PDB Chemical Component YDI

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 YDI

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
S01	C02	1.730	1.705
S01	C05	1.712	1.757
C02	C03	1.385	1.374
C02	N06	1.395	1.385
C03	C04	1.422	1.398
C03	C10	1.446	1.467
C04	C05	1.385	1.341
C05	C19	1.452	1.478
N06	C07	1.378	1.348
C07	N08	1.368	1.347
C07	O09	1.229	1.216
C10	O11	1.225	1.217
C10	N12	1.380	1.347
C14	N15	1.477	1.470
N15	C16	1.484	1.469
N15	C2	1.483	1.468
C16	C17	1.512	1.529
C17	O1	1.420	1.430
C19	C20	1.383	1.397
C19	C24	1.379	1.396
C20	C21	1.384	1.379
C21	C22	1.383	1.388
C22	C23	1.379	1.388
C22	O1	1.386	1.360
C23	C24	1.375	1.379
N06	H06	1.000	0.970
C04	H04	1.080	1.080
N08	H081	1.000	0.971
N08	H082	1.000	0.970
N12	H121	1.000	0.970
N12	H122	1.000	0.970
C14	H141	1.100	1.090
C14	H142	1.100	1.090
C14	H143	1.100	1.090
C16	H161	1.100	1.090
C16	H162	1.100	1.090
C2	H21C	1.100	1.090
C2	H22C	1.100	1.091
C2	H23C	1.100	1.090
C17	H171	1.100	1.090
C17	H172	1.100	1.090
C20	H20	1.080	1.080
C24	H24	1.080	1.080
C21	H21	1.080	1.080
C23	H23	1.080	1.080

Bond Angles for YDI

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C02	S01	C05	93.6	92.0
S01	C02	C03	111.0	110.4
S01	C02	N06	123.7	124.8
S01	C05	C04	109.1	110.2
S01	C05	C19	120.3	124.9
C03	C02	N06	125.2	124.8
C02	C03	C04	110.9	113.7
C02	C03	C10	121.4	123.1
C02	N06	C07	122.0	120.0
C02	N06	H06	119.0	120.1
C04	C03	C10	127.7	123.1
C03	C04	C05	115.3	113.7
C03	C04	H04	122.3	123.2
C03	C10	O11	122.4	120.0
C03	C10	N12	113.5	120.0
C04	C05	C19	130.5	124.9
C05	C04	H04	122.4	123.1
C05	C19	C20	121.9	120.1
C05	C19	C24	119.1	120.1
N06	C07	N08	113.5	120.0
N06	C07	O09	123.6	120.0
C07	N06	H06	119.0	119.9
N08	C07	O09	122.9	120.0
C07	N08	H081	120.0	120.0
C07	N08	H082	120.0	120.0
O11	C10	N12	124.1	120.0
C10	N12	H121	120.0	120.0
C10	N12	H122	120.0	120.1
C14	N15	C16	112.1	111.0
C14	N15	C2	112.0	111.0
N15	C14	H141	109.5	109.5
N15	C14	H142	109.5	109.5
N15	C14	H143	109.5	109.4
C16	N15	C2	112.3	111.0
N15	C16	C17	106.9	109.5
N15	C16	H161	110.4	109.5
N15	C16	H162	110.3	109.5
N15	C2	H21C	109.5	109.5
N15	C2	H22C	109.5	109.4
N15	C2	H23C	109.5	109.5
C16	C17	O1	108.2	109.5
C17	C16	H161	110.4	109.5
C17	C16	H162	110.4	109.5
C16	C17	H171	109.9	109.5
C16	C17	H172	109.9	109.5
C17	O1	C22	109.2	117.0
O1	C17	H171	109.9	109.5
O1	C17	H172	109.9	109.4
C20	C19	C24	119.0	119.8
C19	C20	C21	121.3	119.9
C19	C20	H20	119.4	120.0
C19	C24	C23	120.6	119.9
C19	C24	H24	119.7	120.0
C20	C21	C22	118.6	120.1
C21	C20	H20	119.3	120.0
C20	C21	H21	120.7	119.9
C21	C22	C23	120.6	120.2
C21	C22	O1	123.9	119.9
C22	C21	H21	120.7	120.0
C23	C22	O1	115.5	119.9
C22	C23	C24	119.9	120.1
C22	C23	H23	120.0	120.0
C23	C24	H24	119.7	120.0
C24	C23	H23	120.0	119.9
H081	N08	H082	120.0	120.0
H121	N12	H122	120.0	119.9
H141	C14	H142	109.5	109.5
H141	C14	H143	109.5	109.5
H142	C14	H143	109.5	109.5
H161	C16	H162	108.5	109.5
H21C	C2	H22C	109.5	109.5
H21C	C2	H23C	109.5	109.5
H22C	C2	H23C	109.5	109.4
H171	C17	H172	109.1	109.5

Torsion Angles for YDI

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
C02	S01	C05	C04	359.6	0.0
C02	S01	C05	C19	180.8	180.0
C03	C02	S01	N06	180.1	180.0
S01	C02	C03	C04	0.2	360.0
S01	C02	C03	C10	179.5	180.0
S01	C02	N06	C07	351.9	0.1
S01	C02	N06	H06	171.9	180.0
C05	S01	C02	C03	0.1	0.0
C05	S01	C02	N06	180.0	180.0
C03	C04	C05	S01	0.6	360.0
C04	C05	S01	C19	178.8	180.0
S01	C05	C04	H04	180.6	180.0
S01	C05	C19	C20	359.8	0.0
S01	C05	C19	C24	177.9	179.7
C03	C02	S01	C05	0.1	0.0
S01	C02	C03	N06	179.9	180.0
C03	C02	N06	C07	171.8	180.0
C03	C02	N06	H06	351.8	359.9
C04	C03	C02	C10	180.7	180.0
C02	C03	C04	C05	359.5	0.0
C02	C03	C04	H04	179.5	180.0
C02	C03	C10	O11	2.4	359.9
C02	C03	C10	N12	184.5	180.0
N06	C02	S01	C05	180.0	180.0
S01	C02	N06	C03	180.1	180.0
N06	C02	C03	C04	180.2	180.0
N06	C02	C03	C10	359.5	0.0
C02	N06	C07	N08	191.6	180.0
C02	N06	C07	O09	11.8	360.0
C07	N06	C02	H06	180.0	180.1
S01	C05	C04	C03	0.6	360.0
C04	C03	C02	N06	180.2	180.0
C02	C03	C04	C10	179.2	180.0
C04	C03	C10	O11	181.6	180.0
C04	C03	C10	N12	3.6	0.1
C03	C04	C05	C19	179.2	180.0
C05	C04	C03	H04	180.0	180.1
C10	C03	C02	N06	359.5	0.0
C02	C03	C10	C04	180.8	180.0
C10	C03	C04	C05	180.3	180.0
C10	C03	C04	H04	0.3	359.9
O11	C10	C03	N12	178.0	179.9
C03	C10	N12	H121	177.9	359.9
C03	C10	N12	H122	357.9	180.0
S01	C05	C04	C19	181.4	180.0
C05	C04	C03	C10	180.3	180.0
C03	C04	C05	H04	180.0	179.9
C04	C05	C19	C20	181.3	180.0
C04	C05	C19	C24	359.4	359.7
S01	C05	C19	C04	178.5	180.0
C19	C05	C04	H04	359.2	0.1
C20	C19	C05	C24	181.9	180.3
C05	C19	C20	C21	178.4	180.0
C05	C19	C20	H20	358.4	359.9
C05	C19	C24	C23	181.2	179.8
C05	C19	C24	H24	1.2	0.0
C02	N06	C07	H06	180.0	179.9
N08	C07	N06	O09	179.8	180.0
N06	C07	N08	H081	180.2	0.0
N06	C07	N08	H082	0.2	180.0
N06	C07	N08	O09	180.2	180.0
N08	C07	N06	H06	11.6	0.1
H081	N08	C07	H082	180.0	180.0
N06	C07	O09	N08	179.8	180.0
O09	C07	N06	H06	191.8	180.1
O09	C07	N08	H081	360.0	180.0
O09	C07	N08	H082	180.0	0.0
C03	C10	O11	N12	182.2	180.1
O11	C10	N12	H121	360.0	180.0
O11	C10	N12	H122	180.0	0.1
C03	C10	N12	O11	177.9	179.9
H121	N12	C10	H122	180.0	179.9
C16	N15	C14	C2	127.3	236.0
C14	N15	C16	C17	136.1	195.9
C14	N15	C16	H161	256.1	315.9
C14	N15	C16	H162	16.1	75.9
C14	N15	C2	H21C	180.0	56.1
C14	N15	C2	H22C	300.0	176.0
C14	N15	C2	H23C	60.0	296.0
H141	C14	N15	H142	240.0	240.0
H141	C14	N15	H143	120.0	120.0
H142	C14	N15	H143	240.0	240.0
C14	N15	C16	C2	232.9	123.9
C16	N15	C14	H141	180.0	55.0
C16	N15	C14	H142	300.0	175.0
C16	N15	C14	H143	60.0	295.1
C16	N15	C2	H21C	52.8	180.0
C16	N15	C2	H22C	172.8	300.0
C16	N15	C2	H23C	292.8	60.0
N15	C16	C17	O1	306.4	64.2
C17	C16	N15	H161	240.0	240.0
C17	C16	N15	H162	120.0	120.0
N15	C16	C17	H171	66.4	184.2
N15	C16	C17	H172	186.4	304.3
H161	C16	N15	H162	240.1	240.0
C14	N15	C2	C16	127.2	236.0
C2	N15	C14	H141	52.7	179.0
C2	N15	C14	H142	172.7	299.0
C2	N15	C14	H143	292.7	59.0
C2	N15	C16	C17	263.2	72.0
C2	N15	C16	H161	23.2	191.9
C2	N15	C16	H162	143.2	311.9
H21C	C2	N15	H22C	240.0	240.0
H21C	C2	N15	H23C	120.0	120.1
H22C	C2	N15	H23C	240.0	240.0
C17	C16	N15	C2	263.2	72.0
N15	C16	C17	H161	120.0	120.0
N15	C16	C17	H162	240.0	240.0
C16	C17	O1	C22	164.9	180.0
O1	C17	C16	H171	240.0	240.0
O1	C17	C16	H172	120.0	119.9
H161	C16	C17	H162	120.0	120.0
H171	C17	C16	H172	240.0	239.9
O1	C17	C16	H161	186.4	304.2
O1	C17	C16	H162	66.4	184.3
C16	C17	O1	H171	120.0	120.0
C16	C17	O1	H172	240.0	240.0
C21	C22	O1	C17	1.4	180.0
C23	C22	O1	C17	181.2	360.0
H171	C17	O1	H172	120.0	120.0
C05	C19	C20	C24	178.1	179.7
C20	C19	C24	C23	359.4	359.5
C20	C19	C24	H24	179.4	179.7
C19	C20	C21	C22	0.0	359.9
C21	C20	C19	H20	180.0	180.1
C19	C20	C21	H21	180.1	180.0
C05	C19	C24	C20	181.8	180.3
C24	C19	C20	C21	0.3	0.3
C24	C19	C20	H20	180.3	180.2
C22	C23	C24	C19	0.6	0.5
C23	C24	C19	H24	180.0	179.8
C19	C24	C23	H23	180.6	180.3
C21	C20	C19	C24	0.3	0.3
C19	C20	C21	H20	180.0	179.9
C20	C21	C22	C23	0.0	0.1
C20	C21	C22	O1	179.8	180.0
C22	C21	C20	H21	180.0	179.9
C17	O1	C22	C21	1.4	180.0
C22	C21	C20	H20	180.0	180.0
C20	C21	C22	H21	180.0	180.1
C23	C22	C21	O1	180.2	180.1
C21	C22	C23	C24	359.7	359.7
C21	C22	C23	H23	179.7	179.9
C17	O1	C22	C23	181.2	360.0
C19	C24	C23	C22	0.6	0.5
C21	C22	C23	O1	179.8	179.9
C23	C22	C21	H21	180.0	180.0
C22	C23	C24	H24	180.7	180.3
C24	C23	C22	H23	180.0	179.8
C22	O1	C17	H171	44.9	60.0
C22	O1	C17	H172	284.9	300.0
C21	C22	O1	C23	180.2	180.1
O1	C22	C21	H21	359.8	359.9
O1	C22	C23	C24	179.8	179.8
O1	C22	C23	H23	359.8	360.0
C19	C24	C23	H24	180.0	180.2
C24	C23	C22	O1	179.8	179.8
C22	C23	C24	H23	180.0	180.2
C02	N06	H06	C07	180.0	180.1
H06	N06	C07	N08	11.6	0.1
H06	N06	C07	O09	191.8	180.1
H04	C04	C03	C10	0.3	359.9
C03	C04	H04	C05	180.0	180.1
H04	C04	C05	C19	359.2	0.1
H081	N08	C07	O09	360.0	180.0
C07	N08	H081	H082	180.0	180.0
H082	N08	C07	O09	180.0	0.0
C07	N08	H082	H081	180.0	180.0
C10	N12	H121	H122	180.0	180.1
C10	N12	H122	H121	180.0	179.9
H141	C14	N15	C16	180.0	55.0
H141	C14	N15	C2	52.7	179.0
N15	C14	H141	H142	120.0	120.0
N15	C14	H141	H143	240.0	240.1
H142	C14	H141	H143	120.0	120.0
H142	C14	N15	C16	300.0	175.0
H142	C14	N15	C2	172.7	299.0
N15	C14	H142	H141	240.0	240.0
N15	C14	H142	H143	120.0	120.0
H141	C14	H142	H143	240.0	240.0
H143	C14	N15	C16	60.0	295.1
H143	C14	N15	C2	292.7	59.0
N15	C14	H143	H141	120.0	120.0
N15	C14	H143	H142	240.0	240.0
H141	C14	H143	H142	120.0	120.0
H161	C16	N15	C2	23.2	191.9
N15	C16	H161	C17	242.1	240.0
N15	C16	H161	H162	121.0	120.0
H161	C16	C17	O1	186.4	304.2
C17	C16	H161	H162	239.0	240.0
H161	C16	C17	H171	306.4	64.2
H161	C16	C17	H172	66.4	184.3
H162	C16	N15	C2	143.2	311.9
N15	C16	H162	C17	117.9	120.0
N15	C16	H162	H161	239.0	240.0
H162	C16	C17	O1	66.4	184.3
C17	C16	H162	H161	121.1	120.0
H162	C16	C17	H171	186.4	304.2
H162	C16	C17	H172	306.4	64.3
N15	C2	H21C	H22C	120.0	119.9
N15	C2	H21C	H23C	240.0	239.9
H22C	C2	H21C	H23C	120.0	120.0
N15	C2	H22C	H21C	240.0	240.0
N15	C2	H22C	H23C	120.0	120.0
H21C	C2	H22C	H23C	240.0	240.0
N15	C2	H23C	H21C	120.0	120.1
N15	C2	H23C	H22C	240.0	240.1
H21C	C2	H23C	H22C	120.0	120.0
C16	C17	H171	O1	241.1	240.0
H171	C17	C16	H161	306.4	64.2
H171	C17	C16	H162	186.4	304.2
C16	C17	H171	H172	120.6	120.0
H171	C17	O1	C22	44.9	60.0
O1	C17	H171	H172	239.5	240.0
C16	C17	H172	O1	118.9	120.0
H172	C17	C16	H161	66.4	184.3
H172	C17	C16	H162	306.4	64.3
C16	C17	H172	H171	239.5	239.9
H172	C17	O1	C22	284.9	300.0
O1	C17	H172	H171	120.5	120.0
H20	C20	C19	C24	180.3	180.2
C19	C20	H20	C21	180.0	180.1
H20	C20	C21	C22	180.0	180.0
H20	C20	C21	H21	0.1	0.1
C19	C24	H24	C23	180.0	179.8
H24	C24	C23	H23	0.7	0.1
C20	C21	H21	C22	180.0	179.9
H21	C21	C20	H20	0.1	0.1
H21	C21	C22	C23	180.0	180.0
H21	C21	C22	O1	359.8	359.9
H23	C23	C22	O1	359.8	360.0
C22	C23	H23	C24	180.0	179.8
H23	C23	C24	H24	0.7	0.1