PDB Chemical Component JDT

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 JDT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O5' 1.595 1.611
P OP1 1.485 1.480
P OP2 1.485 1.610
P OP3 1.608 1.610
N1 C2 1.379 1.346
N1 C6 1.377 1.369
N1 C1' 1.476 1.465
C2 O2 1.219 1.216
C2 N3 1.370 1.346
N3 C4 1.379 1.349
C4 O4 1.229 1.217
C4 C5 1.447 1.416
C5 C6 1.340 1.350
C5 C7 1.493 1.507
C7 C72 1.499 1.529
C1' C2' 1.530 1.541
C1' O4' 1.426 1.437
C2' C3' 1.518 1.549
C3' O3' 1.430 1.429
C3' C4' 1.521 1.549
C4' O4' 1.444 1.444
C4' C5' 1.512 1.530
C5' O5' 1.430 1.430
N3 HN3 1.000 0.970
C6 H6 1.080 1.081
C7 H71 1.100 1.090
C7 H72 1.100 1.090
C1' H1' 1.100 1.090
C2' H2' 1.100 1.090
C2' H2'' 1.100 1.090
C3' H3' 1.100 1.091
O3' HO3' 0.950 0.967
C4' H4' 1.100 1.090
C5' H5' 1.100 1.090
C5' H5'' 1.100 1.090
C72 H72A 1.100 1.089
C72 H72B 1.100 1.090
C72 H72C 1.100 1.090
OP2 HOP2 0.949 0.967
OP3 HOP3 0.950 0.967

Bond Angles for JDT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O5' P OP1 108.3 109.5
O5' P OP2 107.7 109.4
O5' P OP3 104.2 109.5
P O5' C5' 121.3 123.0
OP1 P OP2 119.5 109.5
OP1 P OP3 108.9 109.5
OP2 P OP3 107.1 109.5
P OP2 HOP2 109.5 114.0
P OP3 HOP3 109.5 114.0
C2 N1 C6 121.4 120.6
C2 N1 C1' 118.2 119.7
N1 C2 O2 123.2 119.5
N1 C2 N3 114.7 120.9
C6 N1 C1' 120.4 119.7
N1 C6 C5 123.1 119.7
N1 C6 H6 118.4 120.1
N1 C1' C2' 114.1 109.9
N1 C1' O4' 108.2 109.9
N1 C1' H1' 106.5 109.8
O2 C2 N3 122.1 119.5
C2 N3 C4 127.2 120.2
C2 N3 HN3 116.4 119.9
N3 C4 O4 119.8 120.3
N3 C4 C5 115.1 119.4
C4 N3 HN3 116.4 119.9
O4 C4 C5 125.1 120.3
C4 C5 C6 118.4 119.1
C4 C5 C7 119.4 120.4
C6 C5 C7 122.0 120.5
C5 C6 H6 118.5 120.2
C5 C7 C72 120.1 109.5
C5 C7 H71 106.1 109.5
C5 C7 H72 106.1 109.4
C72 C7 H71 106.1 109.5
C72 C7 H72 106.1 109.5
C7 C72 H72A 109.4 109.5
C7 C72 H72B 109.5 109.5
C7 C72 H72C 109.5 109.4
C2' C1' O4' 107.2 107.3
C1' C2' C3' 103.9 104.2
C2' C1' H1' 107.5 109.9
C1' C2' H2' 111.4 110.5
C1' C2' H2'' 111.4 110.5
C1' O4' C4' 109.0 107.0
O4' C1' H1' 113.5 110.0
C2' C3' O3' 111.4 110.9
C2' C3' C4' 102.4 102.1
C3' C2' H2' 111.4 110.5
C3' C2' H2'' 111.3 110.5
C2' C3' H3' 113.1 110.9
O3' C3' C4' 110.4 110.9
O3' C3' H3' 105.6 110.8
C3' O3' HO3' 109.5 114.0
C3' C4' O4' 103.9 103.5
C3' C4' C5' 114.9 110.6
C4' C3' H3' 114.1 111.0
C3' C4' H4' 110.0 110.6
O4' C4' C5' 110.6 110.6
O4' C4' H4' 114.4 110.6
C4' C5' O5' 110.1 109.4
C5' C4' H4' 103.3 110.7
C4' C5' H5' 109.3 109.5
C4' C5' H5'' 109.3 109.5
O5' C5' H5' 109.2 109.5
O5' C5' H5'' 109.2 109.5
H71 C7 H72 112.6 109.4
H2' C2' H2'' 107.5 110.5
H5' C5' H5'' 109.7 109.5
H72A C72 H72B 109.5 109.5
H72A C72 H72C 109.5 109.5
H72B C72 H72C 109.5 109.4

Torsion Angles for JDT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P O5' OP2 130.6 120.0
OP1 P O5' OP3 244.1 239.9
OP2 P O5' OP3 113.5 120.0
O5' P OP2 HOP2 124.1 180.0
O5' P OP3 HOP3 244.6 60.0
C4' C5' O5' P 258.9 180.0
P O5' C5' H5' 138.9 60.0
P O5' C5' H5'' 18.9 300.0
O5' P OP1 OP2 236.2 240.1
O5' P OP1 OP3 112.8 120.0
OP1 P O5' C5' 269.6 305.0
OP2 P OP1 OP3 236.6 240.0
OP1 P OP2 HOP2 0.0 60.0
OP1 P OP3 HOP3 0.0 180.0
O5' P OP2 OP1 124.1 120.0
O5' P OP2 OP3 248.4 240.0
OP2 P O5' C5' 139.0 185.0
OP1 P OP2 OP3 124.3 120.1
OP2 P OP3 HOP3 130.6 300.0
O5' P OP3 OP1 244.5 240.0
O5' P OP3 OP2 114.0 119.9
OP3 P O5' C5' 25.4 65.0
OP1 P OP3 OP2 229.4 240.0
OP3 P OP2 HOP2 235.7 300.0
C6 N1 C2 C1' 179.7 180.2
C2 N1 C6 C5 359.1 0.1
C2 N1 C6 H6 179.2 180.0
C2 N1 C1' C2' 98.4 295.0
C2 N1 C1' O4' 217.6 52.8
C2 N1 C1' H1' 340.0 174.0
O2 C2 N1 N3 180.0 180.0
N1 C2 N3 C4 360.0 0.0
N1 C2 N3 HN3 180.0 180.0
C2 N1 C6 C1' 180.4 179.8
C6 N1 C2 O2 180.3 180.0
C6 N1 C2 N3 0.3 360.0
C6 N1 C1' C2' 278.8 114.7
C6 N1 C1' O4' 37.9 232.6
C6 N1 C1' H1' 160.3 353.8
C4 C5 C6 N1 1.0 359.9
N1 C6 C5 C7 186.0 180.0
C5 C6 N1 H6 180.0 180.1
C2 N1 C1' C6 179.7 180.2
C1' N1 C2 O2 0.6 359.8
C1' N1 C2 N3 180.7 179.7
C1' N1 C6 C5 178.8 180.3
C1' N1 C6 H6 358.8 0.2
C2' C1' N1 O4' 240.8 242.1
N1 C1' C2' C3' 108.1 121.5
C2' C1' N1 H1' 118.5 121.0
N1 C1' C2' H2' 228.1 240.2
N1 C1' C2' H2'' 348.1 2.8
N1 C1' O4' C4' 224.4 214.1
O4' C1' N1 H1' 237.6 238.8
O2 C2 N1 C6 180.3 180.0
O2 C2 N1 C1' 0.6 359.8
N1 C2 O2 N3 180.0 180.0
O2 C2 N3 C4 180.0 180.0
O2 C2 N3 HN3 360.0 360.0
N3 C2 N1 C6 0.3 360.0
N3 C2 N1 C1' 180.7 179.7
N1 C2 N3 O2 180.0 180.0
C2 N3 C4 O4 181.0 180.0
C2 N3 C4 C5 0.2 360.0
C4 N3 C2 HN3 180.0 180.1
C2 N3 C4 HN3 180.0 179.9
O4 C4 N3 C5 180.8 180.1
N3 C4 C5 C6 359.3 0.1
N3 C4 C5 C7 174.5 180.0
N3 C4 O4 C5 179.2 179.9
O4 C4 N3 HN3 1.0 0.1
O4 C4 C5 C6 178.5 180.0
O4 C4 C5 C7 353.7 359.9
N1 C6 C5 C4 1.0 359.9
N3 C4 C5 O4 180.8 180.1
C5 C4 N3 HN3 180.2 180.0
C6 C5 C4 C7 184.9 180.1
C4 C5 C6 H6 181.0 180.0
C4 C5 C7 C72 261.4 275.0
C4 C5 C7 H71 21.4 35.1
C4 C5 C7 H72 141.4 155.0
C5 C6 N1 C1' 178.8 180.3
N1 C6 C5 H6 180.0 179.9
C4 C5 C6 C7 175.0 179.9
C6 C5 C7 C72 76.3 94.9
C6 C5 C7 H71 196.3 215.0
C6 C5 C7 H72 316.3 334.9
C4 C5 C7 C6 185.0 180.1
C7 C5 C6 H6 6.0 0.1
C72 C7 C5 H71 240.0 239.9
C72 C7 C5 H72 120.0 120.0
C5 C7 C72 H72A 300.0 180.0
C5 C7 C72 H72B 60.0 300.1
C5 C7 C72 H72C 180.0 60.0
H71 C7 C5 H72 240.0 240.1
C5 C7 C72 H71 120.0 120.0
C5 C7 C72 H72 240.0 240.1
H71 C7 C72 H72 120.0 120.0
H72A C72 C7 H72B 240.0 240.0
H72A C72 C7 H72C 120.0 120.0
H72B C72 C7 H72C 240.0 240.1
N1 C1' C2' O4' 119.7 119.5
N1 C1' C2' H1' 242.1 239.0
C2' C1' O4' C4' 347.9 333.5
O4' C1' C2' H1' 122.4 119.6
C1' C2' C3' O3' 147.2 139.1
C1' C2' C3' C4' 29.3 20.9
C3' C2' C1' H2' 240.0 241.3
C3' C2' C1' H2'' 120.0 118.7
C1' C2' C3' H3' 266.0 262.6
H2' C2' C1' H2'' 240.0 237.4
N1 C1' O4' C2' 236.6 240.6
N1 C1' O4' H1' 118.0 121.1
O4' C1' C2' C3' 348.4 2.0
C2' C1' O4' H1' 241.4 240.5
O4' C1' C2' H2' 108.4 120.7
O4' C1' C2' H2'' 228.4 243.3
C3' C4' O4' C1' 31.0 40.0
C1' O4' C4' C5' 154.9 158.5
C1' O4' C4' H4' 271.0 281.5
C3' C2' C1' O4' 348.4 2.0
C3' C2' C1' H1' 226.0 242.4
C1' C2' C3' H2' 120.0 118.7
C1' C2' C3' H2'' 240.0 241.3
O3' C3' C2' C4' 118.0 118.2
O3' C3' C2' H3' 241.2 236.5
C2' C3' O3' HO3' 180.0 61.4
C2' C3' C4' O4' 323.0 323.0
C2' C3' C4' C5' 202.0 204.5
C4' C3' C2' H3' 123.3 118.3
C2' C3' C4' H4' 86.0 81.5
H2' C2' C3' H2'' 120.0 122.6
C2' C3' O3' C4' 246.9 247.3
O3' C3' C2' H2' 27.2 20.4
O3' C3' C2' H2'' 267.3 257.8
C2' C3' O3' H3' 123.2 123.6
O3' C3' C4' O4' 204.3 204.8
O3' C3' C4' C5' 83.3 86.3
C4' C3' O3' H3' 236.3 236.3
O3' C3' C4' H4' 327.3 323.3
C1' O4' C4' C3' 31.0 40.0
C2' C3' C4' O3' 118.7 118.2
C4' C3' C2' H2' 269.3 262.2
C4' C3' C2' H2'' 149.3 139.6
C2' C3' C4' H3' 237.4 241.8
O3' C3' C4' H3' 118.7 123.6
C4' C3' O3' HO3' 293.1 174.1
O4' C4' C3' C5' 121.0 118.5
O4' C4' C3' H4' 237.1 241.5
C3' C4' C5' O5' 225.1 185.0
C5' C4' C3' H4' 116.0 123.0
C3' C4' C5' H5' 345.1 305.0
C3' C4' C5' H5'' 105.1 65.0
C4' O4' C1' H1' 106.4 93.0
C3' C4' O4' C5' 236.1 241.5
O4' C4' C3' H3' 85.7 81.2
C3' C4' O4' H4' 120.0 118.5
O4' C4' C5' O5' 107.8 70.9
C5' C4' O4' H4' 243.9 237.0
O4' C4' C5' H5' 227.8 190.9
O4' C4' C5' H5'' 347.8 311.0
P O5' C5' C4' 258.9 180.0
C3' C4' C5' O4' 117.3 114.1
C5' C4' C3' H3' 324.6 322.7
C3' C4' C5' H4' 240.1 237.0
O4' C4' C5' H4' 122.8 123.0
O5' C5' C4' H5' 240.0 240.0
O5' C5' C4' H5'' 120.0 120.0
H5' C5' C4' H5'' 240.0 239.9
C5' O5' P OP1 269.6 305.0
C5' O5' P OP2 139.0 185.0
C5' O5' P OP3 25.4 65.0
O5' C5' C4' H4' 345.0 308.0
C4' C5' O5' H5' 120.0 120.0
C4' C5' O5' H5'' 240.0 240.0
H5' C5' O5' H5'' 120.0 120.0
C2 N3 HN3 C4 180.0 180.1
HN3 N3 C4 O4 1.0 0.1
HN3 N3 C4 C5 180.2 180.0
H6 C6 N1 C1' 358.8 0.2
N1 C6 H6 C5 180.0 180.1
H6 C6 C5 C7 6.0 0.1
C5 C7 H71 C72 231.2 239.9
C5 C7 H71 H72 115.6 119.9
C72 C7 H71 H72 244.4 240.0
H71 C7 C72 H72A 180.0 60.0
H71 C7 C72 H72B 300.0 180.0
H71 C7 C72 H72C 60.0 300.0
C5 C7 H72 C72 128.8 120.0
C5 C7 H72 H71 244.4 240.1
C72 C7 H72 H71 115.6 120.1
H72 C7 C72 H72A 60.0 300.0
H72 C7 C72 H72B 180.0 60.0
H72 C7 C72 H72C 300.0 179.9
N1 C1' H1' C2' 122.7 121.0
N1 C1' H1' O4' 241.1 238.9
C2' C1' H1' O4' 118.4 117.9
H1' C1' C2' C3' 226.0 242.4
H1' C1' C2' H2' 346.0 1.1
H1' C1' C2' H2'' 106.0 123.7
H1' C1' O4' C4' 106.4 93.0
H2' C2' C1' O4' 108.4 120.7
C1' C2' H2' C3' 244.5 245.2
H2' C2' C1' H1' 346.0 1.1
C1' C2' H2' H2'' 122.3 122.6
H2' C2' C3' O3' 27.2 20.4
H2' C2' C3' C4' 269.3 262.2
C3' C2' H2' H2'' 237.8 237.4
H2' C2' C3' H3' 146.0 143.9
H2'' C2' C1' O4' 228.4 243.3
C1' C2' H2'' C3' 115.5 114.8
H2'' C2' C1' H1' 106.0 123.7
C1' C2' H2'' H2' 237.7 237.4
H2'' C2' C3' O3' 267.3 257.8
H2'' C2' C3' C4' 149.3 139.6
C3' C2' H2'' H2' 122.2 122.6
H2'' C2' C3' H3' 26.0 21.3
C2' C3' H3' O3' 237.9 236.4
C2' C3' H3' C4' 116.6 112.7
H3' C3' C2' H2' 146.0 143.9
H3' C3' C2' H2'' 26.0 21.3
O3' C3' H3' C4' 238.6 236.3
H3' C3' O3' HO3' 56.8 297.9
H3' C3' C4' O4' 85.7 81.2
H3' C3' C4' C5' 324.6 322.7
H3' C3' C4' H4' 208.6 199.7
HO3' O3' C3' C4' 293.1 174.1
HO3' O3' C3' H3' 56.8 297.9
C3' C4' H4' O4' 243.4 245.9
C3' C4' H4' C5' 123.2 122.9
H4' C4' C3' H3' 208.6 199.7
O4' C4' H4' C5' 239.7 237.0
H4' C4' C5' O5' 345.0 308.0
H4' C4' C5' H5' 105.0 67.9
H4' C4' C5' H5'' 225.0 188.0
C4' C5' H5' O5' 239.5 240.0
H5' C5' C4' H4' 105.0 67.9
C4' C5' H5' H5'' 119.7 120.0
O5' C5' H5' H5'' 240.3 240.0
C4' C5' H5'' O5' 120.5 120.0
H5'' C5' C4' H4' 225.0 188.0
C4' C5' H5'' H5' 240.3 240.0
O5' C5' H5'' H5' 119.7 120.0
H72A C72 C7 H71 180.0 60.0
H72A C72 C7 H72 60.0 300.0
C7 C72 H72A H72B 120.0 120.0
C7 C72 H72A H72C 240.0 240.0
H72B C72 H72A H72C 120.0 120.0
H72B C72 C7 H71 300.0 180.0
H72B C72 C7 H72 180.0 60.0
C7 C72 H72B H72A 240.0 240.0
C7 C72 H72B H72C 120.0 119.9
H72A C72 H72B H72C 240.0 240.0
H72C C72 C7 H71 60.0 300.0
H72C C72 C7 H72 300.0 179.9
C7 C72 H72C H72A 120.0 120.0
C7 C72 H72C H72B 240.0 240.0
H72A C72 H72C H72B 120.0 120.0
HOP2 OP2 P OP3 235.7 300.0