PDB Chemical Component P2P

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 P2P

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O1P 1.489 1.479
P O2P 1.496 1.610
P O3P 1.486 1.610
P O6' 1.602 1.610
O2P HOP2 0.950 0.967
O3P HOP3 0.950 0.967
O6' C5' 1.452 1.428
C5' C4' 1.515 1.529
C5' H5'1 1.116 1.090
C5' H5'2 1.115 1.088
C4' O5' 1.468 1.446
C4' C3' 1.515 1.544
C4' H4' 1.114 1.090
O5' C1' 1.456 1.443
C3' O3' 1.442 1.429
C3' C2' 1.530 1.544
C3' H3' 1.116 1.089
O3' HO3' 0.950 0.967
C2' O2' 1.440 1.429
C2' C1' 1.529 1.545
C2' H2' 1.116 1.091
O2' HO2' 0.950 0.966
C1' N7 1.514 1.465
C1' H1' 1.115 1.089
C8 N9 1.362 1.303
C8 N7 1.353 1.351
C8 H8 1.103 1.080
N9 C4 1.382 1.346
C4 C5 1.391 1.408
C4 N3 1.351 1.334
C5 N7 1.381 1.380
C5 C6 1.414 1.386
N3 C2 1.354 1.321
C2 N1 1.382 1.324
C2 O11 1.368 1.355
N1 C6 1.362 1.325
C6 H6 1.103 1.080
O11 HO11 0.950 0.966

Bond Angles for P2P

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P 109.9 109.4
O1P P O3P 109.5 109.5
O1P P O6' 109.3 109.5
O2P P O3P 108.7 109.5
O2P P O6' 111.2 109.5
P O2P HOP2 109.9 106.8
O3P P O6' 108.1 109.5
P O3P HOP3 109.5 106.8
P O6' C5' 120.3 106.8
O6' C5' C4' 108.5 109.5
O6' C5' H5'1 112.6 109.4
O6' C5' H5'2 112.5 109.5
C4' C5' H5'1 112.6 109.5
C4' C5' H5'2 112.6 109.5
C5' C4' O5' 109.3 110.4
C5' C4' C3' 116.2 110.7
C5' C4' H4' 103.7 110.3
H5'1 C5' H5'2 97.8 109.4
O5' C4' C3' 105.3 104.7
O5' C4' H4' 115.0 110.4
C4' O5' C1' 110.8 105.4
C3' C4' H4' 107.8 110.3
C4' C3' O3' 113.8 110.5
C4' C3' C2' 98.9 104.2
C4' C3' H3' 114.3 110.5
O5' C1' C2' 102.2 104.8
O5' C1' N7 116.2 110.4
O5' C1' H1' 111.6 110.4
O3' C3' C2' 111.5 110.5
O3' C3' H3' 102.4 110.4
C3' O3' HO3' 113.7 106.8
C2' C3' H3' 116.6 110.5
C3' C2' O2' 107.7 110.6
C3' C2' C1' 105.1 104.1
C3' C2' H2' 114.3 110.5
O2' C2' C1' 112.0 110.6
O2' C2' H2' 107.7 110.4
C2' O2' HO2' 107.7 106.8
C1' C2' H2' 110.2 110.5
C2' C1' N7 113.7 110.3
C2' C1' H1' 114.1 110.4
N7 C1' H1' 99.6 110.3
C1' N7 C8 128.0 126.4
C1' N7 C5 129.1 126.4
N9 C8 N7 114.1 110.2
N9 C8 H8 123.2 124.9
C8 N9 C4 105.5 109.8
N7 C8 H8 122.6 124.9
C8 N7 C5 102.9 107.2
N9 C4 C5 106.4 106.8
N9 C4 N3 126.5 134.5
C5 C4 N3 127.1 118.7
C4 C5 N7 111.1 106.0
C4 C5 C6 118.4 118.7
C4 N3 C2 111.1 120.3
N7 C5 C6 130.6 135.2
C5 C6 N1 116.3 118.7
C5 C6 H6 123.5 120.7
N3 C2 N1 127.1 122.3
N3 C2 O11 116.4 118.9
N1 C2 O11 116.5 118.9
C2 N1 C6 120.0 121.2
C2 O11 HO11 116.4 106.7
N1 C6 H6 120.2 120.6

Torsion Angles for P2P

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2P P O1P O3P 119.4 119.9
O2P P O1P O6' 237.7 240.0
O1P P O2P HOP2 180.0 300.0
O3P P O1P O6' 118.3 120.0
O1P P O3P HOP3 180.0 180.0
O1P P O6' C5' 54.3 60.0
O1P P O2P O3P 240.1 240.0
O1P P O2P O6' 121.2 120.1
O3P P O2P O6' 241.1 240.0
O2P P O3P HOP3 59.9 60.0
O2P P O6' C5' 175.9 179.9
O1P P O3P O2P 120.1 119.9
O1P P O3P O6' 240.9 239.9
O2P P O3P O6' 120.8 120.0
O3P P O2P HOP2 299.9 60.0
O3P P O6' C5' 295.1 299.9
O1P P O6' O2P 238.4 240.0
O1P P O6' O3P 119.2 120.0
O2P P O6' O3P 240.8 240.0
O6' P O2P HOP2 58.8 180.0
O6' P O3P HOP3 299.1 300.0
P O6' C5' C4' 99.0 180.0
P O6' C5' H5'1 224.3 60.0
P O6' C5' H5'2 333.6 300.1
HOP2 O2P P O3P 299.9 60.0
HOP2 O2P P O6' 58.8 180.0
HOP3 O3P P O6' 299.1 300.0
C4' C5' O6' H5'1 234.7 120.0
C4' C5' O6' H5'2 125.3 239.9
O6' C5' C4' O5' 55.0 61.5
O6' C5' C4' C3' 173.9 176.9
O6' C5' C4' H4' 291.9 299.2
H5'1 C5' O6' H5'2 250.6 119.9
O6' C5' C4' H5'1 125.3 240.1
O6' C5' C4' H5'2 234.7 120.1
H5'1 C5' C4' H5'2 109.4 240.0
O5' C4' C5' C3' 241.1 244.6
O5' C4' C5' H4' 123.1 122.3
C5' C4' O5' C1' 106.9 159.4
C3' C4' C5' H4' 241.9 237.7
C5' C4' C3' O3' 157.0 98.6
C5' C4' C3' C2' 275.2 217.3
C5' C4' C3' H3' 39.8 336.0
O6' C5' H5'1 C4' 236.9 120.0
O6' C5' H5'1 H5'2 118.4 240.0
C4' C5' H5'1 H5'2 241.5 120.1
H5'1 C5' C4' O5' 289.7 181.4
H5'1 C5' C4' C3' 48.6 296.8
H5'1 C5' C4' H4' 166.6 59.2
O6' C5' H5'2 C4' 123.0 239.9
O6' C5' H5'2 H5'1 241.6 119.9
C4' C5' H5'2 H5'1 118.5 240.0
H5'2 C5' C4' O5' 180.3 301.4
H5'2 C5' C4' C3' 299.1 56.8
H5'2 C5' C4' H4' 57.2 179.2
O5' C4' C5' H5'1 289.7 181.4
O5' C4' C5' H5'2 180.3 301.4
C5' C4' O5' C3' 125.5 119.1
C5' C4' O5' H4' 244.0 237.8
C3' C4' O5' H4' 118.5 118.6
O5' C4' C3' O3' 278.0 217.5
O5' C4' C3' C2' 36.3 336.2
O5' C4' C3' H3' 160.8 95.0
C4' O5' C1' C2' 352.1 319.6
C4' O5' C1' N7 116.5 78.4
C4' O5' C1' H1' 229.7 200.7
C3' C4' C5' H5'1 48.6 296.8
C3' C4' C5' H5'2 299.1 56.8
C5' C4' C3' O5' 239.0 241.1
C5' C4' C3' H4' 115.8 122.4
O5' C4' C3' H4' 236.8 241.3
C3' C4' O5' C1' 341.4 40.3
O3' C3' C4' C2' 241.7 241.3
O3' C3' C4' H3' 117.2 122.5
C4' C3' O3' HO3' 180.0 178.1
C2' C3' C4' H3' 235.5 241.2
C4' C3' C2' O2' 198.8 241.1
C4' C3' C2' C1' 318.3 360.0
C4' C3' C2' H2' 79.2 118.6
H4' C4' C5' H5'1 166.6 59.2
H4' C4' C5' H5'2 57.2 179.2
C5' C4' H4' O5' 119.2 122.3
C5' C4' H4' C3' 236.3 237.5
O5' C4' H4' C3' 117.1 115.2
H4' C4' O5' C1' 222.9 281.7
H4' C4' C3' O3' 41.2 336.2
H4' C4' C3' C2' 159.5 94.9
H4' C4' C3' H3' 284.0 213.7
C1' O5' C4' C3' 341.4 40.3
C1' O5' C4' H4' 222.9 281.7
C3' C2' C1' O5' 31.4 23.9
O2' C2' C1' O5' 148.0 142.7
O5' C1' C2' H2' 267.9 265.3
C2' C1' O5' N7 235.6 241.2
C2' C1' O5' H1' 122.3 118.9
N7 C1' O5' H1' 246.8 237.7
O5' C1' N7 C8 192.4 344.1
O5' C1' N7 C5 13.1 163.8
O3' C3' C4' H4' 41.2 336.2
C4' C3' O3' C2' 110.8 114.8
C4' C3' O3' H3' 236.1 237.4
C2' C3' O3' H3' 125.3 122.6
O3' C3' C2' O2' 318.8 359.8
O3' C3' C2' C1' 78.3 118.7
O3' C3' C2' H2' 199.2 237.3
C2' C3' C4' H4' 159.5 94.9
C4' C3' C2' O3' 240.0 241.3
C4' C3' C2' H3' 123.0 118.8
O5' C1' C2' C3' 31.4 23.9
O3' C3' C2' H3' 243.0 237.5
C2' C3' O3' HO3' 69.3 63.3
O2' C2' C3' C1' 240.5 241.2
O2' C2' C3' H2' 119.6 122.6
C3' C2' O2' HO2' 180.0 298.5
C1' C2' C3' H2' 239.1 241.4
C3' C2' C1' N7 265.4 265.0
C3' C2' C1' H1' 152.0 142.9
H3' C3' C4' H4' 284.0 213.7
C4' C3' H3' O3' 123.6 122.6
C4' C3' H3' C2' 245.5 245.2
O3' C3' H3' C2' 121.9 122.6
H3' C3' O3' HO3' 303.9 300.7
H3' C3' C2' O2' 75.8 122.4
H3' C3' C2' C1' 195.3 241.2
H3' C3' C2' H2' 316.3 359.8
HO3' O3' C3' C2' 69.3 63.3
HO3' O3' C3' H3' 303.9 300.7
O5' C1' C2' O2' 148.0 142.7
O2' C2' C3' H3' 75.8 122.4
C3' C2' O2' C1' 115.0 114.7
C3' C2' O2' H2' 236.3 237.4
C1' C2' O2' H2' 121.3 122.6
O2' C2' C1' N7 22.0 23.8
O2' C2' C1' H1' 268.6 261.6
O5' C1' C2' N7 126.0 118.9
O5' C1' C2' H1' 239.4 241.1
C1' C2' C3' H3' 195.3 241.2
C3' C2' C1' O2' 243.4 241.2
C3' C2' C1' H2' 123.6 118.6
O2' C2' C1' H2' 240.2 237.4
C1' C2' O2' HO2' 65.0 183.8
N7 C1' C2' H1' 113.4 122.2
C2' C1' N7 C8 310.7 99.6
C2' C1' N7 C5 131.4 279.2
H2' C2' C3' H3' 316.3 359.8
C3' C2' H2' O2' 119.6 122.7
C3' C2' H2' C1' 242.0 245.4
O2' C2' H2' C1' 122.4 122.7
H2' C2' O2' HO2' 303.7 61.2
H2' C2' C1' N7 141.8 146.4
H2' C2' C1' H1' 28.5 24.2
HO2' O2' C2' C1' 65.0 183.8
HO2' O2' C2' H2' 303.7 61.2
O5' C1' N7 C2' 241.7 244.6
O5' C1' N7 H1' 119.9 122.4
N7 C1' C2' H2' 141.8 146.4
C2' C1' N7 H1' 238.2 237.8
N9 C8 N7 C1' 181.6 179.9
C1' N7 C8 H8 1.6 359.9
C8 N7 C1' C5 179.3 180.4
C4 C5 N7 C1' 177.2 179.9
C1' N7 C5 C6 357.9 0.8
O5' C1' H1' C2' 115.3 115.5
O5' C1' H1' N7 236.8 237.6
H1' C1' C2' H2' 28.5 24.2
C2' C1' H1' N7 121.5 122.2
H1' C1' N7 C8 72.5 221.8
H1' C1' N7 C5 253.2 41.4
C1' N7 C8 N9 181.6 179.9
N7 C8 N9 H8 180.0 179.9
N9 C8 N7 C5 1.0 0.3
C8 N9 C4 C5 358.2 359.7
C8 N9 C4 N3 178.8 180.0
C8 N7 C1' H1' 72.5 221.8
C1' N7 C8 C5 180.6 179.7
N9 C8 N7 H8 180.0 180.1
N7 C8 N9 C4 0.5 0.0
C4 C5 N7 C8 357.8 359.6
C8 N7 C5 C6 178.5 180.4
N9 C8 H8 N7 180.0 179.9
H8 C8 N9 C4 180.5 180.1
H8 C8 N7 C5 181.0 180.2
C4 N9 C8 N7 0.5 0.0
C4 N9 C8 H8 180.5 180.1
C5 C4 N9 N3 179.4 179.7
N9 C4 C5 N7 2.5 0.4
N9 C4 C5 C6 181.9 179.7
N9 C4 N3 C2 178.2 179.9
C1' N7 C5 C4 177.2 179.9
C8 N7 C5 C4 357.8 359.6
N9 C4 C5 N3 180.6 180.2
C5 C4 N3 C2 359.0 0.2
N7 C5 C4 C6 180.6 180.7
C4 C5 C6 N1 358.9 0.5
C4 C5 C6 H6 178.9 180.3
N9 C4 N3 C5 179.2 179.7
N3 C4 C5 N7 181.9 180.2
N3 C4 C5 C6 1.3 359.5
C4 N3 C2 N1 0.7 0.1
C4 N3 C2 O11 179.5 180.0
C5 N7 C1' H1' 253.2 41.4
C1' N7 C5 C8 179.4 180.3
C5 N7 C8 H8 181.0 180.2
N7 C5 C4 N3 181.9 180.2
C4 C5 N7 C6 179.3 179.2
N7 C5 C6 N1 178.1 179.6
N7 C5 C6 H6 358.1 359.3
C6 C5 C4 N3 1.3 359.5
C4 C5 C6 N7 180.7 180.9
C2 N1 C6 C5 0.9 359.8
N1 C6 C5 H6 180.0 180.2
N1 C2 N3 O11 181.2 180.1
N3 C2 N1 C6 359.3 359.9
N3 C2 O11 HO11 180.0 90.0
C5 C6 N1 C2 0.9 359.8
N3 C2 N1 O11 178.8 179.9
N1 C2 O11 HO11 358.9 270.0
C2 N1 C6 H6 180.9 180.0
N3 C2 O11 N1 181.1 180.1
O11 C2 N1 C6 180.5 180.0
C5 C6 N1 H6 180.0 179.8
C6 N1 C2 O11 180.5 180.0
C5 C6 H6 N1 180.0 180.2