PDB Chemical Component P5A

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 P5A

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
CB CG 1.520 1.542
CB CA 1.529 1.545
CB HB1 1.115 1.089
CB HB2 1.116 1.090
CG CD 1.554 1.544
CG HG1 1.115 1.089
CG HG2 1.115 1.090
C O 1.237 1.214
C CA 1.538 1.506
C N3S 1.338 1.346
N CD 1.479 1.487
N CA 1.471 1.485
N HT1 1.019 1.008
CD HD1 1.115 1.089
CD HD2 1.114 1.090
CA HA 1.115 1.090
N3S S 1.588 1.656
N3S H3S 1.020 0.970
S O1S 1.478 1.421
S O2S 1.502 1.420
S O5' 1.596 1.522
O5' C5' 1.443 1.428
C5' C4' 1.518 1.529
C5' H1'1 1.115 1.090
C5' H1'2 1.115 1.090
C4' O4' 1.447 1.444
C4' C3' 1.520 1.544
C4' H4' 1.116 1.090
O4' C1' 1.413 1.445
C1' N9 1.475 1.464
C1' C2' 1.532 1.544
C1' H1' 1.116 1.089
N9 C4 1.389 1.372
N9 C8 1.378 1.363
C4 N3 1.374 1.329
C4 C5 1.399 1.405
N3 C2 1.342 1.315
C2 N1 1.357 1.321
C2 H2 1.104 1.079
N1 C6 1.368 1.329
C6 N6 1.330 1.384
C6 C5 1.434 1.405
N6 H61 1.019 0.969
N6 H62 1.020 0.970
C5 N7 1.386 1.355
N7 C8 1.318 1.301
C8 H8 1.102 1.080
C2' O2' 1.417 1.428
C2' C3' 1.524 1.547
C2' H2' 1.115 1.089
O2' HO'2 0.950 0.967
C3' O3' 1.425 1.428
C3' H3' 1.115 1.090
O3' H3T 0.950 0.967

Bond Angles for P5A

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
CG CB CA 101.9 105.1
CG CB HB1 115.1 110.4
CG CB HB2 115.1 110.4
CB CG CD 105.7 105.1
CB CG HG1 113.6 110.4
CB CG HG2 113.6 110.3
CA CB HB1 115.1 110.3
CA CB HB2 115.1 110.3
CB CA C 111.4 110.4
CB CA N 106.7 104.7
CB CA HA 110.5 110.4
HB1 CB HB2 95.3 110.4
CD CG HG1 113.6 110.3
CD CG HG2 113.7 110.3
CG CD N 104.0 104.7
CG CD HD1 114.3 110.4
CG CD HD2 114.2 110.4
HG1 CG HG2 96.8 110.3
O C CA 120.3 120.0
O C N3S 123.0 120.0
CA C N3S 116.7 120.1
C CA N 110.9 110.5
C CA HA 106.3 110.3
C N3S S 125.0 120.1
C N3S H3S 108.2 120.0
CD N CA 110.1 104.2
CD N HT1 112.0 106.7
N CD HD1 114.3 110.5
N CD HD2 114.3 110.3
CA N HT1 111.9 106.9
N CA HA 111.1 110.4
HD1 CD HD2 96.2 110.5
S N3S H3S 126.8 119.9
N3S S O1S 109.3 105.7
N3S S O2S 103.6 105.8
N3S S O5' 107.1 107.4
O1S S O2S 118.9 125.4
O1S S O5' 109.6 105.7
O2S S O5' 107.7 105.8
S O5' C5' 120.9 106.8
O5' C5' C4' 112.3 109.6
O5' C5' H1'1 111.2 109.5
O5' C5' H1'2 111.2 109.4
C4' C5' H1'1 111.1 109.5
C4' C5' H1'2 111.2 109.4
C5' C4' O4' 109.9 110.3
C5' C4' C3' 115.8 110.5
C5' C4' H4' 103.1 110.3
H1'1 C5' H1'2 99.2 109.4
O4' C4' C3' 103.9 104.9
O4' C4' H4' 115.3 110.4
C4' O4' C1' 110.7 105.2
C3' C4' H4' 109.3 110.4
C4' C3' C2' 102.4 104.1
C4' C3' O3' 109.2 110.5
C4' C3' H3' 115.1 110.5
O4' C1' N9 110.0 110.4
O4' C1' C2' 106.9 104.9
O4' C1' H1' 114.2 110.4
N9 C1' C2' 117.6 110.4
N9 C1' H1' 102.5 110.3
C1' N9 C4 124.4 126.3
C1' N9 C8 130.2 126.3
C2' C1' H1' 105.9 110.4
C1' C2' O2' 106.7 110.8
C1' C2' C3' 102.5 104.0
C1' C2' H2' 117.8 110.4
C4 N9 C8 105.4 107.4
N9 C4 N3 127.8 134.9
N9 C4 C5 105.6 106.1
N9 C8 N7 114.2 110.0
N9 C8 H8 124.9 125.0
N3 C4 C5 126.6 119.0
C4 N3 C2 111.9 120.7
C4 C5 C6 116.1 118.2
C4 C5 N7 110.7 107.1
N3 C2 N1 128.0 122.4
N3 C2 H2 115.3 118.8
N1 C2 H2 116.7 118.8
C2 N1 C6 119.1 121.2
N1 C6 N6 117.8 120.8
N1 C6 C5 118.3 118.4
N6 C6 C5 123.9 120.8
C6 N6 H61 117.8 120.0
C6 N6 H62 109.1 119.9
C6 C5 N7 133.2 134.7
H61 N6 H62 109.3 120.1
C5 N7 C8 104.0 109.4
N7 C8 H8 120.9 125.0
O2' C2' C3' 115.5 110.5
O2' C2' H2' 105.3 110.5
C2' O2' HO'2 106.7 106.8
C3' C2' H2' 109.5 110.5
C2' C3' O3' 112.0 110.5
C2' C3' H3' 112.4 110.6
O3' C3' H3' 106.0 110.5
C3' O3' H3T 109.2 106.8

Torsion Angles for P5A

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
CA CB CG HB1 234.7 118.9
CA CB CG HB2 125.3 241.2
CG CB CA C 269.0 217.3
CG CB CA N 30.1 336.3
CG CB CA HA 151.0 95.1
HB1 CB CG HB2 250.6 122.2
CD CG CB HG1 234.7 241.0
CD CG CB HG2 125.3 118.9
CB CG CD N 25.2 23.8
CB CG CD HD1 150.6 142.6
CB CG CD HD2 260.0 265.1
HG1 CG CB HG2 250.6 237.8
CG CB CA HB1 125.3 241.1
CG CB CA HB2 234.8 118.9
CA CB CG CD 326.3 360.0
CA CB CG HG1 91.6 118.9
CA CB CG HG2 201.0 241.1
HB1 CB CA HB2 109.5 237.8
O C CA CB 113.7 88.4
CB CA C N3S 294.1 268.4
C CA CB N 238.8 241.1
C CA CB HA 118.0 122.2
CD N CA CB 344.8 39.3
CB CA N HT1 110.1 152.1
N CA CB HA 239.1 241.2
CG CB HB1 CA 241.8 115.7
CG CB HB1 HB2 120.9 237.8
HB1 CB CG CD 91.6 241.1
HB1 CB CG HG1 216.9 0.0
HB1 CB CG HG2 326.3 122.2
CA CB HB1 HB2 239.0 122.1
HB1 CB CA C 143.7 336.3
HB1 CB CA N 264.8 95.2
HB1 CB CA HA 25.7 214.0
CG CB HB2 CA 118.1 244.4
CG CB HB2 HB1 239.1 122.2
HB2 CB CG CD 201.0 118.8
HB2 CB CG HG1 326.3 237.8
HB2 CB CG HG2 75.7 360.0
CA CB HB2 HB1 121.0 237.9
HB2 CB CA C 34.2 98.4
HB2 CB CA N 155.4 217.4
HB2 CB CA HA 276.2 336.2
CD CG CB CA 326.3 360.0
CD CG CB HB1 91.6 241.1
CD CG CB HB2 201.0 118.8
CB CG CD HG1 125.3 119.0
CB CG CD HG2 234.7 241.1
HG1 CG CD HG2 109.4 122.1
CG CD N CA 353.9 320.7
CG CD N HT1 228.7 207.8
N CD CG HD1 234.7 241.1
N CD CG HD2 125.3 118.7
HD1 CD CG HD2 250.6 237.5
HG1 CG CB CA 91.6 118.9
HG1 CG CB HB1 216.9 0.0
HG1 CG CB HB2 326.3 237.8
CB CG HG1 CD 239.0 244.3
CB CG HG1 HG2 119.5 122.2
CD CG HG1 HG2 240.5 237.9
HG1 CG CD N 259.9 264.8
HG1 CG CD HD1 25.2 23.6
HG1 CG CD HD2 134.7 146.1
HG2 CG CB CA 201.0 241.1
HG2 CG CB HB1 326.3 122.2
HG2 CG CB HB2 75.7 360.0
CB CG HG2 CD 121.0 115.6
CB CG HG2 HG1 240.5 237.8
CD CG HG2 HG1 119.5 122.1
HG2 CG CD N 150.6 142.7
HG2 CG CD HD1 275.9 261.5
HG2 CG CD HD2 25.3 24.0
CB CA C O 113.7 88.4
CA C O N3S 180.4 180.0
O C CA N 355.0 333.0
O C CA HA 234.2 210.7
O C N3S S 359.5 0.1
O C N3S H3S 179.6 180.0
C CA CB HB1 143.7 336.3
C CA CB HB2 34.2 98.4
CB CA C N 118.7 115.3
CB CA C HA 239.6 237.7
O C CA N3S 179.7 180.0
CA C N3S S 179.2 180.0
CA C N3S H3S 359.2 360.0
CD N CA C 106.3 158.2
C CA N HT1 231.5 270.9
N CA C HA 120.9 122.4
O C N3S CA 180.3 180.0
N3S C CA N 175.4 153.1
N3S C CA HA 54.5 30.7
S N3S C H3S 179.9 180.1
C N3S S O1S 51.4 307.4
C N3S S O2S 179.0 172.6
C N3S S O5' 292.7 59.9
CB CA N CD 344.8 39.3
N CD CG HG1 259.9 264.8
N CD CG HG2 150.6 142.7
CG CD N HD1 125.3 118.9
CG CD N HD2 234.8 241.2
C CA N CD 106.3 158.2
CA N CD HT1 125.3 112.9
CD N CA HA 224.3 280.5
HD1 CD N HD2 109.5 122.4
N CA CB HB1 264.8 95.2
N CA CB HB2 155.4 217.4
CB CA N C 238.5 241.1
CB CA N HA 120.5 118.8
N CA C N3S 175.4 153.1
C CA N HA 242.0 237.7
CD N CA HT1 234.7 247.2
CA N CD HD1 228.6 201.9
CA N CD HD2 119.1 79.5
CD N HT1 CA 124.3 111.0
HT1 N CD HD1 103.4 88.9
HT1 N CD HD2 353.9 326.6
HT1 N CA HA 349.6 33.3
HD1 CD CG HG1 25.2 23.6
HD1 CD CG HG2 275.9 261.5
CG CD HD1 N 240.4 244.7
CG CD HD1 HD2 120.1 122.5
HD1 CD N CA 228.6 201.9
HD1 CD N HT1 103.4 88.9
N CD HD1 HD2 239.8 237.7
HD2 CD CG HG1 134.7 146.1
HD2 CD CG HG2 25.3 24.0
CG CD HD2 N 119.6 115.2
CG CD HD2 HD1 239.9 237.5
HD2 CD N CA 119.1 79.5
HD2 CD N HT1 353.9 326.6
N CD HD2 HD1 120.2 122.4
HA CA CB HB1 25.7 214.0
HA CA CB HB2 276.2 336.2
CB CA HA C 121.0 122.3
CB CA HA N 241.8 244.7
HA CA C N3S 54.5 30.7
C CA HA N 120.7 122.4
HA CA N HT1 349.6 33.3
C N3S S H3S 180.1 179.9
O1S S N3S O2S 232.3 134.8
O1S S N3S O5' 118.6 247.5
O2S S N3S O5' 246.3 112.6
N3S S O5' C5' 304.3 90.1
C N3S H3S S 179.9 180.1
H3S N3S S O1S 231.3 127.5
H3S N3S S O2S 359.0 352.6
H3S N3S S O5' 112.7 240.0
O1S S N3S H3S 231.3 127.5
N3S S O1S O2S 118.5 236.8
N3S S O1S O5' 242.9 113.7
O2S S O1S O5' 124.4 236.9
O1S S O5' C5' 185.8 202.6
O2S S N3S H3S 359.0 352.6
N3S S O2S O1S 238.5 123.1
N3S S O2S O5' 113.2 246.2
O1S S O2S O5' 234.7 123.1
O2S S O5' C5' 55.1 337.4
O5' S N3S H3S 112.7 240.0
N3S S O5' O1S 118.5 247.5
N3S S O5' O2S 249.2 112.7
O1S S O5' O2S 130.7 225.2
S O5' C5' C4' 237.7 180.0
S O5' C5' H1'1 2.9 59.9
S O5' C5' H1'2 112.5 300.0
C4' C5' O5' H1'1 234.8 120.1
C4' C5' O5' H1'2 125.3 240.0
O5' C5' C4' O4' 300.0 61.4
O5' C5' C4' C3' 57.3 176.9
O5' C5' C4' H4' 176.6 299.2
H1'1 C5' O5' H1'2 250.5 119.9
O5' C5' C4' H1'1 125.3 239.9
O5' C5' C4' H1'2 234.7 120.0
H1'1 C5' C4' H1'2 109.5 240.0
O4' C4' C5' C3' 242.7 244.5
O4' C4' C5' H4' 123.4 122.2
C5' C4' O4' C1' 147.5 159.5
C3' C4' C5' H4' 240.7 237.7
C5' C4' C3' C2' 203.9 217.0
C5' C4' C3' O3' 85.0 98.3
C5' C4' C3' H3' 326.0 335.7
O5' C5' H1'1 C4' 234.1 120.1
O5' C5' H1'1 H1'2 117.1 240.1
C4' C5' H1'1 H1'2 243.0 120.0
H1'1 C5' C4' O4' 174.7 181.5
H1'1 C5' C4' C3' 292.0 297.0
H1'1 C5' C4' H4' 51.3 59.3
O5' C5' H1'2 C4' 125.9 239.9
O5' C5' H1'2 H1'1 242.9 120.0
C4' C5' H1'2 H1'1 117.0 240.0
H1'2 C5' C4' O4' 65.3 301.4
H1'2 C5' C4' C3' 182.6 56.9
H1'2 C5' C4' H4' 301.9 179.2
O4' C4' C5' H1'1 174.7 181.5
O4' C4' C5' H1'2 65.3 301.4
C5' C4' O4' C3' 124.5 119.0
C5' C4' O4' H4' 244.0 237.9
C3' C4' O4' H4' 119.5 118.9
O4' C4' C3' C2' 324.5 335.9
O4' C4' C3' O3' 205.6 217.2
O4' C4' C3' H3' 86.7 94.6
C4' O4' C1' N9 230.6 200.6
C4' O4' C1' C2' 359.3 319.6
C4' O4' C1' H1' 116.0 78.5
C3' C4' C5' H1'1 292.0 297.0
C3' C4' C5' H1'2 182.6 56.9
C5' C4' C3' O4' 239.4 241.1
C5' C4' C3' H4' 115.9 122.2
O4' C4' C3' H4' 236.5 241.1
C3' C4' O4' C1' 23.0 40.5
C1' C2' C3' C4' 34.5 0.1
O2' C2' C3' C4' 279.0 241.2
C4' C3' C2' H2' 160.4 118.6
C2' C3' C4' O3' 118.9 118.7
C2' C3' C4' H3' 237.8 241.3
O3' C3' C4' H3' 119.0 122.6
C4' C3' O3' H3T 179.9 180.0
H4' C4' C5' H1'1 51.3 59.3
H4' C4' C5' H1'2 301.9 179.2
C5' C4' H4' O4' 119.8 122.2
C5' C4' H4' C3' 236.2 237.6
O4' C4' H4' C3' 116.5 115.4
H4' C4' O4' C1' 263.5 281.6
H4' C4' C3' C2' 88.0 94.8
H4' C4' C3' O3' 329.1 336.1
H4' C4' C3' H3' 210.1 213.5
C1' O4' C4' C3' 23.0 40.5
C1' O4' C4' H4' 263.5 281.6
N9 C1' O4' C2' 231.3 241.1
N9 C1' O4' H1' 114.6 122.2
O4' C1' N9 C4 239.7 207.0
O4' C1' N9 C8 59.1 27.1
C2' C1' O4' H1' 243.3 241.1
O4' C1' C2' O2' 100.1 142.6
O4' C1' C2' C3' 338.3 23.9
O4' C1' C2' H2' 218.1 265.3
O4' C1' N9 C2' 122.6 115.5
O4' C1' N9 H1' 238.2 237.7
C2' C1' N9 H1' 115.6 122.2
N9 C1' C2' O2' 224.2 261.5
N9 C1' C2' C3' 102.4 142.8
N9 C1' C2' H2' 342.3 24.2
C4 N9 C1' C8 180.6 179.9
C1' N9 C4 N3 359.7 0.1
C1' N9 C4 C5 179.2 180.2
C1' N9 C8 N7 180.6 180.0
C1' N9 C8 H8 0.6 360.0
C4' C3' C2' C1' 34.5 0.1
O4' C1' C2' N9 235.9 241.1
O4' C1' C2' H1' 122.1 118.9
N9 C1' C2' H1' 246.2 237.8
C2' C1' N9 C4 117.2 91.5
C2' C1' N9 C8 296.5 271.5
O2' C2' C1' C3' 121.8 118.7
O2' C2' C1' H2' 241.9 237.2
C1' C2' O2' HO'2 180.0 183.9
C3' C2' C1' H2' 120.2 118.5
C1' C2' C3' O3' 151.4 118.8
C1' C2' C3' H3' 270.5 241.4
O4' C1' H1' N9 118.9 122.2
O4' C1' H1' C2' 242.7 244.5
N9 C1' H1' C2' 123.8 122.2
H1' C1' N9 C4 1.5 329.3
H1' C1' N9 C8 180.9 149.3
H1' C1' C2' O2' 338.0 23.7
H1' C1' C2' C3' 216.2 264.9
H1' C1' C2' H2' 96.1 146.4
C4 N9 C1' C2' 117.2 91.5
C4 N9 C1' H1' 1.5 329.3
C1' N9 C4 C8 179.5 180.1
C4 N9 C8 N7 0.0 0.0
C4 N9 C8 H8 180.0 180.0
N3 C4 N9 C5 180.5 179.8
N9 C4 N3 C2 179.9 179.9
N9 C4 C5 C6 179.9 180.3
N9 C4 C5 N7 0.5 359.7
C8 N9 C1' C2' 296.5 271.5
C8 N9 C1' H1' 180.9 149.3
C1' N9 C8 C4 180.5 179.9
C8 N9 C4 N3 180.2 180.0
C8 N9 C4 C5 359.7 0.2
C5 N7 C8 N9 0.3 359.8
N7 C8 N9 H8 180.0 180.0
N3 C4 N9 C8 180.2 180.0
N9 C4 N3 C5 179.4 180.2
N3 C4 C5 C6 359.5 0.5
N3 C4 C5 N7 180.0 179.8
C4 N3 C2 N1 359.7 0.0
C4 N3 C2 H2 179.6 180.0
C5 C4 N9 C8 359.7 0.2
N9 C4 C5 N3 180.5 179.9
C5 C4 N3 C2 0.5 359.7
N1 C6 C5 C4 0.5 359.5
N6 C6 C5 C4 179.9 179.7
C6 C5 C4 N7 179.4 180.6
C4 C5 N7 C8 359.5 0.3
C2 N3 C4 C5 0.5 359.7
N1 C2 N3 H2 180.0 180.0
N3 C2 N1 C6 0.3 360.0
N3 C2 N1 H2 180.0 180.0
C2 N1 C6 N6 180.2 180.1
C2 N1 C6 C5 359.6 0.3
N3 C2 H2 N1 180.0 180.0
H2 C2 N1 C6 180.4 180.0
C4 C5 C6 N1 0.5 359.5
C6 N1 C2 H2 180.4 180.0
N6 C6 N1 C5 180.6 179.8
N1 C6 N6 H61 180.0 360.0
N1 C6 N6 H62 54.7 179.7
N1 C6 C5 N7 179.7 180.4
C4 C5 C6 N6 179.9 179.7
N1 C6 N6 C5 179.4 180.2
N6 C6 C5 N7 359.2 0.6
H61 N6 C6 H62 125.3 180.2
C4 C5 C6 N7 180.7 179.1
N1 C6 C5 N6 180.6 179.8
C5 C6 N6 H61 0.6 179.8
C5 C6 N6 H62 235.3 359.5
C6 C5 N7 C8 180.2 179.5
H61 N6 C6 C5 0.6 179.8
C6 N6 H61 H62 234.7 179.8
H62 N6 C6 C5 235.3 359.5
C6 N6 H62 H61 130.1 180.2
N9 C8 N7 C5 0.3 359.8
C4 C5 N7 C6 179.3 180.8
C5 N7 C8 H8 180.3 179.7
N9 C8 N7 H8 180.0 180.0
N9 C8 H8 N7 180.0 180.0
C4' C3' C2' O2' 279.0 241.2
O2' C2' C1' H1' 338.0 23.7
C1' C2' O2' C3' 246.9 245.3
C1' C2' O2' H2' 126.0 122.7
C3' C2' O2' H2' 239.1 237.4
O2' C2' C3' O3' 35.8 359.9
O2' C2' C3' H3' 155.0 122.5
C2' C3' C4' H4' 88.0 94.8
C4' C3' C2' O3' 243.2 241.3
C4' C3' C2' H3' 124.0 118.7
C3' C2' C1' H1' 216.2 264.9
C1' C2' C3' O2' 115.6 118.9
C1' C2' C3' H2' 234.2 241.5
O2' C2' C3' H2' 118.6 122.6
C3' C2' O2' HO'2 293.1 298.5
O3' C3' C2' H3' 240.8 237.4
C2' C3' O3' H3T 67.3 65.3
H2' C2' C1' H1' 96.1 146.4
C1' C2' H2' O2' 241.2 237.1
C1' C2' H2' C3' 116.4 114.5
O2' C2' H2' C3' 235.3 237.4
H2' C2' O2' HO'2 54.0 61.1
H2' C2' C3' O3' 277.2 237.3
H2' C2' C3' H3' 36.3 359.9
HO'2 O2' C2' C3' 293.1 298.5
HO'2 O2' C2' H2' 54.0 61.1
O3' C3' C4' H4' 329.1 336.1
C4' C3' O3' C2' 112.7 114.7
C4' C3' O3' H3' 235.5 237.4
O3' C3' C2' H2' 277.2 237.3
C2' C3' O3' H3' 122.9 122.7
H3' C3' C4' H4' 210.1 213.5
C4' C3' H3' C2' 243.4 245.3
C4' C3' H3' O3' 120.7 122.6
H3' C3' C2' H2' 36.3 359.9
C2' C3' H3' O3' 237.4 237.3
H3' C3' O3' H3T 304.4 302.6
H3T O3' C3' H3' 304.4 302.6