PDB Chemical Component RDG

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 RDG

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O6 C6 1.348 1.220
N1 C6 1.362 1.351
N1 C2 1.349 1.364
N2 C2 1.428 1.372
N2 C11 1.436 1.465
C6 C5 1.425 1.415
O7 C12 1.330 1.343
O7 C10 1.324 1.343
C2 N3 1.350 1.314
C11 C10 1.520 1.507
C12 C7 1.393 1.345
C10 C9 1.400 1.344
C5 C4 1.372 1.399
C5 N7 1.395 1.355
N3 C4 1.391 1.338
C4 N9 1.381 1.369
C7 C9 1.456 1.414
N7 C8 1.337 1.301
N9 C8 1.352 1.366
N9 C1' 1.544 1.464
C1' O4' 1.493 1.445
C1' C2' 1.525 1.544
O4' C4' 1.378 1.445
OP1 P 1.505 1.479
C2' C3' 1.457 1.546
C4' C5' 1.482 1.530
C4' C3' 1.488 1.546
C5' O5' 1.375 1.430
OP3 P 1.606 1.610
C3' O3' 1.382 1.429
P O5' 1.576 1.610
P OP2 1.548 1.610
OP3 H1 0.950 0.966
OP2 H2 0.950 0.968
C5' H3 1.100 1.090
C5' H4 1.100 1.091
C4' H5 1.100 1.090
C3' H6 1.101 1.090
O3' HO3' 0.950 0.967
C2' H8 1.100 1.090
C2' H9 1.100 1.090
C1' H10 1.100 1.090
C8 H12 1.080 1.080
N2 H13 1.000 0.970
C11 H14 1.100 1.090
C11 H15 1.100 1.089
C9 H16 1.080 1.080
C12 H17 1.080 1.080
C7 H18 1.080 1.081
N1 H11 1.000 0.969

Bond Angles for RDG

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O6 C6 C5 118.5 120.8
N1 C6 C5 118.9 118.4
C6 N1 H11 119.1 119.9
N2 C11 C10 115.3 109.5
C11 N2 H13 119.8 120.0
N2 C11 H14 108.0 109.5
N2 C11 H15 108.0 109.5
C6 C5 N7 133.9 134.1
O7 C12 C7 109.9 108.4
O7 C12 H17 125.1 125.8
C11 C10 C9 125.9 125.8
C10 C11 H14 108.0 109.4
C10 C11 H15 108.0 109.5
C7 C12 H17 125.0 125.8
C12 C7 H18 127.9 126.6
C10 C9 H16 126.9 126.6
C5 N7 C8 107.5 109.3
C4 N9 C8 109.2 107.5
C7 C9 H16 126.9 126.6
N9 C8 N7 109.1 109.8
N7 C8 H12 125.5 125.1
N9 C8 H12 125.4 125.1
N9 C1' H10 104.6 110.5
O4' C1' H10 105.1 110.4
C1' C2' H8 110.7 110.5
C1' C2' H9 110.7 110.6
O4' C4' H5 111.1 110.5
OP1 P O5' 115.2 109.5
C2' C3' H6 110.7 110.6
C4' C5' H3 107.7 109.5
C4' C5' H4 107.7 109.5
C4' C3' O3' 110.6 110.5
C3' C4' H5 109.4 110.3
C4' C3' H6 110.2 110.5
OP3 P O5' 103.9 109.5
OP3 P OP2 115.5 109.5
P OP3 H1 109.5 114.0
O3' C3' H6 111.9 110.5
C3' O3' HO3' 109.5 113.9
P OP2 H2 109.5 114.0
H3 C5' H4 109.4 109.5
H8 C2' H9 109.5 110.4
H14 C11 H15 109.5 109.5

Torsion Angles for RDG

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
N1 C6 O6 C5 180.6 179.9
O6 C6 N1 H11 359.6 0.1
O6 C6 C5 N7 0.6 359.9
O6 C6 N1 C5 179.4 180.1
N1 C6 C5 N7 180.0 180.0
N2 C11 C10 C9 253.7 90.0
C10 C11 N2 H14 239.2 240.0
C10 C11 N2 H15 120.9 120.0
H14 C11 N2 H15 241.7 240.0
C5 C6 N1 H11 180.2 180.0
C6 C5 N7 C8 179.5 180.0
C7 C12 O7 H17 180.0 180.2
O7 C12 C7 H18 180.1 180.1
O7 C10 C11 H14 312.1 149.7
O7 C10 C11 H15 193.8 29.7
O7 C10 C9 H16 180.3 180.3
C10 C11 N2 H13 277.1 0.1
N2 C11 C10 H14 120.8 120.0
N2 C11 C10 H15 239.1 240.0
C11 C10 C9 H16 359.6 0.0
H14 C11 C10 H15 118.3 120.0
O7 C12 C7 H17 180.0 179.8
C12 C7 C9 H16 179.8 179.8
C9 C10 C11 H14 132.9 330.0
C9 C10 C11 H15 14.6 210.0
C7 C9 C10 H16 180.0 180.0
C5 C4 N9 C8 0.2 360.0
N9 C8 N7 C5 0.4 0.0
C5 N7 C8 H12 180.3 180.3
N3 C4 N9 C8 180.3 180.0
C4 N9 C8 N7 359.7 360.0
C4 N9 C8 H12 179.7 179.8
C4 N9 C1' H10 22.2 326.2
C10 C9 C7 H16 180.0 180.0
N9 C8 N7 H12 180.0 179.8
C5 N7 C8 N9 0.4 0.0
N7 C8 N9 H12 180.0 180.2
C8 N9 C1' H10 201.3 145.8
O4' C1' N9 H10 244.4 237.7
N9 C1' C2' H8 263.6 24.1
N9 C1' C2' H9 25.3 261.5
N9 C1' O4' H10 115.3 122.4
O4' C1' C2' H8 130.8 265.3
O4' C1' C2' H9 252.5 142.7
C1' O4' C4' H5 206.4 281.6
C1' C2' C3' H6 209.4 241.3
H8 C2' C1' H9 238.4 122.6
O4' C4' C5' H3 348.1 309.6
O4' C4' C5' H4 106.0 189.6
C3' C4' O4' H5 117.1 118.9
O4' C4' C3' H6 161.7 94.8
OP3 P OP1 O5' 245.4 120.0
OP1 P OP3 H1 360.0 60.0
OP1 P OP2 H2 360.0 180.0
C2' C3' C4' H5 161.8 95.0
C4' C3' C2' H6 117.8 118.6
O3' C3' C2' H6 235.9 237.3
C2' C3' O3' HO3' 180.0 65.4
H3 C5' C4' H4 242.1 120.1
O4' C4' C3' H5 241.7 241.0
C2' C3' C4' H6 241.8 241.2
C3' C4' C5' H3 102.9 65.0
C3' C4' C5' H4 220.8 305.0
O3' C3' C4' H6 124.2 122.6
C4' C3' O3' HO3' 293.3 180.0
OP1 P OP3 O5' 122.0 240.0
OP3 P OP2 H2 239.4 300.0
C2' C3' O3' H6 123.5 122.8
O3' C3' C4' H5 44.1 336.4
C4' C3' O3' H6 236.7 237.4
OP3 P O5' OP2 238.0 120.0
O5' P OP3 H1 238.0 180.0
O5' P OP2 H2 125.1 60.0
OP3 P OP2 O5' 114.3 240.0
OP2 P OP3 H1 122.5 300.0
H1 OP3 P O5' 238.0 180.0
H1 OP3 P OP2 122.5 300.0
C4' C5' H3 H4 116.8 239.9
C4' C5' H4 H3 243.2 120.1
H5 C4' C5' H3 226.9 187.2
H5 C4' C5' H4 344.8 67.2
H5 C4' C3' O3' 44.1 336.4
H5 C4' C3' H6 279.9 213.7
C4' C3' H6 O3' 123.5 122.6
H6 C3' C4' H5 279.9 213.7
H6 C3' O3' HO3' 56.6 302.6
HO3' O3' C3' H6 56.6 302.6
C1' C2' H8 H9 122.4 237.2
H8 C2' C3' H6 90.2 0.1
C1' C2' H9 H8 237.6 122.7
H9 C2' C3' H6 328.6 122.5
H10 C1' C2' H8 21.1 146.5
H10 C1' C2' H9 142.7 23.9
N9 C8 H12 N7 180.0 180.3
H13 N2 C11 C10 277.1 0.1
H13 N2 C11 H14 37.9 120.0
H13 N2 C11 H15 156.2 240.1
N2 C11 H14 C10 234.7 240.0
H14 C11 N2 H13 37.9 120.0
N2 C11 H14 H15 117.4 120.0
H14 C11 C10 C9 132.9 330.0
C10 C11 H14 H15 242.7 240.0
N2 C11 H15 C10 125.3 120.0
H15 C11 N2 H13 156.2 240.1
N2 C11 H15 H14 242.6 240.0
H15 C11 C10 C9 14.6 210.0
C10 C11 H15 H14 117.3 120.0
O7 C12 H17 C7 180.0 180.2
H17 C12 C7 H18 0.0 0.3
H18 C7 C12 H17 0.0 0.3
H18 C7 C9 H16 359.8 359.7
H11 N1 C6 C5 180.2 180.0