PDB Chemical Component TDY

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 TDY

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.455 1.480
P O5' 1.560 1.610
P OP2 1.484 1.611
P OP3 1.562 1.610
O5' C5' 1.434 1.429
C5' C4' 1.518 1.529
C4' O4' 1.460 1.444
C4' C3' 1.506 1.550
O4' C1' 1.413 1.438
C3' O3' 1.415 1.429
C3' C2' 1.525 1.548
C2' C1' 1.518 1.540
C1' N1 1.517 1.464
N1 C2 1.321 1.344
N1 C6 1.470 1.464
C2 O2 1.240 1.216
C2 N3 1.386 1.344
N3 C4 1.396 1.346
C4 O4 1.221 1.212
C4 C5 1.530 1.508
C5 C5M 1.510 1.530
C5 C6 1.552 1.533
C5 N5 1.347 1.470
OP2 HA 0.950 0.967
OP3 HP3 0.950 0.967
C5' HA1 1.100 1.090
C5' HB2 1.100 1.090
C4' HB 1.100 1.090
C3' HC 1.100 1.089
C1' HD 1.100 1.090
O3' H3' 0.950 0.967
C2' HB1 1.100 1.090
C2' HC2 1.100 1.090
C6 H61C 1.100 1.090
C6 H62C 1.100 1.090
N3 H3 1.000 0.970
C5M H5M1 1.100 1.090
C5M H5M2 1.100 1.091
C5M H5M3 1.100 1.090
N5 H51N 1.000 1.009
N5 CM5 1.404 1.469
CM5 HM51 1.100 1.090
CM5 HM52 1.100 1.090
CM5 HM53 1.100 1.090

Bond Angles for TDY

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P O5' 108.0 109.5
OP1 P OP2 121.0 109.5
OP1 P OP3 109.4 109.5
O5' P OP2 110.3 109.5
O5' P OP3 103.2 109.5
P O5' C5' 119.1 123.0
OP2 P OP3 103.4 109.5
P OP2 HA 109.5 114.0
P OP3 HP3 109.5 114.0
O5' C5' C4' 110.3 109.5
O5' C5' HA1 109.2 109.4
O5' C5' HB2 109.0 109.4
C5' C4' O4' 109.0 110.6
C5' C4' C3' 115.5 110.6
C4' C5' HA1 109.2 109.5
C4' C5' HB2 109.0 109.5
C5' C4' HB 104.2 110.6
O4' C4' C3' 104.7 103.5
C4' O4' C1' 108.9 107.0
O4' C4' HB 115.1 110.6
C4' C3' O3' 109.3 110.9
C4' C3' C2' 101.8 102.1
C3' C4' HB 108.6 110.8
C4' C3' HC 115.8 110.9
O4' C1' C2' 107.5 107.3
O4' C1' N1 107.3 109.9
O4' C1' HD 114.6 109.9
O3' C3' C2' 113.3 110.9
O3' C3' HC 104.9 110.8
C3' O3' H3' 109.5 114.1
C3' C2' C1' 104.1 104.2
C2' C3' HC 112.0 110.9
C3' C2' HB1 111.3 110.4
C3' C2' HC2 112.5 110.5
C2' C1' N1 116.0 109.9
C2' C1' HD 105.7 109.9
C1' C2' HB1 111.3 110.5
C1' C2' HC2 112.5 110.5
C1' N1 C2 117.5 119.6
C1' N1 C6 116.9 119.6
N1 C1' HD 105.9 110.0
C2 N1 C6 123.7 120.9
N1 C2 O2 124.6 119.2
N1 C2 N3 119.0 121.6
N1 C6 C5 109.5 109.4
N1 C6 H61C 109.4 109.4
N1 C6 H62C 109.5 109.4
O2 C2 N3 116.4 119.2
C2 N3 C4 123.4 121.0
C2 N3 H3 118.3 119.5
N3 C4 O4 119.3 120.0
N3 C4 C5 117.4 120.0
C4 N3 H3 118.3 119.5
O4 C4 C5 122.8 120.0
C4 C5 C5M 111.0 109.5
C4 C5 C6 110.7 109.1
C4 C5 N5 109.9 109.5
C5M C5 C6 107.8 109.4
C5M C5 N5 112.4 109.5
C5 C5M H5M1 109.5 109.5
C5 C5M H5M2 109.4 109.5
C5 C5M H5M3 109.5 109.5
C6 C5 N5 104.9 109.7
C5 C6 H61C 109.5 109.6
C5 C6 H62C 109.5 109.5
C5 N5 H51N 97.8 111.0
C5 N5 CM5 149.5 111.0
HA1 C5' HB2 110.1 109.5
HB1 C2' HC2 105.4 110.5
H61C C6 H62C 109.5 109.5
H5M1 C5M H5M2 109.5 109.5
H5M1 C5M H5M3 109.4 109.5
H5M2 C5M H5M3 109.5 109.4
CM5 N5 H51N 97.7 111.0
N5 CM5 HM51 109.5 109.5
N5 CM5 HM52 109.5 109.4
N5 CM5 HM53 109.5 109.5
HM51 CM5 HM52 109.5 109.5
HM51 CM5 HM53 109.5 109.5
HM52 CM5 HM53 109.5 109.5

Torsion Angles for TDY

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O5' P OP1 OP2 231.6 240.0
O5' P OP1 OP3 111.7 120.0
OP1 P O5' C5' 186.9 305.0
OP2 P OP1 OP3 240.2 240.0
OP1 P OP2 HA 65.8 60.0
OP1 P OP3 HP3 103.0 180.0
OP1 P O5' OP2 134.3 120.0
OP1 P O5' OP3 244.2 240.0
OP2 P O5' OP3 109.9 120.0
O5' P OP2 HA 193.2 180.0
O5' P OP3 HP3 348.2 60.0
P O5' C5' C4' 164.6 180.0
P O5' C5' HA1 284.6 300.0
P O5' C5' HB2 44.9 60.0
OP1 P OP2 O5' 232.6 240.0
OP1 P OP2 OP3 122.7 120.0
O5' P OP2 OP3 250.2 240.0
OP2 P O5' C5' 52.6 185.0
OP2 P OP3 HP3 233.2 300.0
OP1 P OP3 O5' 114.8 120.0
OP1 P OP3 OP2 229.8 240.0
O5' P OP3 OP2 115.0 120.0
OP3 P O5' C5' 302.7 65.0
OP3 P OP2 HA 303.0 300.0
C5' O5' P OP2 52.6 185.0
C5' O5' P OP3 302.7 65.0
O5' C5' C4' O4' 74.2 66.5
O5' C5' C4' C3' 191.6 180.5
C4' C5' O5' HA1 240.0 240.0
C4' C5' O5' HB2 119.6 120.0
O5' C5' C4' HB 310.7 303.6
HA1 C5' O5' HB2 239.7 240.0
O5' C5' C4' HA1 120.0 120.0
O5' C5' C4' HB2 240.3 240.0
O4' C4' C5' C3' 242.5 246.0
C5' C4' O4' C1' 151.9 158.6
O4' C4' C5' HB 123.4 122.8
C5' C4' C3' O3' 84.2 86.3
C5' C4' C3' C2' 204.3 204.5
C3' C4' C5' HB 240.9 236.9
C5' C4' C3' HC 326.0 322.7
HA1 C5' C4' HB2 120.3 120.0
C5' C4' O4' C3' 124.1 118.5
O4' C4' C5' HA1 314.2 306.5
O4' C4' C5' HB2 193.8 186.4
C5' C4' O4' HB 243.3 237.2
O4' C4' C3' O3' 204.0 204.8
O4' C4' C3' C2' 324.2 323.0
C3' C4' O4' HB 119.2 118.7
O4' C4' C3' HC 85.9 81.2
C4' O4' C1' C2' 352.4 333.5
C4' O4' C1' N1 227.0 214.0
C4' O4' C1' HD 109.7 92.9
C5' C4' C3' O4' 240.1 241.5
C3' C4' C5' HA1 71.6 60.5
C3' C4' C5' HB2 311.3 300.5
C5' C4' C3' HB 116.6 123.0
C3' C4' O4' C1' 27.8 40.1
O4' C4' C3' HB 236.5 241.5
O3' C3' C4' C2' 239.9 241.8
O3' C3' C4' HC 118.1 123.6
C4' C3' O3' H3' 122.7 180.0
C4' C3' C2' C1' 30.9 20.9
C2' C3' C4' HC 238.3 241.7
C4' C3' C2' HB1 150.9 139.6
C4' C3' C2' HC2 268.9 262.2
C1' O4' C4' C3' 27.8 40.1
C1' O4' C4' HB 268.6 281.4
C3' C2' C1' O4' 344.7 2.0
C2' C1' O4' N1 125.4 119.4
C2' C1' O4' HD 242.8 240.6
O4' C1' C2' HB1 224.7 243.4
O4' C1' C2' HC2 106.7 120.7
O4' C1' N1 C2 240.1 53.6
O4' C1' N1 C6 75.2 233.3
N1 C1' O4' HD 117.3 121.1
C4' C3' O3' C2' 112.8 112.7
O3' C3' C4' HB 327.5 323.3
C4' C3' O3' HC 235.2 236.3
O3' C3' C2' C1' 148.2 139.1
C2' C3' O3' HC 122.4 123.7
O3' C3' C2' HB1 268.2 257.8
O3' C3' C2' HC2 26.2 20.4
C4' C3' C2' O3' 242.7 241.8
C2' C3' C4' HB 87.7 81.5
C4' C3' C2' HC 124.4 118.3
O4' C1' C2' C3' 344.7 2.0
O3' C3' C2' HC 241.6 236.4
C2' C3' O3' H3' 10.0 67.3
C3' C2' C1' N1 104.8 121.4
C3' C2' C1' HD 221.9 242.6
C1' C2' C3' HB1 240.0 241.3
C1' C2' C3' HC2 122.0 118.7
HB1 C2' C3' HC2 242.0 237.4
O4' C1' C2' N1 239.9 240.6
O4' C1' C2' HD 122.9 119.4
C1' C2' C3' HC 266.6 262.6
C3' C2' C1' HB1 120.0 118.7
C3' C2' C1' HC2 238.0 241.3
C2' C1' N1 C2 119.9 295.8
C2' C1' N1 C6 314.9 115.4
N1 C1' C2' HD 243.0 238.8
HB1 C2' C1' HC2 118.0 122.6
O4' C1' N1 C2' 120.2 117.8
O4' C1' N1 HD 237.1 238.9
C2' C1' N1 HD 116.9 121.1
N1 C1' C2' HB1 344.8 2.8
N1 C1' C2' HC2 226.8 240.1
C2 N1 C1' C6 164.9 180.3
C1' N1 C2 O2 358.3 5.6
C1' N1 C2 N3 180.3 185.6
C1' N1 C6 C5 203.8 144.1
C1' N1 C6 H61C 323.8 264.2
C1' N1 C6 H62C 83.7 24.2
C1' N1 C2 C6 196.2 179.7
C2 N1 C1' HD 2.9 174.6
C2 N1 C6 C5 39.8 323.8
C2 N1 C6 H61C 159.8 83.9
C2 N1 C6 H62C 279.8 203.8
O2 C2 N1 N3 178.0 180.0
N1 C2 N3 C4 358.0 12.0
N1 C2 N3 H3 178.0 192.0
C1' N1 C6 C2 163.9 180.3
C6 N1 C1' HD 198.0 354.3
C6 N1 C2 O2 162.1 186.0
C6 N1 C2 N3 344.1 6.0
C4 C5 C6 N1 315.5 47.0
C5M C5 C6 N1 77.1 166.8
N1 C6 C5 N5 197.0 287.0
C5 C6 N1 H61C 240.0 239.9
C5 C6 N1 H62C 120.0 119.9
H61C C6 N1 H62C 240.0 240.1
O2 C2 N1 C6 162.1 186.0
N1 C2 O2 N3 181.9 180.0
O2 C2 N3 C4 179.8 192.0
O2 C2 N3 H3 359.8 12.0
N3 C2 N1 C6 344.1 6.0
N1 C2 N3 O2 178.2 180.0
C2 N3 C4 O4 179.4 184.4
C2 N3 C4 C5 352.0 4.4
C4 N3 C2 H3 180.0 180.0
C2 N3 C4 H3 180.0 180.0
O4 C4 N3 C5 187.4 180.0
N3 C4 C5 C5M 272.1 205.8
N3 C4 C5 C6 31.8 325.6
N3 C4 C5 N5 147.2 85.7
N3 C4 O4 C5 172.2 180.0
O4 C4 N3 H3 359.4 4.5
O4 C4 C5 C5M 84.4 25.8
O4 C4 C5 C6 204.1 145.6
O4 C4 C5 N5 319.5 265.7
N1 C6 C5 C4 315.5 47.0
N3 C4 C5 O4 187.7 180.0
C5 C4 N3 H3 172.0 184.4
C5M C5 C4 C6 240.3 240.2
C5M C5 C4 N5 124.9 120.1
C4 C5 C5M H5M1 31.6 60.0
C4 C5 C5M H5M2 151.6 180.1
C4 C5 C5M H5M3 271.6 300.0
C6 C5 C4 N5 244.6 239.9
C4 C5 C6 H61C 195.5 287.0
C4 C5 C6 H62C 75.5 166.9
C4 C5 N5 H51N 271.9 184.0
C4 C5 N5 CM5 151.9 60.0
N1 C6 C5 C5M 77.1 166.8
C4 C5 C5M C6 121.4 119.6
C4 C5 C5M N5 236.5 239.9
C6 C5 C5M N5 115.1 120.3
C5M C5 C6 H61C 317.1 46.8
C5M C5 C6 H62C 197.1 286.7
C5M C5 N5 H51N 147.8 63.9
C5M C5 N5 CM5 27.8 299.9
H5M1 C5M C5 H5M2 240.0 240.0
H5M1 C5M C5 H5M3 120.0 120.0
H5M2 C5M C5 H5M3 240.0 240.1
N1 C6 C5 H61C 120.0 120.0
N1 C6 C5 H62C 240.0 240.1
C4 C5 C6 C5M 238.4 240.2
C4 C5 C6 N5 118.5 120.0
C5M C5 C6 N5 240.1 239.8
C6 C5 C5M H5M1 270.2 300.4
C6 C5 C5M H5M2 30.2 60.5
C6 C5 C5M H5M3 150.2 180.4
C6 C5 N5 H51N 31.0 303.7
C6 C5 N5 CM5 271.0 179.8
H61C C6 C5 H62C 120.0 120.1
C4 C5 N5 C5M 124.1 120.1
C4 C5 N5 C6 241.0 240.2
C5M C5 N5 C6 116.9 120.1
N5 C5 C5M H5M1 155.1 180.1
N5 C5 C5M H5M2 275.1 300.1
N5 C5 C5M H5M3 35.1 60.1
N5 C5 C6 H61C 77.0 167.0
N5 C5 C6 H62C 317.0 46.9
CM5 N5 C5 H51N 240.0 236.0
C5 N5 CM5 HM51 343.5 60.0
C5 N5 CM5 HM52 103.5 180.0
C5 N5 CM5 HM53 223.5 300.0
HA OP2 P OP3 303.0 300.0
O5' C5' HA1 C4' 239.3 240.0
O5' C5' HA1 HB2 119.6 119.9
HA1 C5' C4' O4' 314.2 306.5
HA1 C5' C4' C3' 71.6 60.5
C4' C5' HA1 HB2 240.4 240.0
HA1 C5' C4' HB 190.7 183.6
O5' C5' HB2 C4' 120.5 120.0
O5' C5' HB2 HA1 240.2 240.1
HB2 C5' C4' O4' 193.8 186.4
HB2 C5' C4' C3' 311.3 300.5
C4' C5' HB2 HA1 119.8 120.0
HB2 C5' C4' HB 70.4 63.6
C5' C4' HB O4' 119.4 122.9
C5' C4' HB C3' 236.3 237.0
HB C4' C5' HA1 190.7 183.6
HB C4' C5' HB2 70.4 63.6
O4' C4' HB C3' 117.0 114.1
HB C4' O4' C1' 268.6 281.4
HB C4' C3' O3' 327.5 323.3
HB C4' C3' C2' 87.7 81.5
HB C4' C3' HC 209.4 199.7
C4' C3' HC O3' 120.6 123.6
C4' C3' HC C2' 243.9 247.2
HC C3' C4' HB 209.4 199.7
O3' C3' HC C2' 123.3 123.6
HC C3' O3' H3' 247.5 303.6
HC C3' C2' C1' 266.6 262.6
HC C3' C2' HB1 26.6 21.3
HC C3' C2' HC2 144.6 143.9
O4' C1' HD C2' 241.7 242.2
O4' C1' HD N1 118.1 121.1
C2' C1' HD N1 236.4 238.9
HD C1' C2' HB1 101.8 124.0
HD C1' C2' HC2 343.9 1.3
HD C1' N1 C2 2.9 174.6
HD C1' N1 C6 198.0 354.3
H3' O3' C3' C2' 10.0 67.3
H3' O3' C3' HC 247.5 303.6
C3' C2' HB1 C1' 244.4 245.2
HB1 C2' C3' HC 26.6 21.3
C3' C2' HB1 HC2 122.2 122.6
HB1 C2' C1' N1 344.8 2.8
HB1 C2' C1' HD 101.8 124.0
C1' C2' HB1 HC2 237.8 237.4
C3' C2' HC2 C1' 117.1 114.8
HC2 C2' C3' HC 144.6 143.9
C3' C2' HC2 HB1 238.6 237.5
HC2 C2' C1' N1 226.8 240.1
HC2 C2' C1' HD 343.9 1.3
C1' C2' HC2 HB1 121.4 122.6
N1 C6 H61C C5 240.0 240.0
N1 C6 H61C H62C 120.0 119.9
H61C C6 C5 N5 77.0 167.0
C5 C6 H61C H62C 240.0 239.8
N1 C6 H62C C5 120.0 119.8
N1 C6 H62C H61C 240.0 240.1
H62C C6 C5 N5 317.0 46.9
C5 C6 H62C H61C 120.0 120.2
C2 N3 H3 C4 180.0 180.0
H3 N3 C4 O4 359.4 4.5
H3 N3 C4 C5 172.0 184.4
H5M1 C5M C5 C6 270.2 300.4
H5M1 C5M C5 N5 155.1 180.1
C5 C5M H5M1 H5M2 120.0 120.0
C5 C5M H5M1 H5M3 240.0 240.0
H5M2 C5M H5M1 H5M3 120.0 120.0
H5M2 C5M C5 C6 30.2 60.5
H5M2 C5M C5 N5 275.1 300.1
C5 C5M H5M2 H5M1 240.0 240.0
C5 C5M H5M2 H5M3 120.0 120.0
H5M1 C5M H5M2 H5M3 240.0 240.0
H5M3 C5M C5 C6 150.2 180.4
H5M3 C5M C5 N5 35.1 60.1
C5 C5M H5M3 H5M1 120.0 120.0
C5 C5M H5M3 H5M2 240.0 240.0
H5M1 C5M H5M3 H5M2 120.0 120.0
C5 N5 H51N CM5 206.3 236.1
H51N N5 CM5 HM51 223.5 296.1
H51N N5 CM5 HM52 343.5 56.1
H51N N5 CM5 HM53 103.5 176.1
C5 N5 CM5 H51N 120.0 123.9
HM51 CM5 N5 HM52 240.0 240.0
HM51 CM5 N5 HM53 120.0 120.0
HM52 CM5 N5 HM53 240.0 240.0
HM51 CM5 N5 H51N 223.5 296.1
N5 CM5 HM51 HM52 120.0 120.0
N5 CM5 HM51 HM53 240.0 240.0
HM52 CM5 HM51 HM53 120.0 120.1
HM52 CM5 N5 H51N 343.5 56.1
N5 CM5 HM52 HM51 240.0 240.0
N5 CM5 HM52 HM53 120.0 120.0
HM51 CM5 HM52 HM53 240.0 240.0
HM53 CM5 N5 H51N 103.5 176.1
N5 CM5 HM53 HM51 120.0 120.0
N5 CM5 HM53 HM52 240.0 240.0
HM51 CM5 HM53 HM52 120.0 120.1