PDB Chemical Component P

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 P

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.479 1.481
P OP2 1.482 1.610
P OP3 1.614 1.610
P O5' 1.607 1.610
OP2 HOP2 0.950 0.967
OP3 HOP3 0.949 0.968
O5' C5' 1.430 1.429
C5' C4' 1.522 1.529
C5' H5' 1.100 1.091
C5' H5'' 1.100 1.090
C4' O4' 1.445 1.443
C4' C3' 1.520 1.550
C4' H4' 1.100 1.090
O4' C1' 1.443 1.438
C3' O3' 1.432 1.429
C3' C2' 1.506 1.548
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.968
C2' C1' 1.518 1.541
C2' H2' 1.100 1.090
C2' H2'' 1.100 1.090
C1' N9 1.474 1.465
C1' H1' 1.100 1.090
N9 C8 1.351 1.365
N9 C4 1.378 1.369
C8 N7 1.288 1.301
C8 H8 1.080 1.080
N7 C5 1.399 1.355
C5 C6 1.420 1.412
C5 C4 1.383 1.399
C6 O6 1.231 1.219
C6 N1 1.395 1.356
N1 C2 1.493 1.362
N1 C8A 1.483 1.465
C2 N2 1.388 1.378
C2 N3 1.337 1.319
N2 C6A 1.473 1.469
N2 H2 1.000 0.970
N3 C4 1.345 1.336
C6A C7A 1.519 1.536
C6A H6A1 1.100 1.090
C6A H6A2 1.100 1.090
C7A C8A 1.520 1.529
C7A H7A1 1.100 1.091
C7A H7A2 1.100 1.090
C8A H8A1 1.100 1.090
C8A H8A2 1.100 1.089

Bond Angles for P

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.9 109.5
OP1 P OP3 108.1 109.4
OP1 P O5' 108.2 109.4
OP2 P OP3 108.6 109.5
OP2 P O5' 108.1 109.5
P OP2 HOP2 109.5 114.0
OP3 P O5' 102.5 109.5
P OP3 HOP3 109.5 114.0
P O5' C5' 120.1 123.0
O5' C5' C4' 111.6 109.5
O5' C5' H5' 108.8 109.5
O5' C5' H5'' 108.3 109.5
C4' C5' H5' 108.8 109.5
C4' C5' H5'' 108.3 109.5
C5' C4' O4' 110.6 110.6
C5' C4' C3' 110.5 110.6
C5' C4' H4' 107.7 110.5
H5' C5' H5'' 111.1 109.4
O4' C4' C3' 108.4 103.5
O4' C4' H4' 109.8 110.6
C4' O4' C1' 110.5 107.0
C3' C4' H4' 109.9 110.8
C4' C3' O3' 110.9 110.9
C4' C3' C2' 105.9 102.1
C4' C3' H3' 111.5 110.9
O4' C1' C2' 107.7 107.3
O4' C1' N9 110.8 109.9
O4' C1' H1' 110.1 109.9
O3' C3' C2' 111.3 110.9
O3' C3' H3' 106.2 110.8
C3' O3' HO3' 109.5 114.0
C2' C3' H3' 111.1 110.9
C3' C2' C1' 107.1 104.2
C3' C2' H2' 110.3 110.5
C3' C2' H2'' 110.8 110.5
C1' C2' H2' 110.2 110.5
C1' C2' H2'' 110.8 110.5
C2' C1' N9 110.4 109.9
C2' C1' H1' 110.5 109.9
H2' C2' H2'' 107.7 110.5
N9 C1' H1' 107.4 109.9
C1' N9 C8 129.3 126.2
C1' N9 C4 126.9 126.3
C8 N9 C4 103.8 107.5
N9 C8 N7 117.6 109.8
N9 C8 H8 121.2 125.1
N9 C4 C5 106.3 106.1
N9 C4 N3 125.4 134.3
N7 C8 H8 121.2 125.1
C8 N7 C5 101.9 109.4
N7 C5 C6 129.1 134.3
N7 C5 C4 110.4 107.3
C6 C5 C4 120.5 118.4
C5 C6 O6 127.1 120.7
C5 C6 N1 113.4 118.8
C5 C4 N3 128.4 119.5
O6 C6 N1 119.6 120.6
C6 N1 C2 121.8 120.0
C6 N1 C8A 118.2 118.0
C2 N1 C8A 120.0 122.0
N1 C2 N2 118.4 120.9
N1 C2 N3 122.3 121.4
N1 C8A C7A 112.3 110.6
N1 C8A H8A1 108.5 109.2
N1 C8A H8A2 107.9 109.3
N2 C2 N3 119.3 117.6
C2 N2 C6A 120.8 119.2
C2 N2 H2 119.6 120.4
C2 N3 C4 113.7 121.7
C6A N2 H2 119.6 120.4
N2 C6A C7A 109.2 107.4
N2 C6A H6A1 109.6 109.9
N2 C6A H6A2 109.6 109.9
C7A C6A H6A1 109.6 109.9
C7A C6A H6A2 109.6 109.8
C6A C7A C8A 109.4 108.2
C6A C7A H7A1 109.5 109.7
C6A C7A H7A2 109.5 109.8
H6A1 C6A H6A2 109.3 109.9
C8A C7A H7A1 109.5 109.7
C8A C7A H7A2 109.5 109.7
C7A C8A H8A1 108.6 109.2
C7A C8A H8A2 107.9 109.3
H7A1 C7A H7A2 109.4 109.7
H8A1 C8A H8A2 111.7 109.2

Torsion Angles for P

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 125.1 240.0
OP2 P OP1 O5' 235.5 120.0
OP1 P OP2 HOP2 256.2 180.0
OP3 P OP1 O5' 110.4 240.1
OP1 P OP3 HOP3 14.8 299.9
OP1 P O5' C5' 54.0 55.1
OP1 P OP2 OP3 235.1 120.0
OP1 P OP2 O5' 124.5 240.0
OP3 P OP2 O5' 249.4 120.0
OP2 P OP3 HOP3 243.2 59.9
OP2 P O5' C5' 185.3 295.1
OP1 P OP3 OP2 131.6 240.0
OP1 P OP3 O5' 245.9 119.9
OP2 P OP3 O5' 114.3 239.9
OP3 P OP2 HOP2 21.1 60.0
OP3 P O5' C5' 299.9 175.0
OP1 P O5' OP2 228.7 120.0
OP1 P O5' OP3 114.1 240.1
OP2 P O5' OP3 245.4 120.1
O5' P OP2 HOP2 131.6 299.9
O5' P OP3 HOP3 129.0 180.0
P O5' C5' C4' 169.0 180.0
P O5' C5' H5' 289.0 300.0
P O5' C5' H5'' 49.9 59.9
HOP2 OP2 P OP3 21.1 60.0
HOP2 OP2 P O5' 131.6 299.9
HOP3 OP3 P O5' 129.0 180.0
C4' C5' O5' H5' 240.0 240.0
C4' C5' O5' H5'' 119.1 120.0
O5' C5' C4' O4' 301.5 66.4
O5' C5' C4' C3' 61.6 180.5
O5' C5' C4' H4' 181.6 303.5
H5' C5' O5' H5'' 239.1 240.0
O5' C5' C4' H5' 120.0 120.0
O5' C5' C4' H5'' 240.9 240.0
H5' C5' C4' H5'' 120.9 120.0
O4' C4' C5' C3' 239.9 245.9
O4' C4' C5' H4' 119.9 122.9
C5' C4' O4' C1' 120.5 158.6
C3' C4' C5' H4' 240.0 237.0
C5' C4' C3' O3' 115.3 86.3
C5' C4' C3' C2' 236.1 204.4
C5' C4' C3' H3' 357.1 322.7
O5' C5' H5' C4' 238.3 240.0
O5' C5' H5' H5'' 119.1 120.0
C4' C5' H5' H5'' 240.9 240.0
H5' C5' C4' O4' 181.5 306.4
H5' C5' C4' C3' 301.6 60.5
H5' C5' C4' H4' 61.6 183.5
O5' C5' H5'' C4' 121.2 120.0
O5' C5' H5'' H5' 240.6 240.0
C4' C5' H5'' H5' 119.4 120.0
H5'' C5' C4' O4' 60.6 186.4
H5'' C5' C4' C3' 180.7 300.5
H5'' C5' C4' H4' 300.7 63.6
O4' C4' C5' H5' 181.5 306.4
O4' C4' C5' H5'' 60.6 186.4
C5' C4' O4' C3' 121.3 118.5
C5' C4' O4' H4' 241.3 237.2
C3' C4' O4' H4' 120.0 118.7
O4' C4' C3' O3' 236.7 204.8
O4' C4' C3' C2' 357.5 323.0
O4' C4' C3' H3' 118.6 81.2
C4' O4' C1' C2' 3.8 333.5
C4' O4' C1' N9 242.9 214.1
C4' O4' C1' H1' 124.3 93.0
C3' C4' C5' H5' 301.6 60.5
C3' C4' C5' H5'' 180.7 300.5
C5' C4' C3' O4' 238.6 241.5
C5' C4' C3' H4' 118.6 122.9
O4' C4' C3' H4' 240.0 241.4
C3' C4' O4' C1' 359.2 40.1
O3' C3' C4' C2' 239.2 241.8
O3' C3' C4' H3' 118.1 123.6
C4' C3' O3' HO3' 185.5 180.0
C2' C3' C4' H3' 238.9 241.8
C4' C3' C2' C1' 4.7 20.9
C4' C3' C2' H2' 124.7 139.6
C4' C3' C2' H2'' 243.8 262.2
H4' C4' C5' H5' 61.6 183.5
H4' C4' C5' H5'' 300.7 63.6
C5' C4' H4' O4' 120.5 122.9
C5' C4' H4' C3' 239.6 237.0
O4' C4' H4' C3' 119.1 114.2
H4' C4' O4' C1' 239.1 281.4
H4' C4' C3' O3' 356.6 323.4
H4' C4' C3' C2' 117.5 81.5
H4' C4' C3' H3' 238.5 199.8
C1' O4' C4' C3' 359.2 40.1
C1' O4' C4' H4' 239.1 281.4
C3' C2' C1' O4' 354.7 2.0
O4' C1' C2' H2' 234.7 243.4
O4' C1' C2' H2'' 115.6 120.7
C2' C1' O4' N9 120.9 119.4
C2' C1' O4' H1' 239.5 240.5
N9 C1' O4' H1' 118.6 121.1
O4' C1' N9 C8 65.7 23.6
O4' C1' N9 C4 244.4 203.2
O3' C3' C4' H4' 356.6 323.4
C4' C3' O3' C2' 117.6 112.7
C4' C3' O3' H3' 238.7 236.4
C2' C3' O3' H3' 121.1 123.7
O3' C3' C2' C1' 125.3 139.1
O3' C3' C2' H2' 245.2 257.8
O3' C3' C2' H2'' 4.3 20.4
C2' C3' C4' H4' 117.5 81.5
C4' C3' C2' O3' 239.4 241.8
C4' C3' C2' H3' 121.3 118.2
O4' C1' C2' C3' 354.7 2.0
O3' C3' C2' H3' 241.9 236.4
C2' C3' O3' HO3' 67.8 67.3
C1' C2' C3' H2' 240.0 241.3
C1' C2' C3' H2'' 120.9 118.7
C3' C2' C1' N9 115.8 121.5
C3' C2' C1' H1' 234.5 242.6
H2' C2' C3' H2'' 240.9 237.4
H3' C3' C4' H4' 238.5 199.8
C4' C3' H3' O3' 120.9 123.6
C4' C3' H3' C2' 242.0 247.3
O3' C3' H3' C2' 121.1 123.6
H3' C3' O3' HO3' 306.8 303.6
H3' C3' C2' C1' 243.4 262.7
H3' C3' C2' H2' 3.4 21.4
H3' C3' C2' H2'' 122.5 144.0
HO3' O3' C3' C2' 67.8 67.3
HO3' O3' C3' H3' 306.8 303.6
O4' C1' C2' N9 238.9 240.6
O4' C1' C2' H1' 120.3 119.5
C1' C2' C3' H3' 243.4 262.7
C3' C2' C1' H2' 120.0 118.7
C3' C2' C1' H2'' 239.1 241.3
H2' C2' C1' H2'' 119.1 122.6
N9 C1' C2' H1' 241.4 238.9
C2' C1' N9 C8 306.4 265.7
C2' C1' N9 C4 125.1 85.4
H2' C2' C3' H3' 3.4 21.4
C3' C2' H2' C1' 241.9 245.2
C3' C2' H2' H2'' 120.9 122.6
C1' C2' H2' H2'' 239.0 237.4
H2' C2' C1' N9 355.9 2.8
H2' C2' C1' H1' 114.5 123.9
H2'' C2' C3' H3' 122.5 144.0
C3' C2' H2'' C1' 118.7 114.8
C3' C2' H2'' H2' 239.4 237.4
C1' C2' H2'' H2' 120.6 122.6
H2'' C2' C1' N9 236.8 240.2
H2'' C2' C1' H1' 355.4 1.3
O4' C1' N9 C2' 119.3 117.8
O4' C1' N9 H1' 239.8 238.9
N9 C1' C2' H2' 355.9 2.8
N9 C1' C2' H2'' 236.8 240.2
C2' C1' N9 H1' 120.5 121.1
C8 N9 C1' C4 181.2 180.3
C1' N9 C8 N7 179.0 179.8
C1' N9 C8 H8 359.0 359.8
C1' N9 C4 C5 181.0 180.3
C1' N9 C4 N3 0.9 1.8
O4' C1' H1' C2' 241.1 242.1
O4' C1' H1' N9 120.7 121.1
H1' C1' C2' H2' 114.5 123.9
H1' C1' C2' H2'' 355.4 1.3
C2' C1' H1' N9 239.6 238.9
H1' C1' N9 C8 185.9 144.7
H1' C1' N9 C4 4.6 324.3
C8 N9 C1' H1' 185.9 144.7
C1' N9 C8 C4 179.0 179.7
C8 N9 C4 C5 0.0 360.0
C8 N9 C4 N3 179.9 181.5
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 359.9 360.0
C4 N9 C1' H1' 4.6 324.3
C1' N9 C4 C8 181.0 180.3
C4 N9 C8 N7 0.0 0.0
C4 N9 C8 H8 180.0 180.1
N7 C5 C4 N9 359.9 0.0
C6 C5 C4 N9 179.9 179.6
C5 C4 N9 N3 180.1 178.5
C2 N3 C4 N9 180.3 179.8
N7 C8 N9 C4 0.0 0.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 180.1 180.5
C8 N7 C5 C4 0.1 0.0
H8 C8 N9 C4 180.0 180.1
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 179.9 179.9
N9 C4 C5 N7 359.9 0.0
C5 N7 C8 H8 179.9 179.9
C6 C5 N7 C4 180.0 180.5
N7 C5 C6 O6 359.9 358.1
N7 C5 C6 N1 179.9 178.1
N7 C5 C4 N3 180.0 178.8
N9 C4 C5 C6 179.9 179.6
N7 C5 C6 C4 180.0 179.5
C6 C5 C4 N3 0.0 358.4
O6 C6 C5 N1 180.0 180.0
C5 C6 N1 C2 0.0 4.6
C5 C6 N1 C8A 180.5 186.3
N9 C4 C5 N3 179.9 181.3
N7 C5 C4 C6 180.0 180.4
C4 C5 C6 O6 179.9 178.6
C4 C5 C6 N1 359.9 358.6
C2 N3 C4 C5 0.1 1.5
O6 C6 C5 C4 179.9 178.6
C5 C6 O6 N1 180.0 180.0
O6 C6 N1 C2 180.1 184.6
O6 C6 N1 C8A 0.5 6.3
N1 C6 C5 C4 359.9 358.6
C5 C6 N1 O6 180.0 180.0
C2 N1 C6 C8A 179.5 178.3
C6 N1 C2 N2 180.1 173.8
C6 N1 C2 N3 0.2 355.1
C6 N1 C8A C7A 201.2 205.0
C6 N1 C8A H8A1 321.2 325.2
C6 N1 C8A H8A2 82.4 84.7
C6 N1 C2 C8A 180.5 181.7
C2 N1 C8A C7A 21.7 26.7
C2 N1 C8A H8A1 141.7 146.9
C2 N1 C8A H8A2 262.8 266.4
N2 C2 N1 N3 179.9 178.7
N1 C2 N2 C6A 11.5 17.9
N1 C2 N2 H2 191.4 197.9
N1 C2 N3 C4 359.8 1.8
C6 N1 C8A C2 179.5 178.3
C8A N1 C2 N2 359.6 352.1
C8A N1 C2 N3 179.7 173.4
C6A C7A C8A N1 308.1 307.2
N1 C8A C7A H7A1 188.1 187.5
N1 C8A C7A H7A2 68.1 66.9
C7A C8A N1 H8A1 240.0 239.8
C7A C8A N1 H8A2 118.8 120.3
H8A1 C8A N1 H8A2 238.8 240.6
N2 C2 N1 C8A 359.6 352.1
N1 C2 N2 N3 180.1 181.3
N2 C2 N3 C4 179.8 183.0
C6A N2 C2 H2 180.0 180.0
C2 N2 C6A C7A 317.7 315.4
C2 N2 C6A H6A1 77.7 74.8
C2 N2 C6A H6A2 197.6 195.9
N9 C4 N3 C2 180.3 179.8
C5 C4 N3 C2 0.1 1.5
N3 C2 N1 C8A 179.7 173.4
N1 C2 N3 N2 179.9 178.7
N3 C2 N2 C6A 191.4 196.6
N3 C2 N2 H2 11.4 16.6
C6A N2 C2 N3 191.4 196.6
C2 N2 C6A H2 180.0 180.0
C7A C6A N2 H6A1 240.0 240.5
C7A C6A N2 H6A2 120.1 119.4
N2 C6A C7A C8A 61.6 61.2
N2 C6A C7A H7A1 181.7 180.8
N2 C6A C7A H7A2 301.6 301.4
H6A1 C6A N2 H6A2 240.1 238.9
H2 N2 C2 N3 11.4 16.6
C2 N2 H2 C6A 180.0 180.0
H2 N2 C6A C7A 137.7 135.3
H2 N2 C6A H6A1 257.7 254.8
H2 N2 C6A H6A2 17.6 15.9
N9 C4 N3 C5 180.1 178.3
N1 C8A C7A C6A 308.1 307.2
C7A C6A N2 H2 137.7 135.3
N2 C6A C7A H6A1 120.0 119.5
N2 C6A C7A H6A2 239.9 240.5
H6A1 C6A C7A H6A2 119.9 121.1
C8A C7A C6A H7A1 240.0 240.3
C8A C7A C6A H7A2 120.0 119.7
C6A C7A C8A H8A1 188.1 186.9
C6A C7A C8A H8A2 66.9 67.5
H7A1 C7A C6A H7A2 240.0 239.4
H6A1 C6A N2 H2 257.7 254.8
N2 C6A H6A1 C7A 240.2 242.1
N2 C6A H6A1 H6A2 120.1 121.1
C7A C6A H6A1 H6A2 239.9 239.0
H6A1 C6A C7A C8A 301.6 301.7
H6A1 C6A C7A H7A1 61.6 61.4
H6A1 C6A C7A H7A2 181.6 182.0
H6A2 C6A N2 H2 17.6 15.9
N2 C6A H6A2 C7A 119.9 117.9
N2 C6A H6A2 H6A1 239.9 238.9
C7A C6A H6A2 H6A1 120.1 121.0
H6A2 C6A C7A C8A 181.8 180.6
H6A2 C6A C7A H7A1 301.8 300.3
H6A2 C6A C7A H7A2 61.7 60.9
N1 C8A C7A H8A1 120.0 120.2
N1 C8A C7A H8A2 241.2 239.7
C8A C7A C6A H6A1 301.6 301.7
C8A C7A C6A H6A2 181.8 180.6
C6A C7A C8A H7A1 120.0 119.6
C6A C7A C8A H7A2 240.0 240.3
H7A1 C7A C8A H7A2 120.0 120.6
H8A1 C8A C7A H8A2 121.2 119.4
H7A1 C7A C6A H6A1 61.6 61.4
H7A1 C7A C6A H6A2 301.8 300.3
C6A C7A H7A1 C8A 240.1 241.3
C6A C7A H7A1 H7A2 120.0 120.6
C8A C7A H7A1 H7A2 239.9 239.4
H7A1 C7A C8A H8A1 68.1 67.3
H7A1 C7A C8A H8A2 306.9 307.9
H7A2 C7A C6A H6A1 181.6 182.0
H7A2 C7A C6A H6A2 61.7 60.9
C6A C7A H7A2 C8A 119.9 118.8
C6A C7A H7A2 H7A1 240.0 239.4
C8A C7A H7A2 H7A1 120.0 120.6
H7A2 C7A C8A H8A1 308.1 306.7
H7A2 C7A C8A H8A2 186.9 187.2
N1 C8A H8A1 C7A 237.7 238.9
N1 C8A H8A1 H8A2 118.8 119.5
H8A1 C8A C7A H7A1 68.1 67.3
H8A1 C8A C7A H7A2 308.1 306.7
C7A C8A H8A1 H8A2 241.2 240.6
N1 C8A H8A2 C7A 121.6 121.1
N1 C8A H8A2 H8A1 240.8 240.5
H8A2 C8A C7A H7A1 306.9 307.9
H8A2 C8A C7A H7A2 186.9 187.2
C7A C8A H8A2 H8A1 119.2 119.4