PDB Chemical Component MDA

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 MDA

Atom I	Atom J	Distance (Experimental Model)	Distance (Ideal Model)
C1	C2	1.534	1.531
C1	O1	1.436	1.429
C1	O5	1.437	1.425
C1	H1	1.099	1.090
C2	C3	1.547	1.532
C2	H2	1.099	1.090
C2	H22	1.099	1.089
C3	C4	1.541	1.532
C3	C3'	1.546	1.531
C3	O3	1.417	1.428
C4	C5	1.542	1.529
C4	O4	1.416	1.428
C4	H4	1.098	1.090
C5	C6	1.564	1.530
C5	O5	1.436	1.427
C5	H5	1.100	1.090
C6	H61	1.099	1.089
C6	H62	1.099	1.090
C6	H63	1.099	1.090
C3'	H3'1	1.099	1.090
C3'	H3'2	1.099	1.089
C3'	H3'3	1.100	1.090
O1	HO1	0.950	0.966
O3	HO3	0.957	0.967
O4	HO4	0.960	0.967

Bond Angles for MDA

Atom I	Atom J	Atom K	Angle (Experimental Model)	Angle (Ideal Model)
C2	C1	O1	109.7	109.4
C2	C1	O5	108.5	109.8
C2	C1	H1	109.7	109.4
C1	C2	C3	112.1	109.0
C1	C2	H2	108.5	109.5
C1	C2	H22	106.6	109.5
O1	C1	O5	112.0	109.5
O1	C1	H1	107.2	109.4
C1	O1	HO1	109.6	106.8
O5	C1	H1	109.7	109.5
C1	O5	C5	115.2	107.6
C3	C2	H2	108.5	109.6
C3	C2	H22	110.0	109.6
C2	C3	C4	107.2	108.7
C2	C3	C3'	112.2	109.6
C2	C3	O3	110.0	109.6
H2	C2	H22	111.0	109.6
C4	C3	C3'	110.0	109.6
C4	C3	O3	107.8	109.8
C3	C4	C5	109.1	109.0
C3	C4	O4	110.0	109.6
C3	C4	H4	110.3	109.5
C3'	C3	O3	109.5	109.6
C3	C3'	H3'1	110.3	109.5
C3	C3'	H3'2	112.2	109.5
C3	C3'	H3'3	110.1	109.4
C3	O3	HO3	113.0	106.8
C5	C4	O4	109.1	109.6
C5	C4	H4	110.4	109.6
C4	C5	C6	109.4	109.5
C4	C5	O5	110.3	109.8
C4	C5	H5	107.5	109.5
O4	C4	H4	107.9	109.5
C4	O4	HO4	109.6	106.8
C6	C5	O5	109.1	109.4
C6	C5	H5	114.6	109.4
C5	C6	H61	112.9	109.5
C5	C6	H62	112.6	109.5
C5	C6	H63	109.5	109.5
O5	C5	H5	105.9	109.4
H61	C6	H62	108.4	109.5
H61	C6	H63	106.5	109.4
H62	C6	H63	106.5	109.5
H3'1	C3'	H3'2	107.1	109.5
H3'1	C3'	H3'3	108.0	109.5
H3'2	C3'	H3'3	109.1	109.5

Torsion Angles for MDA

Atom I	Atom J	Atom K	Atom L	Angle (Experimental Model)	Angle (Ideal Model)
O1	C1	C2	O5	122.7	120.1
O1	C1	C2	H1	242.5	240.2
C2	C1	O1	HO1	180.0	179.7
O5	C1	C2	H1	119.8	120.1
C2	C1	O5	C5	302.4	292.5
C3	C2	C1	H2	119.9	240.1
C3	C2	C1	H22	239.5	119.9
C1	C2	C3	C4	302.9	306.3
C1	C2	C3	C3'	182.0	186.5
C1	C2	C3	O3	59.9	66.3
H2	C2	C1	H22	119.6	239.7
C2	C1	O1	O5	239.4	239.7
C2	C1	O1	H1	119.1	119.8
O1	C1	C2	C3	178.6	181.4
O1	C1	C2	H2	58.8	301.2
O1	C1	C2	H22	299.1	61.5
O5	C1	O1	H1	239.7	240.1
O1	C1	O5	C5	181.1	172.4
C2	C1	O5	O1	121.3	120.1
C2	C1	O5	H1	240.1	239.9
O5	C1	C2	C3	55.9	61.2
O5	C1	C2	H2	296.1	181.1
O5	C1	C2	H22	176.4	301.4
O1	C1	O5	H1	118.9	119.9
O5	C1	O1	HO1	300.6	300.0
C4	C5	O5	C1	60.1	67.6
C6	C5	O5	C1	180.2	187.7
C1	O5	C5	H5	304.0	307.5
C2	C1	H1	O1	241.0	240.2
C2	C1	H1	O5	119.1	120.3
H1	C1	C2	C3	296.1	301.1
H1	C1	C2	H2	176.2	61.0
H1	C1	C2	H22	56.6	181.2
O1	C1	H1	O5	238.2	240.1
H1	C1	O1	HO1	60.9	59.9
H1	C1	O5	C5	62.2	52.5
C3	C2	C1	O1	178.6	181.4
C3	C2	C1	O5	55.9	61.2
C3	C2	C1	H1	296.1	301.1
C1	C2	C3	H2	240.2	119.8
C1	C2	C3	H22	118.5	240.2
H2	C2	C3	H22	238.3	120.4
C4	C3	C2	C3'	120.9	119.7
C4	C3	C2	O3	243.0	240.0
C2	C3	C4	C5	56.8	53.8
C2	C3	C4	O4	176.5	173.7
C2	C3	C4	H4	295.4	293.9
C3'	C3	C2	O3	122.1	120.3
C2	C3	C3'	H3'1	177.2	300.0
C2	C3	C3'	H3'2	296.5	60.0
C2	C3	C3'	H3'3	58.1	180.0
C2	C3	O3	HO3	74.7	60.0
H2	C2	C1	O1	58.8	301.2
H2	C2	C1	O5	296.1	181.1
H2	C2	C1	H1	176.2	61.0
C1	C2	H2	C3	122.1	240.5
C1	C2	H2	H22	243.2	120.2
C3	C2	H2	H22	121.1	239.7
H2	C2	C3	C4	62.7	186.4
H2	C2	C3	C3'	301.9	66.7
H2	C2	C3	O3	179.7	306.4
H22	C2	C1	O1	299.1	61.5
H22	C2	C1	O5	176.4	301.4
H22	C2	C1	H1	56.6	181.2
C1	C2	H22	C3	238.2	119.5
C1	C2	H22	H2	118.0	239.8
C3	C2	H22	H2	239.8	120.3
H22	C2	C3	C4	184.4	66.1
H22	C2	C3	C3'	63.5	306.3
H22	C2	C3	O3	301.4	186.1
C4	C3	C2	H2	62.7	186.4
C4	C3	C2	H22	184.4	66.1
C2	C3	C4	C3'	237.8	240.3
C2	C3	C4	O3	118.5	119.9
C3'	C3	C4	O3	240.7	239.6
C4	C3	C3'	H3'1	58.0	180.9
C4	C3	C3'	H3'2	177.2	300.9
C4	C3	C3'	H3'3	298.9	60.9
C4	C3	O3	HO3	191.3	179.3
C5	C4	C3	O4	240.3	240.1
C5	C4	C3	H4	121.4	119.9
C3	C4	C5	C6	181.7	178.6
C3	C4	C5	O5	301.7	298.7
C3	C4	C5	H5	56.7	58.7
O4	C4	C3	H4	241.1	239.8
C3	C4	O4	HO4	58.9	180.1
C3'	C3	C2	H2	301.9	66.7
C3'	C3	C2	H22	63.5	306.3
C2	C3	C3'	C4	119.2	119.1
C2	C3	C3'	O3	237.6	239.7
C4	C3	C3'	O3	118.3	120.6
C3'	C3	C4	C5	179.0	173.5
C3'	C3	C4	O4	298.7	293.4
C3'	C3	C4	H4	57.6	53.6
C3'	C3	O3	HO3	311.0	299.7
H3'1	C3'	C3	H3'2	240.8	240.0
H3'1	C3'	C3	H3'3	119.1	120.0
H3'2	C3'	C3	H3'3	238.3	240.0
O3	C3	C2	H2	179.7	306.4
O3	C3	C2	H22	301.4	186.1
C2	C3	O3	C4	243.4	240.7
C2	C3	O3	C3'	123.7	120.3
C4	C3	O3	C3'	240.3	239.6
O3	C3	C4	C5	298.3	294.0
O3	C3	C4	O4	58.0	53.9
O3	C3	C4	H4	176.9	174.0
O3	C3	C3'	H3'1	299.7	60.3
O3	C3	C3'	H3'2	58.9	180.3
O3	C3	C3'	H3'3	180.6	300.3
C1	O5	C5	C4	60.1	67.6
C5	C4	C3	C3'	179.0	173.5
C5	C4	C3	O3	298.3	294.0
C3	C4	C5	O4	120.3	119.9
C3	C4	C5	H4	238.7	240.1
O4	C4	C5	H4	118.4	120.2
C5	C4	O4	HO4	178.6	299.7
C6	C5	C4	O5	240.0	239.9
C6	C5	C4	H5	125.0	119.9
C4	C5	C6	H61	178.6	180.1
C4	C5	C6	H62	301.8	300.2
C4	C5	C6	H63	60.1	60.1
O5	C5	C4	H5	245.0	240.0
O4	C4	C3	C3'	298.7	293.4
O4	C4	C3	O3	58.0	53.9
C3	C4	O4	C5	240.3	240.4
C3	C4	O4	H4	120.3	120.2
C5	C4	O4	H4	240.0	239.7
O4	C4	C5	C6	61.4	58.7
O4	C4	C5	O5	181.4	178.8
O4	C4	C5	H5	296.4	298.8
H4	C4	C3	C3'	57.6	53.6
H4	C4	C3	O3	176.9	174.0
C3	C4	H4	C5	120.6	119.6
C3	C4	H4	O4	239.8	239.8
C5	C4	H4	O4	119.2	120.2
H4	C4	C5	C6	303.0	298.5
H4	C4	C5	O5	63.0	58.6
H4	C4	C5	H5	178.0	178.6
H4	C4	O4	HO4	298.6	59.9
C1	O5	C5	C6	180.2	187.7
C6	C5	C4	O4	61.4	58.7
C6	C5	C4	H4	303.0	298.5
C4	C5	C6	O5	120.7	120.3
C4	C5	C6	H5	239.2	240.1
O5	C5	C6	H5	118.5	119.8
H61	C6	C5	H62	236.8	240.0
H61	C6	C5	H63	118.5	120.0
H62	C6	C5	H63	241.7	240.0
C5	O5	C1	H1	62.2	52.5
O5	C5	C4	O4	181.4	178.8
O5	C5	C4	H4	63.0	58.6
C4	C5	O5	C6	239.8	239.9
C4	C5	O5	H5	116.1	120.1
C6	C5	O5	H5	236.2	240.2
O5	C5	C6	H61	57.9	59.8
O5	C5	C6	H62	181.1	179.8
O5	C5	C6	H63	299.4	299.8
H5	C5	C4	O4	296.4	298.8
H5	C5	C4	H4	178.0	178.6
C4	C5	H5	C6	121.8	119.9
C4	C5	H5	O5	242.1	239.7
C6	C5	H5	O5	120.3	119.8
H5	C5	C6	H61	299.5	300.0
H5	C5	C6	H62	62.6	60.1
H5	C5	C6	H63	181.0	180.1
H61	C6	C5	O5	57.9	59.8
H61	C6	C5	H5	299.5	300.0
C5	C6	H61	H62	125.5	120.1
C5	C6	H61	H63	239.8	240.0
H62	C6	H61	H63	114.2	119.9
H62	C6	C5	O5	181.1	179.8
H62	C6	C5	H5	62.6	60.1
C5	C6	H62	H61	234.3	239.9
C5	C6	H62	H63	120.1	120.0
H61	C6	H62	H63	245.7	240.1
H63	C6	C5	O5	299.4	299.8
H63	C6	C5	H5	181.0	180.1
C5	C6	H63	H61	122.4	120.0
C5	C6	H63	H62	237.9	240.0
H61	C6	H63	H62	115.5	119.9
H3'1	C3'	C3	O3	299.7	60.3
C3	C3'	H3'1	H3'2	122.3	120.0
C3	C3'	H3'1	H3'3	239.6	240.0
H3'2	C3'	H3'1	H3'3	117.4	120.0
H3'2	C3'	C3	O3	58.9	180.3
C3	C3'	H3'2	H3'1	238.9	240.0
C3	C3'	H3'2	H3'3	122.2	120.0
H3'1	C3'	H3'2	H3'3	243.3	240.0
H3'3	C3'	C3	O3	180.6	300.3
C3	C3'	H3'3	H3'1	120.5	120.0
C3	C3'	H3'3	H3'2	236.5	240.0
H3'1	C3'	H3'3	H3'2	116.1	120.0
HO1	O1	C1	O5	300.6	300.0
HO1	O1	C1	H1	60.9	59.9
HO4	O4	C4	H4	298.6	59.9