PDB Chemical Component D00

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 D00

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP2 P 1.480 1.481
C2' C3' 1.505 1.548
C2' C1' 1.505 1.541
C3' O3' 1.419 1.429
C3' C4' 1.503 1.550
O5' P 1.607 1.610
O5' C5' 1.422 1.428
OP1 P 1.480 1.609
C6 C5 1.347 1.354
C6 N1 1.353 1.362
C5 C4 1.439 1.410
C5' C4' 1.515 1.530
C4' O4' 1.423 1.444
C1' N1 1.475 1.465
C1' O4' 1.430 1.436
N1 C2 1.379 1.346
C4 N4 1.381 1.376
C4 N3 1.351 1.327
C2 N3 1.362 1.331
C2 O2 1.229 1.220
N4 C11 1.470 1.465
C11 C10 1.355 1.531
P OP3 1.614 1.610
OP1 H1 0.950 0.968
C5' H5'' 1.100 1.090
C5' H5' 1.100 1.090
C4' H4' 1.101 1.090
C3' H3' 1.100 1.090
O3' HO3' 0.949 0.968
C2' H2'' 1.100 1.090
C2' H2' 1.100 1.091
C1' H1' 1.100 1.090
N4 H41 1.000 0.970
C5 H5 1.080 1.080
C6 H6 1.080 1.081
C10 H12 1.101 1.091
C10 H11 1.100 1.090
C10 H8 1.100 1.090
C11 H13 1.100 1.090
C11 H14 1.100 1.090
OP3 H9 0.950 0.967

Bond Angles for D00

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP3 108.0 109.4
C2' C3' H3' 108.9 111.0
C2' C1' N1 114.2 109.8
C1' C2' H2'' 111.0 110.5
C1' C2' H2' 111.1 110.5
C2' C1' H1' 114.3 109.9
O3' C3' H3' 110.1 110.8
C3' O3' HO3' 109.5 114.0
C3' C4' H4' 106.7 110.8
O5' P OP3 103.3 109.5
O5' C5' C4' 111.8 109.5
O5' C5' H5'' 108.9 109.5
O5' C5' H5' 108.9 109.4
OP1 P OP3 108.3 109.5
C6 C5 H5 120.5 120.5
C5' C4' O4' 110.5 110.6
C4' C5' H5'' 108.9 109.5
C4' C5' H5' 108.9 109.4
C5' C4' H4' 106.5 110.6
O4' C4' H4' 107.7 110.6
C1' N1 C2 121.2 119.8
N1 C1' H1' 114.8 109.8
N1 C2 N3 117.4 121.1
N1 C2 O2 121.6 119.4
C4 N4 C11 123.6 120.0
C4 N4 H41 118.2 120.0
O2 C2 N3 121.0 119.5
N4 C11 C10 129.3 109.5
C11 N4 H41 118.2 120.0
N4 C11 H13 104.3 109.5
N4 C11 H14 104.3 109.5
C11 C10 H12 109.5 109.4
C11 C10 H11 109.5 109.4
C11 C10 H8 109.5 109.5
P OP3 H9 109.5 114.0
H5'' C5' H5' 109.5 109.5
H2'' C2' H2' 109.5 110.6
H12 C10 H11 109.5 109.5
H12 C10 H8 109.5 109.5
H11 C10 H8 109.4 109.5
H13 C11 H14 109.5 109.5

Torsion Angles for D00

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O5' P OP2 OP3 111.0 120.0
OP1 P OP2 OP3 235.3 240.0
OP2 P OP3 H9 0.0 300.0
O3' C3' C2' H3' 237.3 236.3
C2' C3' O3' HO3' 180.0 67.3
C2' C3' C4' H4' 122.6 81.5
C1' C2' C3' H3' 208.0 262.7
C2' C1' N1 C2 134.9 295.0
N1 C1' C2' H1' 224.9 239.0
H2'' C2' C1' H2' 122.1 122.7
C2' C3' O3' H3' 122.0 123.7
O3' C3' C4' H4' 1.1 323.3
C3' C4' C5' H5'' 309.0 60.5
C3' C4' C5' H5' 189.6 300.5
C5' C4' C3' H4' 121.2 123.0
O4' C4' C3' H4' 246.0 241.5
OP2 P O5' OP3 245.8 240.0
OP1 P O5' OP3 114.7 120.0
O5' P OP3 H9 245.8 180.0
C5' O5' P OP3 296.2 175.0
O5' C5' C4' O4' 307.3 66.5
C4' C5' O5' H5'' 239.7 240.0
C4' C5' O5' H5' 120.4 119.9
O5' C5' C4' H4' 190.6 303.6
H5'' C5' O5' H5' 240.7 240.0
OP2 P OP1 OP3 124.5 120.0
O5' P OP1 OP3 248.7 240.0
OP1 P OP3 H9 131.4 59.9
C6 N1 C1' H1' 178.3 353.7
C5 C4 N4 C11 142.0 180.1
C5 C4 N4 H41 322.0 0.1
C3' C4' C5' H4' 238.7 236.9
O5' C5' C4' H5'' 120.3 120.0
O5' C5' C4' H5' 239.7 240.1
O4' C4' C5' H4' 116.7 122.9
H5'' C5' C4' H5' 119.3 120.0
C3' C4' O4' H4' 113.3 118.6
O4' C4' C5' H5'' 187.0 306.5
O4' C4' C5' H5' 67.6 186.4
C5' C4' O4' H4' 244.0 237.1
N1 C1' C2' H2'' 35.8 2.8
N1 C1' C2' H2' 273.7 240.1
C2' C1' N1 H1' 134.8 121.0
C1' N1 C2 N3 177.8 180.0
C1' N1 C2 O2 357.4 0.0
C1' O4' C4' H4' 272.0 281.5
C2 N1 C1' H1' 0.1 174.0
O2 C2 N1 N3 179.6 180.0
C4 N4 C11 C10 98.5 180.0
C11 N4 C4 H41 180.0 180.0
C4 N4 C11 H13 221.1 300.0
C4 N4 C11 H14 335.9 60.1
N1 C2 N3 O2 179.6 180.0
N1 C2 O2 N3 180.4 180.0
C4 N4 C11 H41 180.0 180.0
N4 C11 C10 H12 180.0 300.1
N4 C11 C10 H11 300.0 60.0
N4 C11 C10 H8 60.0 180.0
H13 C11 N4 H14 245.1 239.9
C10 C11 N4 H41 278.5 360.0
N4 C11 C10 H13 122.6 120.0
N4 C11 C10 H14 237.4 240.0
H12 C10 C11 H11 240.0 240.1
H12 C10 C11 H8 120.0 120.1
H11 C10 C11 H8 240.0 240.0
H1 OP1 P OP3 235.5 60.1
O5' C5' H5'' C4' 237.9 240.0
O5' C5' H5'' H5' 118.9 120.0
H5'' C5' C4' O4' 187.0 306.5
C4' C5' H5'' H5' 241.1 240.0
H5'' C5' C4' H4' 70.2 183.6
O5' C5' H5' C4' 122.1 120.0
O5' C5' H5' H5'' 241.0 240.0
H5' C5' C4' O4' 67.6 186.4
C4' C5' H5' H5'' 118.9 120.0
H5' C5' C4' H4' 310.9 63.6
C5' C4' H4' O4' 118.6 122.9
H4' C4' C5' H5'' 70.2 183.6
H4' C4' C5' H5' 310.9 63.6
H3' C3' O3' HO3' 58.0 303.6
H3' C3' C4' H4' 237.1 199.7
HO3' O3' C3' H3' 58.0 303.6
H2'' C2' C3' H3' 326.9 21.4
H2'' C2' C1' N1 35.8 2.8
C1' C2' H2'' H2' 237.0 237.4
H2'' C2' C1' H1' 170.9 123.8
H2' C2' C3' H3' 89.0 144.0
H2' C2' C1' N1 273.7 240.1
C1' C2' H2' H2'' 123.0 122.7
H2' C2' C1' H1' 48.8 1.1
C2' C1' H1' N1 225.2 239.0
H1' C1' C2' H2'' 170.9 123.8
H1' C1' C2' H2' 48.8 1.1
H1' C1' N1 C2 0.1 174.0
C4 N4 H41 C11 180.0 180.0
H41 N4 C11 C10 278.5 360.0
H41 N4 C11 H13 41.1 119.9
H41 N4 C11 H14 155.9 240.0
H6 C6 C5 H5 0.2 359.9
C11 C10 H12 H11 120.0 119.9
C11 C10 H12 H8 240.0 239.9
H11 C10 H12 H8 120.0 120.0
C11 C10 H11 H12 240.0 240.1
C11 C10 H11 H8 120.0 120.0
H12 C10 H11 H8 240.0 239.9
C11 C10 H8 H12 120.0 120.0
C11 C10 H8 H11 240.0 240.0
H12 C10 H8 H11 120.0 120.0
N4 C11 H13 C10 222.3 240.0
H13 C11 N4 H41 41.1 119.9
N4 C11 H13 H14 111.1 120.1
H13 C11 C10 H12 57.4 180.1
H13 C11 C10 H11 177.4 300.0
H13 C11 C10 H8 297.4 60.0
N4 C11 H14 C10 137.7 120.0
H14 C11 N4 H41 155.9 240.0
N4 C11 H14 H13 248.8 239.9
H14 C11 C10 H12 302.6 60.1
H14 C11 C10 H11 62.6 180.0
H14 C11 C10 H8 182.6 300.0