PDB Chemical Component AMP

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 AMP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O1P 1.541 1.480
P O2P 1.479 1.610
P O3P 1.545 1.609
P O5' 1.613 1.610
O2P HOP2 0.950 0.967
O3P HOP3 0.950 0.967
O5' C5' 1.412 1.429
C5' C4' 1.526 1.530
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.090
C4' O4' 1.419 1.437
C4' C3' 1.522 1.541
C4' H4' 1.100 1.091
O4' C1' 1.416 1.444
C3' O3' 1.410 1.429
C3' C2' 1.520 1.548
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C2' O2' 1.411 1.429
C2' C1' 1.523 1.550
C2' H2' 1.100 1.091
O2' HO2' 0.950 0.966
C1' N9 1.482 1.465
C1' H1' 1.100 1.090
N9 C8 1.367 1.362
N9 C4 1.380 1.372
C8 N7 1.358 1.302
C8 H8 1.080 1.080
N7 C5 1.347 1.354
C5 C6 1.383 1.406
C5 C4 1.397 1.405
C6 N6 1.329 1.383
C6 N1 1.390 1.329
N6 HN61 1.000 0.970
N6 HN62 1.000 0.970
N1 C2 1.383 1.320
C2 N3 1.385 1.316
C2 H2 1.080 1.080
N3 C4 1.369 1.329

Bond Angles for AMP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P 109.1 109.4
O1P P O3P 109.7 109.5
O1P P O5' 110.1 109.5
O2P P O3P 109.8 109.4
O2P P O5' 110.1 109.5
P O2P HOP2 109.5 114.0
O3P P O5' 107.9 109.5
P O3P HOP3 109.5 114.0
P O5' C5' 120.9 122.9
O5' C5' C4' 111.2 109.4
O5' C5' H5'1 109.1 109.5
O5' C5' H5'2 109.0 109.5
C4' C5' H5'1 109.0 109.5
C4' C5' H5'2 109.0 109.4
C5' C4' O4' 110.4 109.9
C5' C4' C3' 112.3 109.9
C5' C4' H4' 108.4 109.9
H5'1 C5' H5'2 109.5 109.5
O4' C4' C3' 107.4 107.3
O4' C4' H4' 109.8 109.9
C4' O4' C1' 112.3 107.0
C3' C4' H4' 108.4 110.0
C4' C3' O3' 110.5 110.5
C4' C3' C2' 105.2 104.2
C4' C3' H3' 109.3 110.5
O4' C1' C2' 106.6 103.5
O4' C1' N9 107.6 110.7
O4' C1' H1' 110.0 110.6
O3' C3' C2' 111.5 110.5
O3' C3' H3' 110.9 110.4
C3' O3' HO3' 109.5 114.0
C2' C3' H3' 109.3 110.6
C3' C2' O2' 111.9 110.9
C3' C2' C1' 105.2 102.1
C3' C2' H2' 109.2 110.9
O2' C2' C1' 110.6 111.0
O2' C2' H2' 110.7 110.8
C2' O2' HO2' 109.5 114.0
C1' C2' H2' 109.1 110.9
C2' C1' N9 115.0 110.6
C2' C1' H1' 108.5 110.6
N9 C1' H1' 109.0 110.7
C1' N9 C8 126.1 126.3
C1' N9 C4 126.4 126.3
C8 N9 C4 107.4 107.5
N9 C8 N7 109.5 110.0
N9 C8 H8 125.3 125.0
N9 C4 C5 106.4 105.9
N9 C4 N3 132.1 135.0
N7 C8 H8 125.2 125.0
C8 N7 C5 107.7 109.4
N7 C5 C6 130.0 134.7
N7 C5 C4 109.0 107.2
C6 C5 C4 121.0 118.1
C5 C6 N6 120.6 120.8
C5 C6 N1 117.2 118.4
C5 C4 N3 121.5 119.1
N6 C6 N1 122.2 120.8
C6 N6 HN61 109.5 120.0
C6 N6 HN62 109.4 120.1
C6 N1 C2 121.5 121.2
HN61 N6 HN62 109.5 120.0
N1 C2 N3 121.0 122.5
N1 C2 H2 119.5 118.8
N3 C2 H2 119.5 118.7
C2 N3 C4 117.9 120.6

Torsion Angles for AMP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2P P O1P O3P 120.4 240.0
O2P P O1P O5' 239.0 120.0
O1P P O2P HOP2 360.0 60.0
O3P P O1P O5' 118.6 239.9
O1P P O3P HOP3 360.0 180.1
O1P P O5' C5' 54.4 305.0
O1P P O2P O3P 239.7 120.0
O1P P O2P O5' 121.0 240.0
O3P P O2P O5' 241.3 120.0
O2P P O3P HOP3 240.1 300.0
O2P P O5' C5' 174.8 185.0
O1P P O3P O2P 119.9 240.0
O1P P O3P O5' 240.0 120.1
O2P P O3P O5' 120.1 240.0
O3P P O2P HOP2 120.3 300.0
O3P P O5' C5' 294.7 65.0
O1P P O5' O2P 239.6 120.0
O1P P O5' O3P 119.7 239.9
O2P P O5' O3P 240.1 120.0
O5' P O2P HOP2 239.0 180.0
O5' P O3P HOP3 120.0 60.0
P O5' C5' C4' 145.7 180.0
P O5' C5' H5'1 265.9 300.0
P O5' C5' H5'2 25.4 60.0
HOP2 O2P P O3P 120.3 300.0
HOP2 O2P P O5' 239.0 180.0
HOP3 O3P P O5' 120.0 60.0
C4' C5' O5' H5'1 239.8 240.0
C4' C5' O5' H5'2 120.3 120.0
O5' C5' C4' O4' 295.7 66.4
O5' C5' C4' C3' 55.6 184.3
O5' C5' C4' H4' 175.4 305.4
H5'1 C5' O5' H5'2 240.5 240.0
O5' C5' C4' H5'1 120.3 120.0
O5' C5' C4' H5'2 239.7 240.0
H5'1 C5' C4' H5'2 119.5 119.9
O4' C4' C5' C3' 240.1 242.1
O4' C4' C5' H4' 120.3 121.0
C5' C4' O4' C1' 125.8 145.9
C3' C4' C5' H4' 240.2 238.9
C5' C4' C3' O3' 126.3 119.8
C5' C4' C3' C2' 246.8 238.5
C5' C4' C3' H3' 4.1 357.3
O5' C5' H5'1 C4' 238.4 240.0
O5' C5' H5'1 H5'2 119.2 120.1
C4' C5' H5'1 H5'2 240.8 240.1
H5'1 C5' C4' O4' 175.4 306.4
H5'1 C5' C4' C3' 295.3 64.3
H5'1 C5' C4' H4' 55.1 185.4
O5' C5' H5'2 C4' 121.6 120.0
O5' C5' H5'2 H5'1 240.8 239.9
C4' C5' H5'2 H5'1 119.2 119.9
H5'2 C5' C4' O4' 55.9 186.5
H5'2 C5' C4' C3' 175.9 304.3
H5'2 C5' C4' H4' 295.6 65.5
O4' C4' C5' H5'1 175.4 306.4
O4' C4' C5' H5'2 55.9 186.5
C5' C4' O4' C3' 122.8 119.5
C5' C4' O4' H4' 240.5 239.0
C3' C4' O4' H4' 117.7 119.5
O4' C4' C3' O3' 247.9 239.3
O4' C4' C3' C2' 8.5 358.0
O4' C4' C3' H3' 125.7 116.8
C4' O4' C1' C2' 346.9 320.0
C4' O4' C1' N9 223.0 201.5
C4' O4' C1' H1' 104.3 78.5
C3' C4' C5' H5'1 295.3 64.3
C3' C4' C5' H5'2 175.9 304.3
C5' C4' C3' O4' 238.4 240.5
C5' C4' C3' H4' 119.8 121.1
O4' C4' C3' H4' 241.4 240.6
C3' C4' O4' C1' 2.9 26.5
O3' C3' C4' C2' 239.5 241.3
O3' C3' C4' H3' 122.2 122.5
C4' C3' O3' HO3' 180.0 180.0
C2' C3' C4' H3' 242.7 241.2
C4' C3' C2' O2' 224.1 220.9
C4' C3' C2' C1' 344.2 339.1
C4' C3' C2' H2' 101.2 97.3
H4' C4' C5' H5'1 55.1 185.4
H4' C4' C5' H5'2 295.6 65.5
C5' C4' H4' O4' 120.7 121.0
C5' C4' H4' C3' 237.8 238.9
O4' C4' H4' C3' 117.1 117.9
H4' C4' O4' C1' 245.2 267.0
H4' C4' C3' O3' 6.5 358.8
H4' C4' C3' C2' 127.1 117.4
H4' C4' C3' H3' 244.3 236.3
C1' O4' C4' C3' 2.9 26.5
C1' O4' C4' H4' 245.2 267.0
C3' C2' C1' O4' 17.8 37.0
O2' C2' C1' O4' 138.7 155.2
O4' C1' C2' H2' 260.7 278.8
C2' C1' O4' N9 123.9 118.5
C2' C1' O4' H1' 242.5 241.5
N9 C1' O4' H1' 118.6 123.0
O4' C1' N9 C8 52.0 23.6
O4' C1' N9 C4 231.9 203.2
O3' C3' C4' H4' 6.5 358.8
C4' C3' O3' C2' 116.7 114.8
C4' C3' O3' H3' 238.7 237.5
C2' C3' O3' H3' 122.0 122.7
O3' C3' C2' O2' 343.9 339.6
O3' C3' C2' C1' 104.1 97.9
O3' C3' C2' H2' 221.1 216.1
C2' C3' C4' H4' 127.1 117.4
C4' C3' C2' O3' 240.2 241.3
C4' C3' C2' H3' 117.2 118.7
O4' C1' C2' C3' 17.8 37.0
O3' C3' C2' H3' 237.0 237.5
C2' C3' O3' HO3' 63.3 65.2
O2' C2' C3' C1' 239.9 241.7
O2' C2' C3' H2' 122.9 123.5
C3' C2' O2' HO2' 180.0 298.6
C1' C2' C3' H2' 243.0 241.8
C3' C2' C1' N9 136.9 155.5
C3' C2' C1' H1' 259.3 278.5
H3' C3' C4' H4' 244.3 236.3
C4' C3' H3' O3' 122.0 122.6
C4' C3' H3' C2' 245.3 245.2
O3' C3' H3' C2' 123.4 122.6
H3' C3' O3' HO3' 301.3 302.5
H3' C3' C2' O2' 106.9 102.1
H3' C3' C2' C1' 227.0 220.4
H3' C3' C2' H2' 344.0 338.6
HO3' O3' C3' C2' 63.3 65.2
HO3' O3' C3' H3' 301.3 302.5
O4' C1' C2' O2' 138.7 155.2
O2' C2' C3' H3' 106.9 102.1
C3' C2' O2' C1' 117.0 112.7
C3' C2' O2' H2' 238.0 236.4
C1' C2' O2' H2' 121.0 123.7
O2' C2' C1' N9 257.9 273.7
O2' C2' C1' H1' 20.3 36.7
O4' C1' C2' N9 240.8 241.5
O4' C1' C2' H1' 118.4 118.5
C1' C2' C3' H3' 227.0 220.4
C3' C2' C1' O2' 239.0 241.8
C3' C2' C1' H2' 117.0 118.2
O2' C2' C1' H2' 238.0 236.4
C1' C2' O2' HO2' 63.0 185.9
N9 C1' C2' H1' 237.6 237.1
C2' C1' N9 C8 293.3 269.5
C2' C1' N9 C4 113.2 89.1
H2' C2' C3' H3' 344.0 338.6
C3' C2' H2' O2' 123.6 123.6
C3' C2' H2' C1' 245.5 247.3
O2' C2' H2' C1' 121.9 123.7
H2' C2' O2' HO2' 302.0 62.2
H2' C2' C1' N9 19.9 37.4
H2' C2' C1' H1' 142.3 160.3
HO2' O2' C2' C1' 63.0 185.9
HO2' O2' C2' H2' 302.0 62.2
O4' C1' N9 C2' 118.6 114.1
O4' C1' N9 H1' 240.8 237.0
N9 C1' C2' H2' 19.9 37.4
C2' C1' N9 H1' 122.1 122.9
C8 N9 C1' C4 180.1 180.3
C1' N9 C8 N7 180.1 180.0
C1' N9 C8 H8 0.1 360.0
C1' N9 C4 C5 179.6 179.9
C1' N9 C4 N3 0.6 0.9
O4' C1' H1' C2' 243.7 245.9
O4' C1' H1' N9 117.8 123.0
H1' C1' C2' H2' 142.3 160.3
C2' C1' H1' N9 234.1 237.1
H1' C1' N9 C8 171.2 146.6
H1' C1' N9 C4 351.1 326.2
C8 N9 C1' H1' 171.2 146.6
C1' N9 C8 C4 179.9 179.7
C8 N9 C4 C5 359.5 359.6
C8 N9 C4 N3 180.5 180.6
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 0.2 0.0
C4 N9 C1' H1' 351.1 326.2
C1' N9 C4 C8 180.1 180.3
C4 N9 C8 N7 0.2 0.3
C4 N9 C8 H8 180.1 180.3
N7 C5 C4 N9 0.6 0.4
C6 C5 C4 N9 180.1 180.2
C5 C4 N9 N3 179.0 179.0
C2 N3 C4 N9 179.5 179.6
N7 C8 N9 C4 0.2 0.3
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 180.1 180.0
C8 N7 C5 C4 359.5 359.7
H8 C8 N9 C4 180.1 180.3
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 180.2 180.0
N9 C4 C5 N7 0.6 0.4
C5 N7 C8 H8 180.2 180.0
C6 C5 N7 C4 180.6 180.3
N7 C5 C6 N6 359.3 0.0
N7 C5 C6 N1 181.0 180.0
N7 C5 C4 N3 179.8 179.6
N9 C4 C5 C6 180.1 180.2
N7 C5 C6 C4 179.4 179.7
C6 C5 C4 N3 359.3 359.4
N6 C6 C5 N1 178.3 180.0
C5 C6 N6 HN61 181.8 359.9
C5 C6 N6 HN62 301.8 180.1
C5 C6 N1 C2 357.6 360.0
N9 C4 C5 N3 180.8 180.8
N7 C5 C4 C6 180.5 180.2
C4 C5 C6 N6 179.9 180.3
C4 C5 C6 N1 1.6 0.3
C2 N3 C4 C5 0.6 0.7
N6 C6 C5 C4 179.9 180.3
C5 C6 N6 N1 181.8 180.0
N6 C6 N1 C2 179.3 179.9
HN61 N6 C6 HN62 240.0 179.9
N1 C6 C5 C4 1.6 0.3
C5 C6 N1 N6 178.3 180.0
N1 C6 N6 HN61 360.0 180.0
N1 C6 N6 HN62 120.0 0.1
C6 N1 C2 N3 2.4 0.1
C6 N1 C2 H2 182.4 180.0
HN61 N6 C6 N1 360.0 180.0
C6 N6 HN61 HN62 120.0 180.1
HN62 N6 C6 N1 120.0 0.1
C6 N6 HN62 HN61 240.0 179.9
N3 C2 N1 H2 180.0 180.1
N1 C2 N3 C4 358.6 359.6
N9 C4 N3 C2 179.5 179.6
C5 C4 N3 C2 0.6 0.7
N1 C2 N3 H2 180.0 179.9
N1 C2 H2 N3 180.0 180.1
H2 C2 N3 C4 178.6 179.6
N9 C4 N3 C5 178.9 178.9
C4 N3 C2 H2 178.6 179.6