	H5	sing	1.09Å	1.10Å
C4	H6	sing	1.09Å	1.10Å
O4	H7	sing	0.97Å	0.95Å
C6	H8	sing	1.09Å	1.10Å
C6	H9	sing	1.09Å	1.10Å
O6	H10	sing	0.97Å	0.95Å
C4'	H11	sing	1.09Å	1.10Å
C3'	H12	sing	1.09Å	1.10Å
C2'	H13	sing	1.09Å	1.10Å
C1'	H14	sing	1.09Å	1.10Å
C	H15	sing	1.09Å	1.10Å
C	H16	sing	1.09Å	1.10Å
OP3	H17	sing	0.97Å	0.95Å
OP1	H18	sing	0.97Å	0.95Å
C5'	H19	sing	1.09Å	1.10Å
C6'	H20	sing	1.09Å	1.10Å
C6'	H21	sing	1.09Å	1.10Å
O6'	H22	sing	0.97Å	0.95Å
O2'	H23	sing	0.97Å	0.95Å
O3'	H24	sing	0.97Å	0.95Å
O2	H25	sing	0.97Å	0.95Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
OP2	P	C	108.7°	109.4°
OP2	P	OP1	112.0°	109.5°
OP2	P	OP3	109.4°	109.5°
C	P	OP1	111.8°	109.5°
C	P	OP3	106.7°	109.4°
P	C	C1'	116.6°	109.4°
P	C	H15	107.7°	109.5°
P	C	H16	107.7°	109.5°
OP1	P	OP3	108.1°	109.5°
P	OP1	H18	109.5°	114.1°
P	OP3	H17	109.5°	114.0°
O3	C3	C4	109.6°	109.5°
O3	C3	C2	109.7°	109.5°
C3	O3	H1	109.5°	114.0°
O3	C3	H2	109.4°	109.6°
C4	C3	C2	111.0°	109.1°
C3	C4	C5	109.3°	109.1°
C3	C4	O4	110.8°	109.5°
C4	C3	H2	108.5°	109.5°
C3	C4	H6	107.8°	109.5°
C3	C2	O2	109.5°	109.5°
C3	C2	C1	112.3°	109.1°
C2	C3	H2	108.6°	109.6°
C3	C2	H3	108.8°	109.6°
O2	C2	C1	108.6°	109.5°
O2	C2	H3	109.4°	109.5°
C2	O2	H25	109.5°	114.0°
C2	C1	O5	111.5°	109.4°
C2	C1	O4'	106.7°	109.5°
C1	C2	H3	108.2°	109.5°
C2	C1	H4	108.0°	109.4°
O5	C1	O4'	112.5°	109.5°
C1	O5	C5	112.0°	114.1°
O5	C1	H4	108.8°	109.5°
C1	O4'	C4'	114.8°	114.0°
O4'	C1	H4	109.2°	109.5°
O5	C5	C4	109.9°	109.5°
O5	C5	C6	108.0°	109.5°
O5	C5	H5	107.9°	109.5°
C4	C5	C6	116.3°	109.5°
C5	C4	O4	112.6°	109.6°
C4	C5	H5	107.2°	109.5°
C5	C4	H6	107.4°	109.5°
C5	C6	O6	113.4°	109.5°
C6	C5	H5	107.1°	109.5°
C5	C6	H8	108.5°	109.4°
C5	C6	H9	108.5°	109.5°
O4	C4	H6	108.7°	109.6°
C4	O4	H7	109.5°	114.0°
O6	C6	H8	108.5°	109.5°
O6	C6	H9	108.5°	109.5°
C6	O6	H10	109.5°	114.0°
O4'	C4'	C5'	102.2°	109.5°
O4'	C4'	C3'	111.5°	109.6°
O4'	C4'	H11	110.2°	109.5°
C5'	C4'	C3'	114.5°	109.2°
C4'	C5'	O5'	116.3°	109.5°
C4'	C5'	C6'	113.7°	109.5°
C5'	C4'	H11	108.9°	109.5°
C4'	C5'	H19	107.2°	109.5°
C4'	C3'	O3'	110.0°	109.6°
C4'	C3'	C2'	110.7°	109.0°
C3'	C4'	H11	109.4°	109.6°
C4'	C3'	H12	109.6°	109.6°
O3'	C3'	C2'	105.5°	109.5°
O3'	C3'	H12	110.7°	109.5°
C3'	O3'	H24	109.5°	114.0°
C3'	C2'	O2'	113.1°	109.5°
C3'	C2'	C1'	108.2°	109.1°
C2'	C3'	H12	110.3°	109.6°
C3'	C2'	H13	109.2°	109.6°
O2'	C2'	C1'	108.9°	109.5°
O2'	C2'	H13	109.1°	109.5°
C2'	O2'	H23	109.5°	114.0°
C2'	C1'	O5'	110.0°	109.4°
C2'	C1'	C	114.1°	109.5°
C1'	C2'	H13	108.3°	109.6°
C2'	C1'	H14	107.4°	109.5°
O5'	C1'	C	110.2°	109.5°
C1'	O5'	C5'	115.7°	114.1°
O5'	C1'	H14	107.9°	109.5°
C	C1'	H14	107.0°	109.5°
C1'	C	H15	107.7°	109.5°
C1'	C	H16	107.7°	109.5°
O5'	C5'	C6'	103.6°	109.5°
O5'	C5'	H19	108.5°	109.5°
C5'	C6'	O6'	115.4°	109.5°
C6'	C5'	H19	107.2°	109.5°
C5'	C6'	H20	108.0°	109.4°
C5'	C6'	H21	108.0°	109.4°
O6'	C6'	H20	108.0°	109.5°
O6'	C6'	H21	108.0°	109.5°
C6'	O6'	H22	109.5°	114.0°
H8	C6	H9	109.5°	109.5°
H15	C	H16	109.4°	109.5°
H20	C6'	H21	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
OP2	P	C	OP1	124.1°	120.1°
OP2	P	C	OP3	117.9°	120.0°
OP2	P	OP1	OP3	120.6°	120.0°
OP2	P	C	C1'	173.5°	55.1°
OP2	P	C	H15	65.5°	175.0°
OP2	P	C	H16	52.4°	65.0°
OP2	P	OP3	H17	0.0°	60.0°
OP2	P	OP1	H18	0.0°	180.0°
C	P	OP1	OP3	117.1°	120.0°
P	C	C1'	C2'	178.3°	175.0°
P	C	C1'	O5'	57.3°	65.0°
P	C	C1'	H15	121.0°	120.0°
P	C	C1'	H16	121.0°	120.0°
P	C	C1'	H14	59.7°	55.0°
P	C	H15	H16	116.8°	120.0°
C	P	OP3	H17	117.4°	180.0°
C	P	OP1	H18	122.2°	60.0°
OP1	P	C	C1'	62.4°	65.0°
OP1	P	C	H15	58.6°	55.0°
OP1	P	C	H16	176.5°	175.0°
OP1	P	OP3	H17	122.2°	60.1°
OP3	P	C	C1'	55.6°	175.0°
OP3	P	C	H15	176.6°	65.0°
OP3	P	C	H16	65.5°	55.0°
OP3	P	OP1	H18	120.6°	60.0°
O3	C3	C4	C2	121.3°	119.8°
O3	C3	C4	H2	119.4°	120.2°
O3	C3	C2	H2	119.5°	120.3°
O3	C3	C2	O2	64.5°	63.3°
O3	C3	C2	C1	174.7°	176.8°
O3	C3	C4	C5	178.8°	176.8°
O3	C3	C4	O4	56.5°	63.3°
O3	C3	C2	H3	55.0°	56.9°
O3	C3	C4	H6	62.4°	57.0°
C4	C3	C2	H2	119.2°	119.9°
C4	C3	C2	O2	174.2°	176.9°
C4	C3	C2	C1	53.4°	57.0°
C3	C4	C5	O5	60.0°	57.6°
C3	C4	C5	O4	123.6°	119.9°
C3	C4	C5	H6	116.7°	119.8°
C3	C4	C5	C6	176.9°	177.6°
C3	C4	O4	H6	118.3°	120.1°
C4	C3	O3	H1	180.0°	180.0°
C4	C3	C2	H3	66.3°	62.9°
C3	C4	C5	H5	57.0°	62.4°
C3	C4	O4	H7	180.0°	60.1°
C3	C2	O2	C1	123.0°	119.7°
C3	C2	O2	H3	119.1°	120.2°
C3	C2	C1	H3	120.1°	119.9°
C3	C2	C1	O5	51.1°	57.6°
C3	C2	C1	O4'	72.0°	62.4°
C2	C3	C4	C5	57.5°	57.0°
C2	C3	C4	O4	177.9°	176.9°
C2	C3	O3	H1	57.9°	60.5°
C3	C2	C1	H4	170.6°	177.6°
C2	C3	C4	H6	59.0°	62.9°
C3	C2	O2	H25	180.0°	180.0°
O2	C2	C1	H3	118.6°	120.2°
O2	C2	C1	O5	172.4°	177.5°
O2	C2	C1	O4'	49.3°	57.5°
O2	C2	C3	H2	55.0°	57.0°
O2	C2	C1	H4	68.1°	62.5°
C2	C1	O5	O4'	119.8°	120.0°
C2	C1	O5	H4	119.0°	119.9°
C2	C1	O4'	H4	116.5°	120.0°
C2	C1	O5	C5	54.1°	61.2°
C2	C1	O4'	C4'	161.4°	151.6°
C1	C2	C3	H2	65.8°	62.9°
C1	C2	O2	H25	57.0°	60.3°
O5	C1	O4'	H4	120.9°	120.1°
C1	O5	C5	C4	59.0°	61.2°
C1	O5	C5	C6	173.1°	178.8°
O5	C1	O4'	C4'	76.0°	88.5°
O5	C1	C2	H3	69.0°	62.3°
C1	O5	C5	H5	57.6°	58.9°
O4'	C1	O5	C5	65.7°	58.8°
C1	O4'	C4'	C5'	150.6°	119.6°
C1	O4'	C4'	C3'	86.6°	120.7°
O4'	C1	C2	H3	167.9°	177.7°
C1	O4'	C4'	H11	35.0°	0.5°
O5	C5	C4	C6	123.1°	120.0°
O5	C5	C4	H5	117.0°	120.0°
O5	C5	C6	H5	116.0°	120.0°
O5	C5	C4	O4	176.3°	177.5°
O5	C5	C6	O6	55.0°	63.7°
C5	O5	C1	H4	173.1°	178.9°
O5	C5	C4	H6	56.7°	62.2°
O5	C5	C6	H8	65.5°	176.3°
O5	C5	C6	H9	175.6°	56.4°
C4	C5	C6	H5	119.9°	120.1°
C5	C4	O4	H6	118.9°	120.2°
C4	C5	C6	O6	69.0°	176.3°
C5	C4	C3	H2	61.8°	63.0°
C5	C4	O4	H7	57.2°	179.7°
C4	C5	C6	H8	170.4°	56.4°
C4	C5	C6	H9	51.6°	63.6°
C6	C5	C4	O4	53.3°	62.5°
C5	C6	O6	H8	120.6°	120.0°
C5	C6	O6	H9	120.6°	120.0°
C6	C5	C4	H6	66.4°	57.7°
C5	C6	H8	H9	118.2°	120.0°
C5	C6	O6	H10	180.0°	174.9°
O4	C4	C3	H2	62.8°	56.9°
O4	C4	C5	H5	66.6°	57.5°
O6	C6	C5	H5	171.1°	56.3°
O6	C6	H8	H9	118.2°	120.0°
O4'	C4'	C5'	C3'	120.7°	119.9°
O4'	C4'	C5'	H11	116.5°	120.1°
O4'	C4'	C3'	H11	122.1°	120.2°
O4'	C4'	C3'	O3'	81.9°	63.3°
O4'	C4'	C3'	C2'	161.9°	176.9°
O4'	C4'	C5'	O5'	152.5°	177.5°
O4'	C4'	C5'	C6'	87.3°	62.4°
C4'	O4'	C1	H4	44.9°	31.6°
O4'	C4'	C3'	H12	40.0°	56.9°
O4'	C4'	C5'	H19	31.0°	57.5°
C5'	C4'	C3'	H11	122.5°	119.9°
C5'	C4'	C3'	O3'	162.7°	176.8°
C5'	C4'	C3'	C2'	46.5°	57.0°
C4'	C5'	O5'	C1'	34.5°	61.1°
C4'	C5'	O5'	C6'	125.5°	120.0°
C4'	C5'	O5'	H19	120.8°	120.0°
C4'	C5'	C6'	H19	118.3°	120.0°
C4'	C5'	C6'	O6'	59.8°	174.1°
C5'	C4'	C3'	H12	75.4°	63.0°
C4'	C5'	C6'	H20	179.3°	54.0°
C4'	C5'	C6'	H21	61.0°	66.0°
C4'	C3'	O3'	C2'	119.4°	119.5°
C4'	C3'	O3'	H12	121.3°	120.2°
C4'	C3'	C2'	H12	121.5°	120.0°
C4'	C3'	C2'	O2'	176.5°	176.9°
C4'	C3'	C2'	C1'	62.7°	57.0°
C3'	C4'	C5'	O5'	31.8°	57.6°
C3'	C4'	C5'	C6'	152.0°	177.6°
C4'	C3'	C2'	H13	54.9°	63.0°
C3'	C4'	C5'	H19	89.7°	62.4°
C4'	C3'	O3'	H24	180.0°	180.0°
O3'	C3'	C2'	H12	119.5°	120.2°
O3'	C3'	C2'	O2'	57.6°	63.3°
O3'	C3'	C2'	C1'	178.3°	176.9°
O3'	C3'	C4'	H11	40.2°	56.9°
O3'	C3'	C2'	H13	64.1°	56.9°
C3'	C2'	O2'	C1'	120.3°	119.6°
C3'	C2'	O2'	H13	121.7°	120.2°
C3'	C2'	C1'	H13	118.2°	120.0°
C3'	C2'	C1'	O5'	64.9°	57.6°
C3'	C2'	C1'	C	59.5°	62.4°
C2'	C3'	C4'	H11	76.0°	62.9°
C3'	C2'	C1'	H14	177.9°	177.7°
C3'	C2'	O2'	H23	180.0°	60.0°
C2'	C3'	O3'	H24	60.6°	60.5°
O2'	C2'	C1'	H13	118.5°	120.1°
O2'	C2'	C1'	O5'	171.8°	177.5°
O2'	C2'	C1'	C	63.7°	57.5°
O2'	C2'	C3'	H12	62.0°	56.9°
O2'	C2'	C1'	H14	54.6°	62.5°
C2'	C1'	O5'	C	126.7°	120.0°
C2'	C1'	O5'	H14	116.8°	120.0°
C2'	C1'	C	H14	118.6°	120.0°
C2'	C1'	O5'	C5'	50.7°	61.1°
C1'	C2'	C3'	H12	58.7°	63.0°
C2'	C1'	C	H15	60.6°	65.0°
C2'	C1'	C	H16	57.3°	55.0°
C1'	C2'	O2'	H23	59.7°	179.7°
O5'	C1'	C	H14	117.0°	120.1°
C1'	O5'	C5'	C6'	160.0°	178.9°
O5'	C1'	C2'	H13	53.3°	62.4°
O5'	C1'	C	H15	63.7°	54.9°
O5'	C1'	C	H16	178.4°	174.9°
C1'	O5'	C5'	H19	86.3°	58.9°
C	C1'	O5'	C5'	76.0°	58.8°
C	C1'	C2'	H13	177.7°	177.6°
C1'	C	H15	H16	116.8°	120.0°
O5'	C5'	C6'	H19	114.6°	120.0°
O5'	C5'	C6'	O6'	67.3°	65.9°
O5'	C5'	C4'	H11	91.0°	62.4°
C5'	O5'	C1'	H14	167.5°	178.9°
O5'	C5'	C6'	H20	53.5°	174.0°
O5'	C5'	C6'	H21	171.8°	54.0°
C5'	C6'	O6'	H20	120.9°	120.0°
C5'	C6'	O6'	H21	120.9°	119.9°
C6'	C5'	C4'	H11	29.2°	57.7°
C5'	C6'	H20	H21	117.3°	119.9°
C5'	C6'	O6'	H22	180.0°	173.9°
O6'	C6'	C5'	H19	178.1°	54.1°
O6'	C6'	H20	H21	117.3°	120.1°
H1	O3	C3	H2	61.1°	59.8°
H2	C3	C2	H3	174.5°	177.2°
H2	C3	C4	H6	178.3°	177.1°
H3	C2	C1	H4	50.5°	57.7°
H3	C2	O2	H25	60.9°	59.8°
H5	C5	C4	H6	173.7°	177.8°
H5	C5	C6	H8	50.5°	63.7°
H5	C5	C6	H9	68.3°	176.3°
H6	C4	O4	H7	61.6°	60.1°
H8	C6	O6	H10	59.4°	65.1°
H9	C6	O6	H10	59.4°	54.9°
H11	C4'	C3'	H12	162.1°	177.1°
H11	C4'	C5'	H19	147.5°	177.6°
H12	C3'	C2'	H13	176.4°	177.1°
H12	C3'	O3'	H24	58.7°	59.8°
H13	C2'	C1'	H14	63.9°	57.7°
H13	C2'	O2'	H23	58.3°	60.2°
H14	C1'	C	H15	179.2°	175.0°
H14	C1'	C	H16	61.3°	65.0°
H19	C5'	C6'	H20	61.0°	66.0°
H19	C5'	C6'	H21	57.2°	174.0°
H20	C6'	O6'	H22	59.2°	53.9°
H21	C6'	O6'	H22	59.1°	66.2°

Release date:	2020-07-29
Last modified:	2020-07-29
Processing site:	RCSB