PDB Chemical Component 2DT

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 2DT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.490 1.479
P OP2 1.498 1.610
P OP3 1.596 1.610
P O5' 1.594 1.609
OP2 HOP2 0.951 0.967
OP3 HOP3 0.951 0.966
O5' C5' 1.445 1.427
N1 C6 1.379 1.368
N1 C2 1.381 1.344
N1 C1' 1.480 1.465
C6 C5 1.348 1.350
C6 H6 1.102 1.081
C2 O2 1.214 1.215
C2 N3 1.381 1.346
N3 C4 1.376 1.349
N3 HN3 1.020 0.970
C4 O4 1.225 1.218
C4 C5 1.460 1.414
C5 C5M 1.498 1.507
C5M H71 1.115 1.090
C5M H72 1.114 1.089
C5M H73 1.115 1.090
C2' C1' 1.530 1.539
C2' C3' 1.516 1.547
C2' H2' 1.116 1.090
C2' H2'' 1.115 1.090
C5' C4' 1.512 1.530
C5' H5' 1.115 1.091
C5' H5'' 1.115 1.090
C4' O4' 1.441 1.446
C4' C3' 1.526 1.549
C4' H4' 1.115 1.090
O4' C1' 1.422 1.436
C1' H1' 1.116 1.091
C3' H3'1 1.115 1.090
C3' H3'2 1.115 1.090

Bond Angles for 2DT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 120.2 109.5
OP1 P OP3 105.1 109.5
OP1 P O5' 110.8 109.4
OP2 P OP3 107.0 109.5
OP2 P O5' 107.6 109.5
P OP2 HOP2 120.2 106.8
OP3 P O5' 104.9 109.5
P OP3 HOP3 105.1 106.8
P O5' C5' 120.7 106.8
O5' C5' C4' 111.2 109.6
O5' C5' H5' 111.6 109.5
O5' C5' H5'' 111.6 109.5
C6 N1 C2 121.2 120.6
C6 N1 C1' 120.9 119.7
N1 C6 C5 123.5 119.7
N1 C6 H6 119.5 120.2
C2 N1 C1' 117.9 119.7
N1 C2 O2 122.8 119.6
N1 C2 N3 114.9 120.9
N1 C1' C2' 116.7 109.9
N1 C1' O4' 107.9 109.8
N1 C1' H1' 104.8 109.9
C5 C6 H6 117.1 120.1
C6 C5 C4 118.1 119.1
C6 C5 C5M 123.1 120.5
O2 C2 N3 122.3 119.5
C2 N3 C4 127.2 120.3
C2 N3 HN3 116.6 119.9
C4 N3 HN3 116.2 119.9
N3 C4 O4 119.9 120.3
N3 C4 C5 115.0 119.4
O4 C4 C5 125.0 120.3
C4 C5 C5M 118.8 120.4
C5 C5M H71 123.1 109.5
C5 C5M H72 107.3 109.5
C5 C5M H73 107.3 109.5
H71 C5M H72 107.4 109.5
H71 C5M H73 107.4 109.5
H72 C5M H73 102.4 109.4
C1' C2' C3' 103.8 104.2
C1' C2' H2' 114.4 110.6
C1' C2' H2'' 114.4 110.5
C2' C1' O4' 107.1 107.5
C2' C1' H1' 105.7 109.9
C3' C2' H2' 114.4 110.5
C3' C2' H2'' 114.4 110.4
C2' C3' C4' 102.7 102.1
C2' C3' H3'1 114.7 110.9
C2' C3' H3'2 114.8 110.9
H2' C2' H2'' 96.1 110.5
C4' C5' H5' 111.6 109.4
C4' C5' H5'' 111.5 109.4
C5' C4' O4' 108.4 110.7
C5' C4' C3' 116.1 110.7
C5' C4' H4' 104.6 110.5
H5' C5' H5'' 98.8 109.4
O4' C4' C3' 105.6 103.6
O4' C4' H4' 115.2 110.5
C4' O4' C1' 110.4 106.8
C3' C4' H4' 107.4 110.6
C4' C3' H3'1 114.8 110.9
C4' C3' H3'2 114.8 110.9
O4' C1' H1' 114.9 109.9
H3'1 C3' H3'2 95.7 110.8

Torsion Angles for 2DT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 239.4 120.0
OP2 P OP1 O5' 126.6 240.0
OP1 P OP2 HOP2 180.0 300.0
OP3 P OP1 O5' 247.2 120.0
OP1 P OP3 HOP3 180.0 180.0
OP1 P O5' C5' 172.5 60.0
OP1 P OP2 OP3 119.7 240.0
OP1 P OP2 O5' 232.0 120.0
OP3 P OP2 O5' 112.3 240.0
OP2 P OP3 HOP3 308.9 60.0
OP2 P O5' C5' 39.2 180.0
OP1 P OP3 OP2 231.1 120.0
OP1 P OP3 O5' 116.9 240.0
OP2 P OP3 O5' 245.8 120.0
OP3 P OP2 HOP2 60.4 60.0
OP3 P O5' C5' 285.4 300.0
OP1 P O5' OP2 133.3 240.0
OP1 P O5' OP3 247.0 120.0
OP2 P O5' OP3 113.8 240.0
O5' P OP2 HOP2 308.1 180.0
O5' P OP3 HOP3 63.1 299.9
P O5' C5' C4' 175.1 180.0
P O5' C5' H5' 300.3 60.0
P O5' C5' H5'' 49.8 300.0
HOP2 OP2 P OP3 60.4 60.0
HOP2 OP2 P O5' 308.1 180.0
HOP3 OP3 P O5' 63.1 299.9
C4' C5' O5' H5' 234.8 120.0
C4' C5' O5' H5'' 125.2 240.0
O5' C5' C4' O4' 299.5 65.7
O5' C5' C4' C3' 58.0 180.0
O5' C5' C4' H4' 176.1 302.9
H5' C5' O5' H5'' 250.5 120.0
C2 N1 C6 C1' 179.8 179.9
C6 N1 C2 O2 177.1 180.1
C6 N1 C2 N3 358.5 0.1
C6 N1 C1' C2' 279.5 120.2
C6 N1 C1' O4' 40.1 238.3
C6 N1 C1' H1' 162.9 359.2
C5 C6 N1 H6 180.0 179.9
N1 C6 C5 C4 0.7 0.2
N1 C6 C5 C5M 180.8 180.0
C6 N1 C2 C1' 180.2 180.1
C2 N1 C6 C5 0.2 359.9
C2 N1 C6 H6 180.2 180.0
C2 N1 C1' C2' 99.7 300.4
C2 N1 C1' O4' 220.3 58.4
C2 N1 C1' H1' 343.1 179.3
O2 C2 N1 N3 178.5 180.0
N1 C2 N3 C4 2.0 359.7
N1 C2 N3 HN3 182.0 180.0
C6 N1 C1' C2 179.8 179.9
C1' N1 C6 C5 180.4 180.1
C1' N1 C6 H6 0.4 0.1
C1' N1 C2 O2 356.9 359.9
C1' N1 C2 N3 178.3 180.0
N1 C1' C2' C3' 100.9 121.4
N1 C1' C2' H2' 226.1 240.1
N1 C1' C2' H2'' 335.6 2.8
C2' C1' N1 O4' 239.4 242.0
C2' C1' N1 H1' 116.6 121.0
C4' O4' C1' N1 234.1 214.1
O4' C1' N1 H1' 237.1 239.1
C5 C6 N1 C2 0.2 359.9
C5 C6 N1 C1' 180.4 180.1
N1 C6 C5 H6 180.0 180.1
N3 C4 C5 C6 359.8 359.6
O4 C4 C5 C6 180.2 180.0
C4 C5 C6 C5M 179.9 180.2
C6 C5 C5M H71 180.0 180.0
C6 C5 C5M H72 305.3 300.0
C6 C5 C5M H73 54.7 59.9
H6 C6 N1 C2 180.2 180.0
H6 C6 N1 C1' 0.4 0.1
N1 C6 H6 C5 180.0 179.9
H6 C6 C5 C4 180.7 180.2
H6 C6 C5 C5M 0.8 360.0
O2 C2 N1 C1' 356.9 359.9
N1 C2 O2 N3 181.6 180.0
O2 C2 N3 C4 183.5 179.8
O2 C2 N3 HN3 3.5 0.0
N3 C2 N1 C1' 178.3 180.0
N1 C2 N3 O2 178.5 180.0
C4 N3 C2 HN3 180.0 179.7
C2 N3 C4 O4 178.4 180.0
C2 N3 C4 C5 358.8 0.4
C6 C5 C4 N3 359.8 359.6
C2 N3 C4 HN3 180.0 180.3
O4 C4 N3 C5 179.6 179.6
N3 C4 C5 C5M 179.6 179.8
C2 N3 HN3 C4 180.0 179.7
HN3 N3 C4 O4 358.4 359.8
HN3 N3 C4 C5 178.8 180.2
C6 C5 C4 O4 180.2 180.0
O4 C4 N3 HN3 358.4 359.8
N3 C4 O4 C5 180.5 180.4
O4 C4 C5 C5M 0.1 0.2
C4 C5 C6 H6 180.7 180.2
C6 C5 C4 C5M 180.1 179.8
C5 C4 N3 HN3 178.8 180.2
N3 C4 C5 O4 179.6 179.6
C4 C5 C5M H71 0.1 359.8
C4 C5 C5M H72 125.4 119.8
C4 C5 C5M H73 234.9 239.8
C5M C5 C6 H6 0.8 360.0
C6 C5 C5M C4 179.9 180.2
H71 C5M C5 H72 234.7 240.0
H71 C5M C5 H73 125.3 120.0
H72 C5M C5 H73 250.5 240.0
C5 C5M H71 H72 125.3 120.0
C5 C5M H71 H73 234.8 240.0
H72 C5M H71 H73 109.5 120.0
C5 C5M H72 H71 225.8 240.0
C5 C5M H72 H73 112.8 120.0
H71 C5M H72 H73 247.0 240.0
C5 C5M H73 H71 134.2 120.0
C5 C5M H73 H72 247.2 240.0
H71 C5M H73 H72 113.0 120.0
N1 C1' C2' O4' 121.0 119.5
N1 C1' C2' H1' 243.9 239.0
C3' C2' C1' H2' 234.7 241.3
C3' C2' C1' H2'' 125.3 118.6
C1' C2' C3' C4' 30.6 20.9
C1' C2' C3' H3'1 155.9 139.1
C1' C2' C3' H3'2 265.3 262.7
H2' C2' C1' H2'' 250.6 237.4
C4' O4' C1' C2' 0.5 333.7
O4' C1' C2' H1' 122.9 119.5
C1' C2' C3' H2' 125.3 118.8
C1' C2' C3' H2'' 234.7 241.3
C3' C2' C1' O4' 339.8 2.0
C3' C2' C1' H1' 216.9 242.4
H2' C2' C3' H2'' 109.5 122.5
C5' C4' C3' C2' 208.9 204.3
O4' C4' C3' C2' 329.0 323.1
C2' C3' C4' H4' 92.4 81.5
C4' C3' C2' H3'1 234.8 241.8
C4' C3' C2' H3'2 125.3 118.2
H3'1 C3' C2' H3'2 250.5 236.4
C1' C2' H2' C3' 240.5 245.2
C1' C2' H2' H2'' 120.2 122.7
H2' C2' C1' O4' 105.1 120.7
H2' C2' C1' H1' 342.2 1.2
C3' C2' H2' H2'' 239.7 237.5
H2' C2' C3' C4' 265.4 262.1
H2' C2' C3' H3'1 30.6 20.4
H2' C2' C3' H3'2 140.1 143.9
C1' C2' H2'' C3' 119.5 114.8
C1' C2' H2'' H2' 239.8 237.3
H2'' C2' C1' O4' 214.5 243.3
H2'' C2' C1' H1' 91.6 123.8
C3' C2' H2'' H2' 120.3 122.5
H2'' C2' C3' C4' 155.9 139.6
H2'' C2' C3' H3'1 281.2 257.8
H2'' C2' C3' H3'2 30.6 21.4
O5' C5' C4' H5' 125.3 239.9
O5' C5' C4' H5'' 234.7 120.0
C2' C3' C4' C5' 208.9 204.3
H5' C5' C4' H5'' 109.5 240.1
O4' C4' C5' C3' 241.5 245.7
O4' C4' C5' H4' 123.4 122.8
C5' C4' O4' C1' 144.3 158.6
C3' C4' C5' H4' 241.9 237.1
C5' C4' C3' H3'1 83.7 86.1
C5' C4' C3' H3'2 334.2 322.5
O5' C5' H5' C4' 235.0 120.1
O5' C5' H5' H5'' 117.5 240.0
C4' C5' H5' H5'' 242.6 119.9
H5' C5' C4' O4' 174.2 185.7
H5' C5' C4' C3' 292.7 300.1
H5' C5' C4' H4' 50.8 63.0
O5' C5' H5'' C4' 125.0 239.9
O5' C5' H5'' H5' 242.5 120.0
C4' C5' H5'' H5' 117.4 240.1
H5'' C5' C4' O4' 64.8 305.7
H5'' C5' C4' C3' 183.3 60.0
H5'' C5' C4' H4' 301.4 182.9
N1 C1' O4' C4' 234.1 214.1
C2' C1' O4' C4' 0.5 333.7
C2' C3' C4' O4' 329.0 323.1
O4' C4' C5' H5' 174.2 185.7
O4' C4' C5' H5'' 64.8 305.7
C5' C4' O4' C3' 125.0 118.7
C5' C4' O4' H4' 243.3 237.2
C3' C4' O4' H4' 118.3 118.5
O4' C4' C3' H3'1 203.8 204.8
O4' C4' C3' H3'2 94.2 81.3
C4' O4' C1' H1' 117.6 93.2
C4' C3' C2' H2' 265.4 262.1
C4' C3' C2' H2'' 155.9 139.6
C2' C3' C4' H3'1 125.2 118.2
C2' C3' C4' H3'2 234.8 241.8
C3' C4' C5' H5' 292.7 300.1
C3' C4' C5' H5'' 183.3 60.0
C5' C4' C3' O4' 240.0 241.2
C5' C4' C3' H4' 116.6 122.8
O4' C4' C3' H4' 236.6 241.6
C3' C4' O4' C1' 19.3 39.9
H3'1 C3' C4' H3'2 109.6 123.5
H4' C4' C5' H5' 50.8 63.0
H4' C4' C5' H5'' 301.4 182.9
C5' C4' H4' O4' 118.8 122.9
C5' C4' H4' C3' 236.1 237.1
O4' C4' H4' C3' 117.3 114.1
H4' C4' O4' C1' 261.0 281.4
H4' C4' C3' H3'1 327.2 323.3
H4' C4' C3' H3'2 217.6 199.7
N1 C1' O4' C2' 233.6 240.5
N1 C1' O4' H1' 116.5 120.9
O4' C1' C2' C3' 339.8 2.0
O4' C1' C2' H2' 105.1 120.7
O4' C1' C2' H2'' 214.5 243.3
C2' C1' O4' H1' 243.0 240.5
C1' O4' C4' C3' 19.3 39.9
C1' O4' C4' H4' 261.0 281.4
N1 C1' H1' C2' 123.9 121.1
N1 C1' H1' O4' 241.7 239.1
H1' C1' C2' C3' 216.9 242.4
H1' C1' C2' H2' 342.2 1.2
H1' C1' C2' H2'' 91.6 123.8
C2' C1' H1' O4' 117.8 118.0
H3'1 C3' C2' H2' 30.6 20.4
H3'1 C3' C2' H2'' 281.2 257.8
C2' C3' H3'1 C4' 241.4 247.3
C2' C3' H3'1 H3'2 120.6 123.7
H3'1 C3' C4' H4' 327.2 323.3
C4' C3' H3'1 H3'2 239.3 236.4
H3'2 C3' C2' H2' 140.1 143.9
H3'2 C3' C2' H2'' 30.6 21.4
C2' C3' H3'2 C4' 118.7 112.7
C2' C3' H3'2 H3'1 239.4 236.3
H3'2 C3' C4' H4' 217.6 199.7
C4' C3' H3'2 H3'1 120.7 123.6