PDB Chemical Component TM2

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 TM2

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O1P 1.480 1.480
P O2P 1.479 1.610
P O3P 1.468 1.610
P O5' 1.600 1.610
O5' C5' 1.424 1.430
C5' C4' 1.518 1.529
C4' O4' 1.450 1.438
C4' C3' 1.523 1.540
O4' C1' 1.416 1.444
C1' N1 1.490 1.465
C1' C2' 1.525 1.549
N1 C6 1.380 1.368
N1 C2 1.379 1.345
C6 C5 1.338 1.350
C2 O2 1.218 1.215
C2 N3 1.373 1.346
N3 C4 1.383 1.349
C4 O4 1.226 1.218
C4 C5 1.440 1.416
C5 C7 1.552 1.507
C2' O2' 1.414 1.429
C2' C3' 1.525 1.549
C3' O3' 1.422 1.429
C7 N8 1.588 1.469
N8 C9 1.525 1.469
C9 C11 1.528 1.530
C11 S12 1.846 1.814
S12 O1S 1.474 1.421
S12 O2S 1.475 1.421
S12 O3S 1.469 1.522
O3S H3S 0.950 0.967
O2P H2P 0.950 0.966
O3P H3P 0.950 0.967
C5' H5'1 1.100 1.089
C5' H5'2 1.100 1.090
C4' H4' 1.100 1.090
C3' H3' 1.099 1.090
C1' H1' 1.100 1.090
C2' H2' 1.100 1.090
C6 H6 1.080 1.081
N3 H3 1.000 0.970
C7 H7C1 1.100 1.091
C7 H7C2 1.100 1.089
O2' HA 0.950 0.967
O3' HB 0.950 0.967
N8 H8 1.000 1.009
C9 H9C1 1.100 1.090
C9 H9C2 1.100 1.090
C11 H111 1.100 1.090
C11 H112 1.100 1.091

Bond Angles for TM2

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1P P O2P 120.1 109.5
O1P P O3P 105.7 109.5
O1P P O5' 109.0 109.5
O2P P O3P 113.4 109.5
O2P P O5' 108.0 109.4
P O2P H2P 109.5 114.0
O3P P O5' 98.5 109.5
P O3P H3P 109.5 113.9
P O5' C5' 120.0 123.0
O5' C5' C4' 110.9 109.5
O5' C5' H5'1 109.0 109.4
O5' C5' H5'2 108.7 109.5
C5' C4' O4' 109.3 109.9
C5' C4' C3' 114.9 109.9
C4' C5' H5'1 109.0 109.5
C4' C5' H5'2 108.7 109.5
C5' C4' H4' 104.7 109.9
O4' C4' C3' 105.5 107.3
C4' O4' C1' 110.0 106.9
O4' C4' H4' 114.1 109.8
C4' C3' C2' 102.2 104.2
C4' C3' O3' 110.0 110.5
C3' C4' H4' 108.5 110.0
C4' C3' H3' 114.5 110.5
O4' C1' N1 108.4 110.6
O4' C1' C2' 106.7 103.5
O4' C1' H1' 113.4 110.6
N1 C1' C2' 113.5 110.6
C1' N1 C6 119.4 119.7
C1' N1 C2 119.3 119.7
N1 C1' H1' 106.6 110.5
C1' C2' O2' 110.2 110.9
C1' C2' C3' 101.5 102.1
C2' C1' H1' 108.3 110.8
C1' C2' H2' 115.1 110.9
C6 N1 C2 121.3 120.6
N1 C6 C5 122.8 119.7
N1 C6 H6 118.6 120.1
N1 C2 O2 123.2 119.5
N1 C2 N3 114.8 120.9
C6 C5 C4 119.2 119.1
C6 C5 C7 129.3 120.4
C5 C6 H6 118.6 120.1
O2 C2 N3 121.9 119.5
C2 N3 C4 127.0 120.3
C2 N3 H3 116.5 119.9
N3 C4 O4 119.8 120.4
N3 C4 C5 114.8 119.3
C4 N3 H3 116.5 119.8
O4 C4 C5 125.4 120.3
C4 C5 C7 111.5 120.4
C5 C7 N8 134.1 109.5
C5 C7 H7C1 102.0 109.4
C5 C7 H7C2 96.3 109.5
O2' C2' C3' 112.4 110.9
O2' C2' H2' 104.9 110.8
C2' O2' HA 109.5 114.0
C2' C3' O3' 111.5 110.4
C2' C3' H3' 113.0 110.4
C3' C2' H2' 113.0 110.9
O3' C3' H3' 105.7 110.6
C3' O3' HB 109.5 114.0
C7 N8 C9 106.1 111.0
N8 C7 H7C1 101.9 109.5
N8 C7 H7C2 96.3 109.5
C7 N8 H8 110.6 111.0
N8 C9 C11 96.7 109.5
C9 N8 H8 110.6 111.0
N8 C9 H9C1 114.0 109.4
N8 C9 H9C2 116.5 109.5
C9 C11 S12 115.7 109.5
C11 C9 H9C1 114.0 109.5
C11 C9 H9C2 116.5 109.5
C9 C11 H111 107.4 109.5
C9 C11 H112 106.0 109.4
C11 S12 O1S 111.1 110.6
C11 S12 O2S 112.1 110.5
C11 S12 O3S 109.3 104.5
S12 C11 H111 107.4 109.5
S12 C11 H112 106.0 109.5
O1S S12 O2S 106.0 121.0
O1S S12 O3S 109.6 104.2
O2S S12 O3S 108.8 104.3
S12 O3S H3S 109.5 114.0
H5'1 C5' H5'2 110.6 109.5
H7C1 C7 H7C2 131.6 109.4
H9C1 C9 H9C2 100.1 109.5
H111 C11 H112 114.5 109.5

Torsion Angles for TM2

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2P P O1P O3P 230.2 240.0
O2P P O1P O5' 125.2 120.0
O1P P O2P H2P 319.5 60.0
O3P P O1P O5' 255.0 240.0
O1P P O3P H3P 244.3 180.1
O1P P O5' C5' 53.7 305.0
O1P P O2P O3P 126.3 120.0
O1P P O2P O5' 234.3 240.0
O3P P O2P O5' 108.0 120.0
O2P P O3P H3P 17.8 300.1
O2P P O5' C5' 281.7 185.0
O1P P O3P O2P 226.4 240.0
O1P P O3P O5' 112.6 120.0
O2P P O3P O5' 246.1 240.0
O3P P O2P H2P 193.2 300.0
O3P P O5' C5' 163.6 65.0
O1P P O5' O2P 132.0 120.0
O1P P O5' O3P 250.1 240.0
O2P P O5' O3P 118.1 120.0
O5' P O2P H2P 85.2 180.0
O5' P O3P H3P 131.7 60.0
P O5' C5' C4' 182.2 180.0
P O5' C5' H5'1 302.2 300.0
P O5' C5' H5'2 62.8 60.0
O5' C5' C4' O4' 268.4 66.4
O5' C5' C4' C3' 26.8 184.3
C4' C5' O5' H5'1 240.0 240.0
C4' C5' O5' H5'2 119.4 120.0
O5' C5' C4' H4' 145.7 305.5
H5'1 C5' O5' H5'2 239.4 240.0
O5' C5' C4' H5'1 120.0 120.0
O5' C5' C4' H5'2 240.6 240.0
O4' C4' C5' C3' 241.6 242.1
C5' C4' O4' C1' 135.6 145.9
O4' C4' C5' H4' 122.7 121.0
C5' C4' C3' C2' 209.0 238.6
C5' C4' C3' O3' 90.4 119.9
C3' C4' C5' H4' 241.1 238.8
C5' C4' C3' H3' 331.6 357.2
H5'1 C5' C4' H5'2 120.6 120.0
C5' C4' O4' C3' 124.1 119.4
O4' C4' C5' H5'1 148.4 306.4
O4' C4' C5' H5'2 27.8 186.4
C5' C4' O4' H4' 243.1 239.0
O4' C4' C3' C2' 329.5 358.0
O4' C4' C3' O3' 210.9 239.4
C3' C4' O4' H4' 119.1 119.6
O4' C4' C3' H3' 92.1 116.7
C4' O4' C1' N1 250.0 201.5
C4' O4' C1' C2' 12.6 319.9
C4' O4' C1' H1' 131.8 78.7
C5' C4' C3' O4' 239.5 240.6
C3' C4' C5' H5'1 266.8 64.3
C3' C4' C5' H5'2 146.2 304.3
C5' C4' C3' H4' 116.7 121.1
C3' C4' O4' C1' 11.5 26.5
O4' C4' C3' H4' 237.3 240.6
C1' C2' C3' C4' 36.8 339.1
O2' C2' C3' C4' 279.1 220.9
C2' C3' C4' O3' 118.6 118.6
C2' C3' C4' H3' 237.4 241.3
C4' C3' C2' H2' 160.7 97.3
O3' C3' C4' H3' 118.8 122.7
C4' C3' O3' HB 251.8 180.1
C1' O4' C4' C3' 11.5 26.5
C1' O4' C4' H4' 252.4 266.9
N1 C1' O4' C2' 237.4 241.5
O4' C1' N1 C6 28.7 233.6
O4' C1' N1 C2 208.7 53.3
N1 C1' O4' H1' 118.2 122.8
O4' C1' C2' O2' 88.1 155.2
O4' C1' C2' C3' 328.8 37.0
C2' C1' O4' H1' 240.8 241.3
O4' C1' C2' H2' 206.4 278.8
O4' C1' N1 C2' 118.4 114.1
O4' C1' N1 H1' 237.5 237.2
N1 C1' C2' O2' 207.4 273.7
N1 C1' C2' C3' 88.2 155.5
C2' C1' N1 H1' 119.2 123.1
N1 C1' C2' H2' 325.7 37.3
C6 N1 C1' C2 180.0 180.2
C1' N1 C6 C5 180.0 180.0
C1' N1 C6 H6 360.0 0.0
C1' N1 C2 O2 0.0 0.0
C1' N1 C2 N3 180.1 180.0
C4' C3' C2' C1' 36.8 339.1
O4' C1' C2' N1 240.7 241.5
O4' C1' C2' H1' 122.5 118.6
C2' C1' N1 C6 270.4 119.5
C2' C1' N1 C2 90.3 299.2
N1 C1' C2' H1' 241.8 237.1
O2' C2' C1' C3' 119.2 118.2
O2' C2' C1' H2' 241.7 236.4
C1' C2' O2' HA 231.6 180.1
C1' C2' C3' O3' 154.2 97.8
C1' C2' C3' H3' 273.1 220.4
C3' C2' C1' H2' 122.5 118.2
C6 N1 C1' C2' 270.4 119.5
C1' N1 C6 C2 180.0 179.8
C6 N1 C1' H1' 151.2 356.4
C6 N1 C2 O2 180.0 179.8
C6 N1 C2 N3 0.0 359.7
N1 C6 C5 C4 0.0 360.0
N1 C6 C5 C7 180.6 180.0
C5 C6 N1 H6 180.0 180.0
C2 N1 C1' C2' 90.3 299.2
C1' N1 C2 C6 180.0 180.2
C2 N1 C1' H1' 331.2 176.1
C2 N1 C6 C5 0.0 0.2
C2 N1 C6 H6 180.0 180.2
O2 C2 N1 N3 180.0 180.0
N1 C2 N3 C4 359.9 0.1
N1 C2 N3 H3 179.9 180.0
C5 C6 N1 C2 0.0 0.2
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 359.9 359.8
O4 C4 C5 C6 180.1 180.0
C4 C5 C6 C7 179.4 180.0
C6 C5 C7 N8 133.8 95.0
C6 C5 C7 H7C1 253.7 215.0
C6 C5 C7 H7C2 28.6 334.9
N1 C2 O2 N3 180.0 180.0
O2 C2 N3 C4 179.9 180.0
O2 C2 N3 H3 359.9 359.9
N1 C2 N3 O2 180.0 180.0
C2 N3 C4 O4 180.0 180.0
C2 N3 C4 C5 0.1 0.2
C4 N3 C2 H3 180.0 180.1
C6 C5 C4 N3 359.9 359.8
C2 N3 C4 H3 180.0 179.9
O4 C4 N3 C5 179.8 179.8
N3 C4 C5 C7 179.4 179.8
C6 C5 C4 O4 180.1 180.0
N3 C4 O4 C5 180.2 180.2
O4 C4 N3 H3 360.0 0.1
O4 C4 C5 C7 359.6 359.9
C6 C5 C4 C7 180.5 180.0
C4 C5 C6 H6 180.0 180.0
N3 C4 C5 O4 179.8 179.8
C5 C4 N3 H3 180.1 180.2
C4 C5 C7 N8 314.3 275.1
C4 C5 C7 H7C1 74.3 35.0
C4 C5 C7 H7C2 209.2 155.0
C6 C5 C7 C4 179.4 180.0
C7 C5 C6 H6 0.6 0.0
C5 C7 N8 C9 254.6 180.0
N8 C7 C5 H7C1 240.0 240.0
N8 C7 C5 H7C2 105.1 120.1
C5 C7 N8 H8 14.6 303.9
H7C1 C7 C5 H7C2 225.1 240.1
C4' C3' C2' O2' 279.1 220.9
C1' C2' O2' C3' 247.6 247.3
O2' C2' C1' H1' 325.6 36.6
C1' C2' O2' H2' 124.5 123.7
O2' C2' C3' O3' 36.5 339.6
O2' C2' C3' H3' 155.5 102.2
C3' C2' O2' H2' 236.9 236.3
C4' C3' C2' O3' 242.5 241.3
C2' C3' C4' H4' 92.2 117.4
C4' C3' C2' H3' 123.6 118.7
C1' C2' C3' O2' 117.7 118.2
C3' C2' C1' H1' 206.4 278.5
C1' C2' C3' H2' 236.1 241.8
O2' C2' C3' H2' 118.4 123.6
C3' C2' O2' HA 344.0 292.7
O3' C3' C2' H3' 241.1 237.4
C2' C3' O3' HB 139.2 65.3
C4' C3' O3' C2' 112.6 114.8
O3' C3' C4' H4' 333.7 358.8
C4' C3' O3' H3' 235.9 237.3
C2' C3' O3' H3' 123.2 122.6
O3' C3' C2' H2' 278.1 216.0
C5 C7 N8 H7C1 120.0 120.0
C5 C7 N8 H7C2 254.9 240.0
C7 N8 C9 C11 153.3 180.0
C9 N8 C7 H8 240.0 236.1
C7 N8 C9 H9C1 273.3 299.9
C7 N8 C9 H9C2 29.2 60.0
H7C1 C7 N8 H7C2 134.9 120.0
C9 N8 C7 H7C1 134.6 60.0
C9 N8 C7 H7C2 359.7 300.0
C7 N8 C9 H8 120.0 123.9
N8 C9 C11 S12 273.2 180.0
C11 C9 N8 H9C1 240.0 240.0
C11 C9 N8 H9C2 124.1 120.0
N8 C9 C11 H111 33.2 300.0
N8 C9 C11 H112 156.1 60.0
H9C1 C9 N8 H9C2 244.1 240.0
C11 C9 N8 H8 33.3 56.1
N8 C9 C11 H9C1 120.0 119.9
N8 C9 C11 H9C2 235.9 240.0
C9 C11 S12 O1S 270.3 291.6
C9 C11 S12 O2S 28.6 68.4
C9 C11 S12 O3S 149.3 180.0
S12 C11 C9 H111 240.0 240.0
S12 C11 C9 H112 117.1 120.0
H9C1 C9 C11 H9C2 115.9 120.1
H111 C11 C9 H112 237.1 240.0
S12 C11 C9 H9C1 153.2 60.0
S12 C11 C9 H9C2 37.4 300.0
C9 C11 S12 H111 120.0 120.0
C9 C11 S12 H112 242.9 240.0
O1S S12 C11 O2S 241.7 223.3
O1S S12 C11 O3S 121.0 111.6
O2S S12 C11 O3S 239.3 248.3
C11 S12 O3S H3S 347.8 180.0
H111 C11 S12 H112 122.9 120.0
C11 S12 O1S O2S 121.9 131.5
C11 S12 O1S O3S 239.2 248.3
O1S S12 C11 H111 150.3 171.6
O1S S12 C11 H112 27.4 51.6
O2S S12 O1S O3S 117.3 116.7
O1S S12 O3S H3S 225.9 63.9
C11 S12 O2S O1S 238.7 228.5
C11 S12 O2S O3S 121.0 111.8
O2S S12 C11 H111 268.6 308.3
O2S S12 C11 H112 145.7 188.3
O1S S12 O2S O3S 242.3 243.3
O2S S12 O3S H3S 110.4 296.1
C11 S12 O3S O1S 121.9 116.1
C11 S12 O3S O2S 237.3 243.9
O3S S12 C11 H111 29.3 60.0
O3S S12 C11 H112 266.4 300.0
O1S S12 O3S O2S 115.4 127.8
H2P O2P P O3P 193.2 300.0
H2P O2P P O5' 85.2 180.0
H3P O3P P O5' 131.7 60.0
O5' C5' H5'1 C4' 238.8 240.0
O5' C5' H5'1 H5'2 119.4 120.0
H5'1 C5' C4' O4' 148.4 306.4
H5'1 C5' C4' C3' 266.8 64.3
C4' C5' H5'1 H5'2 240.6 240.0
H5'1 C5' C4' H4' 25.7 185.5
O5' C5' H5'2 C4' 120.8 120.0
O5' C5' H5'2 H5'1 240.4 240.0
H5'2 C5' C4' O4' 27.8 186.4
H5'2 C5' C4' C3' 146.2 304.3
C4' C5' H5'2 H5'1 119.6 120.0
H5'2 C5' C4' H4' 265.1 65.5
C5' C4' H4' O4' 119.5 121.0
C5' C4' H4' C3' 236.9 238.9
H4' C4' C5' H5'1 25.7 185.5
H4' C4' C5' H5'2 265.1 65.5
O4' C4' H4' C3' 117.4 117.9
H4' C4' O4' C1' 252.4 266.9
H4' C4' C3' C2' 92.2 117.4
H4' C4' C3' O3' 333.7 358.8
H4' C4' C3' H3' 214.8 236.1
C4' C3' H3' C2' 243.5 245.2
C4' C3' H3' O3' 121.2 122.7
H3' C3' C4' H4' 214.8 236.1
C2' C3' H3' O3' 237.7 237.4
H3' C3' C2' H2' 37.0 338.6
H3' C3' O3' HB 16.0 302.7
O4' C1' H1' N1 119.2 122.8
O4' C1' H1' C2' 241.7 245.8
N1 C1' H1' C2' 122.5 123.0
H1' C1' N1 C6 151.2 356.4
H1' C1' N1 C2 331.2 176.1
H1' C1' C2' O2' 325.6 36.6
H1' C1' C2' C3' 206.4 278.5
H1' C1' C2' H2' 83.9 160.2
C1' C2' H2' O2' 238.8 236.4
C1' C2' H2' C3' 116.1 112.7
H2' C2' C1' H1' 83.9 160.2
O2' C2' H2' C3' 237.3 236.3
H2' C2' O2' HA 107.2 56.4
H2' C2' C3' O3' 278.1 216.0
H2' C2' C3' H3' 37.0 338.6
H6 C6 N1 C2 180.0 180.2
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 180.0 180.0
H6 C6 C5 C7 0.6 0.0
C2 N3 H3 C4 180.0 180.1
H3 N3 C4 O4 360.0 0.1
H3 N3 C4 C5 180.1 180.2
C5 C7 H7C1 N8 219.5 240.0
C5 C7 H7C1 H7C2 109.8 119.9
H7C1 C7 N8 C9 134.6 60.0
N8 C7 H7C1 H7C2 250.3 239.9
H7C1 C7 N8 H8 254.6 183.9
C5 C7 H7C2 N8 135.8 120.1
C5 C7 H7C2 H7C1 247.8 240.1
H7C2 C7 N8 C9 359.7 300.0
N8 C7 H7C2 H7C1 112.1 120.0
H7C2 C7 N8 H8 119.7 63.9
HA O2' C2' C3' 344.0 292.7
HA O2' C2' H2' 107.2 56.4
HB O3' C3' H3' 16.0 302.7
C7 N8 H8 C9 242.8 236.1
H8 N8 C7 H7C1 254.6 183.9
H8 N8 C7 H7C2 119.7 63.9
H8 N8 C9 C11 33.3 56.1
H8 N8 C9 H9C1 153.3 176.0
H8 N8 C9 H9C2 269.2 296.1
N8 C9 H9C1 C11 250.3 240.0
H9C1 C9 N8 H8 153.3 176.0
N8 C9 H9C1 H9C2 125.1 120.0
H9C1 C9 C11 S12 153.2 60.0
C11 C9 H9C1 H9C2 234.9 239.9
H9C1 C9 C11 H111 273.2 180.0
H9C1 C9 C11 H112 36.1 300.1
N8 C9 H9C2 C11 113.3 120.0
H9C2 C9 N8 H8 269.2 296.1
N8 C9 H9C2 H9C1 236.6 240.0
H9C2 C9 C11 S12 37.4 300.0
C11 C9 H9C2 H9C1 123.4 120.1
H9C2 C9 C11 H111 157.3 60.0
H9C2 C9 C11 H112 280.2 180.0
C9 C11 H111 S12 234.9 240.0
H111 C11 C9 H9C1 273.2 180.0
H111 C11 C9 H9C2 157.3 60.0
C9 C11 H111 H112 117.4 120.0
H111 C11 S12 O1S 150.3 171.6
H111 C11 S12 O2S 268.6 308.3
H111 C11 S12 O3S 29.3 60.0
S12 C11 H111 H112 242.6 240.0
C9 C11 H112 S12 123.5 120.0
H112 C11 C9 H9C1 36.1 300.1
H112 C11 C9 H9C2 280.2 180.0
C9 C11 H112 H111 241.7 240.0
H112 C11 S12 O1S 27.4 51.6
H112 C11 S12 O2S 145.7 188.3
H112 C11 S12 O3S 266.4 300.0
S12 C11 H112 H111 118.2 120.0