PDB Chemical Component VC6

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 VC6

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O2 C2 1.195 1.220
C2 N3 1.323 1.333
C2 N1 1.323 1.345
C2' C1' 1.575 1.550
C2' C3' 1.551 1.553
N3 C4 1.325 1.327
C1' N1 1.473 1.466
C1' O4' 1.310 1.437
N1 C6 1.327 1.362
O3' C3' 1.479 1.428
C3' C4' 1.326 1.544
C4 N4 1.445 1.376
C4 C5 1.380 1.410
O4' C4' 1.598 1.433
C6 C5 1.386 1.354
C4' C5' 1.493 1.530
O2B PB 1.496 1.480
C5' O5' 1.401 1.429
PB O3A 1.632 1.610
PB O1B 1.518 1.610
PB C3B 1.871 1.823
O3A PA 1.637 1.610
O5' PA 1.632 1.611
F4B C3B 1.389 1.398
C3B CL1 1.756 1.803
C3B PG 1.872 1.824
PA O2A 1.488 1.479
PA O1A 1.498 1.611
O3G PG 1.489 1.480
PG O2G 1.519 1.610
PG O1G 1.504 1.609
N4 H1 1.000 0.971
N4 H2 1.000 0.970
C5 H3 1.080 1.080
C6 H4 1.080 1.080
C1' H5 1.100 1.090
C2' H6 1.100 1.091
C2' H7 1.100 1.090
C3' H8 1.100 1.090
O3' H9 0.950 0.967
C4' H10 1.101 1.090
C5' H11 1.100 1.090
C5' H12 1.100 1.090
O1A H13 0.950 0.966
O1B H14 0.950 0.967
O2G H15 0.950 0.967
O1G H16 0.950 0.967

Bond Angles for VC6

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O2 C2 N1 118.8 119.5
C2' C1' O4' 103.7 105.1
C2' C1' H5 108.6 110.4
C2' C3' C4' 102.6 102.3
C3' C2' H6 110.5 111.1
C3' C2' H7 110.5 111.2
C2' C3' H8 105.7 110.8
C1' O4' C4' 103.2 109.9
O4' C1' H5 112.5 110.3
N1 C6 H4 119.7 120.4
O3' C3' C4' 118.4 110.9
O3' C3' H8 106.5 110.9
C3' C4' O4' 111.9 107.6
C3' C4' C5' 125.9 109.8
C4' C3' H8 108.4 110.8
C3' C4' H10 102.6 109.8
N4 C4 C5 118.6 120.2
C4 N4 H1 120.0 120.0
C4 N4 H2 120.0 120.0
C4 C5 H3 121.5 120.5
O4' C4' C5' 110.5 109.8
O4' C4' H10 100.4 109.8
C6 C5 H3 121.5 120.5
C4' C5' O5' 90.2 109.5
C5' C4' H10 101.2 109.9
C4' C5' H11 114.1 109.5
C4' C5' H12 114.0 109.5
O2B PB C3B 108.6 109.5
C5' O5' PA 118.3 123.0
O5' C5' H11 114.1 109.5
O5' C5' H12 114.1 109.5
O1B PB C3B 111.7 109.5
PB O1B H14 109.5 114.0
PB C3B CL1 107.4 109.5
PB C3B PG 110.0 109.4
O5' PA O2A 111.2 109.5
O5' PA O1A 105.8 109.4
F4B C3B PG 112.2 109.5
CL1 C3B PG 107.5 109.5
C3B PG O2G 107.7 109.5
C3B PG O1G 109.5 109.5
O1A PA O2A 114.1 109.5
PA O1A H13 109.5 114.0
O2G PG O1G 109.6 109.5
PG O2G H15 109.5 114.0
PG O1G H16 109.5 114.0
H1 N4 H2 120.0 120.0
H6 C2' H7 109.5 111.0
H11 C5' H12 109.5 109.4

Torsion Angles for VC6

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 H4 181.2 179.7
C2' C1' O4' C4' 35.2 335.5
O4' C1' C2' H5 119.8 119.0
C3' C2' C1' O4' 328.0 36.5
C3' C2' C1' H5 208.2 277.5
O3' C3' C2' C4' 129.6 118.2
O3' C3' C2' H8 243.1 236.4
C2' C3' C4' O4' 9.1 21.4
C2' C3' C4' C5' 148.2 140.9
C4' C3' C2' H8 113.5 118.2
C2' C3' C4' H10 262.2 261.8
H6 C2' C3' H7 121.4 124.2
N3 C4 N4 H1 0.0 179.7
N3 C4 N4 H2 180.0 359.7
N3 C4 C5 H3 179.2 180.3
C1' N1 C6 H4 357.9 0.0
C2' C1' O4' H5 242.9 240.9
C3' C4' O4' C1' 328.9 1.7
C1' O4' C4' C5' 183.4 242.2
C1' O4' C4' H10 77.2 121.3
N1 C6 C5 H3 179.7 180.0
C2' C3' O3' C4' 238.7 247.1
O3' C3' C2' H6 22.0 326.2
O3' C3' C2' H7 260.7 202.0
C2' C3' O3' H8 116.4 123.6
O3' C3' C4' O4' 241.9 263.2
O3' C3' C4' C5' 21.0 22.7
C4' C3' O3' H8 237.7 236.4
O3' C3' C4' H10 135.0 143.6
C4' C3' C2' H6 252.4 208.0
C4' C3' C2' H7 131.0 83.8
C2' C3' C4' H8 248.5 241.8
C1' O4' C4' C3' 328.9 1.7
O3' C3' C4' H8 121.3 123.6
O4' C4' C3' C5' 220.9 240.5
O4' C4' C3' H10 106.9 119.5
C3' C4' C5' O5' 124.0 175.0
C5' C4' C3' H10 246.0 239.0
C3' C4' C5' H11 240.6 295.0
C3' C4' C5' H12 7.4 55.0
N4 C4 C5 H3 0.5 360.0
H1 N4 C4 H2 180.0 180.0
C5 C4 N4 H1 178.8 0.0
C5 C4 N4 H2 358.7 180.0
C6 C5 C4 H3 180.0 180.1
C4' O4' C1' H5 152.3 94.6
C3' C4' O4' C5' 145.5 119.5
O4' C4' C3' H8 120.6 139.5
C3' C4' O4' H10 251.7 240.5
O4' C4' C5' O5' 263.6 293.1
C5' C4' O4' H10 106.2 121.0
O4' C4' C5' H11 20.2 53.2
O4' C4' C5' H12 147.0 173.1
C4 C5 C6 H3 180.0 179.9
C3' C4' C5' O4' 220.4 241.9
C5' C4' C3' H8 259.7 259.0
C3' C4' C5' H10 114.7 120.9
O4' C4' C5' H10 254.3 239.1
C4' C5' O5' PA 244.8 180.0
O5' C5' C4' H11 243.4 240.0
O5' C5' C4' H12 116.6 120.0
H11 C5' C4' H12 233.2 240.0
O1B PB O2B C3B 236.5 240.0
O2B PB O1B H14 0.0 180.0
O2B PB C3B CL1 98.3 180.0
O2B PB C3B PG 215.0 300.0
O5' C5' C4' H10 9.3 54.1
C4' C5' O5' H11 116.6 120.0
C4' C5' O5' H12 243.4 240.0
C5' O5' PA O2A 161.8 305.0
C5' O5' PA O1A 286.1 65.0
H11 C5' O5' H12 126.8 120.0
O2B PB O1B C3B 121.8 120.0
O1B PB C3B CL1 221.8 300.0
O1B PB C3B PG 338.5 60.0
C3B PB O1B H14 238.3 60.0
F4B C3B PB PG 126.0 120.0
CL1 C3B PB PG 243.3 240.0
PB C3B PG O2G 320.1 60.0
PB C3B PG O1G 201.0 180.0
O3A PA O1A H13 123.2 300.0
PA O5' C5' H11 128.2 59.9
PA O5' C5' H12 1.4 300.0
O1A PA O5' O2A 124.3 120.0
O5' PA O1A H13 237.5 60.0
PB C3B F4B PG 235.2 240.0
CL1 C3B F4B PG 117.6 120.0
F4B C3B PG O2G 193.9 300.0
F4B C3B PG O1G 74.8 60.0
PB C3B CL1 PG 118.3 120.0
F4B C3B CL1 PG 239.4 240.0
CL1 C3B PG O2G 76.7 180.0
CL1 C3B PG O1G 317.6 300.0
PB C3B PG CL1 243.4 240.0
O2G PG C3B O1G 119.1 240.0
C3B PG O2G H15 118.6 60.0
C3B PG O1G H16 240.0 180.0
O5' PA O2A O1A 119.5 120.0
O2A PA O1A H13 0.0 180.0
O5' PA O1A O2A 237.5 240.0
O3G PG O2G H15 0.0 180.0
O3G PG O1G H16 360.0 60.0
C3B PG O2G O1G 241.0 120.0
O2G PG O1G H16 122.1 300.0
C3B PG O1G O2G 117.9 240.0
O1G PG O2G H15 237.6 300.0
H1 N4 C4 C5 178.8 0.0
C4 N4 H1 H2 180.0 180.0
H2 N4 C4 C5 358.7 180.0
C4 N4 H2 H1 180.0 180.0
H4 C6 C5 H3 359.7 0.0
C2' C1' H5 O4' 114.1 115.8
H5 C1' O4' C4' 152.3 94.6
H6 C2' C1' O4' 87.3 154.4
H6 C2' C1' H5 327.6 35.4
H6 C2' C3' C4' 252.4 208.0
C3' C2' H6 H7 238.1 235.7
H6 C2' C3' H8 138.9 89.8
H7 C2' C1' O4' 208.7 278.5
H7 C2' C1' H5 88.9 159.5
H7 C2' C3' C4' 131.0 83.8
C3' C2' H7 H6 121.9 124.3
H7 C2' C3' H8 17.5 325.6
C2' C3' H8 C4' 109.4 112.8
H8 C3' C2' H6 138.9 89.8
H8 C3' C2' H7 17.5 325.6
O3' C3' H8 C4' 231.6 236.4
H8 C3' C4' O4' 120.6 139.5
H8 C3' C4' C5' 259.7 259.0
H8 C3' C4' H10 13.7 20.0
H9 O3' C3' C4' 274.5 174.3
H9 O3' C3' H8 36.8 297.9
C3' C4' H10 O4' 115.5 118.2
C3' C4' H10 C5' 229.0 239.1
H10 C4' C3' H8 13.7 20.0
O4' C4' H10 C5' 113.5 120.9
H10 C4' C5' O5' 9.3 54.1
H10 C4' C5' H11 125.9 174.1
H10 C4' C5' H12 252.7 294.1
C4' C5' H11 O5' 258.3 240.0
H11 C5' C4' H10 125.9 174.1
C4' C5' H11 H12 129.1 120.0
H11 C5' O5' PA 128.2 59.9
O5' C5' H11 H12 230.8 240.0
C4' C5' H12 O5' 101.7 120.0
H12 C5' C4' H10 252.7 294.1
C4' C5' H12 H11 230.9 240.0
H12 C5' O5' PA 1.4 300.0
O5' C5' H12 H11 129.2 120.0
H13 O1A PA O2A 0.0 180.0
H14 O1B PB C3B 238.3 60.0
H15 O2G PG O1G 237.6 300.0