PDB Chemical Component CDK

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 CDK

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
C17	C16	1.529	1.506
C16	N4	1.343	1.355
C16	C15	1.399	1.344
N4	C13	1.479	1.465
N4	C14	1.341	1.341
C14	O3	1.230	1.218
C14	S1	1.703	1.722
S1	C15	1.697	1.772
C15	C	1.392	1.476
C	N	1.346	1.334
C	C12	1.390	1.401
N	C1	1.349	1.324
C12	C11	1.385	1.382
C11	N3	1.321	1.324
N3	C1	1.340	1.325
C1	N1	1.324	1.385
N1	C2	1.324	1.398
C2	C9	1.389	1.389
C2	C3	1.388	1.389
C9	C10	1.383	1.381
C10	C5	1.388	1.382
C3	C4	1.397	1.381
C4	C5	1.397	1.383
C5	S	1.748	1.762
S	O1	1.501	1.421
S	O2	1.510	1.420
S	N2	1.642	1.656
N2	C6	1.475	1.465
C6	C7	1.536	1.530
C7	O	1.451	1.428
O	C8	1.425	1.429
C17	H171	1.100	1.090
C17	H172	1.100	1.090
C17	H173	1.100	1.090
C13	H131	1.100	1.089
C13	H132	1.100	1.090
C13	H133	1.100	1.091
C12	H12	1.080	1.080
C11	H11	1.080	1.080
N1	H1	0.999	0.970
C9	H9	1.080	1.080
C3	H3	1.080	1.080
C10	H10	1.080	1.081
C4	H4	1.080	1.080
N2	H2	1.000	0.970
C6	H61C	1.100	1.090
C6	H62C	1.100	1.090
C7	H71C	1.100	1.090
C7	H72C	1.100	1.091
C8	H81C	1.100	1.090
C8	H82C	1.100	1.090
C8	H83C	1.100	1.089

Bond Angles for CDK

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C17	C16	N4	123.0	121.8
C17	C16	C15	123.4	121.8
C16	C17	H171	109.5	109.5
C16	C17	H172	109.4	109.4
C16	C17	H173	109.5	109.4
N4	C16	C15	113.6	116.3
C16	N4	C13	122.7	121.2
C16	N4	C14	115.1	117.6
C16	C15	S1	108.2	105.1
C16	C15	C	127.4	127.4
C13	N4	C14	122.2	121.2
N4	C13	H131	109.5	109.5
N4	C13	H132	109.4	109.5
N4	C13	H133	109.5	109.5
N4	C14	O3	125.5	127.0
N4	C14	S1	109.7	106.1
O3	C14	S1	124.8	127.0
C14	S1	C15	93.4	94.8
S1	C15	C	124.2	127.5
C15	C	N	120.7	120.6
C15	C	C12	119.0	120.5
N	C	C12	120.2	118.9
C	N	C1	118.5	120.5
C	C12	C11	118.9	118.4
C	C12	H12	120.5	120.8
N	C1	N3	121.9	121.7
N	C1	N1	123.4	119.1
C12	C11	N3	119.1	119.3
C11	C12	H12	120.6	120.8
C12	C11	H11	120.4	120.3
C11	N3	C1	121.3	121.1
N3	C11	H11	120.5	120.4
N3	C1	N1	114.5	119.2
C1	N1	C2	126.9	120.0
C1	N1	H1	116.5	120.1
N1	C2	C9	114.7	120.1
N1	C2	C3	124.7	120.0
C2	N1	H1	116.6	120.0
C9	C2	C3	120.5	119.8
C2	C9	C10	121.4	119.9
C2	C9	H9	119.3	120.0
C2	C3	C4	118.5	119.9
C2	C3	H3	120.8	120.1
C9	C10	C5	118.3	120.1
C10	C9	H9	119.3	120.1
C9	C10	H10	120.9	119.9
C10	C5	C4	120.8	120.2
C10	C5	S	116.5	119.9
C5	C10	H10	120.8	120.0
C3	C4	C5	120.5	120.0
C4	C3	H3	120.7	120.0
C3	C4	H4	119.8	120.0
C4	C5	S	122.7	119.9
C5	C4	H4	119.8	120.0
C5	S	O1	108.0	106.4
C5	S	O2	108.2	106.4
C5	S	N2	112.2	107.2
O1	S	O2	107.4	123.2
O1	S	N2	110.3	106.4
O2	S	N2	110.6	106.4
S	N2	C6	110.1	120.0
S	N2	H2	109.3	120.0
N2	C6	C7	111.4	109.5
C6	N2	H2	109.2	120.0
N2	C6	H61C	108.8	109.5
N2	C6	H62C	108.4	109.5
C6	C7	O	113.4	109.5
C7	C6	H61C	108.9	109.4
C7	C6	H62C	108.4	109.5
C6	C7	H71C	108.2	109.5
C6	C7	H72C	107.3	109.4
C7	O	C8	109.7	114.0
O	C7	H71C	108.2	109.5
O	C7	H72C	107.3	109.5
O	C8	H81C	109.5	109.5
O	C8	H82C	109.5	109.4
O	C8	H83C	109.4	109.5
H171	C17	H172	109.5	109.5
H171	C17	H173	109.4	109.5
H172	C17	H173	109.5	109.5
H131	C13	H132	109.5	109.5
H131	C13	H133	109.4	109.5
H132	C13	H133	109.5	109.4
H61C	C6	H62C	111.0	109.5
H71C	C7	H72C	112.5	109.5
H81C	C8	H82C	109.5	109.5
H81C	C8	H83C	109.5	109.5
H82C	C8	H83C	109.5	109.5

Torsion Angles for CDK

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
N4	C16	C17	C15	181.6	180.3
C17	C16	N4	C13	0.5	0.0
C17	C16	N4	C14	180.0	179.9
C17	C16	C15	S1	179.7	179.9
C17	C16	C15	C	4.2	360.0
H171	C17	C16	H172	240.0	240.0
H171	C17	C16	H173	120.0	120.0
H172	C17	C16	H173	240.0	240.0
C17	C16	N4	C15	178.5	179.7
N4	C16	C17	H171	251.3	0.0
N4	C16	C17	H172	11.3	120.0
N4	C16	C17	H173	131.3	240.0
N4	C16	C15	S1	358.2	359.7
N4	C16	C15	C	182.7	179.7
C13	N4	C16	C14	180.5	180.1
C16	N4	C13	H131	225.1	90.0
C16	N4	C13	H132	345.1	210.0
C16	N4	C13	H133	105.1	329.9
C16	N4	C14	O3	181.3	180.0
C16	N4	C14	S1	359.5	0.1
C17	C16	C15	N4	181.5	180.3
C15	C16	C17	H171	69.7	179.8
C15	C16	C17	H172	189.7	299.7
C15	C16	C17	H173	309.7	59.7
C15	C16	N4	C13	181.9	180.3
C15	C16	N4	C14	1.5	0.2
C14	S1	C15	C16	1.3	0.3
S1	C15	C16	C	175.5	179.9
C16	C15	C	N	209.0	0.1
C16	C15	C	C12	31.9	179.7
C13	N4	C16	C15	181.9	180.3
C16	N4	C13	C14	179.5	179.9
C13	N4	C14	O3	0.8	359.9
C13	N4	C14	S1	179.1	180.0
H131	C13	N4	H132	240.0	239.9
H131	C13	N4	H133	120.0	120.0
H132	C13	N4	H133	240.0	240.1
C14	N4	C16	C15	1.5	0.2
C16	N4	C14	C13	180.5	180.1
C14	N4	C13	H131	45.6	270.0
C14	N4	C13	H132	165.6	30.1
C14	N4	C13	H133	285.6	150.0
O3	C14	N4	S1	181.7	179.9
N4	C14	S1	C15	359.5	359.8
N4	C14	O3	S1	178.0	180.1
O3	C14	S1	C15	177.8	179.9
C16	C15	S1	C14	1.3	0.3
N4	C14	S1	O3	181.7	179.9
C14	S1	C15	C	177.0	180.3
C16	C15	S1	C	184.3	180.1
S1	C15	C	N	34.1	180.1
S1	C15	C	C12	217.0	359.8
C16	C15	C	S1	174.9	179.9
N	C	C15	C12	177.1	180.3
C15	C	N	C1	183.9	180.0
C15	C	C12	C11	177.9	180.1
C15	C	C12	H12	357.9	0.0
C15	C	N	C12	182.9	179.7
N	C	C12	C11	0.8	359.7
N	C	C12	H12	180.8	179.7
C	N	C1	N3	357.6	360.0
C	N	C1	N1	181.4	180.0
C15	C	C12	N	177.1	180.3
C12	C	N	C1	1.0	0.3
C	C12	C11	N3	358.8	360.0
C11	C12	C	H12	180.0	180.0
C	C12	C11	H11	178.8	180.0
C1	N	C	C12	1.0	0.3
C11	N3	C1	N	2.0	359.7
N3	C1	N	N1	176.2	180.0
N	C1	N1	C2	340.8	174.5
N	C1	N1	H1	160.8	354.4
C	C12	C11	H12	180.0	180.0
C12	C11	N3	C1	359.8	0.3
N3	C11	C12	H11	180.0	180.0
N	C1	N3	C11	2.0	359.7
N3	C11	C12	H12	178.8	180.0
C12	C11	N3	H11	180.0	180.0
C11	N3	C1	N1	178.5	179.7
N	C1	N3	N1	183.5	180.0
C1	N3	C11	H11	179.8	180.3
N3	C1	N1	C2	164.4	354.5
N3	C1	N1	H1	344.4	174.4
N	C1	N1	N3	176.4	180.0
C1	N1	C2	C9	173.7	146.5
C1	N1	C2	C3	350.7	326.1
C2	N1	C1	H1	180.0	180.1
C1	N1	C2	H1	180.0	179.9
C9	C2	N1	C3	183.0	180.3
N1	C2	C9	C10	178.3	180.0
N1	C2	C9	H9	358.3	360.0
N1	C2	C3	C4	182.7	180.0
N1	C2	C3	H3	2.7	0.0
N1	C2	C9	C3	177.1	179.7
C9	C2	N1	H1	353.7	326.6
C9	C2	C3	C4	359.6	359.7
C9	C2	C3	H3	179.5	179.7
C2	C9	C10	C5	359.1	360.0
C10	C9	C2	H9	180.0	180.0
C2	C9	C10	H10	179.1	180.0
N1	C2	C3	C9	183.2	180.3
C3	C2	N1	H1	170.7	146.2
C3	C2	C9	C10	1.2	0.3
C3	C2	C9	H9	181.1	180.3
C2	C3	C4	C5	359.5	0.1
C4	C3	C2	H3	180.0	180.0
C2	C3	C4	H4	179.5	180.0
C10	C9	C2	C3	1.2	0.3
C2	C9	C10	H9	180.0	180.0
C9	C10	C5	C4	359.9	359.8
C9	C10	C5	S	181.8	180.0
C5	C10	C9	H10	180.0	180.0
C5	C10	C9	H9	179.1	180.0
C9	C10	C5	H10	180.0	180.0
C3	C4	C5	C10	0.8	0.2
C4	C5	C10	S	178.2	179.8
C10	C5	C4	H4	180.7	180.3
C10	C5	S	O1	98.8	203.5
C10	C5	S	O2	342.9	336.5
C10	C5	S	N2	220.6	90.0
C2	C3	C4	H3	180.0	180.0
C10	C5	C4	C3	0.8	0.2
C3	C4	C5	S	178.8	180.0
C5	C4	C3	H4	180.0	180.1
C10	C5	C4	S	182.0	180.2
C4	C5	C10	H10	179.9	179.8
C5	C4	C3	H3	179.5	180.1
C3	C4	C5	H4	180.0	179.9
C4	C5	S	O1	280.7	23.7
C4	C5	S	O2	164.7	156.7
C4	C5	S	N2	42.5	270.2
C10	C5	S	C4	178.1	179.8
S	C5	C10	H10	1.8	360.0
S	C5	C4	H4	358.8	0.1
O1	S	C5	O2	116.0	227.1
O1	S	C5	N2	238.2	113.5
O2	S	C5	N2	122.3	246.5
C5	S	N2	C6	176.2	65.0
C5	S	N2	H2	296.2	245.0
C5	S	O1	O2	243.5	123.0
C5	S	O1	N2	122.9	245.9
O2	S	O1	N2	239.4	122.9
O1	S	N2	C6	296.6	311.5
O1	S	N2	H2	56.6	131.4
C5	S	O2	O1	116.3	237.0
C5	S	O2	N2	236.8	114.1
O1	S	O2	N2	120.4	237.1
O2	S	N2	C6	55.3	178.6
O2	S	N2	H2	175.3	358.5
C5	S	N2	O1	239.6	113.5
C5	S	N2	O2	120.9	246.5
O1	S	N2	O2	241.3	132.9
S	N2	C6	C7	268.9	165.0
C6	N2	S	H2	240.0	180.1
S	N2	C6	H61C	28.9	285.0
S	N2	C6	H62C	149.7	45.0
S	N2	C6	H2	120.0	179.9
N2	C6	C7	O	104.5	64.9
C7	C6	N2	H61C	240.0	240.0
C7	C6	N2	H62C	119.2	120.1
N2	C6	C7	H71C	224.5	185.0
N2	C6	C7	H72C	346.2	304.9
H61C	C6	N2	H62C	239.2	240.0
C7	C6	N2	H2	148.9	345.1
N2	C6	C7	H61C	120.0	120.0
N2	C6	C7	H62C	240.8	239.9
C6	C7	O	C8	138.1	180.0
O	C7	C6	H71C	240.0	239.9
O	C7	C6	H72C	118.3	120.0
H61C	C6	C7	H62C	120.8	120.0
H71C	C7	C6	H72C	238.3	240.0
O	C7	C6	H61C	344.5	305.0
O	C7	C6	H62C	223.7	185.0
C6	C7	O	H71C	120.0	120.0
C6	C7	O	H72C	241.7	240.1
C7	O	C8	H81C	309.5	300.1
C7	O	C8	H82C	69.5	60.0
C7	O	C8	H83C	189.5	180.0
H71C	C7	O	H72C	121.7	120.0
C8	O	C7	H71C	18.1	59.9
C8	O	C7	H72C	256.4	299.9
H81C	C8	O	H82C	240.0	240.0
H81C	C8	O	H83C	120.0	120.1
H82C	C8	O	H83C	240.0	240.0
H171	C17	C16	N4	251.3	0.0
H171	C17	C16	C15	69.7	179.8
C16	C17	H171	H172	120.0	120.0
C16	C17	H171	H173	240.0	240.0
H172	C17	H171	H173	120.0	120.1
H172	C17	C16	N4	11.3	120.0
H172	C17	C16	C15	189.7	299.7
C16	C17	H172	H171	240.0	240.0
C16	C17	H172	H173	120.0	120.0
H171	C17	H172	H173	240.0	239.9
H173	C17	C16	N4	131.3	240.0
H173	C17	C16	C15	309.7	59.7
C16	C17	H173	H171	120.0	120.0
C16	C17	H173	H172	240.0	240.0
H171	C17	H173	H172	120.0	120.0
H131	C13	N4	C14	45.6	270.0
N4	C13	H131	H132	120.0	120.0
N4	C13	H131	H133	240.0	240.0
H132	C13	H131	H133	120.0	120.0
H132	C13	N4	C14	165.6	30.1
N4	C13	H132	H131	240.0	239.9
N4	C13	H132	H133	120.0	120.0
H131	C13	H132	H133	240.0	240.0
H133	C13	N4	C14	285.6	150.0
N4	C13	H133	H131	120.0	120.0
N4	C13	H133	H132	240.0	240.0
H131	C13	H133	H132	120.0	120.0
C	C12	H12	C11	180.0	180.0
H12	C12	C11	N3	178.8	180.0
H12	C12	C11	H11	358.8	0.0
C12	C11	H11	N3	180.0	180.0
H11	C11	C12	H12	358.8	0.0
H11	C11	N3	C1	179.8	180.3
C1	N1	H1	C2	180.0	180.1
H1	N1	C2	C9	353.7	326.6
H1	N1	C2	C3	170.7	146.2
H9	C9	C2	C3	181.1	180.3
C2	C9	H9	C10	180.0	180.0
H9	C9	C10	C5	179.1	180.0
H9	C9	C10	H10	359.1	360.0
C2	C3	H3	C4	180.0	180.0
H3	C3	C4	C5	179.5	180.1
H3	C3	C4	H4	359.6	360.0
C9	C10	H10	C5	180.0	180.0
H10	C10	C9	H9	359.1	360.0
H10	C10	C5	C4	179.9	179.8
H10	C10	C5	S	1.8	360.0
C3	C4	H4	C5	180.0	180.1
H4	C4	C3	H3	359.6	360.0
H4	C4	C5	S	358.8	0.1
S	N2	H2	C6	239.5	180.1
H2	N2	C6	C7	148.9	345.1
H2	N2	C6	H61C	268.9	105.0
H2	N2	C6	H62C	29.7	225.0
N2	C6	H61C	C7	238.4	240.0
H61C	C6	N2	H2	268.9	105.0
N2	C6	H61C	H62C	119.2	120.0
H61C	C6	C7	O	344.5	305.0
C7	C6	H61C	H62C	240.8	240.0
H61C	C6	C7	H71C	104.5	65.0
H61C	C6	C7	H72C	226.2	185.0
N2	C6	H62C	C7	121.0	120.0
H62C	C6	N2	H2	29.7	225.0
N2	C6	H62C	H61C	240.5	240.0
H62C	C6	C7	O	223.7	185.0
C7	C6	H62C	H61C	119.5	120.0
H62C	C6	C7	H71C	343.7	305.0
H62C	C6	C7	H72C	105.4	65.0
C6	C7	H71C	O	236.8	239.9
H71C	C7	C6	H61C	104.5	65.0
H71C	C7	C6	H62C	343.7	305.0
C6	C7	H71C	H72C	118.4	119.9
H71C	C7	O	C8	18.1	59.9
O	C7	H71C	H72C	241.6	240.0
C6	C7	H72C	O	122.2	120.0
H72C	C7	C6	H61C	226.2	185.0
H72C	C7	C6	H62C	105.4	65.0
C6	C7	H72C	H71C	241.1	240.0
H72C	C7	O	C8	256.4	299.9
O	C7	H72C	H71C	118.9	120.0
O	C8	H81C	H82C	120.0	119.9
O	C8	H81C	H83C	240.0	240.0
H82C	C8	H81C	H83C	120.0	120.0
O	C8	H82C	H81C	240.0	240.0
O	C8	H82C	H83C	120.0	120.0
H81C	C8	H82C	H83C	240.0	239.9
O	C8	H83C	H81C	120.0	120.0
O	C8	H83C	H82C	240.0	240.1
H81C	C8	H83C	H82C	120.0	120.0