PDB Chemical Component YDK

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 YDK

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
S01	C02	1.737	1.706
S01	C05	1.729	1.756
C02	C03	1.386	1.374
C02	N06	1.396	1.385
C03	C04	1.424	1.397
C03	C10	1.459	1.467
C04	C05	1.381	1.341
C05	C19	1.459	1.478
N06	C07	1.368	1.348
C07	N08	1.369	1.347
C07	O09	1.210	1.216
C10	O11	1.212	1.217
C10	N12	1.369	1.347
N12	C13	1.449	1.464
C13	C14	1.507	1.530
C13	C18	1.531	1.532
C14	N15	1.490	1.469
N15	C16	1.494	1.468
C16	C17	1.519	1.531
C17	C18	1.522	1.531
C19	C20	1.379	1.396
C19	C24	1.379	1.396
C20	C21	1.387	1.380
C21	C22	1.379	1.384
C22	C23	1.381	1.384
C23	C24	1.376	1.379
N06	H06	1.000	0.970
C04	H04	1.080	1.079
N08	H081	1.000	0.970
N08	H082	1.000	0.969
N12	H12	1.000	0.970
C13	H13	1.100	1.090
C14	H141	1.099	1.089
C14	H142	1.100	1.090
C18	H181	1.100	1.089
C18	H182	1.100	1.090
N15	H15	1.000	1.009
C16	H161	1.100	1.090
C16	H162	1.100	1.090
C17	H171	1.100	1.090
C17	H172	1.100	1.090
C20	H20	1.080	1.079
C24	H24	1.080	1.080
C21	H21	1.080	1.079
C22	H22	1.080	1.080
C23	H23	1.080	1.080

Bond Angles for YDK

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C02	S01	C05	91.3	92.0
S01	C02	C03	113.1	110.4
S01	C02	N06	120.9	124.8
S01	C05	C04	110.8	110.2
S01	C05	C19	119.6	124.9
C03	C02	N06	126.0	124.8
C02	C03	C04	110.0	113.8
C02	C03	C10	122.2	123.1
C02	N06	C07	121.2	120.0
C02	N06	H06	119.4	120.0
C04	C03	C10	127.8	123.2
C03	C04	C05	114.9	113.7
C03	C04	H04	122.6	123.1
C03	C10	O11	122.2	120.0
C03	C10	N12	117.2	120.0
C04	C05	C19	129.6	124.9
C05	C04	H04	122.6	123.1
C05	C19	C20	122.2	120.1
C05	C19	C24	118.9	120.1
N06	C07	N08	115.1	120.0
N06	C07	O09	123.2	120.0
C07	N06	H06	119.4	120.0
N08	C07	O09	121.7	120.0
C07	N08	H081	120.0	120.0
C07	N08	H082	120.0	120.0
O11	C10	N12	120.6	120.0
C10	N12	C13	119.7	120.0
C10	N12	H12	120.1	120.0
N12	C13	C14	109.0	109.5
N12	C13	C18	111.8	109.5
C13	N12	H12	120.2	120.0
N12	C13	H13	108.7	109.5
C14	C13	C18	110.9	109.3
C13	C14	N15	110.3	109.5
C14	C13	H13	109.7	109.5
C13	C14	H141	109.2	109.5
C13	C14	H142	109.2	109.4
C13	C18	C17	111.0	109.2
C18	C13	H13	106.8	109.5
C13	C18	H181	109.0	109.5
C13	C18	H182	109.0	109.5
C14	N15	C16	113.7	111.2
N15	C14	H141	109.2	109.5
N15	C14	H142	109.2	109.4
C14	N15	H15	108.1	111.0
N15	C16	C17	106.8	109.5
C16	N15	H15	108.1	111.0
N15	C16	H161	110.4	109.5
N15	C16	H162	110.4	109.5
C16	C17	C18	111.9	109.3
C17	C16	H161	110.4	109.4
C17	C16	H162	110.4	109.4
C16	C17	H171	108.7	109.5
C16	C17	H172	108.7	109.5
C17	C18	H181	109.0	109.5
C17	C18	H182	109.0	109.5
C18	C17	H171	108.6	109.5
C18	C17	H172	108.7	109.5
C20	C19	C24	118.8	119.7
C19	C20	C21	121.3	119.8
C19	C20	H20	119.3	120.1
C19	C24	C23	120.9	119.9
C19	C24	H24	119.6	120.1
C20	C21	C22	118.6	120.1
C21	C20	H20	119.3	120.1
C20	C21	H21	120.7	119.9
C21	C22	C23	120.8	120.3
C22	C21	H21	120.7	119.9
C21	C22	H22	119.6	119.8
C22	C23	C24	119.5	120.1
C23	C22	H22	119.6	119.8
C22	C23	H23	120.2	119.9
C23	C24	H24	119.5	120.1
C24	C23	H23	120.3	120.0
H081	N08	H082	120.0	120.0
H141	C14	H142	109.7	109.5
H181	C18	H182	109.9	109.6
H161	C16	H162	108.6	109.5
H171	C17	H172	110.3	109.5

Torsion Angles for YDK

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
C02	S01	C05	C04	359.5	360.0
C02	S01	C05	C19	180.3	180.0
C03	C02	S01	N06	180.6	180.0
S01	C02	C03	C04	359.6	360.0
S01	C02	C03	C10	179.1	180.0
S01	C02	N06	C07	354.1	0.0
S01	C02	N06	H06	174.1	180.0
C05	S01	C02	C03	0.6	0.0
C05	S01	C02	N06	180.0	180.0
C03	C04	C05	S01	0.4	360.0
C04	C05	S01	C19	179.2	180.0
S01	C05	C04	H04	180.4	180.0
S01	C05	C19	C20	186.4	360.0
S01	C05	C19	C24	6.7	179.8
C03	C02	S01	C05	0.6	0.0
S01	C02	C03	N06	179.4	180.0
C03	C02	N06	C07	173.4	180.0
C03	C02	N06	H06	353.4	360.0
C04	C03	C02	C10	180.5	180.0
C02	C03	C04	C05	0.0	0.0
C02	C03	C04	H04	180.0	180.0
C02	C03	C10	O11	359.4	0.0
C02	C03	C10	N12	181.5	180.0
N06	C02	S01	C05	180.0	180.0
S01	C02	N06	C03	180.6	180.1
N06	C02	C03	C04	180.2	180.0
N06	C02	C03	C10	359.6	0.0
C02	N06	C07	N08	194.6	180.0
C02	N06	C07	O09	15.0	360.0
C07	N06	C02	H06	180.0	180.0
S01	C05	C04	C03	0.4	360.0
C04	C03	C02	N06	180.2	180.0
C02	C03	C04	C10	179.4	180.0
C04	C03	C10	O11	178.8	180.0
C04	C03	C10	N12	0.9	0.0
C03	C04	C05	C19	179.5	180.0
C05	C04	C03	H04	180.0	180.0
C10	C03	C02	N06	359.6	0.0
C02	C03	C10	C04	180.6	180.0
C10	C03	C04	C05	180.6	180.0
C10	C03	C04	H04	0.6	360.0
O11	C10	C03	N12	177.9	180.0
C03	C10	N12	C13	160.1	180.0
C03	C10	N12	H12	340.1	359.9
S01	C05	C04	C19	180.9	180.0
C05	C04	C03	C10	180.6	180.0
C03	C04	C05	H04	180.0	180.0
C04	C05	C19	C20	7.4	180.0
C04	C05	C19	C24	187.7	359.8
S01	C05	C19	C04	179.0	180.0
C19	C05	C04	H04	359.5	0.0
C20	C19	C05	C24	179.7	180.2
C05	C19	C20	C21	180.0	180.0
C05	C19	C20	H20	359.9	360.0
C05	C19	C24	C23	180.0	179.7
C05	C19	C24	H24	360.0	359.9
C02	N06	C07	H06	180.0	180.0
N08	C07	N06	O09	179.6	180.0
N06	C07	N08	H081	180.4	0.0
N06	C07	N08	H082	0.4	180.0
N06	C07	N08	O09	180.4	180.0
N08	C07	N06	H06	14.6	360.0
H081	N08	C07	H082	180.0	180.1
N06	C07	O09	N08	179.6	180.0
O09	C07	N06	H06	194.9	180.0
O09	C07	N08	H081	0.0	180.0
O09	C07	N08	H082	180.0	360.0
C03	C10	O11	N12	182.2	180.0
O11	C10	N12	C13	342.1	0.0
O11	C10	N12	H12	162.1	179.9
C03	C10	N12	O11	177.9	180.0
C10	N12	C13	C14	273.6	275.0
C10	N12	C13	C18	150.8	155.2
C13	N12	C10	H12	180.0	180.1
C10	N12	C13	H13	33.2	35.1
C10	N12	C13	H12	180.0	179.9
C14	C13	N12	C18	122.9	119.8
N12	C13	C14	N15	182.9	180.8
C14	C13	N12	H13	240.5	239.9
N12	C13	C14	H141	302.9	300.8
N12	C13	C14	H142	62.9	60.9
N12	C13	C18	C17	174.6	177.6
C18	C13	N12	H13	117.6	120.1
N12	C13	C18	H181	294.6	297.5
N12	C13	C18	H182	54.6	57.7
N12	C13	C14	C18	236.6	240.0
C14	C13	N12	H12	93.6	95.1
N12	C13	C14	H13	118.9	120.1
C14	C13	C18	C17	52.8	57.7
C18	C13	C14	H13	242.3	240.0
C14	C13	C18	H181	172.8	177.6
C14	C13	C18	H182	292.8	297.8
C13	C14	N15	C16	59.6	61.8
N15	C14	C13	H141	240.0	240.0
N15	C14	C13	H142	120.0	120.0
C13	C14	N15	H15	179.6	185.8
H141	C14	C13	H142	240.0	240.0
N12	C13	C18	C14	121.8	120.0
C18	C13	N12	H12	330.8	335.2
N12	C13	C18	H13	241.3	239.9
C18	C13	C14	N15	306.4	300.8
C14	C13	C18	H13	119.4	120.0
C18	C13	C14	H141	66.4	60.8
C18	C13	C14	H142	186.4	180.8
C16	C17	C18	C13	304.0	302.4
C17	C18	C13	H181	240.0	240.1
C17	C18	C13	H182	120.0	119.9
C13	C18	C17	H171	184.0	182.4
C13	C18	C17	H172	64.0	62.3
H181	C18	C13	H182	240.0	239.8
N15	C14	C13	C18	306.4	300.8
N15	C14	C13	H13	64.1	60.8
C13	C14	N15	H141	120.0	120.0
C13	C14	N15	H142	240.0	240.0
C14	N15	C16	C17	299.8	298.2
C16	N15	C14	H15	240.0	236.0
C14	N15	C16	H161	59.8	58.2
C14	N15	C16	H162	179.8	178.2
H141	C14	N15	H142	120.0	120.0
C16	N15	C14	H141	299.6	301.8
C16	N15	C14	H142	179.6	181.7
C14	N15	C16	H15	120.0	124.0
N15	C16	C17	C18	57.7	59.2
C17	C16	N15	H161	240.0	240.0
C17	C16	N15	H162	120.0	120.0
N15	C16	C17	H171	177.7	179.2
N15	C16	C17	H172	297.7	299.3
H161	C16	N15	H162	240.0	240.0
C13	C18	C17	C16	304.0	302.4
C17	C16	N15	H15	179.8	174.2
N15	C16	C17	H161	120.0	120.1
N15	C16	C17	H162	240.0	240.0
C16	C17	C18	H181	184.0	182.4
C16	C17	C18	H182	64.0	62.2
C18	C17	C16	H171	240.0	240.0
C18	C17	C16	H172	120.0	119.9
H161	C16	C17	H162	120.0	119.9
H171	C17	C16	H172	240.0	239.9
C17	C18	C13	H13	293.4	297.7
C13	C18	C17	H181	120.0	119.9
C13	C18	C17	H182	240.0	240.1
C18	C17	C16	H161	297.7	299.1
C18	C17	C16	H162	177.7	179.2
C16	C17	C18	H171	120.0	120.0
C16	C17	C18	H172	240.0	240.1
H181	C18	C17	H182	120.0	120.2
H171	C17	C18	H172	120.0	120.1
C05	C19	C20	C24	180.3	179.8
C20	C19	C24	C23	0.2	359.4
C20	C19	C24	H24	180.2	179.7
C19	C20	C21	C22	0.2	0.0
C21	C20	C19	H20	180.0	180.0
C19	C20	C21	H21	180.2	180.0
C05	C19	C24	C20	179.7	180.2
C24	C19	C20	C21	359.7	0.2
C24	C19	C20	H20	179.7	180.2
C22	C23	C24	C19	359.9	0.6
C23	C24	C19	H24	180.0	179.7
C19	C24	C23	H23	179.9	180.3
C21	C20	C19	C24	359.7	0.2
C19	C20	C21	H20	180.0	180.0
C20	C21	C22	C23	359.9	360.0
C22	C21	C20	H21	180.0	180.1
C20	C21	C22	H22	179.9	179.9
C22	C21	C20	H20	180.3	180.1
C20	C21	C22	H21	180.0	179.9
C21	C22	C23	C24	0.0	359.7
C23	C22	C21	H22	180.0	180.0
C21	C22	C23	H23	180.0	179.9
C19	C24	C23	C22	359.9	0.6
C23	C22	C21	H21	179.9	180.1
C21	C22	C23	H22	180.0	180.0
C22	C23	C24	H24	179.9	180.3
C24	C23	C22	H23	180.0	179.8
C19	C24	C23	H24	180.0	180.3
C24	C23	C22	H22	180.0	179.7
C22	C23	C24	H23	180.0	180.2
C02	N06	H06	C07	180.0	180.0
H06	N06	C07	N08	14.6	360.0
H06	N06	C07	O09	194.9	180.0
H04	C04	C03	C10	0.6	360.0
C03	C04	H04	C05	180.0	180.0
H04	C04	C05	C19	359.5	0.0
H081	N08	C07	O09	0.0	180.0
C07	N08	H081	H082	180.0	179.9
H082	N08	C07	O09	180.0	360.0
C07	N08	H082	H081	180.0	180.1
C10	N12	H12	C13	180.0	180.1
H12	N12	C13	C14	93.6	95.1
H12	N12	C13	C18	330.8	335.2
H12	N12	C13	H13	213.2	215.1
N12	C13	H13	C14	240.9	239.9
N12	C13	H13	C18	120.7	120.1
H13	C13	N12	H12	213.2	215.1
C14	C13	H13	C18	239.8	240.2
H13	C13	C14	N15	64.1	60.8
H13	C13	C14	H141	184.0	180.8
H13	C13	C14	H142	304.0	300.8
H13	C13	C18	C17	293.4	297.7
H13	C13	C18	H181	53.4	57.6
H13	C13	C18	H182	173.3	177.8
H141	C14	C13	C18	66.4	60.8
C13	C14	H141	N15	239.3	239.9
H141	C14	C13	H13	184.0	180.8
C13	C14	H141	H142	119.7	120.0
H141	C14	N15	C16	299.6	301.8
N15	C14	H141	H142	240.3	240.0
H141	C14	N15	H15	59.6	65.8
H142	C14	C13	C18	186.4	180.8
C13	C14	H142	N15	120.7	120.0
H142	C14	C13	H13	304.0	300.8
C13	C14	H142	H141	240.3	240.0
H142	C14	N15	C16	179.6	181.7
N15	C14	H142	H141	119.7	120.0
H142	C14	N15	H15	299.6	305.8
C13	C18	H181	C17	238.7	240.3
H181	C18	C13	H13	53.4	57.6
C13	C18	H181	H182	119.4	120.2
C17	C18	H181	H182	240.6	239.9
H181	C18	C17	H171	64.0	62.5
H181	C18	C17	H172	304.0	302.3
C13	C18	H182	C17	121.3	119.7
H182	C18	C13	H13	173.3	177.8
C13	C18	H182	H181	240.6	239.8
C17	C18	H182	H181	119.4	120.2
H182	C18	C17	H171	304.0	302.3
H182	C18	C17	H172	184.0	182.1
C14	N15	H15	C16	236.5	235.9
H15	N15	C14	H141	59.6	65.8
H15	N15	C14	H142	299.6	305.8
H15	N15	C16	C17	179.8	174.2
H15	N15	C16	H161	299.8	294.2
H15	N15	C16	H162	59.8	54.2
N15	C16	H161	C17	242.2	239.9
H161	C16	N15	H15	299.8	294.2
N15	C16	H161	H162	121.1	120.0
H161	C16	C17	C18	297.7	299.1
C17	C16	H161	H162	238.9	240.1
H161	C16	C17	H171	57.7	59.1
H161	C16	C17	H172	177.7	179.2
N15	C16	H162	C17	117.8	120.1
H162	C16	N15	H15	59.8	54.2
N15	C16	H162	H161	238.9	240.0
H162	C16	C17	C18	177.7	179.2
C17	C16	H162	H161	121.1	119.9
H162	C16	C17	H171	297.6	299.2
H162	C16	C17	H172	57.7	59.3
C16	C17	H171	C18	238.0	240.2
H171	C17	C16	H161	57.7	59.1
H171	C17	C16	H162	297.6	299.2
C16	C17	H171	H172	119.0	120.0
H171	C17	C18	H181	64.0	62.5
H171	C17	C18	H182	304.0	302.3
C18	C17	H171	H172	241.0	239.9
C16	C17	H172	C18	122.0	119.8
H172	C17	C16	H161	177.7	179.2
H172	C17	C16	H162	57.7	59.3
C16	C17	H172	H171	241.0	239.9
H172	C17	C18	H181	304.0	302.3
H172	C17	C18	H182	184.0	182.1
C18	C17	H172	H171	119.0	120.1
H20	C20	C19	C24	179.7	180.2
C19	C20	H20	C21	180.0	180.0
H20	C20	C21	C22	180.3	180.1
H20	C20	C21	H21	0.2	0.0
C19	C24	H24	C23	180.0	179.7
H24	C24	C23	H23	359.9	0.1
C20	C21	H21	C22	180.0	180.1
H21	C21	C20	H20	0.2	0.0
H21	C21	C22	C23	179.9	180.1
H21	C21	C22	H22	359.9	0.0
C21	C22	H22	C23	180.0	180.0
H22	C22	C21	H21	359.9	0.0
H22	C22	C23	C24	180.0	179.7
H22	C22	C23	H23	0.0	360.0
C22	C23	H23	C24	180.0	179.8
H23	C23	C22	H22	0.0	360.0
H23	C23	C24	H24	359.9	0.1