PDB Chemical Component CDW

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 CDW

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.476 1.480
P OP2 1.506 1.609
P O5' 1.592 1.610
P OP3 1.574 1.611
O5' C5' 1.420 1.429
C5' C4' 1.536 1.530
C4' O4' 1.448 1.445
C4' C3' 1.525 1.549
O4' C1' 1.410 1.438
C3' O3' 1.402 1.429
C3' C2' 1.501 1.548
C2' C1' 1.520 1.542
C1' N1 1.439 1.465
N1 C2 1.382 1.342
N1 C6 1.421 1.461
C2 O2 1.219 1.216
C2 N3 1.419 1.343
N3 C4 1.324 1.388
N3 C6 1.501 1.457
C4 C5 1.411 1.314
OP2 HP2 0.950 0.967
OP3 HP3 0.950 0.967
C5' H51 1.100 1.090
C5' H52 1.100 1.090
C4' H4' 1.099 1.089
C3' H3' 1.100 1.090
C1' H1' 1.100 1.090
O3' HA 0.950 0.967
C2' H21 1.100 1.090
C2' H22 1.100 1.089
C6 C5 1.436 1.496
C6 H6 1.100 1.090
C4 H41C 1.080 1.080
C5 H51C 1.080 1.081

Bond Angles for CDW

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 121.4 109.5
OP1 P O5' 105.0 109.5
OP1 P OP3 108.5 109.4
OP2 P O5' 110.1 109.5
OP2 P OP3 106.3 109.5
P OP2 HP2 109.5 114.0
O5' P OP3 104.4 109.4
P O5' C5' 121.8 123.0
P OP3 HP3 109.5 114.0
O5' C5' C4' 109.6 109.5
O5' C5' H51 109.4 109.4
O5' C5' H52 109.4 109.4
C5' C4' O4' 112.0 110.6
C5' C4' C3' 113.1 110.6
C4' C5' H51 109.4 109.5
C4' C5' H52 109.4 109.5
C5' C4' H4' 104.1 110.6
O4' C4' C3' 105.9 103.5
C4' O4' C1' 109.5 107.0
O4' C4' H4' 111.5 110.6
C4' C3' O3' 111.3 110.9
C4' C3' C2' 106.3 102.1
C3' C4' H4' 110.4 110.8
C4' C3' H3' 109.5 110.9
O4' C1' C2' 108.4 107.3
O4' C1' N1 108.7 109.9
O4' C1' H1' 109.9 109.9
O3' C3' C2' 106.7 110.9
O3' C3' H3' 109.1 110.8
C3' O3' HA 109.5 114.0
C3' C2' C1' 105.3 104.2
C2' C3' H3' 113.9 110.9
C3' C2' H21 110.9 110.5
C3' C2' H22 111.8 110.5
C2' C1' N1 107.3 109.9
C2' C1' H1' 111.3 109.9
C1' C2' H21 110.9 110.5
C1' C2' H22 111.8 110.5
C1' N1 C2 133.2 133.9
C1' N1 C6 129.6 133.9
N1 C1' H1' 111.1 110.0
C2 N1 C6 90.2 92.2
N1 C2 O2 130.4 133.8
N1 C2 N3 94.6 92.3
N1 C6 N3 89.5 83.2
N1 C6 C5 134.0 118.7
N1 C6 H6 103.4 118.6
O2 C2 N3 135.0 133.9
C2 N3 C4 134.5 120.5
C2 N3 C6 85.7 92.3
C4 N3 C6 92.4 92.0
N3 C4 C5 91.9 92.2
N3 C4 H41C 134.0 133.9
N3 C6 C5 84.1 82.5
N3 C6 H6 145.2 124.2
C4 C5 C6 91.6 93.3
C5 C4 H41C 134.0 133.9
C4 C5 H51C 134.2 133.3
H51 C5' H52 109.6 109.5
H21 C2' H22 106.3 110.5
C5 C6 H6 107.6 118.6
C6 C5 H51C 134.2 133.4

Torsion Angles for CDW

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 O5' 125.5 239.9
OP2 P OP1 OP3 236.6 120.0
OP1 P OP2 HP2 205.0 180.0
O5' P OP1 OP3 111.1 240.1
OP1 P O5' C5' 178.1 305.0
OP1 P OP3 HP3 127.5 60.1
OP1 P OP2 O5' 236.9 120.0
OP1 P OP2 OP3 124.4 240.0
O5' P OP2 OP3 247.5 120.0
OP2 P O5' C5' 45.9 65.0
OP2 P OP3 HP3 259.6 300.1
OP1 P O5' OP2 132.2 239.9
OP1 P O5' OP3 246.0 119.9
OP2 P O5' OP3 113.8 240.0
O5' P OP2 HP2 328.1 59.9
O5' P OP3 HP3 16.0 180.0
P O5' C5' C4' 173.3 180.0
P O5' C5' H51 293.2 300.0
P O5' C5' H52 53.3 60.0
OP1 P OP3 OP2 228.0 120.0
OP1 P OP3 O5' 111.5 240.0
OP2 P OP3 O5' 243.5 120.0
OP3 P OP2 HP2 80.6 299.9
OP3 P O5' C5' 292.1 185.0
C5' O5' P OP3 292.1 185.0
O5' C5' C4' O4' 278.2 66.5
O5' C5' C4' C3' 37.7 180.5
C4' C5' O5' H51 240.0 240.0
C4' C5' O5' H52 119.9 120.0
O5' C5' C4' H4' 157.5 303.6
H51 C5' O5' H52 239.9 240.0
O5' C5' C4' H51 120.0 120.0
O5' C5' C4' H52 240.1 240.0
O4' C4' C5' C3' 240.5 245.9
C5' C4' O4' C1' 146.1 158.6
O4' C4' C5' H4' 120.6 122.8
C5' C4' C3' O3' 104.6 86.3
C5' C4' C3' C2' 220.4 204.5
C3' C4' C5' H4' 240.2 236.9
C5' C4' C3' H3' 343.9 322.7
H51 C5' C4' H52 120.1 120.0
C5' C4' O4' C3' 123.7 118.5
O4' C4' C5' H51 158.2 306.5
O4' C4' C5' H52 38.1 186.5
C5' C4' O4' H4' 243.8 237.2
O4' C4' C3' O3' 227.6 204.7
O4' C4' C3' C2' 343.4 322.9
C3' C4' O4' H4' 120.1 118.7
O4' C4' C3' H3' 106.9 81.2
C4' O4' C1' C2' 340.6 333.5
C4' O4' C1' N1 224.3 214.1
C4' O4' C1' H1' 102.5 92.9
C5' C4' C3' O4' 237.0 241.5
C3' C4' C5' H51 277.7 60.5
C3' C4' C5' H52 157.6 300.5
C5' C4' C3' H4' 116.2 123.0
C3' C4' O4' C1' 22.4 40.1
O4' C4' C3' H4' 239.1 241.4
O3' C3' C4' C2' 244.2 241.8
O3' C3' C4' H3' 120.7 123.6
C4' C3' O3' HA 232.5 180.0
C4' C3' C2' C1' 5.3 20.9
C2' C3' C4' H3' 236.5 241.8
C4' C3' C2' H21 125.3 139.5
C4' C3' C2' H22 243.8 262.2
C1' O4' C4' C3' 22.4 40.1
C1' O4' C4' H4' 262.3 281.4
C3' C2' C1' O4' 8.1 2.0
C2' C1' O4' N1 116.3 119.4
C2' C1' O4' H1' 238.1 240.6
O4' C1' C2' H21 248.1 243.4
O4' C1' C2' H22 129.7 120.8
O4' C1' N1 C2 300.1 53.5
O4' C1' N1 C6 81.6 233.2
N1 C1' O4' H1' 121.8 121.2
C4' C3' O3' C2' 115.6 112.7
O3' C3' C4' H4' 348.4 323.3
C4' C3' O3' H3' 239.0 236.4
O3' C3' C2' C1' 124.3 139.1
C2' C3' O3' H3' 123.5 123.6
O3' C3' C2' H21 244.3 257.7
O3' C3' C2' H22 2.7 20.5
C4' C3' C2' O3' 241.1 241.8
C2' C3' C4' H4' 104.3 81.5
C4' C3' C2' H3' 120.7 118.3
O4' C1' C2' C3' 8.1 2.0
O3' C3' C2' H3' 239.6 236.5
C2' C3' O3' HA 116.9 67.2
C3' C2' C1' N1 125.4 121.4
C3' C2' C1' H1' 247.1 242.6
C1' C2' C3' H21 240.0 241.4
C1' C2' C3' H22 121.6 118.7
H21 C2' C3' H22 241.6 237.3
O4' C1' C2' N1 242.7 240.6
O4' C1' C2' H1' 121.0 119.4
C1' C2' C3' H3' 244.7 262.6
C3' C2' C1' H21 120.0 118.7
C3' C2' C1' H22 238.4 241.3
C2' C1' N1 C2 183.0 295.7
C2' C1' N1 C6 324.5 115.4
N1 C1' C2' H1' 238.3 238.8
H21 C2' C1' H22 118.4 122.6
O4' C1' N1 C2' 117.1 117.8
O4' C1' N1 H1' 238.9 238.9
C2' C1' N1 H1' 121.8 121.1
N1 C1' C2' H21 5.4 2.8
N1 C1' C2' H22 247.0 240.1
C2 N1 C1' C6 218.4 180.3
C1' N1 C2 O2 330.8 359.3
C1' N1 C2 N3 151.8 179.3
C1' N1 C6 N3 206.5 180.7
C1' N1 C6 C5 287.8 258.3
C1' N1 C6 H6 59.2 55.3
C1' N1 C2 C6 151.4 179.8
C2 N1 C1' H1' 61.1 174.6
C2 N1 C6 N3 359.6 0.5
C2 N1 C6 C5 80.9 78.1
C2 N1 C6 H6 212.2 235.1
O2 C2 N1 N3 179.0 180.1
N1 C2 N3 C4 270.5 266.9
N1 C2 N3 C6 359.6 0.5
C1' N1 C6 C2 207.0 180.2
C6 N1 C1' H1' 202.7 354.3
C6 N1 C2 O2 179.4 179.6
C6 N1 C2 N3 0.4 359.5
C2 N3 C6 N1 0.4 359.5
C4 N3 C6 N1 134.8 120.2
N3 C6 N1 C5 278.7 282.4
N3 C6 N1 H6 147.4 125.4
C4 C5 C6 N1 276.0 282.0
C5 C6 N1 H6 228.6 203.0
N1 C6 C5 H51C 96.0 101.9
O2 C2 N1 C6 179.4 179.6
N1 C2 O2 N3 181.4 179.9
O2 C2 N3 C4 91.6 86.8
O2 C2 N3 C6 180.7 180.4
N3 C2 N1 C6 0.4 359.5
N1 C2 N3 O2 178.9 180.1
N1 C6 N3 C2 0.4 359.5
C4 N3 C2 C6 270.9 266.3
C2 N3 C4 C5 85.8 93.8
C2 N3 C4 H41C 265.8 273.9
C2 N3 C6 C5 226.0 239.3
C2 N3 C6 H6 113.6 119.6
N1 C6 N3 C4 134.8 120.2
C2 N3 C4 C6 86.3 93.8
C4 N3 C6 C5 0.5 0.0
C4 N3 C6 H6 248.0 240.3
N3 C4 C5 C6 0.5 0.0
C5 C4 N3 H41C 180.0 179.9
N3 C4 C5 H51C 180.5 180.1
N1 C6 N3 C5 134.4 120.2
N1 C6 N3 H6 246.9 239.9
C2 N3 C6 C4 225.6 239.3
C6 N3 C4 C5 359.5 360.0
C6 N3 C4 H41C 179.5 180.1
C4 C5 C6 N3 359.6 360.0
C5 C6 N3 H6 112.5 119.7
N3 C6 C5 H51C 179.6 179.9
N1 C6 C5 C4 276.0 282.0
C5 C4 N3 C6 359.5 360.0
N3 C4 C5 H41C 180.0 180.1
N3 C6 C5 C4 359.6 360.0
C4 C5 C6 H6 146.0 125.0
C6 C5 C4 H51C 180.0 179.9
HP2 OP2 P O5' 328.1 59.9
HP2 OP2 P OP3 80.6 299.9
O5' C5' H51 C4' 239.9 240.0
O5' C5' H51 H52 119.9 119.9
H51 C5' C4' O4' 158.2 306.5
H51 C5' C4' C3' 277.7 60.5
C4' C5' H51 H52 240.1 240.0
H51 C5' C4' H4' 37.6 183.6
O5' C5' H52 C4' 120.1 120.0
O5' C5' H52 H51 240.0 240.1
H52 C5' C4' O4' 38.1 186.5
H52 C5' C4' C3' 157.6 300.5
C4' C5' H52 H51 120.0 120.0
H52 C5' C4' H4' 277.5 63.6
C5' C4' H4' O4' 120.9 122.8
C5' C4' H4' C3' 238.4 237.0
H4' C4' C5' H51 37.6 183.6
H4' C4' C5' H52 277.5 63.6
O4' C4' H4' C3' 117.4 114.2
H4' C4' O4' C1' 262.3 281.4
H4' C4' C3' O3' 348.4 323.3
H4' C4' C3' C2' 104.3 81.5
H4' C4' C3' H3' 227.7 199.8
C4' C3' H3' O3' 122.1 123.6
C4' C3' H3' C2' 241.2 247.2
H3' C3' C4' H4' 227.7 199.8
O3' C3' H3' C2' 119.1 123.6
H3' C3' O3' HA 353.5 303.6
H3' C3' C2' C1' 244.7 262.6
H3' C3' C2' H21 4.7 21.3
H3' C3' C2' H22 123.1 144.0
O4' C1' H1' C2' 239.8 242.2
O4' C1' H1' N1 120.4 121.1
C2' C1' H1' N1 240.5 238.9
H1' C1' C2' H21 127.1 123.9
H1' C1' C2' H22 8.7 1.3
H1' C1' N1 C2 61.1 174.6
H1' C1' N1 C6 202.7 354.3
HA O3' C3' C2' 116.9 67.2
HA O3' C3' H3' 353.5 303.6
C3' C2' H21 C1' 243.4 245.3
H21 C2' C3' H3' 4.7 21.3
C3' C2' H21 H22 121.7 122.7
H21 C2' C1' N1 5.4 2.8
H21 C2' C1' H1' 127.1 123.9
C1' C2' H21 H22 238.3 237.4
C3' C2' H22 C1' 117.8 114.8
H22 C2' C3' H3' 123.1 144.0
C3' C2' H22 H21 238.9 237.3
H22 C2' C1' N1 247.0 240.1
H22 C2' C1' H1' 8.7 1.3
C1' C2' H22 H21 121.1 122.6
N1 C6 C5 N3 276.4 282.0
N1 C6 C5 H6 130.0 157.0
N3 C6 C5 H6 213.6 235.0
C6 C5 C4 H41C 180.5 179.9
C4 C5 C6 H51C 180.0 180.1
N1 C6 H6 N3 109.1 101.9
N1 C6 H6 C5 214.5 203.0
N3 C6 H6 C5 105.4 101.0
H6 C6 C5 H51C 326.0 304.9
H41C C4 N3 C6 179.5 180.1
N3 C4 H41C C5 180.0 179.9
H41C C4 C5 C6 180.5 179.9
H41C C4 C5 H51C 0.5 0.1
C4 C5 H51C C6 180.0 179.8
H51C C5 C4 H41C 0.5 0.1
H51C C5 C6 H6 326.0 304.9