PDB Chemical Component B9H

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 B9H

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP2 P 1.494 1.610
C5' C4' 1.505 1.530
C5' O5' 1.406 1.429
C4' O4' 1.422 1.437
C4' C3' 1.507 1.542
P O5' 1.570 1.611
P OP1 1.495 1.480
O4' C1' 1.424 1.444
O2' C21 1.418 1.429
O2' C2' 1.415 1.429
C1' C2' 1.529 1.549
C1' N1 1.476 1.465
C3' O3' 1.453 1.429
C3' C2' 1.507 1.548
N1 C6 1.340 1.386
N1 C2 1.393 1.340
C6 C5 1.378 1.320
O2 C2 1.241 1.216
C2 N3 1.406 1.348
C5 C4 1.373 1.514
N3 C4 1.400 1.473
N3 C31 1.465 1.465
C4 N4 1.349 1.469
C32 C31 1.517 1.530
C32 C33 1.509 1.530
C4 H1 1.100 1.090
C5 H2 1.080 1.080
C6 H3 1.080 1.079
C32 H4 1.100 1.090
C32 H5 1.100 1.090
C1' H6 1.101 1.090
C2' H7 1.100 1.090
C3' H8 1.100 1.090
C31 H9 1.100 1.090
C31 H10 1.100 1.090
C33 H11 1.100 1.090
C33 H12 1.100 1.090
C33 H13 1.100 1.091
C4' H14 1.101 1.090
C5' H15 1.100 1.090
C5' H16 1.100 1.090
N4 H17 1.000 1.009
N4 H18 1.001 1.010
O3' H20 0.950 0.967
OP2 H22 0.950 0.967
C21 H23 1.100 1.090
C21 H24 1.100 1.090
C21 H25 1.100 1.090
P OP3 1.599 1.610
OP3 H19 0.950 0.967

Bond Angles for B9H

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP2 H22 109.5 114.0
OP2 P OP3 109.8 109.5
C5' C4' O4' 111.0 109.9
C5' C4' H14 110.1 110.0
O5' C5' H15 110.2 109.5
O5' C5' H16 110.2 109.4
O4' C4' H14 111.4 109.9
C4' C3' O3' 119.1 110.5
C4' C3' H8 103.7 110.6
O4' C1' H6 109.5 110.7
O2' C21 H23 109.5 109.5
O2' C21 H24 109.5 109.5
O2' C21 H25 109.5 109.5
O2' C2' H7 114.4 110.8
C2' C1' N1 113.2 110.6
C2' C1' H6 108.1 110.6
C1' C2' H7 112.5 111.0
N1 C1' H6 108.8 110.6
O3' C3' H8 104.3 110.5
C3' O3' H20 109.5 114.0
C3' C2' H7 112.9 110.9
N1 C6 H3 118.5 119.4
N1 C2 N3 120.3 121.8
C6 C5 H2 120.1 121.0
C2 N3 C4 119.1 118.3
C2 N3 C31 122.4 120.8
C5 C4 N4 119.8 107.9
C5 C4 H1 90.1 107.9
N3 C4 N4 120.9 107.9
N3 C4 H1 90.1 107.9
N3 C31 H9 107.9 109.5
N3 C31 H10 107.9 109.4
N4 C4 H1 90.1 107.7
C4 N4 H17 109.5 111.1
C4 N4 H18 109.5 111.0
C31 C32 C33 112.8 109.5
C31 C32 H4 108.6 109.5
C31 C32 H5 108.6 109.5
C32 C31 H9 107.9 109.5
C32 C31 H10 107.9 109.5
C33 C32 H4 108.6 109.4
C33 C32 H5 108.6 109.4
C32 C33 H11 109.5 109.5
C32 C33 H12 109.5 109.5
C32 C33 H13 109.5 109.5
H4 C32 H5 109.5 109.5
H9 C31 H10 109.5 109.5
H11 C33 H12 109.5 109.5
H11 C33 H13 109.5 109.5
H12 C33 H13 109.5 109.4
H15 C5' H16 109.5 109.4
H17 N4 H18 109.5 111.0
H23 C21 H24 109.4 109.5
H23 C21 H25 109.5 109.5
H24 C21 H25 109.5 109.5
P OP3 H19 109.5 114.0

Torsion Angles for B9H

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP3 H19 128.0 60.0
O4' C4' C5' H14 123.9 121.2
C5' C4' C3' O3' 54.8 119.9
C5' C4' C3' H8 299.6 357.3
O5' C5' C4' O4' 291.4 66.5
O5' C5' C4' H14 167.6 305.3
H15 C5' O5' H16 121.0 120.0
C5' C4' O4' H14 236.9 238.8
O4' C4' C3' O3' 173.6 239.3
O4' C4' C3' H8 58.4 116.7
C4' O4' C1' H6 115.3 78.5
O3' C3' C4' H8 115.2 122.6
C4' C3' O3' H20 180.0 294.7
C4' C3' C2' H7 166.5 97.4
P O5' C5' H15 41.6 60.0
P O5' C5' H16 280.7 300.0
C2' C1' O4' H6 244.3 241.4
O4' C1' C2' H7 210.0 278.8
N1 C1' O4' H6 121.1 122.9
C21 O2' C2' H7 326.0 26.3
H23 C21 O2' H24 240.0 240.0
H23 C21 O2' H25 120.0 120.0
H24 C21 O2' H25 240.0 240.0
O2' C2' C1' H6 326.2 36.6
C1' C2' O2' H7 126.0 123.7
C3' C2' O2' H7 233.6 236.4
O4' C1' C2' H6 116.6 118.6
O2' C2' C1' H7 232.9 236.4
N1 C1' C2' H6 239.3 237.1
C3' C2' C1' H7 120.2 118.2
O4' C1' N1 H6 238.5 237.0
C2' C1' N1 H6 120.3 122.9
N1 C1' C2' H7 332.6 37.3
C1' N1 C6 H3 358.7 360.0
C1' N1 C2 N3 180.2 180.0
C4' C3' O3' H8 245.0 237.3
O3' C3' C2' H7 301.0 216.0
O2' C2' C3' H7 127.3 123.5
C3' C2' C1' N1 92.9 155.5
C3' C2' C1' H6 213.6 278.4
C1' C2' C3' H7 240.0 241.7
C6 N1 C2 N3 0.6 0.0
N1 C6 C5 H2 181.7 179.9
N1 C2 N3 C4 0.6 0.0
N1 C2 N3 C31 178.7 179.9
C6 C5 C4 N4 179.4 121.9
C6 C5 C4 H1 269.5 238.1
C2 N3 C4 N4 179.6 238.0
C2 N3 C4 H1 89.4 121.9
C2 N3 C31 H9 188.9 330.0
C2 N3 C31 H10 307.1 210.0
C2 N3 C4 C5 359.3 360.0
N3 C4 C5 N4 180.3 238.1
N3 C4 C5 H1 90.1 121.9
N4 C4 C5 H1 269.8 243.9
C5 C4 N4 H17 180.0 56.3
C5 C4 N4 H18 300.0 180.2
C2 N3 C4 C31 178.1 179.9
C5 C4 N3 N4 179.7 122.0
C5 C4 N3 H1 269.9 238.1
N4 C4 N3 H1 90.2 116.1
N3 C4 N4 H17 359.7 183.8
N3 C4 N4 H18 119.7 307.7
C2 N3 C31 C4 181.9 180.1
C31 N3 C4 N4 1.4 58.1
C31 N3 C4 H1 271.3 302.0
N3 C31 C32 H4 282.6 299.9
N3 C31 C32 H5 41.6 60.0
C32 C31 N3 H9 239.1 120.0
C32 C31 N3 H10 120.9 240.0
H9 C31 N3 H10 241.8 120.0
C5 C4 N4 H1 90.1 116.3
N3 C4 N4 H1 269.8 243.8
H17 N4 C4 H18 240.0 236.0
C2 N3 C31 C32 68.0 90.0
N3 C31 C32 H9 120.9 240.0
N3 C31 C32 H10 239.1 119.9
C33 C32 C31 H4 239.5 240.0
C33 C32 C31 H5 120.5 120.0
C31 C32 C33 H11 180.0 179.9
C31 C32 C33 H12 300.0 300.0
C31 C32 C33 H13 60.0 59.9
H4 C32 C31 H5 241.0 240.0
H9 C31 C32 H10 118.2 240.0
C31 C32 C33 H4 120.5 120.0
C31 C32 C33 H5 239.5 240.0
C33 C32 C31 H9 41.2 300.0
C33 C32 C31 H10 283.0 60.0
H4 C32 C33 H5 119.0 120.0
H11 C33 C32 H12 240.0 239.9
H11 C33 C32 H13 120.0 120.0
H12 C33 C32 H13 240.0 240.1
C5 C4 H1 N4 240.2 243.7
N3 C4 H1 N4 120.9 116.2
H1 C4 N4 H17 89.9 300.0
H1 C4 N4 H18 209.9 64.0
H2 C5 C4 N4 359.4 302.0
H2 C5 C4 H1 89.5 58.1
H3 C6 C5 H2 1.7 359.9
C31 C32 H4 C33 236.9 240.0
C31 C32 H4 H5 118.5 120.1
H4 C32 C31 H9 161.7 60.0
H4 C32 C31 H10 43.5 180.0
C33 C32 H4 H5 241.5 240.1
H4 C32 C33 H11 59.5 59.9
H4 C32 C33 H12 179.5 180.0
H4 C32 C33 H13 299.5 299.9
C31 C32 H5 C33 123.1 120.0
C31 C32 H5 H4 241.5 240.0
H5 C32 C31 H9 280.7 180.0
H5 C32 C31 H10 162.5 300.0
C33 C32 H5 H4 118.4 119.9
H5 C32 C33 H11 300.5 300.0
H5 C32 C33 H12 60.5 60.0
H5 C32 C33 H13 180.5 180.0
C2' C1' H6 N1 236.6 237.1
H6 C1' C2' H7 93.3 160.2
H7 C2' C1' N1 332.6 37.3
H7 C2' C1' H6 93.3 160.2
C4' C3' H8 O3' 125.4 122.6
H8 C3' O3' H20 295.0 57.4
H8 C3' C2' H7 60.1 338.6
N3 C31 H9 H10 117.2 240.0
H9 C31 C32 C33 41.2 300.0
H9 C31 C32 H4 161.7 60.0
H9 C31 C32 H5 280.7 180.0
C32 C31 H9 H10 242.8 120.0
N3 C31 H10 H9 242.8 120.0
H10 C31 C32 C33 283.0 60.0
H10 C31 C32 H4 43.5 180.0
H10 C31 C32 H5 162.5 300.0
C32 C31 H10 H9 117.2 240.0
H11 C33 C32 H4 59.5 59.9
H11 C33 C32 H5 300.5 300.0
C32 C33 H11 H12 120.0 120.1
C32 C33 H11 H13 240.0 240.0
H12 C33 H11 H13 120.0 119.9
H12 C33 C32 H4 179.5 180.0
H12 C33 C32 H5 60.5 60.0
C32 C33 H12 H11 240.0 239.9
C32 C33 H12 H13 120.0 120.0
H11 C33 H12 H13 240.0 240.1
H13 C33 C32 H4 299.5 299.9
H13 C33 C32 H5 180.5 180.0
C32 C33 H13 H11 120.0 120.0
C32 C33 H13 H12 240.0 240.0
H11 C33 H13 H12 120.0 120.0
C5' C4' H14 O4' 123.6 121.1
H14 C4' C3' O3' 292.2 358.8
H14 C4' C3' H8 177.0 236.2
H15 C5' C4' O4' 50.9 186.5
H15 C5' C4' H14 287.1 65.3
O5' C5' H15 H16 238.6 240.0
H16 C5' C4' O4' 171.9 306.5
H16 C5' C4' H14 48.1 185.3
O5' C5' H16 H15 121.4 120.0
H17 N4 C4 H1 89.9 300.0
C4 N4 H17 H18 120.0 124.0
H18 N4 C4 H1 209.9 64.0
C4 N4 H18 H17 240.0 236.0
H20 O3' C3' H8 295.0 57.4
H22 OP2 P OP3 231.6 60.0
O2' C21 H23 H24 120.0 120.0
O2' C21 H23 H25 240.0 240.0
H24 C21 H23 H25 120.0 120.0
O2' C21 H24 H23 240.0 240.0
O2' C21 H24 H25 120.0 120.0
H23 C21 H24 H25 240.0 240.0
O2' C21 H25 H23 120.0 120.0
O2' C21 H25 H24 240.0 240.0
H23 C21 H25 H24 120.0 120.0
OP3 P OP2 H22 231.6 60.0