PDB Chemical Component A5A

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 A5A

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N CA 1.457 1.469
N H 1.019 1.008
N HN2 1.020 1.010
CA CB 1.533 1.530
CA C 1.499 1.505
CA HA 1.115 1.090
CB HB1 1.116 1.089
CB HB2 1.115 1.089
CB HB3 1.116 1.090
C O 1.207 1.213
C N3S 1.370 1.347
N3S S 1.614 1.655
N3S H3S 1.020 0.971
S O1S 1.476 1.420
S O2S 1.503 1.421
S O5' 1.597 1.522
O5' C5' 1.434 1.428
C5' C4' 1.514 1.529
C5' H5'1 1.115 1.090
C5' H5'2 1.115 1.090
C4' O4' 1.456 1.437
C4' C3' 1.517 1.540
C4' H4' 1.116 1.090
O4' C1' 1.426 1.443
C3' O3' 1.428 1.428
C3' C2' 1.525 1.551
C3' H3' 1.115 1.090
O3' H3T 0.950 0.967
C2' O2' 1.423 1.429
C2' C1' 1.520 1.549
C2' H2' 1.115 1.090
O2' HO'2 0.950 0.967
C1' N9 1.483 1.466
C1' H1' 1.115 1.090
N9 C8 1.384 1.362
N9 C4 1.388 1.371
C8 N7 1.322 1.301
C8 H8 1.102 1.081
N7 C5 1.388 1.355
C5 C6 1.437 1.405
C5 C4 1.403 1.405
C6 N6 1.338 1.384
C6 N1 1.378 1.329
N6 H61 1.020 0.970
N6 H62 1.020 0.970
N1 C2 1.364 1.320
C2 N3 1.356 1.316
C2 H2 1.104 1.080
N3 C4 1.376 1.329

Bond Angles for A5A

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
CA N H 111.0 106.7
CA N HN2 111.6 106.7
N CA CB 111.0 109.5
N CA C 108.1 109.5
N CA HA 108.8 109.4
H N HN2 111.7 106.7
CB CA C 107.7 109.5
CB CA HA 109.1 109.4
CA CB HB1 111.1 109.5
CA CB HB2 111.7 109.4
CA CB HB3 111.7 109.4
C CA HA 112.0 109.5
CA C O 126.1 120.0
CA C N3S 111.2 120.1
HB1 CB HB2 111.6 109.5
HB1 CB HB3 111.6 109.5
HB2 CB HB3 98.7 109.5
O C N3S 117.4 119.9
C N3S S 125.5 120.1
C N3S H3S 108.3 120.0
S N3S H3S 126.3 120.0
N3S S O1S 110.4 105.8
N3S S O2S 103.9 105.7
N3S S O5' 107.0 107.4
O1S S O2S 118.1 125.4
O1S S O5' 109.7 105.7
O2S S O5' 107.1 105.8
S O5' C5' 120.0 106.9
O5' C5' C4' 112.1 109.5
O5' C5' H5'1 111.3 109.5
O5' C5' H5'2 111.3 109.4
C4' C5' H5'1 111.2 109.5
C4' C5' H5'2 111.2 109.4
C5' C4' O4' 111.1 109.8
C5' C4' C3' 116.2 109.9
C5' C4' H4' 102.1 109.9
H5'1 C5' H5'2 99.1 109.5
O4' C4' C3' 104.3 107.5
O4' C4' H4' 114.4 109.9
C4' O4' C1' 109.9 106.9
C3' C4' H4' 109.1 109.8
C4' C3' O3' 110.3 110.8
C4' C3' C2' 103.2 104.0
C4' C3' H3' 114.7 110.5
O4' C1' C2' 107.6 103.5
O4' C1' N9 108.8 110.6
O4' C1' H1' 113.5 110.7
O3' C3' C2' 114.1 110.5
O3' C3' H3' 104.0 110.4
C3' O3' H3T 110.3 106.9
C2' C3' H3' 111.0 110.4
C3' C2' O2' 114.2 110.9
C3' C2' C1' 103.0 102.1
C3' C2' H2' 111.3 111.0
O2' C2' C1' 111.1 110.9
O2' C2' H2' 103.2 110.8
C2' O2' HO'2 114.2 106.8
C1' C2' H2' 114.3 110.9
C2' C1' N9 115.7 110.7
C2' C1' H1' 106.3 110.6
N9 C1' H1' 105.1 110.5
C1' N9 C8 129.5 126.2
C1' N9 C4 124.9 126.2
C8 N9 C4 105.6 107.5
N9 C8 N7 113.9 110.0
N9 C8 H8 125.0 125.1
N9 C4 C5 105.7 106.0
N9 C4 N3 127.6 135.0
N7 C8 H8 121.1 125.0
C8 N7 C5 104.2 109.5
N7 C5 C6 133.1 134.7
N7 C5 C4 110.7 107.1
C6 C5 C4 116.2 118.2
C5 C6 N6 123.4 120.8
C5 C6 N1 118.4 118.5
C5 C4 N3 126.7 119.0
N6 C6 N1 118.2 120.8
C6 N6 H61 123.4 120.0
C6 N6 H62 107.2 120.0
C6 N1 C2 119.0 121.2
H61 N6 H62 107.3 120.0
N1 C2 N3 127.7 122.5
N1 C2 H2 116.5 118.8
N3 C2 H2 115.8 118.7
C2 N3 C4 112.0 120.7

Torsion Angles for A5A

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
H N CA HN2 125.3 246.2
CB CA N C 242.0 239.9
CB CA N HA 120.1 119.9
N CA CB HB1 180.0 300.0
N CA CB HB2 305.3 60.1
N CA CB HB3 54.7 180.0
C CA N HA 238.1 240.0
N CA C O 0.1 330.0
N CA C N3S 153.6 150.0
CA N H HN2 234.7 113.7
H N CA CB 180.0 300.0
H N CA C 298.0 60.1
H N CA HA 59.9 180.1
CA N HN2 H 124.9 246.3
HN2 N CA CB 54.7 53.7
HN2 N CA C 172.7 173.8
HN2 N CA HA 294.6 293.8
CB CA N H 180.0 300.0
CB CA N HN2 54.7 53.7
N CA CB C 118.2 120.1
N CA CB HA 240.1 240.1
C CA CB HA 121.8 120.0
CB CA C O 120.2 90.0
CB CA C N3S 273.7 270.1
HB1 CB CA HB2 234.7 240.0
HB1 CB CA HB3 125.2 120.0
HB2 CB CA HB3 250.6 240.1
C CA N H 298.0 60.1
C CA N HN2 172.7 173.8
N CA C CB 239.9 240.0
N CA C HA 119.9 120.0
CB CA C HA 240.0 240.0
C CA CB HB1 61.7 180.0
C CA CB HB2 187.1 300.0
C CA CB HB3 296.5 59.9
O C CA N3S 206.6 179.9
CA C N3S S 190.9 180.0
CA C N3S H3S 11.0 359.9
HA CA N H 59.9 180.1
HA CA N HN2 294.6 293.8
N CA HA CB 121.3 119.9
N CA HA C 240.5 240.0
CB CA HA C 119.2 120.0
HA CA CB HB1 299.9 60.0
HA CA CB HB2 65.2 180.0
HA CA CB HB3 174.7 299.9
HA CA C O 240.3 210.0
HA CA C N3S 33.7 30.0
HB1 CB CA C 61.7 180.0
HB1 CB CA HA 299.9 60.0
CA CB HB1 HB2 125.4 120.0
CA CB HB1 HB3 234.7 240.0
HB2 CB HB1 HB3 109.4 120.0
HB2 CB CA C 187.1 300.0
HB2 CB CA HA 65.2 180.0
CA CB HB2 HB1 235.0 240.0
CA CB HB2 HB3 117.6 119.9
HB1 CB HB2 HB3 242.6 239.9
HB3 CB CA C 296.5 59.9
HB3 CB CA HA 174.7 299.9
CA CB HB3 HB1 124.9 120.0
CA CB HB3 HB2 242.4 240.1
HB1 CB HB3 HB2 117.5 120.1
O C CA HA 240.3 210.0
CA C O N3S 152.0 180.1
O C N3S S 346.9 0.0
O C N3S H3S 167.0 180.0
N3S C CA HA 33.7 30.0
CA C N3S O 204.0 179.9
S N3S C H3S 179.9 180.0
C N3S S O1S 51.3 172.6
C N3S S O2S 178.8 307.4
C N3S S O5' 291.9 60.0
C N3S S H3S 180.1 180.0
O1S S N3S O2S 232.4 225.2
O1S S N3S O5' 119.4 112.6
O2S S N3S O5' 246.9 247.4
N3S S O5' C5' 308.4 90.0
C N3S H3S S 179.9 180.0
H3S N3S S O1S 231.2 352.6
H3S N3S S O2S 358.8 127.4
H3S N3S S O5' 111.8 240.0
O1S S N3S H3S 231.2 352.6
N3S S O1S O2S 119.3 123.1
N3S S O1S O5' 242.3 246.3
O2S S O1S O5' 123.0 123.1
O1S S O5' C5' 188.6 337.4
O2S S N3S H3S 358.8 127.4
N3S S O2S O1S 237.3 236.8
N3S S O2S O5' 113.0 113.7
O1S S O2S O5' 235.7 236.9
O2S S O5' C5' 59.3 202.6
O5' S N3S H3S 111.8 240.0
N3S S O5' O1S 119.8 112.6
N3S S O5' O2S 249.1 247.4
O1S S O5' O2S 129.3 134.8
S O5' C5' C4' 226.1 180.0
S O5' C5' H5'1 351.4 300.0
S O5' C5' H5'2 100.9 60.0
C4' C5' O5' H5'1 234.7 240.0
C4' C5' O5' H5'2 125.3 120.0
O5' C5' C4' O4' 304.4 61.7
O5' C5' C4' C3' 63.5 179.7
O5' C5' C4' H4' 182.1 300.7
H5'1 C5' O5' H5'2 250.5 240.0
O5' C5' C4' H5'1 125.3 120.0
O5' C5' C4' H5'2 234.7 240.0
H5'1 C5' C4' H5'2 109.4 120.0
O4' C4' C5' C3' 240.9 242.0
O4' C4' C5' H4' 122.4 121.0
C5' C4' O4' C1' 148.2 146.0
C3' C4' C5' H4' 241.4 239.0
C5' C4' C3' O3' 81.6 119.8
C5' C4' C3' C2' 203.8 238.6
C5' C4' C3' H3' 324.6 357.1
O5' C5' H5'1 C4' 234.2 239.9
O5' C5' H5'1 H5'2 117.2 120.0
C4' C5' H5'1 H5'2 242.9 240.1
H5'1 C5' C4' O4' 179.2 301.7
H5'1 C5' C4' C3' 298.2 59.7
H5'1 C5' C4' H4' 56.8 180.7
O5' C5' H5'2 C4' 125.8 120.0
O5' C5' H5'2 H5'1 242.8 240.0
C4' C5' H5'2 H5'1 117.1 120.0
H5'2 C5' C4' O4' 69.7 181.7
H5'2 C5' C4' C3' 188.8 299.7
H5'2 C5' C4' H4' 307.3 60.7
O4' C4' C5' H5'1 179.2 301.7
O4' C4' C5' H5'2 69.7 181.7
C5' C4' O4' C3' 126.0 119.6
C5' C4' O4' H4' 245.1 239.0
C3' C4' O4' H4' 119.1 119.5
O4' C4' C3' O3' 204.3 239.3
O4' C4' C3' C2' 326.5 358.1
O4' C4' C3' H3' 87.3 116.6
C4' O4' C1' C2' 358.3 320.0
C4' O4' C1' N9 232.2 201.3
C4' O4' C1' H1' 115.6 78.5
C3' C4' C5' H5'1 298.2 59.7
C3' C4' C5' H5'2 188.8 299.7
C5' C4' C3' O4' 237.3 240.5
C5' C4' C3' H4' 114.6 121.0
O4' C4' C3' H4' 237.3 240.5
C3' C4' O4' C1' 22.3 26.4
O3' C3' C4' C2' 237.8 241.2
O3' C3' C4' H3' 116.9 122.7
C4' C3' O3' H3T 180.0 176.2
C2' C3' C4' H3' 239.2 241.5
C4' C3' C2' O2' 271.4 220.8
C4' C3' C2' C1' 32.0 339.0
C4' C3' C2' H2' 155.0 97.2
H4' C4' C5' H5'1 56.8 180.7
H4' C4' C5' H5'2 307.3 60.7
C5' C4' H4' O4' 120.1 121.0
C5' C4' H4' C3' 236.5 239.0
O4' C4' H4' C3' 116.4 118.0
H4' C4' O4' C1' 263.2 267.0
H4' C4' C3' O3' 326.9 358.8
H4' C4' C3' C2' 89.2 117.6
H4' C4' C3' H3' 210.0 236.1
C1' O4' C4' C3' 22.3 26.4
C1' O4' C4' H4' 263.2 267.0
C3' C2' C1' O4' 340.7 37.1
O2' C2' C1' O4' 103.3 155.3
O4' C1' C2' H2' 219.7 278.8
C2' C1' O4' N9 126.1 118.7
C2' C1' O4' H1' 242.7 241.5
N9 C1' O4' H1' 116.6 122.8
O4' C1' N9 C8 54.2 28.5
O4' C1' N9 C4 234.9 208.3
O3' C3' C4' H4' 326.9 358.8
C4' C3' O3' C2' 115.6 114.8
C4' C3' O3' H3' 236.6 237.3
C2' C3' O3' H3' 121.0 122.5
O3' C3' C2' O2' 31.1 339.8
O3' C3' C2' C1' 151.7 98.0
O3' C3' C2' H2' 274.6 216.2
C2' C3' C4' H4' 89.2 117.6
C4' C3' C2' O3' 240.3 241.0
C4' C3' C2' H3' 123.3 118.5
O4' C1' C2' C3' 340.7 37.1
O3' C3' C2' H3' 243.0 237.5
C2' C3' O3' H3T 64.3 61.4
O2' C2' C3' C1' 239.4 241.8
O2' C2' C3' H2' 116.4 123.6
C3' C2' O2' HO'2 180.0 292.7
C1' C2' C3' H2' 237.0 241.8
C3' C2' C1' N9 102.5 155.7
C3' C2' C1' H1' 218.7 278.6
H3' C3' C4' H4' 210.0 236.1
C4' C3' H3' O3' 120.5 123.0
C4' C3' H3' C2' 243.5 245.5
O3' C3' H3' C2' 123.0 122.5
H3' C3' O3' H3T 303.4 298.9
H3' C3' C2' O2' 148.1 102.3
H3' C3' C2' C1' 268.7 220.5
H3' C3' C2' H2' 31.7 338.7
H3T O3' C3' C2' 64.3 61.4
H3T O3' C3' H3' 303.4 298.9
O4' C1' C2' O2' 103.3 155.3
O2' C2' C3' H3' 148.1 102.3
C3' C2' O2' C1' 116.0 112.7
C3' C2' O2' H2' 239.0 236.3
C1' C2' O2' H2' 123.0 123.6
O2' C2' C1' N9 225.2 273.9
O2' C2' C1' H1' 341.4 36.7
O4' C1' C2' N9 238.2 241.4
O4' C1' C2' H1' 121.9 118.6
C1' C2' C3' H3' 268.7 220.5
C3' C2' C1' O2' 237.3 241.8
C3' C2' C1' H2' 121.0 118.3
O2' C2' C1' H2' 243.6 236.4
C1' C2' O2' HO'2 64.0 180.0
N9 C1' C2' H1' 243.8 237.2
C2' C1' N9 C8 293.0 274.3
C2' C1' N9 C4 113.6 94.1
H2' C2' C3' H3' 31.7 338.7
C3' C2' H2' O2' 122.9 123.6
C3' C2' H2' C1' 243.8 247.3
O2' C2' H2' C1' 120.8 123.6
H2' C2' O2' HO'2 301.0 56.4
H2' C2' C1' N9 341.5 37.4
H2' C2' C1' H1' 97.7 160.3
HO'2 O2' C2' C1' 64.0 180.0
HO'2 O2' C2' H2' 301.0 56.4
O4' C1' N9 C2' 121.2 114.2
O4' C1' N9 H1' 238.1 237.1
N9 C1' C2' H2' 341.5 37.4
C2' C1' N9 H1' 116.9 122.9
C8 N9 C1' C4 179.4 180.2
C1' N9 C8 N7 180.6 180.0
C1' N9 C8 H8 0.7 360.0
C1' N9 C4 C5 179.3 179.8
C1' N9 C4 N3 359.6 0.6
O4' C1' H1' C2' 241.9 245.9
O4' C1' H1' N9 118.7 122.9
H1' C1' C2' H2' 97.7 160.3
C2' C1' H1' N9 236.9 237.0
H1' C1' N9 C8 176.1 151.4
H1' C1' N9 C4 356.8 331.2
C8 N9 C1' H1' 176.1 151.4
C1' N9 C8 C4 180.5 179.8
C8 N9 C4 C5 359.8 359.7
C8 N9 C4 N3 180.0 180.5
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 0.0 360.0
C4 N9 C1' H1' 356.8 331.2
C1' N9 C4 C8 179.5 180.2
C4 N9 C8 N7 0.1 0.2
C4 N9 C8 H8 180.1 180.2
N7 C5 C4 N9 0.2 0.3
C6 C5 C4 N9 180.2 180.2
C5 C4 N9 N3 179.8 179.2
C2 N3 C4 N9 179.7 179.6
N7 C8 N9 C4 0.1 0.2
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 179.8 180.0
C8 N7 C5 C4 359.9 359.8
H8 C8 N9 C4 180.1 180.2
N9 C8 H8 N7 180.0 180.1
H8 C8 N7 C5 180.0 180.0
N9 C4 C5 N7 0.2 0.3
C5 N7 C8 H8 180.0 180.0
C6 C5 N7 C4 179.9 180.2
N7 C5 C6 N6 359.9 0.1
N7 C5 C6 N1 180.0 180.0
N7 C5 C4 N3 180.0 179.7
N9 C4 C5 C6 180.2 180.2
N7 C5 C6 C4 180.1 179.8
C6 C5 C4 N3 0.0 359.5
N6 C6 C5 N1 179.9 180.1
C5 C6 N6 H61 180.0 179.9
C5 C6 N6 H62 54.8 0.0
C5 C6 N1 C2 0.1 0.2
N9 C4 C5 N3 180.2 180.6
N7 C5 C4 C6 179.9 180.1
C4 C5 C6 N6 179.8 180.3
C4 C5 C6 N1 359.9 0.2
C2 N3 C4 C5 360.0 0.5
N6 C6 C5 C4 179.8 180.3
C5 C6 N6 N1 180.1 179.9
N6 C6 N1 C2 180.2 180.0
H61 N6 C6 H62 125.2 179.9
N1 C6 C5 C4 359.9 0.2
C5 C6 N1 N6 179.9 180.1
N1 C6 N6 H61 359.9 0.1
N1 C6 N6 H62 234.7 180.1
C6 N1 C2 N3 360.0 359.8
C6 N1 C2 H2 179.9 180.0
H61 N6 C6 N1 359.9 0.1
C6 N6 H61 H62 234.8 180.1
H62 N6 C6 N1 234.7 180.1
C6 N6 H62 H61 134.4 179.9
N3 C2 N1 H2 180.0 179.9
N1 C2 N3 C4 0.0 359.9
N9 C4 N3 C2 179.7 179.6
C5 C4 N3 C2 360.0 0.5
N1 C2 N3 H2 180.0 180.1
N1 C2 H2 N3 180.0 179.9
H2 C2 N3 C4 180.0 179.7
N9 C4 N3 C5 179.7 179.1
C4 N3 C2 H2 180.0 179.7