PDB Chemical Component XPB

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 XPB

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O3' C3' 1.432 1.429
C3' C4' 1.526 1.550
C3' C2' 1.524 1.548
C4' C5' 1.510 1.530
C4' O4' 1.454 1.444
C5' O5' 1.440 1.430
C2' C1' 1.521 1.541
O4' C1' 1.420 1.437
OP1 P 1.479 1.480
C1' N9 1.460 1.465
O5' P 1.600 1.611
P OP2 1.480 1.610
N9 C4 1.375 1.372
N9 C8 1.384 1.365
N3 C4 1.332 1.329
N3 C2 1.347 1.323
N2 C2 1.371 1.385
C4 C5 1.409 1.405
C8 N7 1.305 1.301
C2 N1 1.349 1.327
C5 N7 1.394 1.356
C5 C6 1.413 1.403
N1 C6 1.330 1.326
C6 O6 1.341 1.354
O6 C10 1.441 1.428
C10 C11 1.520 1.530
C11 C12 1.529 1.530
O13 C13 1.221 1.212
C12 C13 1.524 1.506
C13 C14 1.501 1.472
C14 C15 1.403 1.402
C14 C18 1.402 1.399
C15 C16 1.389 1.383
C18 N1' 1.338 1.316
C16 C17 1.397 1.383
N1' C17 1.340 1.321
C8 H8 1.080 1.080
N2 H22 1.000 0.971
N2 H21 1.000 0.970
C10 H10 1.100 1.090
C10 H7 1.100 1.090
C11 H11 1.100 1.090
C11 H9 1.099 1.090
C12 H12 1.099 1.090
C12 H13 1.100 1.090
C15 H15 1.080 1.080
OP2 H2 0.950 0.968
C5' H5' 1.100 1.090
C5' H5'' 1.100 1.090
C4' H4' 1.100 1.090
C3' H3' 1.100 1.090
O3' H3 0.950 0.967
C2' H2'' 1.100 1.090
C2' H2' 1.100 1.090
C1' H1' 1.100 1.090
C16 H16 1.080 1.080
C17 H17 1.080 1.080
C18 H18 1.080 1.081
P OP3   1.610
OP3 H1   0.967

Bond Angles for XPB

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O3' C3' C2' 107.8 111.0
O3' C3' H3' 112.1 110.8
C3' C4' H4' 108.6 110.7
C3' C2' C1' 102.3 104.2
C2' C3' H3' 110.7 110.9
C3' C2' H2'' 111.2 110.5
C3' C2' H2' 111.3 110.4
C4' C5' H5' 109.4 109.5
C4' C5' H5'' 109.3 109.5
C4' O4' C1' 110.8 107.0
O4' C4' H4' 109.6 110.7
O4' C1' C2' 105.9 107.3
C2' C1' N9 112.8 109.9
C1' C2' H2'' 111.2 110.5
C1' C2' H2' 111.2 110.5
C2' C1' H1' 109.3 109.9
O4' C1' N9 107.8 109.9
O4' C1' H1' 110.8 109.9
OP1 P OP2 109.3 109.5
OP1 P OP3   109.5
N9 C1' H1' 110.2 110.0
O5' P OP3   109.4
P OP2 H2 109.5 114.0
OP2 P OP3   109.5
N9 C8 N7 113.4 110.0
N9 C8 H8 123.3 125.0
N2 C2 N3 116.7 118.9
C2 N2 H22 109.5 120.0
C2 N2 H21 109.5 120.0
C4 C5 N7 110.6 107.1
C4 C5 C6 114.4 118.4
C5 N7 C8 104.5 109.5
N7 C8 H8 123.3 125.1
C6 C5 N7 135.0 134.6
C5 C6 O6 126.2 120.7
N1 C6 O6 114.0 120.7
C6 O6 C10 119.7 117.0
O6 C10 C11 106.8 109.5
O6 C10 H10 110.1 109.4
O6 C10 H7 110.1 109.6
C10 C11 C12 111.3 109.5
C11 C10 H10 110.1 109.4
C11 C10 H7 110.2 109.5
C10 C11 H11 109.0 109.4
C10 C11 H9 109.0 109.5
C11 C12 C13 113.0 109.5
C12 C11 H11 109.0 109.4
C12 C11 H9 109.0 109.5
C11 C12 H12 108.6 109.5
C11 C12 H13 108.6 109.5
C12 C13 C14 118.7 120.0
C13 C12 H12 108.6 109.5
C13 C12 H13 108.6 109.5
C13 C14 C15 118.8 120.6
C13 C14 C18 123.7 120.6
C15 C14 C18 117.5 118.8
C14 C15 C16 119.1 118.3
C14 C15 H15 120.5 120.9
C14 C18 N1' 124.1 120.6
C14 C18 H18 117.9 119.7
C15 C16 C17 118.4 119.3
C16 C15 H15 120.5 120.9
C15 C16 H16 120.8 120.3
C17 C16 H16 120.8 120.3
C16 C17 H17 118.1 119.5
N1' C17 H17 118.1 119.4
H22 N2 H21 109.5 120.0
H10 C10 H7 109.5 109.4
H11 C11 H9 109.5 109.5
H12 C12 H13 109.5 109.4
H5' C5' H5'' 109.4 109.5
H2'' C2' H2' 109.5 110.6
P OP3 H1   114.0

Torsion Angles for XPB

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O3' C3' C4' H4' 5.3 323.3
O3' C3' C2' C1' 95.4 139.1
C2' C3' O3' H3' 122.1 123.6
O3' C3' C2' H2'' 214.2 257.8
O3' C3' C2' H2' 336.5 20.5
C3' C4' C5' H5' 175.5 60.5
C3' C4' C5' H5'' 295.3 300.5
C3' C4' O4' C1' 15.4 40.1
O4' C4' C3' H4' 243.1 241.4
O3' C3' C2' H3' 237.0 236.4
C2' C3' C4' H4' 121.3 81.6
O4' C1' C2' C3' 29.9 2.1
C3' C2' C1' N9 147.6 121.5
C1' C2' C3' H2'' 241.2 241.3
C1' C2' C3' H2' 118.8 118.6
C3' C2' C1' H1' 270.6 242.6
H2'' C2' C3' H2' 237.7 237.3
H5' C5' C4' H5'' 240.2 120.0
C3' C4' O4' H4' 116.2 118.7
O4' C4' C5' H5' 57.9 306.5
O4' C4' C5' H5'' 177.7 186.4
C4' O4' C1' C2' 330.7 333.4
C4' O4' C1' N9 209.8 214.0
C4' O4' C1' H1' 89.1 92.9
C5' O5' P OP3   185.0
C1' C2' C3' H3' 218.4 262.7
C3' C2' C1' H2'' 118.8 118.7
C3' C2' C1' H2' 241.1 241.4
O4' C1' C2' N9 242.3 240.6
O4' C1' C2' H1' 119.4 119.5
N9 C1' C2' H1' 237.0 238.9
H2'' C2' C1' H2' 122.3 122.7
C3' C2' C1' O4' 29.9 2.1
C1' O4' C4' H4' 259.2 281.4
C2' C1' O4' N9 120.9 119.4
O4' C1' C2' H2'' 271.1 243.4
O4' C1' C2' H2' 148.8 120.7
C2' C1' O4' H1' 241.6 240.5
N9 C1' O4' H1' 120.7 121.1
O5' P OP1 OP3   240.0
OP1 P OP2 H2 360.0 180.0
OP2 P OP1 OP3   120.0
OP1 P OP3 H1   60.0
O4' C1' N9 C2' 116.5 117.8
N9 C1' C2' H2'' 28.8 2.8
N9 C1' C2' H2' 266.4 240.1
C2' C1' N9 H1' 122.5 121.1
O4' C1' N9 H1' 239.0 238.9
C1' N9 C8 N7 179.7 179.8
C1' N9 C8 H8 359.7 0.1
OP1 P O5' OP3   120.0
O5' P OP2 H2 232.6 60.0
OP2 P O5' OP3   240.0
O5' P OP3 H1   180.0
OP1 P OP2 OP3   240.0
O5' P OP2 OP3   120.0
OP2 P OP3 H1   300.0
N9 C4 C5 N7 360.0 0.2
C5 N7 C8 N9 0.0 0.3
N7 C8 N9 H8 180.0 179.7
N3 C4 C5 N7 180.1 179.9
N3 C2 N2 H22 0.0 360.0
N3 C2 N2 H21 120.0 180.0
H22 N2 C2 H21 240.0 180.0
C4 C5 N7 C8 0.0 359.7
C6 C5 C4 N7 179.6 180.0
C4 C5 C6 O6 180.7 180.0
N9 C8 N7 H8 180.0 180.3
C6 C5 N7 C8 180.5 179.7
N9 C8 N7 C5 0.0 0.3
C4 C5 N7 C6 179.5 180.0
C5 N7 C8 H8 180.0 180.0
N7 C5 C6 O6 0.3 0.0
C4 C5 C6 N7 180.5 180.0
N1 C6 C5 O6 179.6 180.0
C5 C6 O6 C10 272.3 180.0
N1 C6 C5 N7 179.8 180.0
C5 C6 N1 O6 180.4 180.0
N1 C6 O6 C10 92.8 0.1
O6 C6 C5 N7 0.3 0.0
C6 O6 C10 C11 261.1 180.0
C6 O6 C10 H10 20.7 299.9
C6 O6 C10 H7 141.5 59.9
O6 C10 C11 C12 229.9 180.0
C11 C10 O6 H10 240.4 240.0
C11 C10 O6 H7 119.6 120.0
O6 C10 C11 H11 350.2 300.0
O6 C10 C11 H9 109.6 59.9
H10 C10 O6 H7 239.2 240.0
O6 C10 C11 H10 119.6 120.0
O6 C10 C11 H7 240.4 239.9
C10 C11 C12 C13 158.9 180.0
C12 C11 C10 H11 239.7 240.0
C12 C11 C10 H9 120.3 120.0
C10 C11 C12 H12 279.4 300.0
C10 C11 C12 H13 38.4 59.9
H10 C10 C11 H7 120.9 120.0
H11 C11 C10 H9 240.5 240.0
C12 C11 C10 H10 110.3 60.0
C12 C11 C10 H7 349.5 300.1
C10 C11 C12 H11 120.3 120.0
C10 C11 C12 H9 239.7 239.9
C11 C12 C13 C14 179.5 180.0
C13 C12 C11 H12 239.5 240.0
C13 C12 C11 H13 120.5 120.0
H11 C11 C12 H9 119.5 120.0
H12 C12 C11 H13 241.0 240.1
O13 C13 C12 H12 239.0 240.0
O13 C13 C12 H13 120.1 120.0
C13 C12 C11 H11 38.6 60.0
C13 C12 C11 H9 279.2 300.0
C11 C12 C13 H12 120.5 120.0
C11 C12 C13 H13 239.5 240.0
C12 C13 C14 C15 178.9 180.0
C12 C13 C14 C18 358.9 359.7
H12 C12 C13 H13 119.0 120.0
C14 C13 C12 H12 59.0 60.0
C14 C13 C12 H13 300.0 300.0
C15 C14 C13 C18 180.0 180.3
C13 C14 C15 C16 180.1 180.0
C13 C14 C15 H15 0.0 359.9
C13 C14 C18 N1' 180.0 179.8
C13 C14 C18 H18 360.0 360.0
C13 C14 C15 C18 180.0 179.7
C15 C14 C18 N1' 0.0 359.5
C15 C14 C18 H18 180.0 179.7
C14 C15 C16 C17 360.0 359.9
C16 C15 C14 H15 180.0 180.1
C14 C15 C16 H16 180.0 180.0
C13 C14 C18 C15 180.0 180.3
C18 C14 C15 C16 0.0 0.3
C18 C14 C15 H15 180.0 180.2
C16 C15 C14 C18 0.0 0.3
C14 C15 C16 H15 180.0 179.9
C17 C16 C15 H16 180.0 179.9
C15 C16 C17 H17 180.0 180.0
C14 C18 N1' H18 180.0 180.2
C18 N1' C17 H17 180.0 179.7
C17 C16 C15 H15 180.0 180.0
C15 C16 C17 H16 180.0 180.1
N1' C17 C16 H17 180.0 180.0
C14 C18 N1' C17 360.0 0.5
N1' C17 C16 H16 180.0 180.0
C16 C17 N1' H17 180.0 180.0
N9 C8 H8 N7 180.0 179.6
H22 N2 C2 N3 0.0 360.0
C2 N2 H22 H21 120.0 180.0
H21 N2 C2 N3 120.0 180.0
C2 N2 H21 H22 239.9 180.0
O6 C10 H10 C11 242.5 240.0
O6 C10 H10 H7 121.2 120.1
H10 C10 C11 C12 110.3 60.0
C11 C10 H10 H7 238.7 240.0
H10 C10 C11 H11 230.6 180.0
H10 C10 C11 H9 350.1 300.0
O6 C10 H7 C11 117.6 120.0
O6 C10 H7 H10 238.8 240.0
H7 C10 C11 C12 349.5 300.1
C11 C10 H7 H10 121.2 120.0
H7 C10 C11 H11 109.8 60.0
H7 C10 C11 H9 229.2 180.0
C10 C11 H11 C12 238.3 240.0
H11 C11 C10 H10 230.6 180.0
H11 C11 C10 H7 109.8 60.0
C10 C11 H11 H9 119.2 120.0
H11 C11 C12 C13 38.6 60.0
C12 C11 H11 H9 240.8 240.0
H11 C11 C12 H12 159.2 180.0
H11 C11 C12 H13 278.1 300.0
C10 C11 H9 C12 121.7 120.1
H9 C11 C10 H10 350.1 300.0
H9 C11 C10 H7 229.2 180.0
C10 C11 H9 H11 240.9 240.0
H9 C11 C12 C13 279.2 300.0
C12 C11 H9 H11 119.2 119.9
H9 C11 C12 H12 39.7 60.1
H9 C11 C12 H13 158.7 180.0
C11 C12 H12 C13 236.8 239.9
H12 C12 C11 H11 159.2 180.0
H12 C12 C11 H9 39.7 60.1
C11 C12 H12 H13 118.4 119.9
H12 C12 C13 C14 59.0 60.0
C13 C12 H12 H13 241.6 240.0
C11 C12 H13 C13 123.2 120.1
H13 C12 C11 H11 278.1 300.0
H13 C12 C11 H9 158.7 180.0
C11 C12 H13 H12 241.6 240.1
H13 C12 C13 C14 300.0 300.0
C13 C12 H13 H12 118.4 120.0
H15 C15 C14 C18 180.0 180.2
C14 C15 H15 C16 180.0 180.1
H15 C15 C16 C17 180.0 180.0
H15 C15 C16 H16 0.0 0.1
H2 OP2 P OP3   300.1
C4' C5' H5' H5'' 119.8 239.9
C4' C5' H5'' H5' 240.2 120.1
H4' C4' C5' H5' 298.2 183.6
H4' C4' C5' H5'' 58.0 63.5
H4' C4' O4' C1' 259.2 281.4
O3' C3' H3' C2' 120.5 123.7
H3' C3' C4' H4' 242.3 199.7
H3' C3' C2' C1' 218.4 262.7
H3' C3' C2' H2'' 337.2 21.4
H3' C3' C2' H2' 99.5 144.1
H3 O3' C3' C2' 64.2 67.2
H3 O3' C3' H3' 302.1 303.6
C3' C2' H2'' C1' 246.7 245.3
H2'' C2' C3' H3' 337.2 21.4
C3' C2' H2'' H2' 123.4 122.6
H2'' C2' C1' N9 28.8 2.8
C1' C2' H2'' H2' 236.7 237.3
H2'' C2' C1' H1' 151.7 123.9
C3' C2' H2' C1' 113.3 114.7
H2' C2' C3' H3' 99.5 144.1
C3' C2' H2' H2'' 236.7 237.4
H2' C2' C1' N9 266.4 240.1
C1' C2' H2' H2'' 123.3 122.7
H2' C2' C1' H1' 29.4 1.2
O4' C1' H1' C2' 243.7 242.1
C2' C1' H1' N9 235.5 238.9
H1' C1' C2' H2'' 151.7 123.9
H1' C1' C2' H2' 29.4 1.2
O4' C1' H1' N9 119.2 121.1
C15 C16 H16 C17 180.0 179.9
H16 C16 C15 H15 0.0 0.1
H16 C16 C17 H17 0.0 360.0
H17 C17 C16 H16 0.0 360.0
C14 C18 H18 N1' 180.0 179.8
OP1 P OP3 OP2   120.0
OP3 P OP2 H2   300.1