PDB Chemical Component Y9Z

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 Y9Z

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O C 1.268 1.219
C N 1.328 1.352
C C3 1.458 1.414
N C1 1.361 1.363
C3 N3 1.336 1.356
C3 C2 1.474 1.400
N3 C4 1.354 1.301
C1 N1 1.336 1.372
C1 N2 1.340 1.314
C4 N4 1.335 1.365
C2 N2 1.347 1.339
C2 N4 1.318 1.368
O1 C6 1.416 1.429
O9 P 1.567 1.480
N4 C5 1.466 1.465
C6 C5 1.507 1.545
C6 C7 1.511 1.545
C5 O11 1.416 1.444
P O3 1.579 1.609
P O10 1.459 1.610
P O4 1.639 1.610
O3 C9 1.433 1.429
O8 P1 1.461 1.480
C7 O2 1.396 1.429
C7 C8 1.520 1.545
O11 C8 1.440 1.444
O4 P1 1.609 1.610
P1 O7 1.576 1.610
P1 O5 1.559 1.610
C8 C9 1.524 1.529
C11 C10 1.520 1.530
C11 N5 1.460 1.465
O5 C10 1.432 1.429
N5 C12 1.346 1.348
O6 C12 1.206 1.213
C12 C13 1.526 1.506
N H1 1.000 0.970
N1 H2 1.000 0.971
N1 H3 1.001 0.970
O1 H4 0.949 0.968
O2 H5 0.951 0.967
C4 H6 1.080 1.080
C5 H7 1.100 1.090
N5 H8 1.000 0.969
C6 H9 1.100 1.090
C7 H10 1.100 1.090
O7 H11 0.950 0.968
C8 H12 1.100 1.091
C9 H13 1.100 1.090
C9 H14 1.100 1.090
C10 H15 1.100 1.090
C10 H16 1.100 1.090
O10 H17 0.950 0.967
C11 H18 1.100 1.091
C11 H19 1.101 1.089
C13 H20 1.100 1.090
C13 H21 1.100 1.090
C13 H22 1.100 1.090

Bond Angles for Y9Z

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O C C3 120.9 120.9
C N C1 122.7 120.4
C N H1 118.6 119.8
C C3 N3 134.3 134.1
C C3 C2 117.9 118.6
N C1 N1 118.2 119.1
N C1 N2 124.7 121.9
C1 N H1 118.6 119.9
C3 N3 C4 106.9 109.3
C3 C2 N4 104.2 106.1
N3 C4 N4 110.3 109.8
N3 C4 H6 124.8 125.0
N1 C1 N2 117.0 119.0
C1 N1 H2 120.0 120.0
C1 N1 H3 120.0 120.0
C1 N2 C2 117.5 121.2
C2 N4 C4 110.7 107.5
C4 N4 C5 126.8 126.2
N4 C4 H6 124.9 125.2
N2 C2 N4 135.2 134.2
C2 N4 C5 122.3 126.3
O1 C6 C5 108.5 110.5
O1 C6 C7 115.2 110.5
C6 O1 H4 109.5 114.0
O1 C6 H9 110.9 110.5
O9 P O10 114.1 109.4
N4 C5 O11 108.0 110.4
N4 C5 H7 109.9 110.4
C6 C5 O11 107.7 104.8
C6 C5 H7 109.4 110.4
C6 C7 C8 103.0 104.1
C7 C6 H9 109.5 110.6
C6 C7 H10 111.6 110.5
C5 O11 C8 108.3 105.3
O11 C5 H7 110.7 110.3
O3 P O10 112.8 109.5
O3 P O4 99.6 109.5
P O3 C9 119.3 123.0
O4 P O10 108.3 109.5
P O10 H17 109.5 114.0
P O4 P1 125.0 134.0
O3 C9 C8 107.5 109.5
O3 C9 H13 109.9 109.5
O3 C9 H14 110.0 109.5
C7 O2 H5 109.5 114.0
C7 C8 C9 109.7 110.4
C8 C7 H10 111.4 110.6
C7 C8 H12 109.2 110.4
O11 C8 H12 110.3 110.5
O4 P1 O7 108.1 109.4
O4 P1 O5 105.4 109.5
O5 P1 O7 105.9 109.5
P1 O7 H11 109.5 114.0
P1 O5 C10 119.2 123.0
C9 C8 H12 109.1 110.3
C8 C9 H13 110.0 109.5
C8 C9 H14 110.0 109.5
C11 C10 H15 108.2 109.4
C11 C10 H16 108.2 109.5
C11 N5 C12 125.6 120.0
C11 N5 H8 117.2 120.0
O5 C10 H15 108.2 109.5
O5 C10 H16 108.2 109.5
N5 C12 O6 125.9 120.0
N5 C12 C13 114.7 120.0
C12 N5 H8 117.2 120.0
O6 C12 C13 119.1 120.0
C12 C13 H20 109.5 109.5
C12 C13 H21 109.5 109.5
C12 C13 H22 109.5 109.5
H2 N1 H3 120.0 120.0
H13 C9 H14 109.4 109.4
H15 C10 H16 109.4 109.5
H18 C11 H19 109.5 109.5
H20 C13 H21 109.5 109.4
H20 C13 H22 109.5 109.5
H21 C13 H22 109.4 109.5

Torsion Angles for Y9Z

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O C N C1 179.5 180.0
O C N H1 359.5 359.8
O C C3 N3 359.3 360.0
O C C3 C2 178.9 180.5
C N C1 N1 182.5 179.8
C N C1 N2 5.7 359.8
C1 N C H1 180.0 180.2
C3 C N C1 356.2 359.9
C3 C N H1 176.2 179.7
C C3 N3 C4 180.1 180.0
C C3 C2 N4 177.9 180.4
C N C1 H1 180.0 179.8
N1 C1 N N2 176.7 180.0
N C1 N1 H2 183.1 0.0
N C1 N1 H3 3.0 180.0
N C1 N2 C2 354.6 0.0
C C3 N3 C2 179.7 180.5
N3 C3 C2 N4 357.6 0.8
C3 N3 C4 N4 1.6 0.0
C3 N3 C4 H6 181.6 180.0
C C3 C2 N3 180.3 179.6
C3 C2 N4 C4 3.4 359.2
N2 C2 C3 N4 179.9 178.8
C3 C2 N4 C5 177.8 178.5
C2 N4 C4 N3 356.7 0.5
N3 C4 N4 C5 182.5 181.3
N4 C4 N3 H6 180.0 180.0
N C1 N1 N2 183.0 180.0
N1 C1 N H1 2.5 359.9
N1 C1 N2 C2 177.8 180.0
H2 N1 C1 H3 180.0 180.0
N C1 N2 N1 176.8 180.0
N2 C1 N H1 185.8 179.9
N2 C1 N1 H2 0.0 180.0
N2 C1 N1 H3 180.0 360.0
C1 N2 C2 N4 183.5 178.9
N3 C4 N4 H6 180.0 180.0
N2 C2 N4 C4 183.5 180.7
C2 N4 C4 C5 174.1 179.2
C4 N4 C5 O11 64.3 22.6
C4 N4 C5 H7 185.2 144.9
C C3 C2 N2 357.8 359.2
C3 C2 N2 N4 180.2 181.6
N2 C2 N4 C5 358.0 359.9
N3 C4 N4 C2 356.7 0.5
C4 N4 C2 C5 185.6 180.8
C2 N4 C4 H6 176.7 180.5
C2 N4 C5 O11 250.8 203.6
C2 N4 C5 H7 11.7 325.8
O1 C6 C5 O11 153.6 142.6
O1 C6 C5 H7 33.3 23.8
O1 C6 C7 C8 211.9 241.3
C7 C6 O1 H9 234.8 237.2
O1 C6 C7 H10 92.3 122.6
O3 P O9 O10 231.9 240.0
O4 P O9 O10 122.7 120.0
O9 P O10 H17 0.0 180.0
C2 N4 C5 C4 186.5 180.9
C5 N4 C4 H6 2.5 1.3
O1 C6 C5 N4 271.7 261.5
C6 C5 N4 O11 242.1 244.6
C6 C5 N4 H7 121.3 122.4
N4 C5 O11 C8 221.0 200.7
O11 C5 N4 H7 239.1 237.8
O1 C6 C5 C7 122.4 118.7
C5 C6 O1 H4 180.0 180.0
O1 C6 C5 H9 238.7 237.4
N4 C5 C6 O11 118.1 118.9
N4 C5 C6 H7 238.4 237.6
C6 C5 O11 C8 341.2 319.5
O11 C5 C6 H7 120.3 118.8
O1 C6 C7 C5 242.3 241.4
C7 C6 O1 H4 294.4 294.7
O1 C6 C7 H9 125.9 122.7
C7 C6 C5 O11 31.2 24.0
C7 C6 C5 H7 270.9 265.2
C6 C7 O2 H5 180.0 61.4
C6 C7 C8 C9 260.0 217.2
C8 C7 C6 H10 119.6 118.8
C6 C7 C8 H12 140.4 95.0
N4 C5 O11 H7 120.4 122.3
C6 C5 O11 H7 240.5 241.1
C5 O11 C8 H12 239.4 281.6
O9 P O3 O10 128.8 120.0
O4 P O3 O10 245.3 240.0
O3 P O10 H17 126.7 300.0
O3 P O4 P1 181.2 199.9
P O3 C9 C8 205.3 180.0
P O3 C9 H13 325.0 300.1
P O3 C9 H14 85.6 60.0
O3 P O10 O4 250.7 240.0
O10 P O3 C9 63.2 295.0
O10 P O4 P1 63.1 79.9
O9 P O4 O10 234.0 240.0
O3 P O4 O10 118.1 120.0
O4 P O3 C9 308.6 175.0
O4 P O10 H17 236.0 60.0
P O4 P1 O7 138.2 80.0
P O4 P1 O5 251.1 200.0
C9 O3 P O10 63.2 295.0
C9 O3 P O4 308.6 175.0
C7 C8 C9 O3 50.0 185.0
O3 C9 C8 H12 169.6 307.2
C8 C9 O3 H13 240.3 240.0
C8 C9 O3 H14 119.7 120.1
H13 C9 O3 H14 239.4 240.1
O8 P1 O7 H11 360.0 180.0
O8 P1 O5 C10 354.4 55.0
O1 C6 C7 O2 326.0 0.0
C8 C7 C6 H9 86.0 118.6
C6 C7 C8 H10 240.3 241.3
C5 O11 C8 C7 358.6 40.5
O3 C9 C8 C7 50.0 185.0
C8 C7 O2 H5 291.1 176.1
O11 C8 C7 H12 240.1 241.1
C9 C8 C7 H12 119.5 122.2
C7 C8 C9 H13 290.4 65.0
C7 C8 C9 H14 169.7 305.1
C8 O11 C5 H7 100.7 78.4
O11 C8 C7 H10 140.2 94.8
C7 C8 O11 H12 119.2 118.8
C9 C8 O11 H12 239.2 237.7
O11 C8 C9 H13 171.4 309.6
O11 C8 C9 H14 50.8 189.7
P1 O4 P O10 63.1 79.9
O5 P1 O4 O7 113.0 120.0
O4 P1 O7 H11 232.9 60.0
O4 P1 O5 C10 119.0 175.1
O4 P1 O7 O5 112.6 120.0
O7 P1 O5 C10 233.5 295.0
O4 P1 O5 O7 245.5 240.0
O5 P1 O7 H11 120.3 300.0
P1 O5 C10 H15 311.1 299.9
P1 O5 C10 H16 192.6 59.9
C5 O11 C8 C9 118.6 159.4
O3 C9 C8 H13 119.7 120.0
O3 C9 C8 H14 240.3 239.9
C9 C8 C7 H10 19.7 335.9
C7 C8 C9 H12 240.4 237.8
O11 C8 C9 H12 121.5 122.4
H13 C9 C8 H14 120.6 119.9
C10 C11 N5 C12 266.3 180.0
C10 C11 N5 H8 86.3 0.0
O5 C10 C11 H15 239.2 119.9
O5 C10 C11 H16 120.8 239.9
H15 C10 C11 H16 241.5 120.0
C11 N5 C12 O6 335.8 0.0
C11 N5 C12 C13 149.2 180.0
C12 N5 C11 H8 180.0 180.0
C10 O5 P1 O7 233.5 295.0
C11 C10 O5 H15 120.8 240.1
C11 C10 O5 H16 239.2 120.1
H15 C10 O5 H16 118.4 240.0
C11 N5 C12 H8 180.0 180.0
O6 C12 N5 C13 186.6 180.0
N5 C12 C13 H20 186.1 0.1
N5 C12 C13 H21 306.1 120.0
N5 C12 C13 H22 66.1 240.0
N5 C12 O6 C13 173.1 180.0
O6 C12 N5 H8 155.8 180.0
O6 C12 C13 H20 0.0 180.0
O6 C12 C13 H21 120.0 300.0
O6 C12 C13 H22 240.0 60.0
N5 C12 C13 O6 186.1 180.0
C13 C12 N5 H8 329.2 360.0
H20 C13 C12 H21 240.0 240.0
H20 C13 C12 H22 120.0 120.0
H21 C13 C12 H22 240.0 240.0
C N H1 C1 180.0 180.2
H1 N C1 N1 2.5 359.9
H1 N C1 N2 185.8 179.9
H2 N1 C1 N2 0.0 180.0
C1 N1 H2 H3 180.0 180.0
H3 N1 C1 N2 180.0 360.0
C1 N1 H3 H2 180.0 180.0
H4 O1 C6 C5 180.0 180.0
H4 O1 C6 C7 294.4 294.7
H4 O1 C6 H9 59.6 57.4
N3 C4 H6 N4 180.0 180.0
H6 C4 N4 C5 2.5 1.3
N4 C5 H7 O11 240.8 237.7
C6 C5 H7 O11 118.5 115.3
H7 C5 O11 C8 100.7 78.4
C11 N5 H8 C12 180.0 180.0
H8 N5 C12 O6 155.8 180.0
H8 N5 C12 C13 329.2 360.0
O1 C6 H9 C5 119.8 122.6
O1 C6 H9 C7 231.7 237.3
H9 C6 O1 H4 59.6 57.4
H9 C6 C5 O11 274.9 265.2
H9 C6 C5 H7 154.5 146.4
H9 C6 C7 C8 86.0 118.6
H9 C6 C7 H10 326.4 359.9
C6 C7 H10 C8 114.5 114.7
H10 C7 C6 H9 326.4 359.9
H10 C7 O2 H5 54.9 298.8
H10 C7 C8 C9 19.7 335.9
H10 C7 C8 H12 260.2 213.7
C7 C8 H12 C9 119.9 122.3
H12 C8 C7 H10 260.2 213.7
H12 C8 C9 H13 49.9 187.2
H12 C8 C9 H14 289.3 67.3
O3 C9 H13 C8 241.8 240.0
O3 C9 H13 H14 120.9 120.0
H13 C9 C8 H12 49.9 187.2
C8 C9 H13 H14 239.1 240.0
O3 C9 H14 C8 118.2 120.1
O3 C9 H14 H13 239.1 240.1
H14 C9 C8 H12 289.3 67.3
C8 C9 H14 H13 120.9 120.0
C11 C10 H15 H16 117.6 240.0
O5 C10 H15 H16 242.4 120.1
C11 C10 H16 H15 242.3 119.9
O5 C10 H16 H15 117.6 240.0
H18 C11 C10 H15 349.2 185.0
H18 C11 C10 H16 107.6 65.1
H18 C11 N5 C12 146.3 300.0
H18 C11 N5 H8 326.3 120.0
H19 C11 C10 H15 109.1 65.1
H19 C11 C10 H16 227.6 305.1
H19 C11 N5 C12 26.4 60.0
H19 C11 N5 H8 206.4 240.0
C12 C13 H20 H21 120.0 120.0
C12 C13 H20 H22 240.0 239.9
H21 C13 H20 H22 119.9 120.0
C12 C13 H21 H20 240.0 240.0
C12 C13 H21 H22 120.0 120.0
H20 C13 H21 H22 240.0 240.0
C12 C13 H22 H20 120.0 120.0
C12 C13 H22 H21 240.0 240.0
H20 C13 H22 H21 120.0 119.9