PDB Chemical Component 5DK

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 5DK

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
NH2	CZ	1.257	1.304
CZ	NE	1.470	1.376
CZ	NH1	1.470	1.374
NE	CD	1.470	1.465
OXT	C	1.256	1.208
C	O	1.242	1.342
C	CA	1.533	1.507
CG	CD	1.547	1.530
CG	CB	1.550	1.531
CB	CA	1.533	1.530
CA	N	1.462	1.465
N	C4A	1.260	1.293
O3P	P	1.510	1.479
O1P	P	1.526	1.610
C4A	C4	1.559	1.476
P	O4P	1.637	1.610
P	O2P	1.540	1.610
O3	C3	1.393	1.358
O4P	C5A	1.397	1.429
C4	C3	1.394	1.404
C4	C5	1.396	1.399
C3	C2	1.387	1.388
C5A	C5	1.532	1.507
C5	C6	1.389	1.380
C2	C2A	1.535	1.507
C2	N1	1.328	1.316
C6	N1	1.314	1.320
C6	H1	1.080	1.080
CB	H2	1.100	1.089
CB	H3	1.100	1.090
O3	H4	0.950	0.968
O1P	H5	0.950	0.967
O2P	H6	0.950	0.967
C2A	H9	1.100	1.090
C2A	H10	1.100	1.090
C2A	H11	1.100	1.090
C4A	H12	1.080	1.080
C5A	H14	1.100	1.090
C5A	H15	1.101	1.090
CA	H16	1.100	1.090
O	H17	0.950	0.966
CG	H18	1.100	1.089
CG	H19	1.100	1.089
CD	H20	1.100	1.090
CD	H21	1.100	1.090
NE	H22	1.000	0.970
NH1	H23	0.999	0.971
NH1	H24	1.000	0.970
NH2	H25	1.000	0.970

Bond Angles for 5DK

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
CZ	NE	H22	119.8	120.0
CZ	NH1	H23	120.0	120.0
CZ	NH1	H24	120.0	120.0
NE	CD	H20	109.5	109.4
NE	CD	H21	109.5	109.4
C	O	H17	109.5	117.0
C	CA	H16	109.1	109.5
CD	CG	H18	109.3	109.5
CD	CG	H19	109.3	109.5
CG	CD	H20	109.5	109.5
CG	CD	H21	109.5	109.5
CG	CB	H2	108.7	109.5
CG	CB	H3	108.7	109.5
CB	CA	N	107.7	109.5
CA	CB	H2	108.6	109.5
CA	CB	H3	108.6	109.4
CB	CA	H16	109.2	109.4
N	C4A	H12	123.1	120.0
O1P	P	O3P	110.3	109.5
O3P	P	O4P	108.9	109.5
O1P	P	O4P	112.4	109.4
O1P	P	O2P	109.0	109.4
P	O1P	H5	109.5	114.0
P	O4P	C5A	117.2	123.0
P	O2P	H6	109.5	114.0
O4P	C5A	H14	110.5	109.5
O4P	C5A	H15	110.5	109.5
C4	C5	C6	120.6	119.0
C3	C2	C2A	117.2	119.6
C3	C2	N1	121.3	120.8
C5	C6	N1	121.3	121.0
C5	C6	H1	119.4	119.5
C2A	C2	N1	121.5	119.6
C2	C2A	H9	109.5	109.5
C2	C2A	H10	109.4	109.5
C2	C2A	H11	109.5	109.5
C2	N1	C6	120.4	122.1
N1	C6	H1	119.4	119.5
H2	CB	H3	109.5	109.5
H9	C2A	H10	109.5	109.4
H9	C2A	H11	109.5	109.5
H10	C2A	H11	109.5	109.5
H14	C5A	H15	109.5	109.5
H18	CG	H19	109.5	109.5
H20	CD	H21	109.5	109.5
H23	NH1	H24	120.0	120.0

Torsion Angles for 5DK

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
NH2	CZ	NE	H22	339.1	360.0
NH2	CZ	NH1	H23	178.8	180.0
NH2	CZ	NH1	H24	358.8	0.0
CZ	NE	CD	H20	316.9	60.0
CZ	NE	CD	H21	76.9	300.0
NH1	CZ	NE	H22	157.9	180.0
H23	NH1	CZ	H24	180.0	180.0
NE	CD	CG	H18	32.3	60.0
NE	CD	CG	H19	152.1	300.0
CG	CD	NE	H20	240.0	120.0
CG	CD	NE	H21	120.0	240.0
H20	CD	NE	H21	240.0	119.9
OXT	C	O	H17	0.0	0.1
OXT	C	CA	H16	287.6	120.0
O	C	CA	H16	106.7	300.0
C	CA	CB	H2	141.3	305.0
C	CA	CB	H3	22.3	65.0
CB	CA	C	H16	119.3	120.0
NE	CD	CG	H20	120.0	240.0
NE	CD	CG	H21	240.0	120.0
CD	CG	CB	H2	329.8	60.0
CD	CG	CB	H3	88.9	300.0
H18	CG	CD	H19	240.2	120.1
H20	CD	CG	H21	120.0	240.0
CA	CB	CG	H2	239.5	120.0
CA	CB	CG	H3	120.5	240.0
CG	CB	CA	H16	21.1	305.0
H2	CB	CG	H3	240.9	120.0
C	CA	CB	H16	240.7	240.0
CG	CB	CA	H2	120.5	240.0
CG	CB	CA	H3	239.5	120.0
H2	CB	CA	H3	119.0	240.0
N	CA	CB	H2	20.2	185.0
N	CA	CB	H3	261.1	305.0
CB	CA	N	H16	241.0	240.0
CA	N	C4A	H12	16.0	359.9
CB	CA	N	C4A	300.0	240.1
O1P	P	O3P	O4P	236.3	120.0
O1P	P	O3P	O2P	118.0	240.0
O3P	P	O1P	H5	0.0	180.0
O3P	P	O4P	C5A	72.0	55.0
O3P	P	O2P	H6	0.0	300.1
O3P	P	O1P	O4P	121.7	239.9
O1P	P	O4P	C5A	194.5	295.0
O1P	P	O2P	H6	241.2	60.1
O1P	P	O4P	O3P	122.5	240.0
O1P	P	O4P	O2P	238.4	119.9
O4P	P	O1P	H5	238.3	300.0
O4P	P	O2P	H6	117.6	180.0
P	O4P	C5A	H14	298.2	60.0
P	O4P	C5A	H15	59.5	300.0
O1P	P	O2P	O3P	241.2	120.0
O1P	P	O2P	O4P	123.6	240.1
O2P	P	O1P	H5	116.3	60.0
O3	C3	C2	C2A	0.7	360.0
O3	C3	C2	N1	179.5	179.7
H14	C5A	O4P	H15	238.7	120.0
C4	C3	C2	C2A	181.2	180.0
C4	C3	C2	N1	0.0	359.7
C4	C5	C6	N1	0.6	0.4
C4	C5	C6	H1	180.5	179.9
C2A	C2	C3	N1	181.1	180.3
C3	C2	C2A	H9	178.9	269.7
C3	C2	C2A	H10	298.9	29.7
C3	C2	C2A	H11	58.9	149.7
C3	C2	N1	C6	359.6	0.6
C5A	C5	C6	N1	179.3	180.3
C5A	C5	C6	H1	359.2	359.9
C2	N1	C6	C5	0.1	359.4
N1	C6	C5	H1	180.0	180.4
C3	C2	C2A	N1	178.9	179.7
C2A	C2	N1	C6	178.5	180.3
H9	C2A	C2	H10	240.0	240.0
H9	C2A	C2	H11	120.0	120.0
H10	C2A	C2	H11	240.0	240.0
C3	C2	N1	C2A	181.2	180.3
C5	C6	N1	C2	0.1	359.4
N1	C2	C2A	H9	0.0	90.0
N1	C2	C2A	H10	120.0	210.0
N1	C2	C2A	H11	240.0	330.0
C2	N1	C6	H1	180.1	179.8
C5	C6	N1	H1	180.0	179.6
C5	C6	H1	N1	180.0	180.4
CG	CB	H2	H3	118.5	240.0
H2	CB	CA	N	20.2	185.0
CA	CB	H2	H3	241.5	120.0
H2	CB	CA	H16	260.6	65.0
CG	CB	H3	H2	241.5	120.0
H3	CB	CA	N	261.1	305.0
CA	CB	H3	H2	118.5	240.0
H3	CB	CA	H16	141.6	185.0
H5	O1P	P	O3P	0.0	180.0
H5	O1P	P	O4P	238.3	300.0
H5	O1P	P	O2P	116.3	60.0
H9	C2A	C2	N1	0.0	90.0
C2	C2A	H9	H10	120.0	120.0
C2	C2A	H9	H11	240.0	240.0
H10	C2A	H9	H11	120.0	120.0
H10	C2A	C2	N1	120.0	210.0
C2	C2A	H10	H9	240.0	240.0
C2	C2A	H10	H11	120.0	120.0
H9	C2A	H10	H11	240.0	240.0
H11	C2A	C2	N1	240.0	330.0
C2	C2A	H11	H9	120.0	120.0
C2	C2A	H11	H10	240.0	240.0
H9	C2A	H11	H10	120.0	120.0
O4P	C5A	H14	H15	121.9	240.0
O4P	C5A	H15	H14	238.1	120.0
CB	CA	H16	N	118.0	120.0
H16	CA	CB	H2	260.6	65.0
H16	CA	CB	H3	141.6	185.0
CD	CG	H18	H19	119.7	240.0
H18	CG	CD	H20	272.3	180.0
H18	CG	CD	H21	152.3	300.1
H18	CG	CB	H2	209.8	180.0
H18	CG	CB	H3	328.8	60.0
CD	CG	H19	H18	240.3	120.1
H19	CG	CD	H20	32.1	59.9
H19	CG	CD	H21	272.1	180.0
H19	CG	CB	H2	89.9	300.1
H19	CG	CB	H3	209.0	180.0
NE	CD	H20	H21	120.1	240.1
H20	CD	CG	H18	272.3	180.0
H20	CD	CG	H19	32.1	59.9
CG	CD	H20	H21	240.0	120.1
NE	CD	H21	H20	239.9	119.9
H21	CD	CG	H18	152.3	300.1
H21	CD	CG	H19	272.1	180.0
CG	CD	H21	H20	120.0	239.9
H22	NE	CD	H20	136.9	240.0
H22	NE	CD	H21	257.0	120.0
CZ	NH1	H23	H24	180.0	180.0
CZ	NH1	H24	H23	180.0	180.0