PDB Chemical Component 5YL

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for 5YL

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
O3P	P	1.515	1.610
O3P	HOP3	0.950	0.966
P	O1P	1.497	1.480
P	O2P	1.505	1.610
P	C17	1.656	1.823
O2P	HOP2	0.950	0.968
C17	C16	1.533	1.530
C17	H171	1.115	1.090
C17	H172	1.114	1.090
C16	C15	1.561	1.529
C16	H161	1.116	1.089
C16	H162	1.116	1.089
C15	C14	1.558	1.530
C15	H151	1.114	1.091
C15	H152	1.115	1.089
C14	C13	1.542	1.530
C14	H141	1.115	1.090
C14	H142	1.116	1.089
C13	C5	1.509	1.506
C13	H131	1.115	1.090
C13	H132	1.114	1.090
C5	C4	1.469	1.403
C5	C6	1.497	1.367
C4	O4	1.252	1.219
C4	N3	1.317	1.346
N3	C2	1.327	1.345
N3	HN3	1.019	0.971
C2	O2	1.238	1.216
C2	N1	1.332	1.346
N1	C6	1.349	1.373
N1	HN1	1.021	0.970
C6	N7	1.362	1.371
N7	C8	1.454	1.465
N7	HN7	1.020	0.970
C8	C9	1.538	1.529
C8	H81	1.116	1.090
C8	H82	1.115	1.089
C9	O9	1.425	1.429
C9	C10	1.535	1.529
C9	H91	1.116	1.090
O9	HO9	0.950	0.967
C10	O10	1.425	1.429
C10	C11	1.537	1.530
C10	H101	1.116	1.090
O10	H10O	0.951	0.967
C11	O11	1.426	1.429
C11	C12	1.539	1.529
C11	H111	1.115	1.089
O11	H11O	0.951	0.968
C12	O12	1.411	1.429
C12	H121	1.115	1.090
C12	H122	1.115	1.089
O12	H12O	0.951	0.967

Bond Angles for 5YL

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
P	O3P	HOP3	112.3	106.9
O3P	P	O1P	112.3	109.5
O3P	P	O2P	112.5	109.5
O3P	P	C17	104.0	109.5
O1P	P	O2P	113.5	109.5
O1P	P	C17	107.0	109.5
O2P	P	C17	106.7	109.5
P	O2P	HOP2	112.6	106.8
P	C17	C16	122.5	109.5
P	C17	H171	107.5	109.4
P	C17	H172	107.6	109.5
C16	C17	H171	107.6	109.5
C16	C17	H172	107.5	109.5
C17	C16	C15	115.8	109.5
C17	C16	H161	109.9	109.5
C17	C16	H162	109.9	109.5
H171	C17	H172	102.3	109.5
C15	C16	H161	109.9	109.4
C15	C16	H162	109.9	109.5
C16	C15	C14	115.5	109.5
C16	C15	H151	110.0	109.4
C16	C15	H152	110.0	109.5
H161	C16	H162	100.3	109.5
C14	C15	H151	110.0	109.4
C14	C15	H152	110.0	109.5
C15	C14	C13	112.7	109.5
C15	C14	H141	111.1	109.4
C15	C14	H142	111.0	109.5
H151	C15	H152	100.3	109.5
C13	C14	H141	111.1	109.5
C13	C14	H142	111.0	109.4
C14	C13	C5	111.1	109.5
C14	C13	H131	111.6	109.4
C14	C13	H132	111.6	109.5
H141	C14	H142	99.3	109.5
C5	C13	H131	111.6	109.5
C5	C13	H132	111.6	109.5
C13	C5	C4	113.7	120.5
C13	C5	C6	131.2	120.4
H131	C13	H132	98.8	109.4
C4	C5	C6	114.6	119.0
C5	C4	O4	120.7	120.2
C5	C4	N3	120.2	119.6
C5	C6	N1	118.1	119.4
C5	C6	N7	122.8	120.3
O4	C4	N3	119.1	120.2
C4	N3	C2	122.5	120.6
C4	N3	HN3	118.4	119.8
C2	N3	HN3	119.1	119.7
N3	C2	O2	116.6	119.6
N3	C2	N1	122.4	120.9
O2	C2	N1	121.0	119.5
C2	N1	C6	122.3	120.4
C2	N1	HN1	118.3	119.8
C6	N1	HN1	119.5	119.8
N1	C6	N7	119.1	120.3
C6	N7	C8	121.6	120.0
C6	N7	HN7	107.9	120.0
C8	N7	HN7	107.9	120.0
N7	C8	C9	111.5	109.5
N7	C8	H81	111.5	109.4
N7	C8	H82	111.5	109.5
C9	C8	H81	111.4	109.4
C9	C8	H82	111.4	109.5
C8	C9	O9	111.1	109.5
C8	C9	C10	111.2	109.5
C8	C9	H91	107.1	109.4
H81	C8	H82	98.9	109.5
O9	C9	C10	109.3	109.5
O9	C9	H91	109.1	109.4
C9	O9	HO9	111.1	106.8
C10	C9	H91	108.9	109.5
C9	C10	O10	110.1	109.5
C9	C10	C11	111.9	109.5
C9	C10	H101	107.3	109.5
O10	C10	C11	109.2	109.5
O10	C10	H101	110.1	109.4
C10	O10	H10O	110.1	106.8
C11	C10	H101	108.2	109.4
C10	C11	O11	110.2	109.5
C10	C11	C12	112.5	109.5
C10	C11	H111	106.6	109.5
O11	C11	C12	108.5	109.5
O11	C11	H111	110.7	109.4
C11	O11	H11O	110.2	106.8
C12	C11	H111	108.3	109.5
C11	C12	O12	109.7	109.5
C11	C12	H121	112.1	109.5
C11	C12	H122	112.1	109.5
O12	C12	H121	112.1	109.4
O12	C12	H122	112.1	109.5
C12	O12	H12O	109.7	106.9
H121	C12	H122	98.3	109.4

Torsion Angles for 5YL

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
O1P	P	O3P	O2P	129.6	240.0
O1P	P	O3P	C17	244.7	120.0
O2P	P	O3P	C17	115.1	240.0
O3P	P	O2P	HOP2	180.0	60.0
O3P	P	C17	C16	182.0	180.0
O3P	P	C17	H171	307.2	60.0
O3P	P	C17	H172	56.8	300.0
HOP3	O3P	P	O1P	180.0	300.0
HOP3	O3P	P	O2P	50.4	60.0
HOP3	O3P	P	C17	295.3	180.0
O1P	P	O3P	HOP3	180.0	300.0
O3P	P	O1P	O2P	230.9	120.0
O3P	P	O1P	C17	113.5	240.0
O2P	P	O1P	C17	242.6	120.0
O1P	P	O2P	HOP2	51.0	180.0
O1P	P	C17	C16	301.1	60.0
O1P	P	C17	H171	66.3	300.0
O1P	P	C17	H172	175.8	180.0
O2P	P	O3P	HOP3	50.4	60.0
O3P	P	O2P	O1P	129.0	240.0
O3P	P	O2P	C17	246.5	120.1
O1P	P	O2P	C17	117.6	240.0
O2P	P	C17	C16	62.9	300.0
O2P	P	C17	H171	188.1	180.1
O2P	P	C17	H172	297.6	60.0
C17	P	O3P	HOP3	295.3	180.0
O3P	P	C17	O1P	241.0	120.0
O3P	P	C17	O2P	119.2	240.0
O1P	P	C17	O2P	238.2	120.0
C17	P	O2P	HOP2	293.4	300.0
C16	C17	P	H171	234.8	120.0
C16	C17	P	H172	125.2	240.0
P	C17	C16	C15	221.8	180.0
P	C17	C16	H161	347.0	60.1
P	C17	C16	H162	96.5	300.0
H171	C17	P	H172	250.5	120.0
HOP2	O2P	P	C17	293.4	300.0
P	C17	C16	H171	125.2	240.1
P	C17	C16	H172	234.7	120.0
H171	C17	C16	H172	109.5	240.0
C15	C16	C17	H161	234.7	119.9
C15	C16	C17	H162	125.3	240.0
C17	C16	C15	C14	198.8	180.0
C17	C16	C15	H151	324.1	60.0
C17	C16	C15	H152	73.6	300.0
H161	C16	C17	H162	250.5	120.0
P	C17	H171	C16	226.2	120.0
P	C17	H171	H172	113.1	240.0
C16	C17	H171	H172	246.9	120.0
H171	C17	C16	C15	96.5	299.9
H171	C17	C16	H161	221.8	180.0
H171	C17	C16	H162	331.3	59.9
P	C17	H172	C16	133.8	240.0
P	C17	H172	H171	246.9	120.0
C16	C17	H172	H171	113.1	240.0
H172	C17	C16	C15	347.0	60.0
H172	C17	C16	H161	112.3	300.0
H172	C17	C16	H162	221.7	180.0
C15	C16	C17	H171	96.5	299.9
C15	C16	C17	H172	347.0	60.0
C17	C16	C15	H161	125.3	240.0
C17	C16	C15	H162	234.7	120.0
H161	C16	C15	H162	109.4	240.0
C14	C15	C16	H151	234.7	119.9
C14	C15	C16	H152	125.2	239.9
C16	C15	C14	C13	71.0	180.0
C16	C15	C14	H141	196.4	60.1
C16	C15	C14	H142	305.8	300.0
H151	C15	C16	H152	250.5	120.0
H161	C16	C17	H171	221.8	180.0
H161	C16	C17	H172	112.3	300.0
C17	C16	H161	C15	231.4	120.0
C17	C16	H161	H162	115.7	240.0
C15	C16	H161	H162	244.3	120.0
H161	C16	C15	C14	73.5	299.9
H161	C16	C15	H151	198.8	180.0
H161	C16	C15	H152	308.3	60.0
H162	C16	C17	H171	331.3	59.9
H162	C16	C17	H172	221.7	180.0
C17	C16	H162	C15	128.6	240.0
C17	C16	H162	H161	244.3	120.0
C15	C16	H162	H161	115.7	240.1
H162	C16	C15	C14	324.1	60.0
H162	C16	C15	H151	89.3	300.0
H162	C16	C15	H152	198.9	180.0
C14	C15	C16	H161	73.5	299.9
C14	C15	C16	H162	324.1	60.0
C16	C15	C14	H151	125.3	240.1
C16	C15	C14	H152	234.8	120.1
H151	C15	C14	H152	109.5	240.0
C13	C14	C15	H141	234.7	120.0
C13	C14	C15	H142	125.2	240.0
C15	C14	C13	C5	165.3	180.0
C15	C14	C13	H131	290.6	60.0
C15	C14	C13	H132	40.1	300.1
H141	C14	C15	H142	250.6	120.0
H151	C15	C16	H161	198.8	180.0
H151	C15	C16	H162	89.3	300.0
C16	C15	H151	C14	231.7	120.0
C16	C15	H151	H152	115.8	240.0
C14	C15	H151	H152	244.2	120.0
H151	C15	C14	C13	305.8	300.0
H151	C15	C14	H141	71.1	180.0
H151	C15	C14	H142	180.5	60.0
H152	C15	C16	H161	308.3	60.0
H152	C15	C16	H162	198.9	180.0
C16	C15	H152	C14	128.3	239.9
C16	C15	H152	H151	244.1	120.0
C14	C15	H152	H151	115.8	240.0
H152	C15	C14	C13	196.2	59.9
H152	C15	C14	H141	321.6	300.0
H152	C15	C14	H142	71.0	179.9
C13	C14	C15	H151	305.8	300.0
C13	C14	C15	H152	196.2	59.9
C15	C14	C13	H141	125.3	240.1
C15	C14	C13	H142	234.8	120.0
H141	C14	C13	H142	109.4	239.9
C5	C13	C14	H131	234.8	120.0
C5	C13	C14	H132	125.2	239.9
C14	C13	C5	C4	281.6	270.0
C14	C13	C5	C6	93.4	90.0
H131	C13	C14	H132	250.5	119.9
H141	C14	C15	H151	71.1	180.0
H141	C14	C15	H152	321.6	300.0
C15	C14	H141	C13	233.8	120.0
C15	C14	H141	H142	116.9	240.0
C13	C14	H141	H142	243.1	120.0
H141	C14	C13	C5	40.0	299.9
H141	C14	C13	H131	165.3	179.9
H141	C14	C13	H132	274.8	60.0
H142	C14	C15	H151	180.5	60.0
H142	C14	C15	H152	71.0	179.9
C15	C14	H142	C13	126.2	240.0
C15	C14	H142	H141	243.1	120.0
C13	C14	H142	H141	116.9	240.0
H142	C14	C13	C5	290.6	60.0
H142	C14	C13	H131	55.8	300.0
H142	C14	C13	H132	165.3	180.0
C5	C13	C14	H141	40.0	299.9
C5	C13	C14	H142	290.6	60.0
C14	C13	C5	H131	125.3	240.0
C14	C13	C5	H132	234.8	120.0
H131	C13	C5	H132	109.5	240.0
C4	C5	C13	C6	188.2	180.0
C13	C5	C4	O4	354.3	0.0
C13	C5	C4	N3	174.9	180.0
C13	C5	C6	N1	187.4	180.3
C13	C5	C6	N7	6.0	0.1
H131	C13	C14	H141	165.3	179.9
H131	C13	C14	H142	55.8	300.0
C14	C13	H131	C5	235.0	120.0
C14	C13	H131	H132	117.5	240.1
C5	C13	H131	H132	242.5	120.0
H131	C13	C5	C4	156.3	30.0
H131	C13	C5	C6	328.1	210.0
H132	C13	C14	H141	274.8	60.0
H132	C13	C14	H142	165.3	180.0
C14	C13	H132	C5	125.0	240.0
C14	C13	H132	H131	242.5	119.9
C5	C13	H132	H131	117.5	240.0
H132	C13	C5	C4	46.8	150.0
H132	C13	C5	C6	218.7	330.0
C4	C5	C13	H131	156.3	30.0
C4	C5	C13	H132	46.8	150.0
C13	C5	C4	C6	173.2	180.0
C4	C5	C6	N1	359.2	0.2
C4	C5	C6	N7	177.8	180.0
O4	C4	C5	N3	179.4	180.0
C5	C4	N3	C2	358.9	0.0
C5	C4	N3	HN3	178.9	180.0
C6	C5	C13	H131	328.1	210.0
C6	C5	C13	H132	218.7	330.0
C13	C5	C6	C4	188.2	180.0
C6	C5	C4	O4	181.1	180.0
C6	C5	C4	N3	1.7	0.0
C2	N1	C6	C5	359.4	359.4
C5	C6	N1	HN1	179.4	180.1
N1	C6	C5	N7	181.4	180.2
C5	C6	N7	C8	156.3	179.9
C5	C6	N7	HN7	31.1	359.9
O4	C4	C5	C6	181.1	180.0
C5	C4	O4	N3	180.6	180.0
O4	C4	N3	C2	179.4	180.0
O4	C4	N3	HN3	359.5	0.0
N3	C4	C5	C6	1.7	0.0
C5	C4	N3	O4	179.4	180.0
C2	N3	C4	HN3	180.0	180.0
C4	N3	C2	O2	179.0	180.0
C4	N3	C2	N1	359.6	359.6
C4	N3	C2	HN3	180.0	180.0
O2	C2	N3	N1	179.4	180.4
N3	C2	N1	C6	1.2	0.6
N3	C2	N1	HN1	181.3	180.0
C4	N3	HN3	C2	180.0	180.0
HN3	N3	C2	O2	359.0	0.0
HN3	N3	C2	N1	179.6	179.6
O2	C2	N3	HN3	359.0	0.0
N3	C2	O2	N1	180.6	179.6
O2	C2	N1	C6	181.9	180.2
O2	C2	N1	HN1	1.9	359.6
C5	C6	N1	C2	359.4	359.4
N1	C2	N3	HN3	179.6	179.6
N3	C2	N1	O2	179.3	180.4
C6	N1	C2	HN1	180.0	180.6
C2	N1	C6	N7	180.8	179.6
C5	C6	N1	N7	178.7	179.8
C2	N1	C6	HN1	180.0	179.4
N1	C6	N7	C8	334.9	359.7
N1	C6	N7	HN7	209.7	179.7
C2	N1	HN1	C6	180.0	180.6
HN1	N1	C6	N7	0.8	0.3
C5	C6	N7	N1	181.4	180.2
N7	C6	N1	HN1	0.8	0.3
C8	N7	C6	HN7	125.3	180.0
C6	N7	C8	C9	91.7	180.0
C6	N7	C8	H81	216.9	60.1
C6	N7	C8	H82	326.5	300.1
C6	N7	C8	HN7	234.7	180.0
C9	C8	N7	H81	234.8	119.9
C9	C8	N7	H82	125.2	239.9
N7	C8	C9	O9	286.5	300.1
N7	C8	C9	C10	164.5	180.0
N7	C8	C9	H91	45.6	60.1
H81	C8	N7	H82	250.5	120.0
C6	N7	HN7	C8	133.0	180.0
HN7	N7	C8	C9	216.9	359.9
HN7	N7	C8	H81	342.2	240.1
HN7	N7	C8	H82	91.7	120.1
C9	C8	N7	HN7	216.9	359.9
N7	C8	C9	H81	125.3	240.1
N7	C8	C9	H82	234.7	120.1
H81	C8	C9	H82	109.5	240.0
O9	C9	C8	C10	122.0	120.1
O9	C9	C8	H91	240.9	240.1
C8	C9	O9	HO9	180.0	300.0
C10	C9	C8	H91	118.9	120.0
C8	C9	C10	O10	56.7	300.1
C8	C9	C10	C11	295.1	180.1
C8	C9	C10	H101	176.5	60.1
H81	C8	N7	HN7	342.2	240.1
N7	C8	H81	C9	234.7	119.9
N7	C8	H81	H82	117.4	239.9
C9	C8	H81	H82	242.7	120.0
H81	C8	C9	O9	161.2	60.0
H81	C8	C9	C10	39.2	299.9
H81	C8	C9	H91	280.3	179.9
H82	C8	N7	HN7	91.7	120.1
N7	C8	H82	C9	125.3	239.9
N7	C8	H82	H81	242.6	120.0
C9	C8	H82	H81	117.3	240.1
H82	C8	C9	O9	51.8	180.0
H82	C8	C9	C10	289.7	59.9
H82	C8	C9	H91	170.8	299.9
O9	C9	C8	H81	161.2	60.0
O9	C9	C8	H82	51.8	180.0
C8	C9	O9	C10	236.9	239.9
C8	C9	O9	H91	117.9	119.9
C10	C9	O9	H91	241.0	240.0
O9	C9	C10	O10	293.7	180.0
O9	C9	C10	C11	172.0	60.0
O9	C9	C10	H101	53.5	300.0
C10	C9	C8	H81	39.2	299.9
C10	C9	C8	H82	289.7	59.9
C8	C9	C10	O9	123.0	120.1
C8	C9	C10	H91	242.2	240.0
O9	C9	C10	H91	119.1	120.0
C10	C9	O9	HO9	303.1	60.0
O10	C10	C9	C11	121.7	120.0
O10	C10	C9	H101	240.2	240.0
C9	C10	O10	H10O	180.0	300.0
C11	C10	C9	H101	118.5	120.0
C9	C10	C11	O11	306.7	300.1
C9	C10	C11	C12	185.5	180.0
C9	C10	C11	H111	66.9	60.0
H91	C9	C8	H81	280.3	179.9
H91	C9	C8	H82	170.8	299.9
C8	C9	H91	O9	239.7	240.0
C8	C9	H91	C10	120.4	120.0
O9	C9	H91	C10	240.7	240.0
H91	C9	O9	HO9	62.1	180.0
H91	C9	C10	O10	174.6	60.0
H91	C9	C10	C11	52.9	300.0
H91	C9	C10	H101	294.4	180.0
HO9	O9	C9	C10	303.1	60.0
HO9	O9	C9	H91	62.1	180.0
O10	C10	C9	H91	174.6	60.0
C9	C10	O10	C11	236.7	239.9
C9	C10	O10	H101	118.1	120.0
C11	C10	O10	H101	241.4	240.1
O10	C10	C11	O11	184.5	180.0
O10	C10	C11	C12	63.3	59.9
O10	C10	C11	H111	304.7	299.9
C11	C10	C9	H91	52.9	300.0
C9	C10	C11	O10	122.2	120.1
C9	C10	C11	H101	242.0	240.0
O10	C10	C11	H101	119.8	119.9
C11	C10	O10	H10O	303.3	60.0
O11	C11	C10	C12	121.2	120.1
O11	C11	C10	H111	239.8	240.1
C10	C11	O11	H11O	180.1	300.0
C12	C11	C10	H111	118.6	120.0
C10	C11	C12	O12	55.0	179.9
C10	C11	C12	H121	180.3	60.0
C10	C11	C12	H122	289.8	300.1
H101	C10	C9	H91	294.4	180.0
C9	C10	H101	O10	240.2	239.9
C9	C10	H101	C11	121.0	120.0
O10	C10	H101	C11	240.8	240.1
H101	C10	O10	H10O	61.9	179.9
H101	C10	C11	O11	64.7	60.1
H101	C10	C11	C12	303.5	300.0
H101	C10	C11	H111	184.9	180.0
H10O	O10	C10	C11	303.3	60.0
H10O	O10	C10	H101	61.9	179.9
O11	C11	C10	H101	64.7	60.1
C10	C11	O11	C12	236.5	239.9
C10	C11	O11	H111	117.7	120.0
C12	C11	O11	H111	241.2	240.1
O11	C11	C12	O12	292.9	59.9
O11	C11	C12	H121	58.2	299.9
O11	C11	C12	H122	167.7	180.0
C12	C11	C10	H101	303.5	300.0
C10	C11	C12	O11	122.1	120.1
C10	C11	C12	H111	242.4	240.0
O11	C11	C12	H111	120.3	119.9
C12	C11	O11	H11O	303.6	60.1
O12	C12	C11	H121	234.8	120.0
O12	C12	C11	H122	125.3	239.9
C11	C12	O12	H12O	180.0	180.0
H121	C12	C11	H122	250.5	119.9
H111	C11	C10	H101	184.9	180.0
C10	C11	H111	O11	240.2	240.0
C10	C11	H111	C12	121.3	120.1
O11	C11	H111	C12	241.1	240.0
H111	C11	O11	H11O	62.4	180.0
H111	C11	C12	O12	172.6	300.0
H111	C11	C12	H121	297.9	180.0
H111	C11	C12	H122	47.4	60.1
H11O	O11	C11	C12	303.6	60.1
H11O	O11	C11	H111	62.4	180.0
O12	C12	C11	H111	172.6	300.0
C11	C12	O12	H121	125.3	240.0
C11	C12	O12	H122	234.7	120.1
H121	C12	O12	H122	109.5	240.1
H121	C12	C11	H111	297.9	180.0
C11	C12	H121	O12	236.1	120.0
C11	C12	H121	H122	118.1	240.0
O12	C12	H121	H122	242.0	120.0
H121	C12	O12	H12O	54.7	300.0
H122	C12	C11	H111	47.4	60.1
C11	C12	H122	O12	123.9	239.9
C11	C12	H122	H121	241.9	120.0
O12	C12	H122	H121	118.0	240.1
H122	C12	O12	H12O	305.2	59.8
H12O	O12	C12	H121	54.7	300.0
H12O	O12	C12	H122	305.2	59.8