PDB Chemical Component A2M

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 A2M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.484 1.480
P OP3 1.486 1.610
P O5' 1.593 1.611
OP3 HOP3 0.950 0.967
O5' C5' 1.419 1.429
C5' C4' 1.508 1.530
C5' H5' 1.100 1.090
C5' H5'' 1.100 1.090
C4' O4' 1.446 1.438
C4' C3' 1.521 1.541
C4' H4' 1.100 1.090
O4' C1' 1.397 1.444
C3' O3' 1.441 1.429
C3' C2' 1.525 1.548
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.968
C2' O2' 1.398 1.429
C2' C1' 1.520 1.549
C2' H2' 1.100 1.090
O2' CM' 1.469 1.429
C1' N9 1.453 1.465
C1' H1' 1.100 1.090
CM' HM'1 1.100 1.090
CM' HM'2 1.100 1.090
CM' HM'3 1.100 1.090
N9 C8 1.371 1.362
N9 C4 1.369 1.372
C8 N7 1.314 1.301
C8 H8 1.080 1.080
N7 C5 1.391 1.355
C5 C6 1.406 1.406
C5 C4 1.377 1.405
C6 N6 1.335 1.383
C6 N1 1.356 1.329
N6 H61 1.000 0.971
N6 H62 1.000 0.970
N1 C2 1.340 1.321
C2 N3 1.333 1.316
C2 H2 1.080 1.080
N3 C4 1.346 1.329
P OP2 1.720 1.610
OP2 HOP2 0.950 0.967

Bond Angles for A2M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 119.7 109.5
OP1 P O5' 105.5 109.5
OP1 P OP2 103.7 109.5
OP3 P O5' 110.6 109.5
P OP3 HOP3 109.5 114.0
OP3 P OP2 98.1 109.5
P O5' C5' 120.8 123.0
O5' P OP2 119.9 109.5
O5' C5' C4' 110.3 109.5
O5' C5' H5' 109.2 109.5
O5' C5' H5'' 109.2 109.5
C4' C5' H5' 109.2 109.5
C4' C5' H5'' 109.2 109.5
C5' C4' O4' 109.7 109.9
C5' C4' C3' 111.2 109.9
C5' C4' H4' 107.1 109.9
H5' C5' H5'' 109.8 109.4
O4' C4' C3' 106.1 107.3
O4' C4' H4' 112.1 109.9
C4' O4' C1' 109.7 107.0
C3' C4' H4' 110.7 110.0
C4' C3' O3' 108.7 110.5
C4' C3' C2' 104.9 104.2
C4' C3' H3' 116.6 110.5
O4' C1' C2' 109.7 103.5
O4' C1' N9 109.8 110.6
O4' C1' H1' 113.8 110.5
O3' C3' C2' 118.5 110.5
O3' C3' H3' 102.4 110.4
C3' O3' HO3' 109.5 114.0
C2' C3' H3' 106.4 110.6
C3' C2' O2' 115.9 110.9
C3' C2' C1' 101.1 102.1
C3' C2' H2' 110.6 110.9
O2' C2' C1' 108.4 110.9
O2' C2' H2' 103.6 110.8
C2' O2' CM' 111.5 114.0
C1' C2' H2' 117.9 110.9
C2' C1' N9 120.2 110.7
C2' C1' H1' 101.5 110.7
O2' CM' HM'1 109.5 109.5
O2' CM' HM'2 109.5 109.5
O2' CM' HM'3 109.4 109.4
N9 C1' H1' 101.4 110.7
C1' N9 C8 131.2 126.3
C1' N9 C4 122.7 126.2
HM'1 CM' HM'2 109.5 109.5
HM'1 CM' HM'3 109.4 109.4
HM'2 CM' HM'3 109.5 109.5
C8 N9 C4 106.2 107.5
N9 C8 N7 113.4 110.0
N9 C8 H8 123.3 125.0
N9 C4 C5 105.9 105.9
N9 C4 N3 126.9 134.9
N7 C8 H8 123.3 125.0
C8 N7 C5 103.8 109.4
N7 C5 C6 132.4 134.6
N7 C5 C4 110.7 107.2
C6 C5 C4 116.9 118.2
C5 C6 N6 123.4 120.8
C5 C6 N1 117.7 118.4
C5 C4 N3 127.2 119.1
N6 C6 N1 118.8 120.8
C6 N6 H61 109.5 120.0
C6 N6 H62 109.5 120.0
C6 N1 C2 118.5 121.2
H61 N6 H62 109.4 120.0
N1 C2 N3 129.1 122.5
N1 C2 H2 115.4 118.7
N3 C2 H2 115.4 118.8
C2 N3 C4 110.6 120.6
P OP2 HOP2 109.5 114.0

Torsion Angles for A2M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP3 P OP1 O5' 125.4 240.0
OP1 P OP3 HOP3 0.0 180.0
OP3 P OP1 OP2 252.2 120.0
OP1 P O5' C5' 195.0 305.0
O5' P OP1 OP2 126.8 240.0
OP1 P OP2 HOP2 360.0 60.0
OP1 P OP3 O5' 237.1 120.0
OP1 P OP3 OP2 110.9 240.0
OP3 P O5' C5' 64.1 65.0
O5' P OP3 OP2 233.8 120.0
OP3 P OP2 HOP2 123.4 300.0
OP1 P O5' OP3 130.9 240.0
OP1 P O5' OP2 243.7 120.0
O5' P OP3 HOP3 122.9 60.0
OP3 P O5' OP2 112.9 240.0
P O5' C5' C4' 169.3 180.0
P O5' C5' H5' 289.3 300.0
P O5' C5' H5'' 49.3 60.0
O5' P OP2 HOP2 242.8 180.0
HOP3 OP3 P O5' 122.9 60.0
HOP3 OP3 P OP2 249.1 300.0
C5' O5' P OP2 311.2 185.0
C4' C5' O5' H5' 240.0 240.0
C4' C5' O5' H5'' 120.0 120.0
O5' C5' C4' O4' 301.2 66.5
O5' C5' C4' C3' 58.3 184.3
O5' C5' C4' H4' 179.4 305.4
H5' C5' O5' H5'' 240.0 240.0
O5' C5' C4' H5' 120.0 120.0
O5' C5' C4' H5'' 240.0 240.0
H5' C5' C4' H5'' 120.0 120.0
O4' C4' C5' C3' 242.9 242.2
O4' C4' C5' H4' 121.9 121.0
C5' C4' O4' C1' 112.8 145.9
C3' C4' C5' H4' 238.9 238.9
C5' C4' C3' O3' 136.3 119.9
C5' C4' C3' C2' 263.9 238.5
C5' C4' C3' H3' 21.3 357.4
O5' C5' H5' C4' 239.3 240.0
O5' C5' H5' H5'' 119.7 120.0
C4' C5' H5' H5'' 240.3 240.0
H5' C5' C4' O4' 181.3 306.4
H5' C5' C4' C3' 298.3 64.3
H5' C5' C4' H4' 59.4 185.4
O5' C5' H5'' C4' 120.7 120.0
O5' C5' H5'' H5' 240.3 240.0
C4' C5' H5'' H5' 119.7 120.0
H5'' C5' C4' O4' 61.2 186.5
H5'' C5' C4' C3' 178.3 304.3
H5'' C5' C4' H4' 299.4 65.4
O4' C4' C5' H5' 181.3 306.4
O4' C4' C5' H5'' 61.2 186.5
C5' C4' O4' C3' 120.2 119.4
C5' C4' O4' H4' 241.1 239.0
C3' C4' O4' H4' 120.9 119.6
O4' C4' C3' O3' 255.6 239.3
O4' C4' C3' C2' 23.2 358.0
O4' C4' C3' H3' 140.6 116.8
C4' O4' C1' C2' 348.2 320.0
C4' O4' C1' N9 214.0 201.4
C4' O4' C1' H1' 101.2 78.5
C3' C4' C5' H5' 298.3 64.3
C3' C4' C5' H5'' 178.3 304.3
C5' C4' C3' O4' 240.7 240.6
C5' C4' C3' H4' 118.9 121.1
O4' C4' C3' H4' 238.2 240.5
C3' C4' O4' C1' 352.6 26.5
O3' C3' C4' C2' 232.4 241.3
O3' C3' C4' H3' 115.0 122.5
C4' C3' O3' HO3' 180.0 298.6
C2' C3' C4' H3' 242.6 241.2
C4' C3' C2' O2' 214.6 220.9
C4' C3' C2' C1' 331.5 339.1
C4' C3' C2' H2' 97.1 97.4
H4' C4' C5' H5' 59.4 185.4
H4' C4' C5' H5'' 299.4 65.4
C5' C4' H4' O4' 120.4 121.0
C5' C4' H4' C3' 238.7 238.9
O4' C4' H4' C3' 118.2 117.9
H4' C4' O4' C1' 231.7 266.9
H4' C4' C3' O3' 17.4 358.8
H4' C4' C3' C2' 145.0 117.5
H4' C4' C3' H3' 262.4 236.3
C1' O4' C4' C3' 352.6 26.5
C1' O4' C4' H4' 231.7 266.9
C3' C2' C1' O4' 25.4 37.0
O2' C2' C1' O4' 147.7 155.2
O4' C1' C2' H2' 264.8 278.8
C2' C1' O4' N9 134.2 118.5
C2' C1' O4' H1' 247.1 241.5
N9 C1' O4' H1' 112.9 122.9
O4' C1' N9 C8 75.5 23.6
O4' C1' N9 C4 255.8 203.3
O3' C3' C4' H4' 17.4 358.8
C4' C3' O3' C2' 119.4 114.8
C4' C3' O3' H3' 236.1 237.4
C2' C3' O3' H3' 116.6 122.7
O3' C3' C2' O2' 336.0 339.6
O3' C3' C2' C1' 92.8 97.8
O3' C3' C2' H2' 218.5 216.1
C2' C3' C4' H4' 145.0 117.5
C4' C3' C2' O3' 238.6 241.3
C4' C3' C2' H3' 124.1 118.8
O4' C1' C2' C3' 25.4 37.0
O3' C3' C2' H3' 245.5 237.5
C2' C3' O3' HO3' 60.5 183.8
O2' C2' C3' C1' 243.1 241.8
O2' C2' C3' H2' 117.5 123.5
C3' C2' O2' CM' 260.1 268.5
C1' C2' C3' H2' 234.3 241.7
C3' C2' C1' N9 154.1 155.5
C3' C2' C1' H1' 264.7 278.6
H3' C3' C4' H4' 262.4 236.3
C4' C3' H3' O3' 118.5 122.6
C4' C3' H3' C2' 243.5 245.1
O3' C3' H3' C2' 125.0 122.6
H3' C3' O3' HO3' 303.9 61.1
H3' C3' C2' O2' 90.5 102.1
H3' C3' C2' C1' 207.3 220.3
H3' C3' C2' H2' 333.0 338.6
HO3' O3' C3' C2' 60.5 183.8
HO3' O3' C3' H3' 303.9 61.1
O4' C1' C2' O2' 147.7 155.2
O2' C2' C3' H3' 90.5 102.1
C3' C2' O2' C1' 112.7 112.7
C3' C2' O2' H2' 238.7 236.4
C1' C2' O2' H2' 126.0 123.7
O2' C2' C1' N9 276.4 273.7
O2' C2' C1' H1' 27.0 36.8
C2' O2' CM' HM'1 180.0 180.0
C2' O2' CM' HM'2 300.0 300.1
C2' O2' CM' HM'3 60.0 60.0
O4' C1' C2' N9 231.3 241.5
O4' C1' C2' H1' 120.7 118.4
C1' C2' C3' H3' 207.3 220.3
C3' C2' C1' O2' 237.7 241.8
C3' C2' C1' H2' 120.6 118.2
O2' C2' C1' H2' 242.9 236.4
C1' C2' O2' CM' 147.3 155.8
N9 C1' C2' H1' 249.4 236.9
C2' C1' N9 C8 306.9 269.5
C2' C1' N9 C4 127.2 89.2
H2' C2' C3' H3' 333.0 338.6
C3' C2' H2' O2' 124.8 123.6
C3' C2' H2' C1' 244.5 247.3
O2' C2' H2' C1' 119.6 123.7
H2' C2' O2' CM' 21.4 32.1
H2' C2' C1' N9 33.5 37.3
H2' C2' C1' H1' 144.1 160.4
CM' O2' C2' C1' 147.3 155.8
CM' O2' C2' H2' 21.4 32.1
HM'1 CM' O2' HM'2 240.0 239.9
HM'1 CM' O2' HM'3 120.0 119.9
HM'2 CM' O2' HM'3 240.0 240.0
O4' C1' N9 C2' 128.7 114.1
O4' C1' N9 H1' 239.3 237.2
N9 C1' C2' H2' 33.5 37.3
C2' C1' N9 H1' 110.6 123.1
C8 N9 C1' C4 179.7 180.3
C1' N9 C8 N7 180.4 180.0
C1' N9 C8 H8 0.4 360.0
C1' N9 C4 C5 179.5 179.9
C1' N9 C4 N3 359.9 0.8
O4' C1' H1' C2' 242.2 245.9
O4' C1' H1' N9 117.9 122.9
H1' C1' C2' H2' 144.1 160.4
C2' C1' H1' N9 235.6 236.9
H1' C1' N9 C8 196.2 146.5
H1' C1' N9 C4 16.5 326.1
O2' CM' HM'1 HM'2 120.0 120.1
O2' CM' HM'1 HM'3 240.0 240.1
HM'2 CM' HM'1 HM'3 120.0 120.0
O2' CM' HM'2 HM'1 240.0 239.9
O2' CM' HM'2 HM'3 120.0 119.9
HM'1 CM' HM'2 HM'3 240.0 240.0
O2' CM' HM'3 HM'1 120.0 120.0
O2' CM' HM'3 HM'2 240.0 240.0
HM'1 CM' HM'3 HM'2 120.0 120.1
C8 N9 C1' H1' 196.2 146.5
C1' N9 C8 C4 180.3 179.7
C8 N9 C4 C5 359.8 359.6
C8 N9 C4 N3 180.1 180.5
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 0.1 360.0
C4 N9 C1' H1' 16.5 326.1
C1' N9 C4 C8 179.8 180.3
C4 N9 C8 N7 0.1 0.3
C4 N9 C8 H8 180.1 180.2
N7 C5 C4 N9 0.3 0.4
C6 C5 C4 N9 180.5 180.2
C5 C4 N9 N3 179.7 179.1
C2 N3 C4 N9 180.0 179.6
N7 C8 N9 C4 0.1 0.3
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 179.5 180.0
C8 N7 C5 C4 359.8 359.8
H8 C8 N9 C4 180.1 180.2
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 180.0 180.0
N9 C4 C5 N7 0.3 0.4
C5 N7 C8 H8 180.0 180.0
C6 C5 N7 C4 179.7 180.2
N7 C5 C6 N6 359.0 0.0
N7 C5 C6 N1 179.5 180.0
N7 C5 C4 N3 180.0 179.7
N9 C4 C5 C6 180.5 180.2
N7 C5 C6 C4 180.3 179.7
C6 C5 C4 N3 0.2 359.5
N6 C6 C5 N1 179.5 180.0
C5 C6 N6 H61 180.5 360.0
C5 C6 N6 H62 300.5 180.0
C5 C6 N1 C2 0.8 360.0
N9 C4 C5 N3 180.3 180.7
N7 C5 C4 C6 179.8 180.2
C4 C5 C6 N6 178.7 180.3
C4 C5 C6 N1 359.2 0.3
C2 N3 C4 C5 0.3 0.6
N6 C6 C5 C4 178.7 180.3
C5 C6 N6 N1 180.5 180.0
N6 C6 N1 C2 181.2 179.9
H61 N6 C6 H62 240.1 179.9
N1 C6 C5 C4 359.2 0.3
C5 C6 N1 N6 179.5 180.0
N1 C6 N6 H61 0.0 180.0
N1 C6 N6 H62 120.0 0.1
C6 N1 C2 N3 359.8 0.1
C6 N1 C2 H2 179.8 180.0
H61 N6 C6 N1 0.0 180.0
C6 N6 H61 H62 120.0 180.1
H62 N6 C6 N1 120.0 0.1
C6 N6 H62 H61 240.0 179.9
N3 C2 N1 H2 180.0 180.1
N1 C2 N3 C4 359.6 359.7
N9 C4 N3 C2 180.0 179.6
C5 C4 N3 C2 0.3 0.6
N1 C2 N3 H2 180.0 179.9
N1 C2 H2 N3 180.0 180.1
H2 C2 N3 C4 179.6 179.7
N9 C4 N3 C5 179.6 179.0
C4 N3 C2 H2 179.6 179.7
OP1 P OP2 OP3 236.6 120.0
OP1 P OP2 O5' 117.2 240.0
OP3 P OP2 O5' 240.6 120.0
OP2 P OP3 HOP3 249.1 300.0
OP2 P O5' C5' 311.2 185.0