PDB Chemical Component 85Y

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 85Y

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C32 C33 1.395 1.361
C32 C31 1.396 1.394
C33 C27 1.377 1.405
C31 C30 1.411 1.361
C27 C28 1.410 1.405
C27 C26 1.469 1.418
C30 C26 1.401 1.405
C28 C29 1.369 1.361
C26 C25 1.394 1.405
C29 C24 1.417 1.394
C25 C24 1.362 1.361
C24 C23 1.495 1.507
C23 N22 1.474 1.465
N22 C20 1.408 1.348
C20 O21 1.384 1.216
C20 C5 1.482 1.471
O4 C4 1.254 1.218
C4 C5 1.486 1.472
C4 N3 1.327 1.349
C5 C6 1.421 1.381
N3 C2 1.369 1.344
C6 N1 1.327 1.359
C2 N1 1.430 1.343
C2 O2 1.277 1.216
N1 C1' 1.458 1.465
C2' C1' 1.494 1.545
C2' C3' 1.512 1.545
C1' O4' 1.405 1.444
O3' C3' 1.430 1.429
C3' C4' 1.529 1.545
O4' C4' 1.441 1.444
C4' C5' 1.549 1.531
O5' C5' 1.448 1.428
O5' P 1.645 1.610
OP2 P 1.502 1.610
P OP3 1.465 1.610
C30 H1 1.080 1.080
C33 H2 1.080 1.080
C23 H3 1.100 1.090
C23 H4 1.100 1.089
C25 H5 1.080 1.080
N3 H6 1.000 0.971
C6 H7 1.080 1.079
C1' H8 1.100 1.090
C2' H9 1.100 1.091
C2' H10 1.100 1.090
C3' H11 1.100 1.090
O3' H12 0.950 0.967
C4' H13 1.100 1.089
C5' H14 1.100 1.090
C5' H15 1.100 1.090
OP3 HOP3 0.950 0.967
OP2 HOP2 0.950 0.967
N22 H18 1.000 0.970
C28 H19 1.080 1.080
C29 H20 1.080 1.081
C31 H21 1.080 1.080
C32 H22 1.080 1.081
P OP1 1.515 1.480

Bond Angles for 85Y

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C32 C33 H2 120.4 120.2
C32 C31 H21 118.9 119.5
C33 C27 C28 121.5 121.3
C33 C27 C26 119.9 119.4
C27 C33 H2 120.4 120.2
C31 C30 H1 121.5 120.2
C27 C28 C29 120.8 119.6
C27 C28 H19 119.6 120.1
C30 C26 C25 120.9 121.3
C26 C30 H1 121.4 120.2
C29 C28 H19 119.6 120.2
C28 C29 H20 120.1 119.5
C26 C25 H5 119.6 120.2
C24 C23 N22 118.5 109.5
C24 C23 H3 107.2 109.5
C24 C23 H4 107.2 109.5
N22 C23 H3 107.1 109.5
N22 C23 H4 107.1 109.5
C23 N22 H18 121.7 120.0
C5 C20 O21 114.3 120.0
C20 C5 C4 124.4 121.0
C20 C5 C6 114.6 120.9
O4 C4 N3 118.1 120.8
C5 C4 N3 118.1 118.5
C4 C5 C6 120.2 118.1
C4 N3 H6 119.9 119.8
C5 C6 N1 118.7 119.3
C5 C6 H7 120.6 120.4
N3 C2 N1 122.7 122.1
N3 C2 O2 119.1 119.0
C2 N1 C6 119.7 121.5
C6 N1 C1' 124.8 119.3
N1 C6 H7 120.7 120.4
O2 C2 N1 118.1 118.9
C2 N1 C1' 115.1 119.3
N1 C1' O4' 111.2 110.4
N1 C1' H8 108.3 110.3
C2' C1' H8 107.8 110.5
C2' C3' C4' 103.3 104.1
C3' C2' H9 111.3 110.5
C3' C2' H10 111.2 110.6
C2' C3' H11 109.3 110.5
C1' O4' C4' 107.3 105.3
O4' C1' H8 109.0 110.4
O3' C3' C4' 109.9 110.5
O3' C3' H11 110.4 110.6
O4' C4' C3' 106.7 104.8
C3' C4' C5' 111.1 110.4
C4' C3' H11 109.1 110.5
C3' C4' H13 109.9 110.3
O4' C4' C5' 108.2 110.4
O4' C4' H13 111.2 110.4
C5' C4' H13 109.7 110.4
C4' C5' H14 109.4 109.4
C4' C5' H15 109.4 109.4
O5' C5' H14 109.4 109.5
O5' C5' H15 109.4 109.5
O5' P OP3 108.0 109.5
O5' P OP1 96.3 109.4
OP2 P OP1 104.9 109.5
P OP3 HOP3 109.5 114.0
OP3 P OP1 118.0 109.5
H3 C23 H4 109.5 109.5
H9 C2' H10 109.5 110.5
H14 C5' H15 109.5 109.5

Torsion Angles for 85Y

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C27 C33 C32 H2 180.0 180.1
C31 C32 C33 H2 180.8 180.0
C32 C31 C30 H1 177.3 180.0
C32 C33 C27 H2 180.0 179.9
C33 C27 C28 C29 175.5 179.7
C33 C27 C28 H19 355.5 360.0
C26 C30 C31 H1 180.0 180.0
C33 C27 C28 C26 176.4 180.0
C28 C27 C33 H2 358.2 0.0
C29 C28 C27 H19 180.0 179.8
C27 C28 C29 H20 184.5 180.0
C33 C27 C26 C28 183.5 180.0
C26 C27 C33 H2 174.6 180.0
C27 C26 C30 H1 178.0 180.0
C27 C26 C25 H5 186.3 180.1
C33 C27 C26 C30 6.2 0.0
C31 C30 C26 H1 180.0 180.0
C30 C26 C25 H5 359.2 0.1
C27 C28 C29 H19 180.0 180.2
C33 C27 C26 C25 179.0 180.1
C25 C26 C30 H1 5.3 360.0
C29 C24 C23 H3 282.2 29.7
C29 C24 C23 H4 39.6 149.8
C25 C24 C23 N22 341.5 90.0
C25 C24 C23 H3 102.8 210.0
C25 C24 C23 H4 220.2 330.0
N22 C23 C24 H3 238.7 240.0
N22 C23 C24 H4 121.3 120.0
C24 C23 N22 H18 269.0 0.0
H3 C23 C24 H4 242.6 240.0
C24 C23 N22 H3 121.3 120.0
C24 C23 N22 H4 238.7 240.0
H3 C23 N22 H4 117.4 120.0
O21 C20 C5 C4 158.4 174.1
O21 C20 C5 C6 327.5 354.4
C20 C5 C4 N3 174.4 180.1
C4 C5 C20 C6 190.9 179.7
C20 C5 C6 N1 183.3 180.2
C20 C5 C6 H7 3.2 360.0
C5 C4 O4 N3 185.0 179.8
O4 C4 C5 C6 180.9 180.0
O4 C4 N3 H6 2.5 359.9
C4 C5 C20 O21 158.4 174.1
C20 C5 C4 C6 168.6 180.3
O4 C4 C5 N3 175.0 180.2
C5 C4 N3 H6 177.8 180.0
C4 C5 C6 N1 352.9 0.5
C4 C5 C6 H7 172.8 180.3
N3 C4 C5 C6 5.9 359.8
C4 N3 C2 N1 359.9 0.0
C4 N3 C2 O2 182.7 180.3
C6 C5 C20 O21 327.5 354.4
C20 C5 C6 C4 190.4 179.7
C6 C5 C4 N3 5.9 359.8
C2 N1 C6 C5 4.7 359.5
C5 C6 N1 C1' 177.7 179.5
N1 C6 C5 H7 180.0 180.2
N3 C2 N1 C6 358.9 0.3
O2 C2 N3 N1 182.8 180.3
N3 C2 N1 C1' 185.2 180.2
C5 C6 N1 H7 180.0 179.8
O2 C2 N1 C6 176.1 180.0
C2 N1 C6 C1' 187.0 180.0
C6 N1 C1' O4' 121.5 233.5
C6 N1 C1' H8 241.2 355.8
C5 C6 N1 C2 4.7 359.5
N3 C2 N1 O2 182.8 180.3
C6 N1 C2 C1' 173.6 180.0
C2 N1 C6 H7 184.8 179.7
C2 N1 C1' O4' 294.7 53.6
C2 N1 C1' H8 54.4 175.8
N3 C2 O2 N1 177.3 179.7
O2 C2 N1 C1' 2.5 359.9
C2 N1 C1' C6 173.3 180.0
C1' N1 C6 H7 357.7 359.7
C2' C1' N1 H8 120.9 122.4
N1 C1' O4' C4' 198.5 200.7
O4' C1' N1 H8 240.3 237.8
N1 C1' C2' H8 238.9 237.7
C2' C1' O4' C4' 324.0 319.5
O4' C1' C2' H8 116.1 118.9
C3' C2' C1' H8 283.5 265.1
O3' C3' C2' C4' 119.6 118.7
O3' C3' C2' H11 235.5 237.3
O4' C4' C3' C2' 7.3 336.1
C2' C3' C4' C5' 249.5 217.2
C4' C3' C2' H11 116.0 118.6
C2' C3' C4' H13 128.0 94.9
H9 C2' C3' H10 122.3 122.7
N1 C1' O4' H8 119.3 122.2
C2' C1' O4' H8 244.7 241.0
C1' O4' C4' C3' 17.6 40.5
C1' O4' C4' C5' 137.2 159.3
C1' O4' C4' H13 257.8 281.7
C2' C3' O3' C4' 244.2 245.3
O3' C3' C2' H9 333.1 0.0
O3' C3' C2' H10 210.8 237.3
C2' C3' O3' H11 123.8 122.7
O4' C4' C3' O3' 244.6 217.4
O3' C3' C4' C5' 126.9 98.5
C4' C3' O3' H11 239.6 237.3
O3' C3' C4' H13 5.3 336.2
C4' C3' C2' H9 213.6 241.4
C4' C3' C2' H10 91.3 118.7
C2' C3' C4' H11 243.9 241.4
O3' C3' C4' H11 121.2 122.7
O4' C4' C3' C5' 117.7 118.9
O4' C4' C3' H13 239.3 241.2
C5' C4' C3' H13 121.6 122.3
C3' C4' C5' H14 173.3 301.9
C3' C4' C5' H15 293.2 61.9
C2' C3' C4' O4' 7.3 336.1
C4' O4' C1' H8 79.2 78.4
O3' C3' C4' O4' 244.6 217.4
C3' C4' O4' C5' 240.4 241.2
O4' C4' C3' H11 123.4 94.7
C3' C4' O4' H13 119.9 118.8
C5' C4' O4' H13 239.4 237.7
O4' C4' C5' H14 56.5 186.5
O4' C4' C5' H15 176.4 306.4
O4' C4' C5' C3' 243.2 244.6
C5' C4' C3' H11 5.7 335.8
C3' C4' C5' H13 238.3 237.7
O4' C4' C5' H13 121.5 122.3
O5' C5' C4' H14 239.9 240.0
O5' C5' C4' H15 120.1 120.0
H14 C5' C4' H15 240.1 240.0
O5' C5' C4' H13 174.9 304.1
C4' C5' O5' H14 120.0 120.0
C4' C5' O5' H15 239.9 240.0
H14 C5' O5' H15 119.9 120.0
P O5' C5' H14 52.1 60.0
P O5' C5' H15 292.2 300.0
OP2 P O5' OP1 252.9 240.0
O5' P OP3 HOP3 252.4 60.0
OP3 P O5' OP1 122.1 120.0
O5' P OP2 OP1 100.5 120.0
OP2 P OP3 HOP3 132.4 300.0
OP3 P OP2 OP1 222.4 240.0
O5' P OP3 OP1 252.4 240.1
OP2 P OP3 OP1 132.4 120.1
H1 C30 C26 C25 5.3 360.0
H2 C33 C27 C28 358.2 0.0
H2 C33 C27 C26 174.6 180.0
C24 C23 H3 N22 231.8 240.0
C24 C23 H3 H4 115.9 120.0
N22 C23 H3 H4 244.1 240.0
H3 C23 N22 H18 147.7 240.0
C24 C23 H4 N22 128.2 120.0
C24 C23 H4 H3 244.1 240.0
N22 C23 H4 H3 115.9 120.0
H4 C23 N22 H18 30.2 120.0
H6 N3 C2 N1 179.9 180.0
H6 N3 C2 O2 2.7 0.3
C5 C6 H7 N1 180.0 180.2
H7 C6 N1 C1' 357.7 359.7
N1 C1' H8 O4' 238.9 237.8
H8 C1' O4' C4' 79.2 78.4
H9 C2' C1' H8 42.4 23.7
H9 C2' C3' C4' 213.6 241.4
C3' C2' H9 H10 236.7 237.3
H9 C2' C3' H11 97.6 122.7
H10 C2' C1' H8 164.7 146.4
H10 C2' C3' C4' 91.3 118.7
C3' C2' H10 H9 123.4 122.6
H10 C2' C3' H11 335.3 0.0
C2' C3' H11 C4' 112.3 114.6
H11 C3' C2' H9 97.6 122.7
H11 C3' C2' H10 335.3 0.0
O3' C3' H11 C4' 239.1 237.3
H11 C3' C4' C5' 5.7 335.8
H11 C3' C4' H13 244.1 213.5
H12 O3' C3' C4' 295.8 176.1
H12 O3' C3' H11 56.1 298.8
O4' C4' H13 C3' 117.9 115.4
C3' C4' H13 C5' 122.4 122.3
H13 C4' C3' H11 244.1 213.5
O4' C4' H13 C5' 240.3 237.7
H13 C4' C5' H14 295.0 64.1
H13 C4' C5' H15 54.9 184.1
H14 C5' C4' H13 295.0 64.1
C4' C5' H14 H15 119.8 120.0
O5' C5' H14 H15 240.2 240.0
H15 C5' C4' H13 54.9 184.1
C4' C5' H15 H14 240.2 240.0
O5' C5' H15 H14 119.8 120.0
HOP3 OP3 P OP1 360.0 179.9
HOP2 OP2 P OP1 360.0 60.0
H18 N22 C23 H3 147.7 240.0
H18 N22 C23 H4 30.2 120.0
C27 C28 H19 C29 180.0 179.8
H19 C28 C29 H20 4.4 359.8
H20 C29 C28 H19 4.4 359.8
H21 C31 C30 H1 357.3 360.0
H22 C32 C33 H2 0.7 360.0
H22 C32 C31 H21 3.6 0.1
O5' P OP1 OP3 114.3 120.0
OP1 P OP3 HOP3 360.0 179.9