PDB Chemical Component DNR

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 DNR

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.481 1.501
P OP2 1.480 1.618
P O5' 1.616 1.619
P OP3   1.616
OP2 HOP2 0.949 0.981
O5' C5' 1.433 1.418
C5' C4' 1.524 1.523
C5' H5' 1.085 1.092
C5' H5'' 1.091 1.093
C4' O4' 1.450 1.441
C4' C3' 1.520 1.522
C4' H4' 1.088 1.094
O4' C1' 1.445 1.434
C1' N1 1.484 1.434
C1' C2' 1.513 1.520
C1' H1' 1.079 1.095
N1 C6 1.361 1.390
N1 C2 1.396 1.406
C6 C5 1.344 1.335
C6 H6 1.086 1.085
C2 O2 1.230 1.224
C2 N3 1.368 1.447
N3 C4 1.344 1.329
N3 HN3 1.021 1.017
C4 N4 1.330 1.323
C4 C5 1.429 1.483
N4 H41 1.009 1.016
N4 H42 1.010 1.017
C5 H5 1.090 1.084
C2' C3' 1.499 1.511
C2' H2' 1.088 1.097
C2' H2'' 1.080 1.095
C3' O3' 1.435 1.426
C3' H3' 1.093 1.094
O3' HO3' 0.950 0.973
OP3 HOP3   0.981

Bond Angles for DNR

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.8 115.3
OP1 P O5' 108.1 115.0
OP1 P OP3   115.0
OP2 P O5' 108.1 103.7
OP2 P OP3   103.3
P OP2 HOP2 119.8 118.9
O5' P OP3   102.9
P O5' C5' 120.5 118.5
P OP3 HOP3   118.9
O5' C5' C4' 112.4 108.9
O5' C5' H5' 108.9 109.0
O5' C5' H5'' 109.2 108.9
C4' C5' H5' 108.1 110.3
C4' C5' H5'' 109.1 110.3
C5' C4' O4' 110.9 107.9
C5' C4' C3' 111.7 112.9
C5' C4' H4' 109.1 109.5
H5' C5' H5'' 109.0 109.3
O4' C4' C3' 107.4 106.2
O4' C4' H4' 108.7 107.9
C4' O4' C1' 109.6 109.3
C3' C4' H4' 109.0 112.2
C4' C3' C2' 104.4 103.1
C4' C3' O3' 111.0 109.9
C4' C3' H3' 109.8 113.5
O4' C1' N1 110.9 109.3
O4' C1' C2' 106.4 107.4
O4' C1' H1' 109.1 108.0
N1 C1' C2' 112.2 112.8
N1 C1' H1' 109.5 107.8
C1' N1 C6 120.4 118.3
C1' N1 C2 118.2 120.7
C2' C1' H1' 108.7 111.5
C1' C2' C3' 105.2 102.5
C1' C2' H2' 111.2 110.6
C1' C2' H2'' 109.6 111.7
C6 N1 C2 121.4 121.0
N1 C6 C5 120.9 122.7
N1 C6 H6 119.5 116.1
N1 C2 O2 120.2 126.8
N1 C2 N3 118.3 115.0
C5 C6 H6 119.6 121.2
C6 C5 C4 117.8 119.3
C6 C5 H5 121.1 121.1
O2 C2 N3 121.5 118.2
C2 N3 C4 120.4 125.3
C2 N3 HN3 119.7 118.6
C4 N3 HN3 119.7 116.1
N3 C4 N4 119.6 125.3
N3 C4 C5 121.2 116.8
N4 C4 C5 119.2 118.0
C4 N4 H41 119.8 120.6
C4 N4 H42 120.1 120.5
C4 C5 H5 121.1 119.6
H41 N4 H42 120.1 118.8
C3' C2' H2' 110.4 109.7
C3' C2' H2'' 109.8 114.1
C2' C3' O3' 111.3 109.7
C2' C3' H3' 109.9 113.2
H2' C2' H2'' 110.5 108.3
O3' C3' H3' 110.2 107.4
C3' O3' HO3' 111.0 107.3

Torsion Angles for DNR

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 O5' 124.3 120.6
OP2 P OP1 OP3   239.9
OP1 P OP2 HOP2 180.0 48.8
O5' P OP1 OP3   119.3
OP1 P O5' C5' 181.7 179.9
OP1 P OP3 HOP3   312.0
OP1 P OP2 O5' 235.7 233.4
OP1 P OP2 OP3   126.3
O5' P OP2 OP3   252.9
OP2 P O5' C5' 50.7 53.2
OP2 P OP3 HOP3   78.5
OP1 P O5' OP2 131.0 126.8
OP1 P O5' OP3   234.2
OP2 P O5' OP3   107.4
O5' P OP2 HOP2 304.3 175.4
O5' P OP3 HOP3   186.2
P O5' C5' C4' 181.9 180.0
P O5' C5' H5' 62.1 300.4
P O5' C5' H5'' 303.1 59.6
OP1 P OP3 OP2   233.5
OP1 P OP3 O5'   125.8
OP2 P OP3 O5'   252.3
OP3 P OP2 HOP2   282.5
OP3 P O5' C5'   305.8
HOP2 OP2 P O5' 304.3 175.4
HOP2 OP2 P OP3   282.5
C5' O5' P OP3   305.8
C4' C5' O5' H5' 119.8 239.6
C4' C5' O5' H5'' 238.8 120.4
O5' C5' C4' O4' 305.9 62.4
O5' C5' C4' C3' 65.7 179.5
O5' C5' C4' H4' 186.2 305.3
H5' C5' O5' H5'' 118.9 240.8
O5' C5' C4' H5' 239.7 119.6
O5' C5' C4' H5'' 121.3 240.5
H5' C5' C4' H5'' 241.6 120.9
O4' C4' C5' C3' 240.2 242.9
O4' C4' C5' H4' 119.7 117.1
C5' C4' O4' C1' 120.1 108.6
C3' C4' C5' H4' 239.5 234.2
C5' C4' C3' C2' 255.9 271.2
C5' C4' C3' O3' 135.9 154.2
C5' C4' C3' H3' 13.7 34.0
O5' C5' H5' C4' 122.5 240.5
O5' C5' H5' H5'' 241.0 119.0
C4' C5' H5' H5'' 118.5 238.5
H5' C5' C4' O4' 66.2 302.9
H5' C5' C4' C3' 186.0 60.0
H5' C5' C4' H4' 306.5 185.7
O5' C5' H5'' C4' 236.8 119.4
O5' C5' H5'' H5' 118.9 241.0
C4' C5' H5'' H5' 242.1 121.5
H5'' C5' C4' O4' 184.6 181.9
H5'' C5' C4' C3' 304.4 299.0
H5'' C5' C4' H4' 64.9 64.8
O4' C4' C5' H5' 66.2 302.9
O4' C4' C5' H5'' 184.6 181.9
C5' C4' O4' C3' 122.4 121.4
C5' C4' O4' H4' 240.1 241.8
C3' C4' O4' H4' 117.8 120.5
O4' C4' C3' C2' 17.7 29.2
O4' C4' C3' O3' 257.7 272.3
O4' C4' C3' H3' 135.5 152.1
C4' O4' C1' N1 223.7 228.3
C4' O4' C1' C2' 345.9 351.0
C4' O4' C1' H1' 103.0 111.3
C3' C4' C5' H5' 186.0 60.0
C3' C4' C5' H5'' 304.4 299.0
C5' C4' C3' O4' 238.2 241.9
C5' C4' C3' H4' 120.6 124.3
O4' C4' C3' H4' 242.4 242.4
C3' C4' O4' C1' 357.7 347.3
C1' C2' C3' C4' 334.2 326.6
C4' C3' C2' H2' 94.3 84.1
C4' C3' C2' H2'' 216.4 205.7
C2' C3' C4' O3' 120.0 116.9
C2' C3' C4' H3' 242.2 237.2
O3' C3' C4' H3' 122.2 120.2
C4' C3' O3' HO3' 180.0 232.0
H4' C4' C5' H5' 306.5 185.7
H4' C4' C5' H5'' 64.9 64.8
C5' C4' H4' O4' 121.0 117.1
C5' C4' H4' C3' 237.8 233.8
O4' C4' H4' C3' 116.8 116.7
H4' C4' O4' C1' 240.0 226.8
H4' C4' C3' C2' 135.3 146.9
H4' C4' C3' O3' 15.3 29.9
H4' C4' C3' H3' 253.1 269.7
C1' O4' C4' C3' 357.7 347.3
C1' O4' C4' H4' 240.0 226.8
N1 C1' O4' C2' 237.8 237.3
N1 C1' O4' H1' 120.7 117.0
O4' C1' N1 C6 53.4 32.9
O4' C1' N1 C2 235.7 212.9
C2' C1' O4' H1' 242.9 239.7
O4' C1' C2' C3' 25.0 26.9
O4' C1' C2' H2' 265.4 270.0
O4' C1' C2' H2'' 143.0 149.4
O4' C1' N1 C2' 118.8 119.4
O4' C1' N1 H1' 239.6 242.9
C2' C1' N1 H1' 120.8 123.5
N1 C1' C2' C3' 146.4 147.4
N1 C1' C2' H2' 26.8 30.6
N1 C1' C2' H2'' 264.4 269.9
C6 N1 C1' C2 177.7 180.0
C1' N1 C6 C5 182.8 180.0
C1' N1 C6 H6 3.5 360.0
C1' N1 C2 O2 357.7 359.9
C1' N1 C2 N3 177.3 180.0
C4' C3' C2' C1' 334.2 326.6
O4' C1' C2' N1 238.6 239.5
O4' C1' C2' H1' 117.3 118.1
N1 C1' C2' H1' 238.7 238.6
C2' C1' N1 C6 294.6 273.5
C2' C1' N1 C2 116.9 93.5
C3' C2' C1' H2' 119.6 116.9
C3' C2' C1' H2'' 242.0 237.5
C1' C2' C3' O3' 94.1 83.6
C1' C2' C3' H3' 216.5 203.6
H2' C2' C1' H2'' 122.4 120.7
O4' C1' H1' N1 121.6 118.0
O4' C1' H1' C2' 244.4 242.3
N1 C1' H1' C2' 122.9 124.3
H1' C1' N1 C6 173.8 150.0
H1' C1' N1 C2 356.1 330.0
H1' C1' C2' C3' 267.7 268.8
H1' C1' C2' H2' 148.1 151.9
H1' C1' C2' H2'' 25.7 31.3
C6 N1 C1' C2' 294.6 273.5
C6 N1 C1' H1' 173.8 150.0
C1' N1 C6 C2 182.4 180.0
C6 N1 C2 O2 180.0 180.0
C6 N1 C2 N3 359.6 0.0
C5 C6 N1 H6 179.3 180.0
N1 C6 C5 C4 359.8 360.0
N1 C6 C5 H5 179.8 180.0
C2 N1 C1' C2' 116.9 93.5
C2 N1 C1' H1' 356.1 330.0
C1' N1 C2 C6 177.7 180.0
C2 N1 C6 C5 0.5 360.0
C2 N1 C6 H6 181.1 180.0
O2 C2 N1 N3 180.4 179.9
N1 C2 N3 C4 0.0 0.0
N1 C2 N3 HN3 185.5 179.9
C5 C6 N1 C2 0.5 360.0
N1 C6 C5 H6 180.7 180.0
N3 C4 C5 C6 359.8 0.1
N4 C4 C5 C6 179.7 180.1
C4 C5 C6 H5 180.0 180.0
H6 C6 N1 C2 181.1 180.0
N1 C6 H6 C5 179.4 180.0
H6 C6 C5 C4 179.2 180.0
H6 C6 C5 H5 359.1 0.0
N1 C2 O2 N3 179.6 180.1
O2 C2 N3 C4 179.6 180.1
O2 C2 N3 HN3 5.1 360.0
N1 C2 N3 O2 180.4 180.0
C4 N3 C2 HN3 174.5 180.1
C2 N3 C4 N4 180.4 179.9
C2 N3 C4 C5 0.2 360.0
C6 C5 C4 N3 359.8 0.1
C2 N3 C4 HN3 185.5 179.9
N4 C4 N3 C5 180.2 180.0
N3 C4 N4 H41 359.9 257.0
N3 C4 N4 H42 179.8 76.9
N3 C4 C5 H5 179.9 180.0
C2 N3 HN3 C4 174.6 180.1
HN3 N3 C4 N4 354.9 0.0
HN3 N3 C4 C5 174.7 180.0
C6 C5 C4 N4 179.7 180.1
N4 C4 N3 HN3 354.9 0.0
N3 C4 N4 C5 179.8 180.0
N4 C4 C5 H5 359.7 0.0
H41 N4 C4 H42 180.1 180.0
C4 C5 C6 H6 179.2 180.0
C6 C5 C4 H5 180.0 180.0
C5 C4 N3 HN3 174.7 180.0
N3 C4 C5 N4 180.2 180.0
C5 C4 N4 H41 180.1 76.9
C5 C4 N4 H42 360.0 256.9
H41 N4 C4 C5 180.1 76.9
C4 N4 H41 H42 179.9 180.0
H42 N4 C4 C5 360.0 256.9
C4 N4 H42 H41 180.1 180.0
H5 C5 C6 H6 359.1 0.0
C6 C5 H5 C4 180.0 180.0
C2' C3' C4' H4' 135.3 146.9
C4' C3' C2' O3' 240.2 242.9
C4' C3' C2' H3' 117.7 123.0
C3' C2' C1' H1' 267.7 268.8
C1' C2' C3' H2' 239.9 242.5
C1' C2' C3' H2'' 117.9 120.8
H2' C2' C3' H2'' 237.9 238.3
O3' C3' C2' H3' 237.6 240.1
C2' C3' O3' HO3' 64.1 119.3
H2' C2' C1' H1' 148.1 151.9
C1' C2' H2' C3' 116.4 112.3
C1' C2' H2' H2'' 238.1 237.3
C3' C2' H2' H2'' 121.7 125.1
H2' C2' C3' O3' 214.2 201.1
H2' C2' C3' H3' 336.6 321.1
H2'' C2' C1' H1' 25.7 31.3
C1' C2' H2'' C3' 244.9 244.4
C1' C2' H2'' H2' 122.8 122.0
C3' C2' H2'' H2' 238.0 237.5
H2'' C2' C3' O3' 336.2 322.8
H2'' C2' C3' H3' 98.6 82.7
O3' C3' C4' H4' 15.3 29.9
C4' C3' O3' C2' 115.8 112.7
C4' C3' O3' H3' 238.1 236.1
O3' C3' C2' H2' 214.2 201.1
O3' C3' C2' H2'' 336.2 322.8
C2' C3' O3' H3' 122.2 123.4
H3' C3' C4' H4' 253.1 269.7
C4' C3' H3' C2' 245.7 242.9
C4' C3' H3' O3' 122.6 121.7
H3' C3' C2' H2' 336.6 321.1
H3' C3' C2' H2'' 98.6 82.7
C2' C3' H3' O3' 237.0 238.7
H3' C3' O3' HO3' 301.9 355.9
HO3' O3' C3' H3' 301.9 355.9