PDB Chemical Component V3L

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 V3L

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C6 1.360 1.330
N1 C2 1.354 1.321
C2 N3 1.343 1.315
C2 H2 1.080 1.080
C4 N3 1.352 1.329
C5 C4 1.461 1.404
C4 N9 1.325 1.373
C6 C5 1.471 1.406
C5 N7 1.344 1.354
N6 C6 1.337 1.384
N6 HN6 1.000 0.971
N6 HN6A 1.001 0.969
N7 C8 1.331 1.302
C8 N9 1.341 1.363
C8 H8 1.080 1.079
N9 C1' 1.478 1.465
OP1 P 1.520 1.480
P O5' 1.604 1.611
P OP3 1.521 1.610
P OP2 1.507 1.610
O15 PB 1.596 1.609
O2B PB 1.509 1.480
PB O3B 1.506 1.611
PB O1B 1.497 1.610
O2' C10 1.427 1.430
C10 C12 1.527 1.540
C10 O14 1.426 1.437
C10 H1'' 1.100 1.090
O4' C1' 1.409 1.444
C1' C2' 1.533 1.550
C1' H1' 1.100 1.090
OP3 HOP3 0.950 0.967
O1B HO1B 0.950 0.967
O12 C12 1.421 1.429
C12 C13 1.526 1.549
C12 H2'' 1.101 1.090
O12 HO2' 0.950 0.966
C3' C2' 1.534 1.549
C2' O2' 1.436 1.429
C2' H2' 1.100 1.090
O13 C13 1.433 1.429
C13 C14 1.522 1.550
C13 H3'' 1.100 1.090
O13 HO13 0.951 0.967
C4' C3' 1.525 1.540
C3' O3' 1.429 1.429
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
OP2 HOP2 0.950 0.967
O3B HO3B 0.951 0.967
O14 C14 1.435 1.444
C14 C15 1.526 1.530
C14 H4'' 1.100 1.090
O4' C4' 1.433 1.438
C5' C4' 1.518 1.530
C4' H4' 1.100 1.091
C15 O15 1.427 1.429
C15 H5'' 1.100 1.090
C15 H5AA 1.100 1.089
C5' O5' 1.443 1.429
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.090

Bond Angles for V3L

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 121.0 121.2
N1 C6 C5 118.6 118.4
N1 C2 N3 123.2 122.5
N1 C2 H2 118.4 118.7
N3 C2 H2 118.4 118.8
C5 C4 N9 104.5 106.0
C4 N9 C8 109.9 107.4
C4 N9 C1' 125.1 126.3
C6 C5 N7 135.8 134.7
C5 N7 C8 107.2 109.4
HN6 N6 HN6A 109.4 120.0
N7 C8 N9 110.8 110.0
N7 C8 H8 124.6 125.0
N9 C8 H8 124.6 125.1
C8 N9 C1' 124.7 126.2
N9 C1' C2' 107.0 110.7
N9 C1' H1' 110.3 110.5
OP1 P O5' 105.7 109.5
OP1 P OP2 115.2 109.5
OP3 P O5' 103.8 109.5
OP2 P O5' 101.5 109.5
P O5' C5' 121.0 123.0
OP3 P OP2 113.2 109.5
P OP3 HOP3 109.5 114.0
P OP2 HOP2 109.5 114.0
O2B PB O3B 113.2 109.5
O1B PB O3B 116.1 109.5
PB O3B HO3B 109.5 114.0
PB O1B HO1B 109.5 114.0
O2' C10 O14 108.4 109.8
O2' C10 H1'' 111.8 110.0
C12 C10 O14 104.2 107.3
C12 C10 H1'' 110.3 109.9
C10 C12 C13 103.2 104.2
C10 C12 H2'' 109.3 110.5
O14 C10 H1'' 111.8 109.9
C10 O14 C14 109.0 107.0
O4' C1' H1' 111.3 110.7
C2' C1' H1' 109.5 110.6
C1' C2' O2' 108.7 110.9
C1' C2' H2' 109.2 110.9
O12 C12 C13 112.3 110.5
O12 C12 H2'' 110.8 110.6
C13 C12 H2'' 109.3 110.4
C12 C13 C14 103.8 102.1
C12 C13 H3'' 109.7 110.9
C3' C2' H2' 109.3 110.9
O2' C2' H2' 110.6 110.8
O13 C13 C14 109.8 110.9
O13 C13 H3'' 111.0 110.9
C14 C13 H3'' 109.8 110.9
C13 C14 C15 112.8 110.6
C13 C14 H4'' 108.5 110.6
C4' C3' H3' 109.1 110.6
O3' C3' H3' 110.4 110.5
C3' O3' HO3' 109.5 113.9
O14 C14 C15 109.7 110.7
O14 C14 H4'' 109.7 110.7
C15 C14 H4'' 108.4 110.6
C14 C15 O15 111.4 109.5
C14 C15 H5'' 109.0 109.5
C14 C15 H5AA 108.9 109.5
O4' C4' H4' 110.1 109.8
C5' C4' H4' 109.0 109.9
O15 C15 H5'' 109.0 109.5
O15 C15 H5AA 109.0 109.4
H5'' C15 H5AA 109.5 109.5
O5' C5' H5' 109.1 109.5
O5' C5' H5'A 109.1 109.5
H5' C5' H5'A 109.5 109.5

Torsion Angles for V3L

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C6 N1 C2 N3 1.4 360.0
C6 N1 C2 H2 181.4 180.0
N1 C6 C5 N7 180.9 180.0
C2 N1 C6 C5 357.3 0.0
N3 C2 N1 H2 180.0 180.0
N3 C2 N1 C6 1.4 360.0
N1 C2 N3 H2 180.0 180.0
H2 C2 N1 C6 181.4 180.0
N1 C2 H2 N3 180.0 180.0
C4 N3 C2 H2 180.1 180.0
N1 C6 C5 C4 2.5 359.9
C5 C4 N9 C8 357.7 360.0
C5 C4 N9 C1' 184.0 180.0
N7 C8 N9 C4 2.8 0.0
C4 N9 C8 H8 182.8 180.0
C8 N9 C4 C1' 173.7 180.0
C4 N9 C1' C2' 104.0 84.9
C4 N9 C1' H1' 345.0 322.1
C6 C5 C4 N9 180.0 180.1
C6 C5 N7 C8 182.0 179.9
N7 C5 C4 N9 1.1 360.0
C5 N7 C8 N9 358.1 360.0
C5 N7 C8 H8 178.0 180.0
N6 C6 C5 N7 359.0 0.0
C4 N9 C8 N7 2.8 0.0
N9 C8 N7 H8 180.0 180.0
N7 C8 N9 C1' 176.5 180.0
C4 N9 C8 C1' 186.3 180.0
N7 C8 N9 H8 180.0 180.0
C8 N9 C1' C2' 291.3 265.0
C8 N9 C1' H1' 172.2 142.1
N7 C8 H8 N9 180.0 180.0
H8 C8 N9 C1' 356.5 360.0
C4 N9 C1' C8 172.8 180.0
C1' N9 C8 H8 356.5 360.0
O4' C1' N9 H1' 235.2 237.0
C2' C1' N9 H1' 119.1 122.9
N9 C1' C2' O2' 271.5 273.7
N9 C1' C2' H2' 32.2 37.3
OP3 P OP1 O5' 246.0 240.0
OP2 P OP1 O5' 111.2 120.0
OP1 P O5' C5' 302.7 55.0
OP3 P OP1 OP2 134.8 120.0
OP1 P OP3 HOP3 0.0 300.0
OP1 P OP2 HOP2 0.0 179.9
OP1 P O5' OP2 120.5 120.0
OP3 P O5' OP2 242.3 240.0
O5' P OP3 HOP3 244.9 180.0
O5' P OP2 HOP2 113.7 299.9
P O5' C5' H5' 45.2 60.0
P O5' C5' H5'A 285.7 300.0
OP1 P OP3 O5' 115.1 120.0
OP1 P OP3 OP2 224.3 240.0
OP2 P OP3 O5' 250.8 240.0
OP3 P O5' C5' 64.5 175.0
OP3 P OP2 HOP2 224.3 59.9
OP1 P OP2 O5' 246.4 240.0
OP3 P OP2 O5' 110.6 120.0
OP2 P O5' C5' 182.1 295.0
OP2 P OP3 HOP3 135.7 60.0
O15 PB O3B HO3B 244.7 180.0
O15 PB O1B HO1B 115.4 60.0
O1B PB O2B O3B 226.3 120.0
O2B PB O3B HO3B 360.0 60.0
O2B PB O1B HO1B 360.0 180.0
O3B PB O1B HO1B 227.7 300.0
O2B PB O1B O3B 132.3 240.0
O1B PB O3B HO3B 131.8 300.0
C12 C10 O2' O14 113.4 117.9
C12 C10 O2' H1'' 237.0 238.9
O2' C10 C12 C13 278.8 242.6
O2' C10 C12 H2'' 162.5 124.0
O14 C10 O2' H1'' 123.6 121.1
O2' C10 O14 C14 85.9 93.0
O2' C10 C12 O14 243.9 240.6
O2' C10 C12 H1'' 123.8 121.1
O14 C10 C12 H1'' 239.9 240.5
C12 C10 O14 C14 328.6 333.5
O12 C12 C10 C13 120.9 118.6
O12 C12 C10 H2'' 237.1 237.3
C13 C12 C10 H2'' 116.2 118.6
C10 C12 C13 C14 334.7 20.9
C10 C12 C13 H3'' 217.5 262.7
O2' C10 O14 H1'' 236.4 238.9
C12 C10 O14 H1'' 119.1 119.5
O14 C10 C12 C13 34.8 2.0
O14 C10 C12 H2'' 278.6 243.4
C10 O14 C14 C15 138.3 158.5
C10 O14 C14 H4'' 257.3 281.5
O2' C10 H1'' O14 121.7 121.0
C12 C10 H1'' O14 244.6 242.1
H1'' C10 C12 C13 154.9 121.5
H1'' C10 C12 H2'' 38.7 2.9
H1'' C10 O14 C14 209.5 214.1
N9 C1' O4' H1' 124.3 122.9
C2' C1' O4' H1' 240.9 241.4
O4' C1' C2' H2' 272.0 278.8
N9 C1' C2' H1' 240.4 237.2
O4' C1' C2' H1' 120.2 118.6
C3' C2' C1' H2' 116.1 118.2
O2' C2' C1' H2' 239.3 236.4
N9 C1' H1' C2' 117.6 122.9
H1' C1' C2' O2' 31.1 36.6
H1' C1' C2' H2' 151.8 160.2
HOP3 OP3 P O5' 244.9 180.0
HOP3 OP3 P OP2 135.7 60.0
HO1B O1B PB O3B 227.7 300.0
O12 C12 C10 O14 155.7 120.7
O12 C12 C10 H1'' 275.8 240.1
C10 C12 O12 C13 244.6 245.2
C10 C12 O12 H2'' 122.0 122.7
C13 C12 O12 H2'' 237.4 237.5
O12 C12 C13 C14 214.4 262.2
O12 C12 C13 H3'' 97.2 144.0
C13 C12 C10 O14 34.8 2.0
C13 C12 C10 H1'' 154.9 121.5
C10 C12 C13 H2'' 243.8 241.3
O12 C12 C13 H2'' 123.4 122.6
O13 C13 C12 C14 118.7 118.2
O13 C13 C12 H3'' 235.9 236.4
C14 C13 C12 H3'' 117.2 118.1
C12 C13 C14 C15 246.2 204.5
C12 C13 C14 H4'' 126.1 81.7
H2'' C12 C10 O14 278.6 243.4
H2'' C12 C10 H1'' 38.7 2.9
C10 C12 H2'' C13 112.3 114.8
O12 C12 H2'' C13 235.7 237.4
H2'' C12 C13 C14 91.0 139.6
H2'' C12 C13 H3'' 333.8 21.4
HO2' O12 C12 C13 295.4 176.3
HO2' O12 C12 H2'' 58.0 298.8
C3' C2' C1' H1' 267.9 278.3
C1' C2' C3' H2' 243.9 241.9
O2' C2' C3' H2' 125.4 123.6
C2' O2' C10 O14 78.3 72.2
C2' O2' C10 H1'' 314.7 311.1
O2' C2' C1' H1' 31.1 36.6
C1' C2' O2' H2' 119.9 123.6
C3' C2' O2' H2' 235.2 236.3
H2' C2' C1' H1' 151.8 160.2
C1' C2' H2' O2' 240.4 236.4
O13 C13 C12 H2'' 209.6 257.8
C12 C13 O13 C14 244.9 247.3
C12 C13 O13 H3'' 123.4 123.6
C14 C13 O13 H3'' 238.5 236.3
O13 C13 C14 C15 125.6 86.3
O13 C13 C14 H4'' 5.5 323.4
C10 O14 C14 C13 15.1 40.0
C14 C13 C12 H2'' 91.0 139.6
C12 C13 C14 H3'' 242.9 241.9
O13 C13 C14 H3'' 122.3 123.7
O14 C14 C13 C15 121.2 118.6
O14 C14 C13 H4'' 241.4 241.4
C15 C14 C13 H4'' 120.1 122.8
C13 C14 C15 O15 51.2 185.0
C13 C14 C15 H5'' 171.5 305.0
C13 C14 C15 H5AA 290.9 65.1
H3'' C13 C12 H2'' 333.8 21.4
C12 C13 H3'' C14 113.4 112.6
O13 C13 H3'' C14 238.4 236.3
H3'' C13 C14 C15 3.3 322.6
H3'' C13 C14 H4'' 243.2 199.8
HO13 O13 C13 C14 295.1 174.1
HO13 O13 C13 H3'' 56.6 297.8
C4' C3' C2' H2' 91.8 97.3
O3' C3' C4' H3' 121.2 122.6
C4' C3' O3' HO3' 296.7 294.7
O3' C3' C2' H2' 211.7 216.0
C4' C3' O3' H3' 239.6 237.3
H3' C3' C2' H2' 335.4 338.5
H3' C3' O3' HO3' 57.1 57.4
HO3' O3' C3' H3' 57.1 57.4
HOP2 OP2 P O5' 113.7 299.9
C14 O14 C10 H1'' 209.5 214.1
O14 C14 C13 H3'' 124.6 81.2
C13 C14 O14 C15 236.9 241.5
C13 C14 O14 H4'' 117.9 118.5
C15 C14 O14 H4'' 241.0 237.1
O14 C14 C15 O15 291.1 70.9
O14 C14 C15 H5'' 51.4 190.9
O14 C14 C15 H5AA 170.8 311.0
C15 C14 C13 H3'' 3.3 322.6
C13 C14 C15 H4'' 239.9 237.2
O14 C14 C15 H4'' 119.8 123.0
O15 C15 C14 H5'' 239.7 240.0
O15 C15 C14 H5AA 120.3 119.9
H5'' C15 C14 H5AA 240.6 239.9
H4'' C14 C13 H3'' 243.2 199.8
C13 C14 H4'' C15 122.8 122.8
O14 C14 H4'' C15 240.2 237.0
H4'' C14 C15 O15 171.3 307.9
H4'' C14 C15 H5'' 291.6 67.8
H4'' C14 C15 H5AA 51.1 187.9
C4' O4' C1' H1' 97.6 78.6
O4' C4' C3' H3' 129.0 116.7
C5' C4' O4' H4' 241.6 239.0
P O5' C5' C4' 165.4 180.0
C5' C4' C3' H3' 10.4 357.1
O4' C4' C5' H4' 119.1 121.0
H4' C4' C3' H3' 248.1 236.1
O15 C15 C14 H4'' 171.3 307.9
C14 C15 O15 H5'' 120.3 120.0
C14 C15 O15 H5AA 239.7 240.0
H5'' C15 O15 H5AA 119.4 120.0
H5'' C15 C14 H4'' 291.6 67.8
C14 C15 H5'' O15 238.2 240.0
C14 C15 H5'' H5AA 119.1 120.0
O15 C15 H5'' H5AA 240.9 240.0
H5AA C15 C14 H4'' 51.1 187.9
C14 C15 H5AA O15 121.8 120.0
C14 C15 H5AA H5'' 240.9 240.0
O15 C15 H5AA H5'' 119.1 120.0
O5' C5' C4' H4' 177.0 306.1
H5' C5' O5' H5'A 119.5 120.1
H5' C5' C4' H4' 297.2 66.0
O5' C5' H5' H5'A 240.7 240.0
H5'A C5' C4' H4' 56.7 186.1
O5' C5' H5'A H5' 119.3 120.0