PDB Chemical Component D3N

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 D3N

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O3' C3' 1.482 1.429
C2' C3' 1.525 1.549
C2' C1' 1.503 1.540
C3' C4' 1.496 1.549
C1' N1 1.443 1.465
C1' O4' 1.419 1.437
O2 C2 1.238 1.216
N1 C2 1.349 1.347
N1 C6 1.408 1.393
C2 N3 1.358 1.347
C7 C6 1.347 1.376
C7 C8 1.409 1.394
C6 C5 1.414 1.410
C4' O4' 1.401 1.444
C4' C5' 1.514 1.530
C8 C9 1.364 1.363
N3 C4 1.410 1.393
C5 C4 1.380 1.409
C5 C10 1.414 1.412
C4 C13 1.403 1.376
C9 C10 1.373 1.405
C10 C11 1.412 1.405
C13 C12 1.404 1.393
C5' O5' 1.387 1.429
C11 C12 1.374 1.364
O5' P 1.611 1.610
O2P P 1.460 1.480
P O1P 1.504 1.610
O1P H1 0.950 0.967
C5' H3 1.099 1.090
C5' H4 1.100 1.090
C4' H5 1.100 1.091
C3' H6 1.100 1.090
O3' H7 0.950 0.967
C2' H8 1.101 1.090
C2' H9 1.100 1.091
C1' H10 1.100 1.090
N3 H11 1.000 0.970
C7 H12 1.080 1.080
C8 H13 1.080 1.080
C9 H14 1.080 1.080
C11 H15 1.080 1.080
C12 H16 1.080 1.080
C13 H17 1.080 1.080
P OP3   1.611
OP3 H2   0.967

Bond Angles for D3N

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O3' C3' H6 112.0 110.8
C2' C3' H6 111.3 110.9
C2' C1' N1 120.6 109.9
C1' C2' H8 110.5 110.5
C1' C2' H9 110.5 110.5
C2' C1' H10 107.6 109.9
C3' C4' H5 109.8 110.8
C1' N1 C2 119.2 119.8
C1' N1 C6 116.8 119.9
N1 C1' H10 108.3 109.8
O2 C2 N3 120.1 118.8
C2 N1 C6 123.8 120.4
N1 C2 N3 117.1 122.4
N1 C6 C5 117.2 118.7
C2 N3 C4 123.8 120.4
C2 N3 H11 118.1 119.8
C7 C8 C9 123.0 121.5
C8 C7 H12 120.2 119.8
C7 C8 H13 118.5 119.3
C6 C5 C10 120.9 120.2
O4' C4' H5 111.2 110.6
C4' C5' H3 108.9 109.5
C4' C5' H4 108.8 109.4
C8 C9 C10 118.4 119.9
C9 C8 H13 118.5 119.3
C8 C9 H14 120.8 120.1
N3 C4 C13 120.2 122.2
C4 N3 H11 118.1 119.8
C5 C4 C13 122.2 119.1
C5 C10 C9 119.6 118.9
C5 C10 C11 118.9 118.9
C4 C13 C12 119.1 120.4
C4 C13 H17 120.5 119.8
C9 C10 C11 121.5 122.2
C10 C9 H14 120.8 120.0
C10 C11 C12 121.9 119.8
C10 C11 H15 119.1 120.1
C13 C12 H16 120.3 119.3
C12 C11 H15 119.1 120.1
C11 C12 H16 120.4 119.2
O5' P OP3   109.5
O2P P OP3   109.5
P O1P H1 109.5 113.9
H3 C5' H4 109.5 109.5
H8 C2' H9 109.5 110.5
P OP3 H2   113.9

Torsion Angles for D3N

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2' C3' O3' H6 127.3 123.6
O3' C3' C4' H5 342.1 323.4
O3' C3' C2' H6 232.3 236.4
C2' C3' C4' H5 101.2 81.6
C1' C2' C3' H6 250.4 262.7
C2' C1' N1 C2 309.7 291.7
C2' C1' N1 C6 134.2 111.4
N1 C1' C2' H10 235.3 239.1
H8 C2' C1' H9 121.3 122.7
O4' C4' C3' H5 238.5 241.4
C3' C4' C5' H3 326.7 60.5
C3' C4' C5' H4 86.0 300.5
N1 C1' C2' H8 0.4 2.8
N1 C1' C2' H9 239.1 240.1
C2' C1' N1 H10 124.4 121.0
C2 N1 C1' C6 175.5 180.3
C1' N1 C2 N3 184.1 180.0
C1' N1 C6 C5 175.3 179.8
C1' O4' C4' H5 261.7 281.4
O2 C2 N1 C6 179.5 180.3
N1 C2 O2 N3 179.7 179.9
O2 C2 N3 C4 181.4 180.0
O2 C2 N3 H11 1.3 360.0
C1' N1 C2 C6 184.9 179.7
C2 N1 C1' H10 185.4 170.7
O2 C2 N1 N3 180.3 180.1
C2 N1 C6 C5 0.0 359.5
N1 C2 N3 C4 1.7 0.1
N1 C2 N3 H11 181.7 180.0
C1' N1 C6 C2 175.3 180.3
C6 N1 C1' H10 9.9 350.4
C6 N1 C2 N3 359.2 0.2
N1 C6 C5 C10 179.4 180.3
N3 C2 N1 C6 359.2 0.2
C2 N3 C4 C13 179.2 179.9
C4 N3 C2 H11 180.0 180.0
C7 C6 C5 C10 359.7 0.1
C7 C8 C9 C10 358.6 359.4
C9 C8 C7 H13 180.0 180.0
C7 C8 C9 H14 178.5 180.0
C6 C5 C4 C13 179.9 179.8
C6 C5 C10 C9 358.8 359.4
C6 C5 C10 C11 178.7 180.2
C3' C4' O4' H5 120.6 118.7
O4' C4' C5' H3 208.8 306.4
O4' C4' C5' H4 328.1 186.4
H3 C5' C4' H4 240.7 120.0
C9 C8 C7 H12 179.9 180.0
C7 C8 C9 H13 180.0 180.0
C5 C10 C9 C8 2.0 0.9
C8 C9 C10 C11 182.2 180.0
C10 C9 C8 H14 180.0 179.5
C2 N3 C4 H11 180.0 180.0
C5 C4 N3 C13 179.0 180.0
N3 C4 C13 C12 179.8 180.0
N3 C4 C13 H17 359.8 0.0
N1 C6 C5 C4 359.9 0.5
N3 C4 C5 C13 181.0 180.0
C5 C4 N3 H11 178.3 180.0
C5 C4 C13 C12 0.8 360.0
C5 C4 C13 H17 180.8 180.0
C8 C9 C10 C5 2.0 0.9
C10 C5 C4 C13 0.4 360.0
C9 C10 C5 C11 180.2 179.1
C5 C10 C9 H14 182.0 180.3
C5 C10 C11 C12 2.1 360.0
C5 C10 C11 H15 182.1 180.0
C13 C4 N3 H11 359.2 360.0
C4 C13 C12 H16 179.4 180.1
C10 C9 C8 H13 178.6 179.4
C8 C9 C10 H14 180.0 180.5
C5 C10 C9 C11 179.8 180.9
C9 C10 C11 C12 182.0 180.9
C9 C10 C11 H15 2.0 0.9
C5 C10 C11 C9 180.2 179.1
C11 C10 C9 H14 2.2 359.4
C12 C11 C10 H15 180.0 180.0
C10 C11 C12 H16 179.1 180.0
C4 C13 C12 H17 180.0 180.0
C13 C12 C11 H15 179.1 180.0
C11 C12 C13 H16 180.0 179.9
C5' O5' P OP3   175.0
C4 C13 C12 C11 359.4 0.0
C10 C11 C12 H15 180.0 180.0
C13 C12 C11 H16 180.0 180.1
O2P P O5' OP3   240.0
O5' P O1P H1 231.8 300.0
O5' P OP3 H2   180.1
O5' P O2P OP3   120.0
O2P P O1P H1 360.0 180.0
O2P P OP3 H2   300.0
C4' C5' H3 H4 118.9 240.0
C4' C5' H4 H3 241.1 120.0
H5 C4' C5' H3 88.2 183.6
H5 C4' C5' H4 207.5 63.6
H6 C3' C4' H5 221.5 199.7
H7 O3' C3' H6 52.6 303.7
H8 C2' C3' H6 9.8 21.4
H8 C2' C1' N1 0.4 2.8
C1' C2' H8 H9 238.1 237.4
H8 C2' C1' H10 125.1 123.7
H9 C2' C3' H6 131.1 144.0
H9 C2' C1' N1 239.1 240.1
C1' C2' H9 H8 121.9 122.7
H9 C2' C1' H10 3.8 1.1
C2' C1' H10 N1 228.2 239.0
H10 C1' C2' H8 125.1 123.7
H10 C1' C2' H9 3.8 1.1
H10 C1' N1 C2 185.4 170.7
H10 C1' N1 C6 9.9 350.4
C2 N3 H11 C4 180.0 180.0
H11 N3 C4 C13 359.2 360.0
H12 C7 C8 C9 179.9 180.0
H12 C7 C8 H13 359.9 360.0
C7 C8 H13 C9 180.0 180.0
H13 C8 C7 H12 359.9 360.0
H13 C8 C9 C10 178.6 179.4
H13 C8 C9 H14 358.5 360.0
C8 C9 H14 C10 180.0 179.5
H14 C9 C8 H13 358.5 360.0
H14 C9 C10 C11 2.2 359.4
C10 C11 H15 C12 180.0 180.0
H15 C11 C12 H16 359.1 359.9
H16 C12 C11 H15 359.1 359.9
C4 C13 H17 C12 180.0 180.0
H17 C13 C12 H16 359.4 0.0
OP3 P O1P H1   60.0