# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 15:07:57 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-[(~{E})-[(~{E})-16-azido-2-oxidanylidene-hexadec-3-enylidene]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN=CC(=O)/C=C/CCCCCCCCCCCCN=[N+]=[N-]
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 8XO  8XO  '2-[(~{E})-[(~{E})-16-azido-2-oxidanylidene-hexadec-3-enylidene]amino]ethanoic acid'  ligand  54  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8XO
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 8XO  C15  C  C1     0  -0.118   -7.6698  -0.6490  -0.0644
 8XO  C14  C  C      0   0.312   -6.6180   0.2824  -0.5839
 8XO  C13  C  C1     0  -0.383   -5.3788   0.3143   0.2056
 8XO  C12  C  C1     0  -0.120   -4.3471   1.1087  -0.0963
 8XO  C16  C  CH2    0  -0.475   -9.7375  -1.6721  -0.1381
 8XO  C11  C  CH2    0  -0.495   -3.0721   1.1689   0.6663
 8XO  O2   O  O      0  -0.585  -10.3661   0.1813   1.2430
 8XO  C17  C  C      0   0.409  -10.7611  -0.8794   0.7388
 8XO  O1   O  OC    -1  -0.609  -11.8651  -1.4344   0.8758
 8XO  N    N  N      0  -0.282   -8.7415  -0.8149  -0.7060
 8XO  O    O  O      0  -0.405   -6.7986   0.9474  -1.5852
 8XO  C10  C  CH2    0  -0.423   -1.8527   0.8955  -0.2176
 8XO  C9   C  CH2    0  -0.415   -0.5492   0.9410   0.5694
 8XO  C8   C  CH2    0  -0.413    0.6829   0.7289  -0.3006
 8XO  C7   C  CH2    0  -0.413    1.9799   0.6896   0.4986
 8XO  C    C  CH2    0  -0.412    3.2186   0.5357  -0.3746
 8XO  C1   C  CH2    0  -0.413    4.5126   0.4371   0.4238
 8XO  C2   C  CH2    0  -0.412    5.7511   0.3260  -0.4563
 8XO  C3   C  CH2    0  -0.412    7.0459   0.1967   0.3359
 8XO  C4   C  CH2    0  -0.423    8.2799   0.1154  -0.5541
 8XO  C5   C  CH2    0  -0.435    9.5746  -0.0281   0.2363
 8XO  C6   C  CH2    0  -0.302   10.7846  -0.0828  -0.6851
 8XO  N1   N  N      0  -0.363   12.0602  -0.1645   0.0411
 8XO  N2   N  N      1   0.353   12.3191  -1.2311   0.5633
 8XO  N3   N  N     -1  -0.232   12.6480  -2.1750   1.0808
 8XO  H1   H  H      0   0.226   -7.4458  -1.1718   0.8717
 8XO  H2   H  H      0   0.262   -5.3197  -0.3436   1.0665
 8XO  H3   H  H      0   0.265   -4.4228   1.7630  -0.9614
 8XO  H4   H  HCH2   0   0.224   -9.3031  -2.4459   0.5119
 8XO  H5   H  HCH2   0   0.239  -10.2751  -2.1774  -0.9414
 8XO  H6   H  HCH2   0   0.250   -2.9729   2.1730   1.0943
 8XO  H7   H  HCH2   0   0.242   -3.0974   0.4676   1.5043
 8XO  H9   H  HCH2   0   0.225   -1.9579  -0.0846  -0.6928
 8XO  H10  H  HCH2   0   0.223   -1.8210   1.6299  -1.0289
 8XO  H11  H  HCH2   0   0.213   -0.4691   1.9045   1.0845
 8XO  H12  H  HCH2   0   0.213   -0.5769   0.1783   1.3553
 8XO  H13  H  HCH2   0   0.209    0.5778  -0.2063  -0.8620
 8XO  H14  H  HCH2   0   0.209    0.7400   1.5264  -1.0497
 8XO  H15  H  HCH2   0   0.207    2.0688   1.6043   1.0956
 8XO  H16  H  HCH2   0   0.208    1.9349  -0.1364   1.2172
 8XO  H17  H  HCH2   0   0.207    3.1129  -0.3566  -1.0021
 8XO  H18  H  HCH2   0   0.207    3.2822   1.3837  -1.0658
 8XO  H19  H  HCH2   0   0.207    4.6080   1.3138   1.0744
 8XO  H20  H  HCH2   0   0.207    4.4607  -0.4300   1.0920
 8XO  H21  H  HCH2   0   0.208    5.6466  -0.5377  -1.1226
 8XO  H22  H  HCH2   0   0.208    5.8111   1.2043  -1.1088
 8XO  H23  H  HCH2   0   0.211    7.1455   1.0500   1.0157
 8XO  H24  H  HCH2   0   0.211    6.9963  -0.6939   0.9722
 8XO  H25  H  HCH2   0   0.217    8.1757  -0.7308  -1.2417
 8XO  H26  H  HCH2   0   0.217    8.3328   1.0120  -1.1814
 8XO  H27  H  HCH2   0   0.230    9.6854   0.8116   0.9282
 8XO  H28  H  HCH2   0   0.225    9.5305  -0.9363   0.8462
 8XO  H29  H  HCH2   0   0.246   10.6921  -0.9171  -1.3871
 8XO  H30  H  HCH2   0   0.253   10.8478   0.8303  -1.2744

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 8XO  C3   C2   single  1.523  0.020  1.523
 8XO  C3   C4   single  1.524  0.020  1.524
 8XO  C1   C2   single  1.523  0.020  1.523
 8XO  C1   C    single  1.524  0.020  1.524
 8XO  C7   C    single  1.523  0.020  1.523
 8XO  C7   C8   single  1.524  0.020  1.524
 8XO  C4   C5   single  1.524  0.020  1.524
 8XO  C5   C6   single  1.522  0.020  1.522
 8XO  C8   C9   single  1.523  0.020  1.523
 8XO  C9   C10  single  1.523  0.020  1.523
 8XO  C6   N1   single  1.470  0.020  1.470
 8XO  N1   N2   double  1.215  0.020  1.215
 8XO  C10  C11  single  1.531  0.020  1.531
 8XO  N2   N3   double  1.126  0.020  1.126
 8XO  C11  C12  single  1.487  0.020  1.487
 8XO  C12  C13  double  1.337  0.020  1.337
 8XO  C13  C14  single  1.470  0.020  1.470
 8XO  C14  C15  single  1.498  0.020  1.498
 8XO  C14  O    double  1.216  0.020  1.216
 8XO  C15  N    double  1.260  0.020  1.260
 8XO  N    C16  single  1.432  0.020  1.432
 8XO  C16  C17  single  1.564  0.020  1.564
 8XO  C17  O2   deloc   1.239  0.020  1.239
 8XO  C17  O1   deloc   1.243  0.020  1.243
 8XO  C15  H1   single  0.930  0.020  1.080
 8XO  C13  H2   single  0.930  0.020  1.080
 8XO  C12  H3   single  0.930  0.020  1.080
 8XO  C16  H4   single  0.970  0.020  1.090
 8XO  C16  H5   single  0.970  0.020  1.090
 8XO  C11  H6   single  0.970  0.020  1.090
 8XO  C11  H7   single  0.970  0.020  1.090
 8XO  C10  H9   single  0.970  0.020  1.090
 8XO  C10  H10  single  0.970  0.020  1.090
 8XO  C9   H11  single  0.970  0.020  1.090
 8XO  C9   H12  single  0.970  0.020  1.090
 8XO  C8   H13  single  0.970  0.020  1.090
 8XO  C8   H14  single  0.970  0.020  1.090
 8XO  C7   H15  single  0.970  0.020  1.090
 8XO  C7   H16  single  0.970  0.020  1.090
 8XO  C    H17  single  0.970  0.020  1.090
 8XO  C    H18  single  0.970  0.020  1.090
 8XO  C1   H19  single  0.970  0.020  1.090
 8XO  C1   H20  single  0.970  0.020  1.090
 8XO  C2   H21  single  0.970  0.020  1.090
 8XO  C2   H22  single  0.970  0.020  1.090
 8XO  C3   H23  single  0.970  0.020  1.090
 8XO  C3   H24  single  0.970  0.020  1.090
 8XO  C4   H25  single  0.970  0.020  1.090
 8XO  C4   H26  single  0.970  0.020  1.090
 8XO  C5   H27  single  0.970  0.020  1.090
 8XO  C5   H28  single  0.970  0.020  1.090
 8XO  C6   H29  single  0.970  0.020  1.090
 8XO  C6   H30  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 8XO  H1   C15  N    123.11  3.000
 8XO  H1   C15  C14  116.72  3.000
 8XO  N    C15  C14  120.16  3.000
 8XO  O    C14  C13  123.78  3.000
 8XO  O    C14  C15  121.44  3.000
 8XO  C13  C14  C15  114.78  3.000
 8XO  H2   C13  C12  119.83  3.000
 8XO  H2   C13  C14  117.32  3.000
 8XO  C12  C13  C14  122.84  3.000
 8XO  H3   C12  C11  116.32  3.000
 8XO  H3   C12  C13  118.92  3.000
 8XO  C11  C12  C13  124.75  3.000
 8XO  H5   C16  H4   107.69  3.000
 8XO  H5   C16  N    109.16  3.000
 8XO  H4   C16  N    112.39  3.000
 8XO  H5   C16  C17  108.98  3.000
 8XO  H4   C16  C17  106.49  3.000
 8XO  N    C16  C17  111.99  3.000
 8XO  H7   C11  H6   106.89  3.000
 8XO  H7   C11  C10  110.28  3.000
 8XO  H6   C11  C10  108.48  3.000
 8XO  H7   C11  C12  110.33  3.000
 8XO  H6   C11  C12  108.36  3.000
 8XO  C10  C11  C12  112.32  3.000
 8XO  O1   C17  O2   128.34  3.000
 8XO  O1   C17  C16  114.64  3.000
 8XO  O2   C17  C16  116.97  3.000
 8XO  C16  N    C15  117.94  3.000
 8XO  H10  C10  H9   106.37  3.000
 8XO  H10  C10  C9   109.76  3.000
 8XO  H9   C10  C9   109.47  3.000
 8XO  H10  C10  C11  109.34  3.000
 8XO  H9   C10  C11  109.52  3.000
 8XO  C9   C10  C11  112.21  3.000
 8XO  H12  C9   H11  106.07  3.000
 8XO  H12  C9   C8   109.47  3.000
 8XO  H11  C9   C8   109.38  3.000
 8XO  H12  C9   C10  109.16  3.000
 8XO  H11  C9   C10  109.38  3.000
 8XO  C8   C9   C10  113.14  3.000
 8XO  H14  C8   H13  106.02  3.000
 8XO  H14  C8   C7   109.45  3.000
 8XO  H13  C8   C7   109.16  3.000
 8XO  H14  C8   C9   109.35  3.000
 8XO  H13  C8   C9   109.51  3.000
 8XO  C7   C8   C9   113.11  3.000
 8XO  H16  C7   H15  105.97  3.000
 8XO  H16  C7   C    109.46  3.000
 8XO  H15  C7   C    109.31  3.000
 8XO  H16  C7   C8   109.17  3.000
 8XO  H15  C7   C8   109.46  3.000
 8XO  C    C7   C8   113.21  3.000
 8XO  H18  C    H17  105.93  3.000
 8XO  H18  C    C1   109.35  3.000
 8XO  H17  C    C1   109.22  3.000
 8XO  H18  C    C7   109.30  3.000
 8XO  H17  C    C7   109.39  3.000
 8XO  C1   C    C7   113.37  3.000
 8XO  H20  C1   H19  105.97  3.000
 8XO  H20  C1   C2   109.45  3.000
 8XO  H19  C1   C2   109.30  3.000
 8XO  H20  C1   C    109.30  3.000
 8XO  H19  C1   C    109.47  3.000
 8XO  C2   C1   C    113.10  3.000
 8XO  H22  C2   H21  105.95  3.000
 8XO  H22  C2   C3   109.34  3.000
 8XO  H21  C2   C3   109.29  3.000
 8XO  H22  C2   C1   109.27  3.000
 8XO  H21  C2   C1   109.34  3.000
 8XO  C3   C2   C1   113.38  3.000
 8XO  H24  C3   H23  106.07  3.000
 8XO  H24  C3   C4   109.43  3.000
 8XO  H23  C3   C4   109.29  3.000
 8XO  H24  C3   C2   109.42  3.000
 8XO  H23  C3   C2   109.50  3.000
 8XO  C4   C3   C2   112.90  3.000
 8XO  H26  C4   H25  106.11  3.000
 8XO  H26  C4   C5   109.46  3.000
 8XO  H25  C4   C5   109.49  3.000
 8XO  H26  C4   C3   109.26  3.000
 8XO  H25  C4   C3   109.32  3.000
 8XO  C5   C4   C3   112.97  3.000
 8XO  H28  C5   H27  106.77  3.000
 8XO  H28  C5   C6   109.84  3.000
 8XO  H27  C5   C6   109.28  3.000
 8XO  H28  C5   C4   109.44  3.000
 8XO  H27  C5   C4   109.99  3.000
 8XO  C6   C5   C4   111.40  3.000
 8XO  H30  C6   H29  107.28  3.000
 8XO  H30  C6   N1   105.29  3.000
 8XO  H29  C6   N1   110.36  3.000
 8XO  H30  C6   C5   110.10  3.000
 8XO  H29  C6   C5   110.40  3.000
 8XO  N1   C6   C5   113.13  3.000
 8XO  N2   N1   C6   116.48  3.000
 8XO  N3   N2   N1   174.65  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 8XO  Var_01  C11  C12  C13  C14  -179.58   0.0  2
 8XO  Var_02  C12  C13  C14  C15  -178.54  30.0  1
 8XO  Var_03  C17  C16  N    C15    92.04  30.0  3
 8XO  Var_04  C10  C11  C12  C13   123.79  30.0  1
 8XO  Var_05  N    C15  C14  C13  -175.85  30.0  2
 8XO  Var_06  C9   C10  C11  C12  -179.30  30.0  1
 8XO  Var_07  C8   C9   C10  C11  -177.61  30.0  2
 8XO  Var_08  N    C16  C17  O2    -26.01  30.0  2
 8XO  Var_09  C7   C8   C9   C10  -176.49  30.0  2
 8XO  Var_10  C    C7   C8   C9   -177.60  30.0  2
 8XO  Var_11  C1   C    C7   C8   -177.58  30.0  3
 8XO  Var_12  C2   C1   C    C7   -178.25  30.0  1
 8XO  Var_13  C3   C2   C1   C    -178.75  30.0  3
 8XO  Var_14  C4   C3   C2   C1   -178.81  30.0  1
 8XO  Var_15  C5   C4   C3   C2   -179.42  30.0  3
 8XO  Var_16  C6   C5   C4   C3   -179.06  30.0  3
 8XO  Var_17  N1   C6   C5   C4    177.59  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 8XO  plan-1  C15  0.020
 8XO  plan-1  C14  0.020
 8XO  plan-1  C13  0.020
 8XO  plan-1  O    0.020
 8XO  plan-2  C16  0.020
 8XO  plan-2  O2   0.020
 8XO  plan-2  C17  0.020
 8XO  plan-2  O1   0.020
 8XO  plan-3  C6   0.020
 8XO  plan-3  N1   0.020
 8XO  plan-3  N2   0.020
 8XO  plan-3  N3   0.020
 8XO  plan-4  C14  0.020
 8XO  plan-4  C13  0.020
 8XO  plan-4  C12  0.020
 8XO  plan-4  C11  0.020
 8XO  plan-4  H2   0.020
 8XO  plan-4  H3   0.020
 8XO  plan-5  C15  0.020
 8XO  plan-5  C14  0.020
 8XO  plan-5  C16  0.020
 8XO  plan-5  N    0.020
 8XO  plan-5  H1   0.020

