PDB Chemical Component XMP

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 XMP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O1P 1.490 1.610
P O2P 1.460 1.610
P O5' 1.605 1.610
P O3P 1.504 1.480
O1P HOP1 0.950 0.967
O2P HOP2 0.950 0.967
O5' C5' 1.418 1.429
C5' C4' 1.492 1.530
C5' H5'2 1.100 1.090
C5' H5'1 1.100 1.090
C4' O4' 1.452 1.437
C4' C3' 1.518 1.541
C4' H4' 1.100 1.090
O4' C1' 1.435 1.443
C1' N9 1.451 1.465
C1' C2' 1.527 1.550
C1' H1' 1.100 1.090
N9 C4 1.360 1.359
N9 C8 1.366 1.364
C4 N3 1.332 1.377
C4 C5 1.385 1.389
N3 C2 1.339 1.345
N3 H3 1.000 0.970
N1 C2 1.363 1.343
N1 C6 1.394 1.350
N1 H1 1.000 0.970
C2 O2 1.229 1.216
C6 O6 1.231 1.218
C6 C5 1.388 1.464
C5 N7 1.390 1.355
N7 C8 1.306 1.302
N7 H7 1.000 0.969
C8 H8 1.080 1.080
C2' O2' 1.386 1.429
C2' C3' 1.510 1.548
C2' H2' 1.100 1.091
O2' H2O1 0.950 0.967
C3' O3' 1.468 1.429
C3' H3' 1.100 1.090
O3' H3O1 0.950 0.967

Bond Angles for XMP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P 121.2 109.5
O1P P O5' 109.3 109.4
O1P P O3P 104.0 109.5
P O1P HOP1 109.5 114.0
O2P P O5' 108.2 109.5
O2P P O3P 110.2 109.4
P O2P HOP2 109.5 114.0
O5' P O3P 102.2 109.5
P O5' C5' 113.5 123.0
O5' C5' C4' 112.6 109.5
O5' C5' H5'2 108.4 109.4
O5' C5' H5'1 107.7 109.4
C4' C5' H5'2 108.5 109.5
C4' C5' H5'1 107.7 109.5
C5' C4' O4' 109.5 109.9
C5' C4' C3' 119.1 109.8
C5' C4' H4' 100.6 109.8
H5'2 C5' H5'1 111.9 109.4
O4' C4' C3' 101.3 107.3
O4' C4' H4' 118.6 109.9
C4' O4' C1' 104.9 107.0
C3' C4' H4' 108.9 110.0
C4' C3' C2' 95.8 104.2
C4' C3' O3' 111.5 110.5
C4' C3' H3' 118.9 110.5
O4' C1' N9 101.6 110.6
O4' C1' C2' 106.6 103.5
O4' C1' H1' 118.0 110.6
N9 C1' C2' 114.7 110.6
N9 C1' H1' 110.5 110.5
C1' N9 C4 127.5 126.2
C1' N9 C8 124.9 126.2
C2' C1' H1' 105.8 110.8
C1' C2' O2' 111.3 110.9
C1' C2' C3' 97.9 102.1
C1' C2' H2' 116.5 110.9
C4 N9 C8 107.6 107.6
N9 C4 N3 125.8 134.4
N9 C4 C5 104.8 106.4
N9 C8 N7 112.7 109.5
N9 C8 H8 123.6 125.3
N3 C4 C5 129.3 119.2
C4 N3 C2 114.5 120.8
C4 N3 H3 122.8 119.6
C4 C5 C6 116.9 118.3
C4 C5 N7 110.7 107.4
C2 N3 H3 122.8 119.7
N3 C2 N1 118.9 122.3
N3 C2 O2 120.2 118.8
C2 N1 C6 127.8 120.9
C2 N1 H1 116.1 119.5
N1 C2 O2 120.9 118.9
C6 N1 H1 116.1 119.6
N1 C6 O6 119.3 120.8
N1 C6 C5 112.5 118.5
O6 C6 C5 128.1 120.7
C6 C5 N7 132.4 134.3
C5 N7 C8 104.2 109.0
C5 N7 H7 127.9 125.5
C8 N7 H7 127.9 125.4
N7 C8 H8 123.6 125.2
O2' C2' C3' 111.9 110.9
O2' C2' H2' 103.6 110.8
C2' O2' H2O1 109.5 114.0
C3' C2' H2' 115.9 110.9
C2' C3' O3' 115.0 110.5
C2' C3' H3' 115.5 110.5
O3' C3' H3' 101.0 110.5
C3' O3' H3O1 109.5 114.0

Torsion Angles for XMP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2P P O1P O5' 126.9 240.0
O2P P O1P O3P 235.4 120.0
O1P P O2P HOP2 274.7 60.0
O5' P O1P O3P 108.5 240.0
O1P P O5' C5' 342.7 175.0
O1P P O2P O5' 232.6 120.0
O1P P O2P O3P 121.7 240.0
O2P P O1P HOP1 252.7 59.9
O5' P O2P O3P 249.0 120.0
O2P P O5' C5' 208.8 295.0
O1P P O5' O2P 133.9 240.0
O1P P O5' O3P 250.3 120.0
O5' P O1P HOP1 125.8 179.9
O2P P O5' O3P 116.3 240.0
O5' P O2P HOP2 42.0 300.0
P O5' C5' C4' 233.1 180.0
P O5' C5' H5'2 353.1 300.0
P O5' C5' H5'1 114.5 59.9
O1P P O3P O2P 228.6 120.0
O1P P O3P O5' 113.7 240.0
O3P P O1P HOP1 17.3 300.0
O2P P O3P O5' 245.1 120.0
O3P P O2P HOP2 153.0 180.0
O3P P O5' C5' 92.5 55.0
HOP1 O1P P O2P 252.7 59.9
HOP1 O1P P O5' 125.8 179.9
HOP1 O1P P O3P 17.3 300.0
HOP2 O2P P O5' 42.0 300.0
HOP2 O2P P O3P 153.0 180.0
C5' O5' P O3P 92.5 55.0
C4' C5' O5' H5'2 240.0 240.0
C4' C5' O5' H5'1 118.6 120.1
O5' C5' C4' O4' 213.0 66.4
O5' C5' C4' C3' 328.7 184.2
O5' C5' C4' H4' 87.4 305.4
H5'2 C5' O5' H5'1 238.7 240.1
O5' C5' C4' H5'2 120.0 119.9
O5' C5' C4' H5'1 241.3 240.0
H5'2 C5' C4' H5'1 121.3 120.0
O4' C4' C5' C3' 244.3 242.2
O4' C4' C5' H4' 125.6 121.0
C5' C4' O4' C1' 91.3 145.9
C3' C4' C5' H4' 241.3 238.8
C5' C4' C3' C2' 295.1 238.5
C5' C4' C3' O3' 175.3 119.9
C5' C4' C3' H3' 58.5 357.2
O5' C5' H5'2 C4' 237.4 240.0
O5' C5' H5'2 H5'1 118.7 119.9
C4' C5' H5'2 H5'1 241.3 239.9
H5'2 C5' C4' O4' 93.0 306.5
H5'2 C5' C4' C3' 208.7 64.3
H5'2 C5' C4' H4' 327.4 185.5
O5' C5' H5'1 C4' 121.7 120.0
O5' C5' H5'1 H5'2 240.9 240.1
C4' C5' H5'1 H5'2 119.1 120.1
H5'1 C5' C4' O4' 331.7 186.5
H5'1 C5' C4' C3' 87.3 304.3
H5'1 C5' C4' H4' 206.0 65.4
O4' C4' C5' H5'2 93.0 306.5
O4' C4' C5' H5'1 331.7 186.5
C5' C4' O4' C3' 126.6 119.4
C5' C4' O4' H4' 245.5 239.0
C3' C4' O4' H4' 118.9 119.7
O4' C4' C3' C2' 55.0 357.9
O4' C4' C3' O3' 295.2 239.3
O4' C4' C3' H3' 178.4 116.6
C4' O4' C1' N9 241.0 201.4
C4' O4' C1' C2' 1.4 319.9
C4' O4' C1' H1' 120.1 78.6
C3' C4' C5' H5'2 208.7 64.3
C3' C4' C5' H5'1 87.3 304.3
C5' C4' C3' O4' 240.0 240.6
C5' C4' C3' H4' 114.4 121.0
O4' C4' C3' H4' 234.3 240.4
C3' C4' O4' C1' 324.8 26.6
C1' C2' C3' C4' 308.4 339.2
O2' C2' C3' C4' 191.6 220.9
C4' C3' C2' H2' 73.0 97.4
C2' C3' C4' O3' 119.8 118.6
C2' C3' C4' H3' 236.6 241.3
O3' C3' C4' H3' 116.8 122.7
C4' C3' O3' H3O1 121.8 180.0
H4' C4' C5' H5'2 327.4 185.5
H4' C4' C5' H5'1 206.0 65.4
C5' C4' H4' O4' 119.2 121.0
C5' C4' H4' C3' 234.1 239.0
O4' C4' H4' C3' 114.9 118.0
H4' C4' O4' C1' 205.8 266.9
H4' C4' C3' C2' 180.7 117.5
H4' C4' C3' O3' 60.9 358.8
H4' C4' C3' H3' 304.1 236.2
C1' O4' C4' C3' 324.8 26.6
C1' O4' C4' H4' 205.8 266.9
N9 C1' O4' C2' 239.6 241.5
N9 C1' O4' H1' 120.9 122.8
O4' C1' N9 C4 238.9 203.5
O4' C1' N9 C8 57.1 23.2
C2' C1' O4' H1' 241.3 241.3
O4' C1' C2' O2' 150.1 155.2
O4' C1' C2' C3' 32.8 37.0
O4' C1' C2' H2' 268.5 278.8
O4' C1' N9 C2' 114.6 114.1
O4' C1' N9 H1' 234.0 237.1
C2' C1' N9 H1' 119.4 123.1
N9 C1' C2' O2' 261.7 273.8
N9 C1' C2' C3' 144.4 155.5
N9 C1' C2' H2' 20.1 37.3
C4 N9 C1' C8 181.8 180.3
C1' N9 C4 N3 359.5 0.1
C1' N9 C4 C5 178.3 180.0
C1' N9 C8 N7 181.0 179.8
C1' N9 C8 H8 1.0 0.0
C4' C3' C2' C1' 308.4 339.2
O4' C1' C2' N9 248.4 241.5
O4' C1' C2' H1' 126.4 118.6
N9 C1' C2' H1' 238.0 237.1
C2' C1' N9 C4 124.3 89.4
C2' C1' N9 C8 302.5 269.2
O2' C2' C1' C3' 117.3 118.2
O2' C2' C1' H2' 241.5 236.5
C1' C2' O2' H2O1 70.6 180.0
C3' C2' C1' H2' 124.2 118.2
C1' C2' C3' O3' 65.4 97.8
C1' C2' C3' H3' 182.5 220.4
O4' C1' H1' N9 116.2 122.9
O4' C1' H1' C2' 240.9 245.9
N9 C1' H1' C2' 124.6 123.0
H1' C1' N9 C4 4.9 326.4
H1' C1' N9 C8 183.1 146.1
H1' C1' C2' O2' 23.7 36.7
H1' C1' C2' C3' 266.4 278.5
H1' C1' C2' H2' 142.1 160.2
C4 N9 C1' C2' 124.3 89.4
C4 N9 C1' H1' 4.9 326.4
C1' N9 C4 C8 178.5 179.8
C4 N9 C8 N7 359.5 359.6
C4 N9 C8 H8 179.5 179.8
N3 C4 N9 C5 181.2 180.1
N9 C4 N3 C2 180.2 180.0
N9 C4 N3 H3 0.2 359.9
N9 C4 C5 C6 178.9 180.0
N9 C4 C5 N7 0.8 0.1
C8 N9 C1' C2' 302.5 269.2
C8 N9 C1' H1' 183.1 146.1
C1' N9 C8 C4 181.5 180.2
C8 N9 C4 N3 181.1 180.3
C8 N9 C4 C5 359.8 0.2
C5 N7 C8 N9 1.0 0.5
N9 C8 N7 H7 181.0 180.2
N7 C8 N9 H8 180.0 179.8
N3 C4 N9 C8 181.1 180.3
N9 C4 N3 C5 178.4 179.9
N3 C4 C5 C6 357.6 360.0
N3 C4 C5 N7 179.5 180.0
C2 N3 C4 H3 180.0 180.1
C4 N3 C2 N1 358.8 360.0
C4 N3 C2 O2 180.8 180.0
C5 C4 N9 C8 359.8 0.2
N9 C4 C5 N3 181.3 180.1
C5 C4 N3 C2 1.8 0.1
C5 C4 N3 H3 181.8 180.0
N1 C6 C5 C4 2.3 360.0
O6 C6 C5 C4 179.8 180.1
C6 C5 C4 N7 178.1 180.0
C4 C5 N7 C8 358.9 359.7
C4 C5 N7 H7 178.9 179.9
C2 N3 C4 C5 1.8 0.1
C4 N3 C2 H3 180.0 179.9
N3 C2 N1 C6 1.7 359.9
N3 C2 N1 H1 181.7 180.0
N1 C2 N3 O2 178.0 180.0
H3 N3 C4 C5 181.8 180.0
C4 N3 H3 C2 180.0 180.1
H3 N3 C2 N1 178.8 180.1
H3 N3 C2 O2 0.8 0.0
N1 C2 N3 H3 178.8 180.1
N3 C2 N1 O2 182.0 180.0
C6 N1 C2 H1 180.0 179.9
C2 N1 C6 O6 180.0 180.0
C2 N1 C6 C5 357.8 0.1
C4 C5 C6 N1 2.3 360.0
C2 N1 C6 H1 180.0 180.1
C6 N1 C2 O2 179.7 180.0
O6 C6 N1 C5 182.2 179.9
N1 C6 C5 N7 179.8 180.0
C2 N1 H1 C6 180.0 179.9
H1 N1 C2 O2 359.7 0.0
H1 N1 C6 O6 360.0 359.9
H1 N1 C6 C5 177.8 180.0
O2 C2 N3 H3 0.8 0.0
N3 C2 O2 N1 178.0 180.0
O2 C2 N1 C6 179.7 180.0
O2 C2 N1 H1 359.7 0.0
C4 C5 C6 O6 179.8 180.1
O6 C6 N1 H1 360.0 359.9
N1 C6 O6 C5 177.4 180.1
O6 C6 C5 N7 357.4 0.0
C4 C5 C6 N7 182.4 180.0
C5 C6 N1 H1 177.8 180.0
N1 C6 C5 O6 182.4 179.9
C6 C5 N7 C8 181.2 179.7
C6 C5 N7 H7 1.2 360.0
N9 C8 N7 C5 1.0 0.5
C4 C5 N7 C6 177.7 180.0
C8 N7 C5 H7 180.0 179.8
C5 N7 C8 H8 181.0 180.2
N9 C8 N7 H8 180.0 180.2
C5 N7 C8 H7 180.0 180.2
C5 N7 H7 C8 180.0 179.7
H7 N7 C8 H8 1.0 360.0
N9 C8 H8 N7 180.0 179.8
H8 C8 N7 H7 1.0 360.0
C4' C3' C2' O2' 191.6 220.9
O2' C2' C1' H1' 23.7 36.7
C1' C2' O2' C3' 251.6 247.2
C1' C2' O2' H2' 126.0 123.6
C3' C2' O2' H2' 234.4 236.3
O2' C2' C3' O3' 308.6 339.6
O2' C2' C3' H3' 65.7 102.2
C2' C3' C4' H4' 180.7 117.5
C4' C3' C2' O3' 243.0 241.4
C4' C3' C2' H3' 125.9 118.7
C3' C2' C1' H1' 266.4 278.5
C1' C2' C3' O2' 116.8 118.2
C1' C2' C3' H2' 235.4 241.8
O2' C2' C3' H2' 118.6 123.6
C3' C2' O2' H2O1 179.1 292.7
O3' C3' C2' H3' 242.9 237.4
C2' C3' O3' H3O1 14.1 65.2
H2' C2' C1' H1' 142.1 160.2
C1' C2' H2' O2' 237.4 236.4
C1' C2' H2' C3' 114.4 112.7
O2' C2' H2' C3' 237.0 236.4
H2' C2' O2' H2O1 304.7 56.4
H2' C2' C3' O3' 190.0 216.0
H2' C2' C3' H3' 307.1 338.6
H2O1 O2' C2' C3' 179.1 292.7
H2O1 O2' C2' H2' 304.7 56.4
O3' C3' C4' H4' 60.9 358.8
C4' C3' O3' C2' 107.6 114.7
C4' C3' O3' H3' 232.8 237.3
O3' C3' C2' H2' 190.0 216.0
C2' C3' O3' H3' 125.1 122.6
H3' C3' C4' H4' 304.1 236.2
C4' C3' H3' C2' 247.0 245.2
C4' C3' H3' O3' 122.2 122.6
H3' C3' C2' H2' 307.1 338.6
C2' C3' H3' O3' 235.2 237.4
H3' C3' O3' H3O1 249.0 302.6
H3O1 O3' C3' H3' 249.0 302.6