PDB Chemical Component TMP

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 TMP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O1P 1.527 1.480
P O2P 1.644 1.610
P O3P 1.562 1.610
P O5' 1.613 1.610
O2P HOP2 0.950 0.968
O3P HOP3 0.950 0.967
O5' C5' 1.423 1.429
C5' C4' 1.515 1.530
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.090
C4' O4' 1.434 1.446
C4' C3' 1.510 1.550
C4' H4' 1.100 1.090
O4' C1' 1.415 1.438
C3' O3' 1.429 1.429
C3' C2' 1.527 1.548
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C2' C1' 1.524 1.540
C2' H2'1 1.100 1.090
C2' H2'2 1.100 1.090
C1' N1 1.479 1.465
C1' H1' 1.100 1.091
N1 C2 1.354 1.346
N1 C6 1.365 1.368
C2 O2 1.258 1.216
C2 N3 1.327 1.346
N3 C4 1.333 1.348
N3 HN3 1.000 0.970
C4 O4 1.246 1.218
C4 C5 1.463 1.415
C5 C5M 1.512 1.507
C5 C6 1.374 1.350
C5M H51 1.100 1.090
C5M H52 1.100 1.090
C5M H53 1.100 1.091
C6 H6 1.080 1.079

Bond Angles for TMP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P 112.9 109.5
O1P P O3P 111.1 109.5
O1P P O5' 108.0 109.5
O2P P O3P 116.3 109.5
O2P P O5' 101.9 109.4
P O2P HOP2 109.5 106.8
O3P P O5' 105.6 109.4
P O3P HOP3 109.5 106.8
P O5' C5' 122.9 106.8
O5' C5' C4' 111.2 109.5
O5' C5' H5'1 108.9 109.4
O5' C5' H5'2 108.5 109.5
C4' C5' H5'1 108.9 109.5
C4' C5' H5'2 108.5 109.5
C5' C4' O4' 106.3 110.8
C5' C4' C3' 113.0 110.6
C5' C4' H4' 109.2 110.5
H5'1 C5' H5'2 110.8 109.5
O4' C4' C3' 109.1 103.6
O4' C4' H4' 113.1 110.5
C4' O4' C1' 107.4 106.8
C3' C4' H4' 106.4 110.6
C4' C3' O3' 110.1 110.9
C4' C3' C2' 104.3 102.1
C4' C3' H3' 111.7 110.9
O4' C1' C2' 110.1 107.4
O4' C1' N1 107.7 109.9
O4' C1' H1' 111.4 109.8
O3' C3' C2' 107.3 110.9
O3' C3' H3' 108.9 110.8
C3' O3' HO3' 109.5 106.8
C2' C3' H3' 114.3 110.9
C3' C2' C1' 100.9 104.2
C3' C2' H2'1 112.4 110.5
C3' C2' H2'2 114.2 110.4
C1' C2' H2'1 112.4 110.5
C1' C2' H2'2 114.3 110.5
C2' C1' N1 112.5 109.9
C2' C1' H1' 106.4 109.9
H2'1 C2' H2'2 103.1 110.5
N1 C1' H1' 108.9 109.8
C1' N1 C2 119.5 119.7
C1' N1 C6 120.4 119.7
C2 N1 C6 120.1 120.6
N1 C2 O2 120.0 119.5
N1 C2 N3 120.3 120.9
N1 C6 C5 121.5 119.7
N1 C6 H6 119.3 120.1
O2 C2 N3 119.6 119.5
C2 N3 C4 123.3 120.3
C2 N3 HN3 118.3 119.8
C4 N3 HN3 118.4 119.9
N3 C4 O4 123.1 120.3
N3 C4 C5 118.3 119.4
O4 C4 C5 118.6 120.3
C4 C5 C5M 121.7 120.4
C4 C5 C6 116.5 119.1
C5M C5 C6 121.8 120.4
C5 C5M H51 109.5 109.5
C5 C5M H52 109.5 109.5
C5 C5M H53 109.5 109.4
C5 C6 H6 119.3 120.2
H51 C5M H52 109.5 109.5
H51 C5M H53 109.4 109.4
H52 C5M H53 109.5 109.5

Torsion Angles for TMP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2P P O1P O3P 132.8 120.1
O2P P O1P O5' 248.1 240.0
O1P P O2P HOP2 295.2 300.0
O3P P O1P O5' 115.3 119.9
O1P P O3P HOP3 3.6 180.0
O1P P O5' C5' 69.1 54.9
O1P P O2P O3P 229.8 240.0
O1P P O2P O5' 115.6 120.0
O3P P O2P O5' 245.8 240.1
O2P P O3P HOP3 232.6 59.9
O2P P O5' C5' 188.2 175.0
O1P P O3P O2P 131.1 120.1
O1P P O3P O5' 243.2 240.0
O2P P O3P O5' 112.1 120.0
O3P P O2P HOP2 65.4 60.0
O3P P O5' C5' 310.2 295.0
O1P P O5' O2P 240.9 240.0
O1P P O5' O3P 118.9 120.0
O2P P O5' O3P 238.1 240.0
O5' P O2P HOP2 179.6 180.0
O5' P O3P HOP3 120.4 299.9
P O5' C5' C4' 196.5 180.0
P O5' C5' H5'1 316.6 60.0
P O5' C5' H5'2 77.2 300.0
HOP2 O2P P O3P 65.4 60.0
HOP2 O2P P O5' 179.6 180.0
HOP3 O3P P O5' 120.4 299.9
C4' C5' O5' H5'1 240.0 120.0
C4' C5' O5' H5'2 119.3 240.0
O5' C5' C4' O4' 285.8 70.7
O5' C5' C4' C3' 45.4 185.0
O5' C5' C4' H4' 163.5 307.9
H5'1 C5' O5' H5'2 239.3 120.0
O5' C5' C4' H5'1 120.0 240.1
O5' C5' C4' H5'2 240.7 120.0
H5'1 C5' C4' H5'2 120.7 240.0
O4' C4' C5' C3' 240.4 245.7
O4' C4' C5' H4' 122.3 122.8
C5' C4' O4' C1' 119.2 158.5
C3' C4' C5' H4' 241.8 237.1
C5' C4' C3' O3' 147.2 86.1
C5' C4' C3' C2' 262.1 204.3
C5' C4' C3' H3' 26.1 322.5
O5' C5' H5'1 C4' 238.6 120.0
O5' C5' H5'1 H5'2 119.3 240.0
C4' C5' H5'1 H5'2 240.7 120.0
H5'1 C5' C4' O4' 165.8 190.7
H5'1 C5' C4' C3' 285.4 305.0
H5'1 C5' C4' H4' 43.5 67.9
O5' C5' H5'2 C4' 121.0 239.9
O5' C5' H5'2 H5'1 240.5 119.9
C4' C5' H5'2 H5'1 119.5 240.0
H5'2 C5' C4' O4' 45.1 310.7
H5'2 C5' C4' C3' 164.6 65.0
H5'2 C5' C4' H4' 282.8 187.9
O4' C4' C5' H5'1 165.8 190.7
O4' C4' C5' H5'2 45.1 310.7
C5' C4' O4' C3' 122.1 118.7
C5' C4' O4' H4' 240.3 237.2
C3' C4' O4' H4' 118.1 118.5
O4' C4' C3' O3' 265.2 204.8
O4' C4' C3' C2' 20.0 323.0
O4' C4' C3' H3' 144.0 81.3
C4' O4' C1' C2' 344.1 333.7
C4' O4' C1' N1 221.2 214.1
C4' O4' C1' H1' 101.9 93.2
C3' C4' C5' H5'1 285.4 305.0
C3' C4' C5' H5'2 164.6 65.0
C5' C4' C3' O4' 242.1 241.3
C5' C4' C3' H4' 119.8 122.8
O4' C4' C3' H4' 237.7 241.6
C3' C4' O4' C1' 357.1 39.9
O3' C3' C4' C2' 245.1 241.8
O3' C3' C4' H3' 121.2 123.6
C4' C3' O3' HO3' 113.9 174.2
C2' C3' C4' H3' 236.0 241.8
C4' C3' C2' C1' 332.7 20.9
C4' C3' C2' H2'1 92.7 262.2
C4' C3' C2' H2'2 209.7 139.6
H4' C4' C5' H5'1 43.5 67.9
H4' C4' C5' H5'2 282.8 187.9
C5' C4' H4' O4' 118.1 123.0
C5' C4' H4' C3' 237.7 237.1
O4' C4' H4' C3' 119.7 114.2
H4' C4' O4' C1' 238.9 281.3
H4' C4' C3' O3' 27.4 323.3
H4' C4' C3' C2' 142.3 81.5
H4' C4' C3' H3' 266.3 199.7
C1' O4' C4' C3' 357.1 39.9
C1' O4' C4' H4' 238.9 281.3
C3' C2' C1' O4' 27.4 1.9
O4' C1' C2' H2'1 267.4 120.6
O4' C1' C2' H2'2 150.4 243.3
C2' C1' O4' N1 122.9 119.6
C2' C1' O4' H1' 242.2 240.5
N1 C1' O4' H1' 119.3 120.9
O4' C1' N1 C2 220.6 53.4
O4' C1' N1 C6 42.0 233.3
O3' C3' C4' H4' 27.4 323.3
C4' C3' O3' C2' 112.9 112.7
C4' C3' O3' H3' 237.2 236.4
C2' C3' O3' H3' 124.3 123.7
O3' C3' C2' C1' 89.5 139.1
O3' C3' C2' H2'1 209.5 20.4
O3' C3' C2' H2'2 326.5 257.8
C2' C3' C4' H4' 142.3 81.5
C4' C3' C2' O3' 243.2 241.8
C4' C3' C2' H3' 122.3 118.2
O4' C1' C2' C3' 27.4 1.9
O3' C3' C2' H3' 239.1 236.4
C2' C3' O3' HO3' 1.0 61.5
C1' C2' C3' H2'1 240.0 118.7
C1' C2' C3' H2'2 123.0 241.3
C3' C2' C1' N1 147.4 121.4
C3' C2' C1' H1' 266.6 242.5
H2'1 C2' C3' H2'2 243.0 122.6
H3' C3' C4' H4' 266.3 199.7
C4' C3' H3' O3' 121.9 123.6
C4' C3' H3' C2' 241.9 247.3
O3' C3' H3' C2' 120.0 123.7
H3' C3' O3' HO3' 236.7 297.8
H3' C3' C2' C1' 210.4 262.7
H3' C3' C2' H2'1 330.4 144.0
H3' C3' C2' H2'2 87.4 21.4
HO3' O3' C3' C2' 1.0 61.5
HO3' O3' C3' H3' 236.7 297.8
O4' C1' C2' N1 239.9 240.5
O4' C1' C2' H1' 120.8 119.5
C1' C2' C3' H3' 210.4 262.7
C3' C2' C1' H2'1 120.0 241.3
C3' C2' C1' H2'2 237.0 118.6
H2'1 C2' C1' H2'2 117.0 237.3
N1 C1' C2' H1' 240.8 239.0
C2' C1' N1 C2 99.1 295.3
C2' C1' N1 C6 280.6 115.3
H2'1 C2' C3' H3' 330.4 144.0
C3' C2' H2'1 C1' 247.0 114.8
C3' C2' H2'1 H2'2 123.5 237.5
C1' C2' H2'1 H2'2 236.5 122.7
H2'1 C2' C1' N1 27.5 240.1
H2'1 C2' C1' H1' 146.6 1.1
H2'2 C2' C3' H3' 87.4 21.4
C3' C2' H2'2 C1' 115.4 245.2
C3' C2' H2'2 H2'1 237.7 122.6
C1' C2' H2'2 H2'1 122.3 237.3
H2'2 C2' C1' N1 270.4 2.8
H2'2 C2' C1' H1' 29.6 123.8
O4' C1' N1 C2' 121.4 118.0
O4' C1' N1 H1' 239.1 239.1
N1 C1' C2' H2'1 27.5 240.1
N1 C1' C2' H2'2 270.4 2.8
C2' C1' N1 H1' 117.7 121.1
C2 N1 C1' C6 178.6 180.1
C1' N1 C2 O2 358.2 360.0
C1' N1 C2 N3 181.1 179.9
C1' N1 C6 C5 180.6 180.1
C1' N1 C6 H6 0.6 0.1
O4' C1' H1' C2' 240.0 242.0
O4' C1' H1' N1 118.6 120.9
H1' C1' C2' H2'1 146.6 1.1
H1' C1' C2' H2'2 29.6 123.8
C2' C1' H1' N1 238.5 238.9
H1' C1' N1 C2 341.4 174.3
H1' C1' N1 C6 162.9 354.2
C2 N1 C1' H1' 341.4 174.3
C1' N1 C2 C6 181.4 179.9
C2 N1 C6 C5 2.1 360.0
C2 N1 C6 H6 182.1 180.0
O2 C2 N1 N3 177.1 180.1
N1 C2 N3 C4 358.5 359.8
N1 C2 N3 HN3 178.5 180.0
C6 N1 C1' H1' 162.9 354.2
C1' N1 C6 C2 178.5 180.1
C6 N1 C2 O2 176.7 180.0
C6 N1 C2 N3 359.6 360.0
C4 C5 C6 N1 358.1 0.2
C5M C5 C6 N1 178.3 180.0
C5 C6 N1 H6 180.0 180.0
O2 C2 N1 C6 176.7 180.0
N1 C2 O2 N3 182.9 179.9
O2 C2 N3 C4 181.4 179.8
O2 C2 N3 HN3 1.5 359.9
N3 C2 N1 C6 359.6 360.0
N1 C2 N3 O2 177.1 180.1
C4 N3 C2 HN3 180.0 179.8
C2 N3 C4 O4 181.0 180.0
C2 N3 C4 C5 1.5 0.4
C2 N3 C4 HN3 180.0 180.2
O4 C4 N3 C5 179.5 179.6
N3 C4 C5 C5M 179.9 179.8
N3 C4 C5 C6 0.2 359.6
C2 N3 HN3 C4 180.0 179.8
HN3 N3 C4 O4 1.0 359.8
HN3 N3 C4 C5 181.5 180.2
O4 C4 N3 HN3 1.0 359.8
N3 C4 O4 C5 180.5 180.5
O4 C4 C5 C5M 0.4 0.3
O4 C4 C5 C6 180.6 180.0
N1 C6 C5 C4 358.1 0.2
C5 C4 N3 HN3 181.5 180.2
N3 C4 C5 O4 179.5 179.6
C5M C5 C4 C6 179.8 180.3
C4 C5 C5M H51 157.3 269.7
C4 C5 C5M H52 277.3 29.7
C4 C5 C5M H53 37.3 149.7
C4 C5 C6 H6 178.1 180.2
N1 C6 C5 C5M 178.3 180.0
C4 C5 C5M C6 180.3 179.7
C5M C5 C6 H6 358.3 360.0
H51 C5M C5 H52 240.0 240.0
H51 C5M C5 H53 120.0 120.0
H52 C5M C5 H53 240.0 240.0
N1 C6 C5 H6 180.0 180.0
C4 C5 C6 C5M 179.8 180.3
C6 C5 C5M H51 337.0 90.0
C6 C5 C5M H52 97.0 210.0
C6 C5 C5M H53 217.0 330.0
H51 C5M C5 C6 337.0 90.0
C5 C5M H51 H52 120.0 120.1
C5 C5M H51 H53 240.0 240.0
H52 C5M H51 H53 120.0 120.0
H52 C5M C5 C6 97.0 210.0
C5 C5M H52 H51 239.9 239.9
C5 C5M H52 H53 120.0 120.0
H51 C5M H52 H53 240.1 240.0
H53 C5M C5 C6 217.0 330.0
C5 C5M H53 H51 120.0 120.0
C5 C5M H53 H52 240.0 240.0
H51 C5M H53 H52 119.9 120.0
N1 C6 H6 C5 180.0 180.0