PDB Chemical Component RPL

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 RPL

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O1P P 1.450 1.480
O2P P 1.493 1.610
O2P HO2P 0.950 0.967
O3P P 1.446 1.609
O3P HO3P 0.950 0.967
P O5' 1.619 1.610
O5' C5' 1.412 1.427
C5' C4' 1.528 1.531
C5' H5'1 1.115 1.089
C5' H5'2 1.116 1.090
C4' O4' 1.422 1.438
C4' C3' 1.513 1.549
C4' H4 1.114 1.090
O4' C1' 1.475 1.424
C3' O3' 1.432 1.430
C3' C2' 1.550 1.555
C3' H3 1.115 1.089
O3' HO3' 0.950 0.967
C2' O2' 1.423 1.429
C2' C1' 1.557 1.537
C2' H2 1.115 1.090
O2' HO2' 0.950 0.967
C1' N1 1.360 1.466
C1' C4 1.437 1.508
N1 C2 1.378 1.347
N1 HN1 1.021 0.970
C2 O2 1.183 1.217
C2 N3 1.388 1.338
N3 C4 1.379 1.350
N3 C5A 1.475 1.465
C4 O4 1.229 1.212
C5A C6A 1.537 1.529
C5A H51 1.114 1.090
C5A H52 1.114 1.090
C6A C7A 1.550 1.530
C6A H61 1.115 1.089
C6A H62 1.115 1.089
C7A C8A 1.561 1.529
C7A H71 1.115 1.090
C7A H72 1.114 1.091
C8A C9A 1.530 1.507
C8A NAA 1.517 1.468
C8A H81 1.115 1.089
C9A OJA 1.348 1.342
C9A OKA 1.347 1.208
OJA H91 0.950 0.967
NAA OAA 1.461 1.462
NAA CBA 1.465 1.469
OAA H10 0.950 0.967
CBA OBA 1.426 1.429
CBA H111 1.115 1.089
CBA H112 1.115 1.091
OBA H11 0.950 0.967

Bond Angles for RPL

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P 108.5 109.5
O1P P O3P 109.7 109.5
O1P P O5' 108.6 109.4
P O2P HO2P 108.5 106.9
O2P P O3P 110.0 109.4
O2P P O5' 108.1 109.5
P O3P HO3P 109.7 106.8
O3P P O5' 111.9 109.5
P O5' C5' 123.9 106.8
O5' C5' C4' 111.4 109.5
O5' C5' H5'1 111.5 109.5
O5' C5' H5'2 111.4 109.5
C4' C5' H5'1 111.5 109.5
C4' C5' H5'2 111.5 109.4
C5' C4' O4' 110.6 110.3
C5' C4' C3' 113.8 110.4
C5' C4' H4 104.2 110.2
H5'1 C5' H5'2 98.9 109.4
O4' C4' C3' 104.4 105.2
O4' C4' H4 113.7 110.3
C4' O4' C1' 113.3 109.6
C3' C4' H4 110.5 110.3
C4' C3' O3' 110.5 111.1
C4' C3' C2' 100.3 101.0
C4' C3' H3 114.7 111.2
O4' C1' C2' 101.3 108.4
O4' C1' N1 109.7 111.5
O4' C1' C4 117.4 111.3
O3' C3' C2' 109.8 111.1
O3' C3' H3 106.1 111.0
C3' O3' HO3' 110.5 106.8
C2' C3' H3 115.4 111.1
C3' C2' O2' 108.3 110.9
C3' C2' C1' 104.8 102.0
C3' C2' H2 113.5 110.9
O2' C2' C1' 110.3 111.0
O2' C2' H2 108.3 110.8
C2' O2' HO2' 108.3 106.8
C1' C2' H2 111.6 110.9
C2' C1' N1 107.4 110.6
C2' C1' C4 116.3 110.8
N1 C1' C4 104.3 104.3
C1' N1 C2 110.7 106.3
C1' N1 HN1 111.8 126.9
C1' C4 N3 110.3 105.4
C1' C4 O4 129.5 127.3
C2 N1 HN1 111.8 126.8
N1 C2 O2 124.0 123.8
N1 C2 N3 108.9 112.4
O2 C2 N3 127.1 123.8
C2 N3 C4 105.8 111.6
C2 N3 C5A 128.2 124.2
C4 N3 C5A 126.1 124.2
N3 C4 O4 120.3 127.3
N3 C5A C6A 110.0 109.5
N3 C5A H51 112.0 109.5
N3 C5A H52 112.0 109.4
C6A C5A H51 112.0 109.5
C6A C5A H52 112.0 109.5
C5A C6A C7A 111.7 109.5
C5A C6A H61 111.4 109.5
C5A C6A H62 111.4 109.5
H51 C5A H52 98.4 109.4
C7A C6A H61 111.4 109.4
C7A C6A H62 111.4 109.4
C6A C7A C8A 109.9 109.5
C6A C7A H71 112.1 109.5
C6A C7A H72 112.1 109.4
H61 C6A H62 98.9 109.5
C8A C7A H71 112.0 109.5
C8A C7A H72 112.1 109.5
C7A C8A C9A 111.1 109.5
C7A C8A NAA 112.4 109.4
C7A C8A H81 105.4 109.5
H71 C7A H72 98.3 109.4
C9A C8A NAA 106.6 109.4
C9A C8A H81 111.3 109.5
C8A C9A OJA 119.0 120.0
C8A C9A OKA 121.2 120.0
NAA C8A H81 110.1 109.6
C8A NAA OAA 110.1 106.8
C8A NAA CBA 111.1 106.7
OJA C9A OKA 119.8 119.9
C9A OJA H91 119.0 120.1
OAA NAA CBA 109.5 106.7
NAA OAA H10 110.0 106.8
NAA CBA OBA 111.7 109.5
NAA CBA H111 111.4 109.5
NAA CBA H112 111.4 109.4
OBA CBA H111 111.4 109.5
OBA CBA H112 111.4 109.5
CBA OBA H11 111.7 106.8
H111 CBA H112 98.9 109.5

Torsion Angles for RPL

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P HO2P 179.9 300.0
O2P P O1P O3P 239.9 120.0
O2P P O1P O5' 117.3 240.0
O1P P O3P HO3P 180.0 180.1
O3P P O1P O5' 237.4 120.0
O1P P O5' C5' 47.9 60.0
O1P P O2P O3P 119.9 240.0
O1P P O2P O5' 242.4 120.0
O2P P O3P HO3P 299.2 60.1
O3P P O2P O5' 122.5 240.0
O2P P O5' C5' 290.4 180.0
HO2P O2P P O3P 60.0 60.0
HO2P O2P P O5' 297.5 180.1
O1P P O3P O2P 240.8 120.0
O1P P O3P O5' 120.6 240.0
O3P P O2P HO2P 60.0 60.0
O2P P O3P O5' 239.8 120.0
O3P P O5' C5' 169.1 300.0
HO3P O3P P O5' 59.4 300.0
O1P P O5' O2P 117.5 240.0
O1P P O5' O3P 238.8 120.0
O5' P O2P HO2P 297.5 180.1
O2P P O5' O3P 121.3 240.0
O5' P O3P HO3P 59.4 300.0
P O5' C5' C4' 139.2 180.0
P O5' C5' H5'1 264.5 59.9
P O5' C5' H5'2 13.9 299.9
C4' C5' O5' H5'1 234.7 120.1
C4' C5' O5' H5'2 125.3 240.1
O5' C5' C4' O4' 289.1 61.4
O5' C5' C4' C3' 46.1 177.2
O5' C5' C4' H4 166.6 299.3
H5'1 C5' O5' H5'2 250.6 120.0
O5' C5' C4' H5'1 125.3 239.9
O5' C5' C4' H5'2 234.8 120.0
H5'1 C5' C4' H5'2 109.5 240.1
O4' C4' C5' C3' 242.9 244.2
O4' C4' C5' H4 122.5 122.1
C5' C4' O4' C1' 97.4 143.4
C3' C4' C5' H4 239.6 237.9
C5' C4' C3' O3' 161.4 87.0
C5' C4' C3' C2' 277.2 204.9
C5' C4' C3' H3 41.5 322.9
O5' C5' H5'1 C4' 234.8 120.1
O5' C5' H5'1 H5'2 117.3 240.0
C4' C5' H5'1 H5'2 242.5 119.9
H5'1 C5' C4' O4' 163.8 181.5
H5'1 C5' C4' C3' 280.9 297.3
H5'1 C5' C4' H4 41.3 59.4
O5' C5' H5'2 C4' 125.2 240.0
O5' C5' H5'2 H5'1 242.7 120.1
C4' C5' H5'2 H5'1 117.5 240.0
H5'2 C5' C4' O4' 54.3 301.5
H5'2 C5' C4' C3' 171.4 57.3
H5'2 C5' C4' H4 291.8 179.4
O4' C4' C5' H5'1 163.8 181.5
O4' C4' C5' H5'2 54.3 301.5
C5' C4' O4' C3' 122.7 119.0
C5' C4' O4' H4 243.2 238.0
C3' C4' O4' H4 120.5 119.0
O4' C4' C3' O3' 282.0 206.0
O4' C4' C3' C2' 37.8 323.9
O4' C4' C3' H3 162.1 81.9
C4' O4' C1' C2' 1.0 358.1
C4' O4' C1' N1 247.7 236.1
C4' O4' C1' C4 128.9 120.1
C3' C4' C5' H5'1 280.9 297.3
C3' C4' C5' H5'2 171.4 57.3
C5' C4' C3' O4' 239.3 241.0
C5' C4' C3' H4 116.8 122.1
O4' C4' C3' H4 237.4 241.0
C3' C4' O4' C1' 334.6 24.4
O3' C3' C4' C2' 244.2 242.1
O3' C3' C4' H3 119.9 124.1
C4' C3' O3' HO3' 180.0 298.5
C2' C3' C4' H3 235.7 242.0
C4' C3' C2' O2' 204.7 275.4
C4' C3' C2' C1' 322.4 33.6
C4' C3' C2' H2 84.4 151.8
H4 C4' C5' H5'1 41.3 59.4
H4 C4' C5' H5'2 291.8 179.4
C5' C4' H4 O4' 120.5 122.1
C5' C4' H4 C3' 237.4 237.8
O4' C4' H4 C3' 116.9 115.8
H4 C4' O4' C1' 214.1 265.4
H4 C4' C3' O3' 44.6 324.9
H4 C4' C3' C2' 160.4 82.9
H4 C4' C3' H3 284.7 200.8
C1' O4' C4' C3' 334.6 24.4
C1' O4' C4' H4 214.1 265.4
C3' C2' C1' O4' 23.2 339.1
O2' C2' C1' O4' 139.5 97.3
O4' C1' C2' H2 260.0 220.9
C2' C1' O4' N1 113.3 122.0
C2' C1' O4' C4 232.1 238.0
N1 C1' O4' C4 118.9 116.0
O4' C1' N1 C2 233.5 239.6
O4' C1' N1 HN1 108.2 59.6
O4' C1' C4 N3 121.3 120.6
O4' C1' C4 O4 301.6 300.4
O3' C3' C4' H4 44.6 324.9
C4' C3' O3' C2' 109.8 111.6
C4' C3' O3' H3 235.1 235.8
C2' C3' O3' H3 125.3 124.2
O3' C3' C2' O2' 321.1 33.3
O3' C3' C2' C1' 78.8 151.5
O3' C3' C2' H2 200.8 269.7
C2' C3' C4' H4 160.4 82.9
C4' C3' C2' O3' 243.6 242.1
C4' C3' C2' H3 123.8 118.0
O4' C1' C2' C3' 23.2 339.1
O3' C3' C2' H3 240.2 235.9
C2' C3' O3' HO3' 70.2 186.9
O2' C2' C3' C1' 242.3 241.8
O2' C2' C3' H2 120.3 123.6
C3' C2' O2' HO2' 180.0 298.5
C1' C2' C3' H2 238.0 241.8
C3' C2' C1' N1 138.3 101.6
C3' C2' C1' C4 254.6 216.7
H3 C3' C4' H4 284.7 200.8
C4' C3' H3 O3' 122.3 124.2
C4' C3' H3 C2' 244.1 248.3
O3' C3' H3 C2' 121.8 124.2
H3 C3' O3' HO3' 304.9 62.7
H3 C3' C2' O2' 80.9 157.4
H3 C3' C2' C1' 198.6 275.6
H3 C3' C2' H2 320.6 33.8
HO3' O3' C3' C2' 70.2 186.9
HO3' O3' C3' H3 304.9 62.7
O4' C1' C2' O2' 139.5 97.3
O2' C2' C3' H3 80.9 157.4
C3' C2' O2' C1' 114.1 112.6
C3' C2' O2' H2 236.5 236.3
C1' C2' O2' H2 122.4 123.7
O2' C2' C1' N1 254.6 219.8
O2' C2' C1' C4 11.0 334.9
O4' C1' C2' N1 244.9 237.5
O4' C1' C2' C4 128.6 122.4
C1' C2' C3' H3 198.6 275.6
C3' C2' C1' O2' 243.7 241.8
C3' C2' C1' H2 123.2 118.2
O2' C2' C1' H2 239.6 236.4
C1' C2' O2' HO2' 65.9 185.9
N1 C1' C2' C4 243.6 244.9
C2' C1' N1 C2 124.2 119.0
C2' C1' N1 HN1 358.9 298.9
C2' C1' C4 N3 241.6 241.2
C2' C1' C4 O4 61.9 61.0
H2 C2' C3' H3 320.6 33.8
C3' C2' H2 O2' 120.3 123.7
C3' C2' H2 C1' 241.9 247.4
O2' C2' H2 C1' 121.6 123.7
H2 C2' O2' HO2' 303.5 62.2
H2 C2' C1' N1 15.0 343.4
H2 C2' C1' C4 131.4 98.5
HO2' O2' C2' C1' 65.9 185.9
HO2' O2' C2' H2 303.5 62.2
O4' C1' N1 C2' 109.3 120.7
O4' C1' N1 C4 233.3 239.8
N1 C1' C2' H2 15.0 343.4
C2' C1' N1 C4 124.0 119.1
N1 C1' C4 N3 359.6 0.3
N1 C1' C4 O4 179.9 180.1
C2 N1 C1' HN1 125.3 180.0
C1' N1 C2 O2 179.7 180.0
C1' N1 C2 N3 0.1 360.0
O4' C1' C4 C2' 239.7 239.3
O4' C1' C4 N1 121.7 120.3
C4 C1' C2' H2 131.4 98.5
C2' C1' C4 N1 242.0 241.0
C4 C1' N1 C2 0.2 359.8
C4 C1' N1 HN1 234.9 179.8
C2 N3 C4 C1' 0.5 359.7
C1' C4 N3 C5A 179.8 179.9
N3 C4 C1' O4 179.7 180.2
C2 N1 C1' C4 0.2 359.8
C1' N1 C2 HN1 234.7 180.0
O2 C2 N1 N3 179.6 180.0
N1 C2 N3 C4 359.6 0.2
N1 C2 N3 C5A 180.3 180.0
HN1 N1 C1' C4 234.9 179.8
C1' N1 HN1 C2 124.7 180.0
HN1 N1 C2 O2 305.0 360.0
HN1 N1 C2 N3 125.4 180.0
O2 C2 N1 HN1 305.0 360.0
N1 C2 O2 N3 180.5 180.0
O2 C2 N3 C4 180.1 180.3
O2 C2 N3 C5A 0.7 0.1
C1' C4 N3 C2 0.5 359.7
N3 C2 N1 HN1 125.4 180.0
N1 C2 N3 O2 179.6 180.0
C4 N3 C2 C5A 179.3 180.2
C2 N3 C4 O4 180.2 179.9
C2 N3 C5A C6A 53.6 90.0
C2 N3 C5A H51 178.9 329.9
C2 N3 C5A H52 288.4 210.0
C1' C4 N3 O4 180.3 179.8
C2 N3 C4 C5A 180.7 179.8
C4 N3 C5A C6A 234.4 269.8
C4 N3 C5A H51 359.7 149.7
C4 N3 C5A H52 109.2 29.8
C2 N3 C5A C4 179.2 180.2
C5A N3 C4 O4 359.5 0.1
C6A C5A N3 H51 234.7 120.1
C6A C5A N3 H52 125.3 240.0
N3 C5A C6A C7A 66.4 180.0
N3 C5A C6A H61 191.7 60.0
N3 C5A C6A H62 301.1 299.9
H51 C5A N3 H52 250.5 119.9
C1' C4 O4 N3 179.7 180.3
O4 C4 N3 C5A 359.5 0.1
N3 C5A C6A H51 125.2 239.9
N3 C5A C6A H52 234.8 119.9
H51 C5A C6A H52 109.5 240.0
C7A C6A C5A H61 234.7 120.0
C7A C6A C5A H62 125.2 240.1
C5A C6A C7A C8A 194.0 180.0
C5A C6A C7A H71 319.2 59.9
C5A C6A C7A H72 68.7 300.0
H61 C6A C5A H62 250.6 120.1
N3 C5A H51 C6A 235.9 120.1
N3 C5A H51 H52 117.9 240.1
C6A C5A H51 H52 242.1 120.0
H51 C5A C6A C7A 301.1 300.1
H51 C5A C6A H61 66.4 180.1
H51 C5A C6A H62 175.9 60.0
N3 C5A H52 C6A 124.1 240.0
N3 C5A H52 H51 242.1 120.0
C6A C5A H52 H51 117.9 240.0
H52 C5A C6A C7A 191.6 60.1
H52 C5A C6A H61 316.9 300.1
H52 C5A C6A H62 66.4 180.0
C7A C6A C5A H51 301.1 300.1
C7A C6A C5A H52 191.6 60.1
C5A C6A C7A H61 125.3 240.0
C5A C6A C7A H62 234.7 120.0
H61 C6A C7A H62 109.4 240.0
C8A C7A C6A H71 234.8 120.1
C8A C7A C6A H72 125.3 240.0
C6A C7A C8A C9A 167.9 180.0
C6A C7A C8A NAA 287.2 299.9
C6A C7A C8A H81 47.2 60.0
H71 C7A C6A H72 250.5 119.9
H61 C6A C5A H51 66.4 180.1
H61 C6A C5A H52 316.9 300.1
C5A C6A H61 C7A 234.6 120.0
C5A C6A H61 H62 117.3 240.0
C7A C6A H61 H62 242.7 119.9
H61 C6A C7A C8A 68.7 300.0
H61 C6A C7A H71 193.9 180.0
H61 C6A C7A H72 303.4 60.1
H62 C6A C5A H51 175.9 60.0
H62 C6A C5A H52 66.4 180.0
C5A C6A H62 C7A 125.4 240.0
C5A C6A H62 H61 242.7 120.0
C7A C6A H62 H61 117.3 240.1
H62 C6A C7A C8A 319.3 60.0
H62 C6A C7A H71 84.5 299.9
H62 C6A C7A H72 194.0 180.0
C8A C7A C6A H61 68.7 300.0
C8A C7A C6A H62 319.3 60.0
C6A C7A C8A H71 125.3 240.0
C6A C7A C8A H72 234.7 120.0
H71 C7A C8A H72 109.4 240.0
C9A C8A C7A NAA 240.7 240.1
C9A C8A C7A H81 120.7 120.0
C7A C8A C9A OJA 157.5 90.0
C7A C8A C9A OKA 338.4 270.0
NAA C8A C7A H81 240.1 239.9
C7A C8A NAA OAA 319.9 293.8
C7A C8A NAA CBA 81.4 180.0
H71 C7A C6A H61 193.9 180.0
H71 C7A C6A H62 84.5 299.9
C6A C7A H71 C8A 236.0 120.1
C6A C7A H71 H72 118.0 240.1
C8A C7A H71 H72 242.0 120.0
H71 C7A C8A C9A 42.7 300.0
H71 C7A C8A NAA 162.0 59.9
H71 C7A C8A H81 281.9 180.0
H72 C7A C6A H61 303.4 60.1
H72 C7A C6A H62 194.0 180.0
C6A C7A H72 C8A 124.1 240.0
C6A C7A H72 H71 242.0 119.9
C8A C7A H72 H71 117.9 240.0
H72 C7A C8A C9A 293.2 60.0
H72 C7A C8A NAA 52.5 179.9
H72 C7A C8A H81 172.5 300.0
C9A C8A C7A H71 42.7 300.0
C9A C8A C7A H72 293.2 60.0
C7A C8A C9A NAA 122.8 119.9
C7A C8A C9A H81 242.8 240.0
NAA C8A C9A H81 120.0 120.1
C9A C8A NAA OAA 81.9 53.8
C9A C8A NAA CBA 203.3 299.9
OJA C9A C8A OKA 179.1 180.0
C8A C9A OJA H91 179.9 180.0
NAA C8A C7A H71 162.0 59.9
NAA C8A C7A H72 52.5 179.9
C7A C8A NAA C9A 238.0 240.0
C7A C8A NAA H81 117.2 120.0
C9A C8A NAA H81 239.1 240.0
NAA C8A C9A OJA 34.7 330.0
NAA C8A C9A OKA 215.6 150.0
OAA NAA C8A CBA 238.5 113.8
C8A NAA OAA H10 180.1 66.2
C8A NAA CBA OBA 160.5 300.1
C8A NAA CBA H111 285.8 180.1
C8A NAA CBA H112 35.2 60.1
H81 C8A C7A H71 281.9 180.0
H81 C8A C7A H72 172.5 300.0
C7A C8A H81 C9A 120.6 120.0
C7A C8A H81 NAA 238.5 240.0
C9A C8A H81 NAA 117.9 120.0
H81 C8A C9A OJA 274.6 210.0
H81 C8A C9A OKA 95.6 30.0
H81 C8A NAA OAA 202.7 173.8
H81 C8A NAA CBA 324.2 59.9
OJA C9A C8A NAA 34.7 330.0
OJA C9A C8A H81 274.6 210.0
C8A C9A OJA OKA 180.9 180.0
OKA C9A C8A NAA 215.6 150.0
OKA C9A C8A H81 95.6 30.0
C8A C9A OKA OJA 179.1 180.0
OKA C9A OJA H91 359.0 0.0
H91 OJA C9A OKA 359.0 0.0
OAA NAA C8A H81 202.7 173.8
C8A NAA OAA CBA 122.4 246.2
OAA NAA CBA OBA 282.3 186.2
OAA NAA CBA H111 47.6 66.2
OAA NAA CBA H112 157.1 306.2
CBA NAA C8A H81 324.2 59.9
C8A NAA CBA OAA 238.2 113.9
CBA NAA OAA H10 57.7 180.0
OBA CBA NAA H111 234.7 120.0
OBA CBA NAA H112 125.3 240.0
NAA CBA OBA H11 180.0 180.0
H111 CBA NAA H112 250.5 120.0
H10 OAA NAA CBA 57.7 180.0
NAA CBA OBA H111 125.3 240.0
NAA CBA OBA H112 234.7 120.0
H111 CBA OBA H112 109.5 240.0
NAA CBA H111 OBA 234.6 120.0
NAA CBA H111 H112 117.3 240.1
OBA CBA H111 H112 242.7 120.0
H111 CBA OBA H11 54.8 300.0
NAA CBA H112 OBA 125.4 240.0
NAA CBA H112 H111 242.7 120.0
OBA CBA H112 H111 117.3 240.0
H112 CBA OBA H11 305.3 60.0
H11 OBA CBA H111 54.8 300.0
H11 OBA CBA H112 305.3 60.0