# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 19:03:40 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: tetradecyl hydrogen (R)-(3-azidopropyl)phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCO[P](O)(=O)CCCN=[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
 1QY  1QY  'tetradecyl hydrogen (R)-(3-azidopropyl)phosphonate'  ligand  59  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1QY
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
 1QY  C14  C  CH3    0  -0.662  -14.0034   0.6183   0.0562
 1QY  C13  C  CH2    0  -0.419  -12.7274  -0.0159  -0.4793
 1QY  C12  C  CH2    0  -0.407  -11.4657   0.5549   0.1564
 1QY  C11  C  CH2    0  -0.411  -10.1861  -0.0795  -0.3727
 1QY  C10  C  CH2    0  -0.412   -8.9210   0.4839   0.2621
 1QY  C9   C  CH2    0  -0.412   -7.6474  -0.1593  -0.2712
 1QY  C8   C  CH2    0  -0.413   -6.3745   0.3966   0.3546
 1QY  C7   C  CH2    0  -0.412   -5.1101  -0.2552  -0.1904
 1QY  C6   C  CH2    0  -0.413   -3.8262   0.2948   0.4175
 1QY  C5   C  CH2    0  -0.412   -2.5740  -0.3640  -0.1469
 1QY  C4   C  CH2    0  -0.411   -1.2775   0.1835   0.4353
 1QY  C3   C  CH2    0  -0.425   -0.0401  -0.4813  -0.1543
 1QY  C2   C  CH2    0  -0.458    1.2671   0.0741   0.3963
 1QY  C1   C  CH2    0  -0.124    2.4705  -0.6121  -0.2206
 1QY  O1   O  O2     0  -0.636    3.6606  -0.0188   0.2671
 1QY  P1   P  P      0   1.275    5.0754  -0.8662   0.1036
 1QY  O2   O  O      0  -0.815    5.1912  -1.3571  -1.3175
 1QY  C1H  C  CH2    0  -0.724    6.2295   0.5210   0.3915
 1QY  C2H  C  CH2    0  -0.443    7.6804   0.0541   0.3287
 1QY  C3H  C  CH2    0  -0.294    8.6430   1.2156   0.5329
 1QY  N1   N  N      0  -0.364   10.0514   0.7942   0.5437
 1QY  N2   N  N      1   0.353   10.5335   0.4865  -0.5287
 1QY  N3   N  N     -1  -0.232   11.0721   0.1860  -1.4703
 1QY  H1   H  HCH3   0   0.225  -14.8911   0.1903  -0.4109
 1QY  H2   H  HCH3   0   0.215  -14.0941   0.4722   1.1343
 1QY  H3   H  HCH3   0   0.215  -14.0182   1.6939  -0.1299
 1QY  H4   H  HCH2   0   0.210  -12.7578  -1.0972  -0.3120
 1QY  H5   H  HCH2   0   0.210  -12.6782   0.1194  -1.5643
 1QY  H6   H  HCH2   0   0.206  -11.4323   1.6372  -0.0120
 1QY  H7   H  HCH2   0   0.205  -11.5157   0.4213   1.2430
 1QY  H8   H  HCH2   0   0.206  -10.2234  -1.1620  -0.2064
 1QY  H9   H  HCH2   0   0.206  -10.1368   0.0555  -1.4591
 1QY  H10  H  HCH2   0   0.206   -8.8800   1.5658   0.0937
 1QY  H11  H  HCH2   0   0.206   -8.9691   0.3499   1.3486
 1QY  H12  H  HCH2   0   0.206   -7.6908  -1.2413  -0.1028
 1QY  H13  H  HCH2   0   0.206   -7.6030  -0.0267  -1.3581
 1QY  H14  H  HCH2   0   0.206   -6.3279   1.4781   0.1853
 1QY  H15  H  HCH2   0   0.206   -6.4145   0.2630   1.4414
 1QY  H16  H  HCH2   0   0.206   -5.1579  -1.3364  -0.0189
 1QY  H17  H  HCH2   0   0.206   -5.0777  -0.1257  -1.2782
 1QY  H18  H  HCH2   0   0.206   -3.7765   1.3760   0.2468
 1QY  H19  H  HCH2   0   0.207   -3.8507   0.1619   1.5049
 1QY  H20  H  HCH2   0   0.207   -2.6229  -1.4444   0.0292
 1QY  H21  H  HCH2   0   0.207   -2.5607  -0.2383  -1.2354
 1QY  H22  H  HCH2   0   0.208   -1.2273   1.2639   0.2610
 1QY  H23  H  HCH2   0   0.209   -1.2796   0.0525   1.5229
 1QY  H24  H  HCH2   0   0.212   -0.0876  -1.5601   0.0310
 1QY  H25  H  HCH2   0   0.211   -0.0542  -0.3628  -1.2434
 1QY  H26  H  HCH2   0   0.217    1.3197   1.1497   0.1988
 1QY  H27  H  HCH2   0   0.217    1.2935  -0.0485   1.4836
 1QY  H28  H  HCH2   0   0.191    2.4313  -1.6836   0.0142
 1QY  H29  H  HCH2   0   0.195    2.4216  -0.5278  -1.3127
 1QY  H31  H  HCH2   0   0.240    6.0557   1.2978  -0.3585
 1QY  H32  H  HCH2   0   0.242    6.0256   0.9694   1.3680
 1QY  H33  H  HCH2   0   0.235    7.8626  -0.7054   1.0918
 1QY  H34  H  HCH2   0   0.230    7.8723  -0.4139  -0.6410
 1QY  H35  H  HCH2   0   0.246    8.4806   1.9832  -0.2297
 1QY  H36  H  HCH2   0   0.252    8.4732   1.6795   1.5029
 1QY  O3   O  OP    -1  -0.808    5.1847  -1.8648   1.2273

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
 1QY  C2H  C3H  single  1.522  0.020  1.522
 1QY  C2H  C1H  single  1.525  0.020  1.525
 1QY  C3H  N1   single  1.470  0.020  1.470
 1QY  N3   N2   double  1.126  0.020  1.126
 1QY  O2   P1   deloc   1.508  0.020  1.508
 1QY  N2   N1   double  1.215  0.020  1.215
 1QY  C1H  P1   single  1.827  0.020  1.827
 1QY  P1   O1   single  1.657  0.020  1.657
 1QY  O1   C1   single  1.416  0.020  1.416
 1QY  C3   C4   single  1.523  0.020  1.523
 1QY  C3   C2   single  1.523  0.020  1.523
 1QY  C1   C2   single  1.516  0.020  1.516
 1QY  C4   C5   single  1.523  0.020  1.523
 1QY  C13  C14  single  1.522  0.020  1.522
 1QY  C13  C12  single  1.524  0.020  1.524
 1QY  C7   C6   single  1.523  0.020  1.523
 1QY  C7   C8   single  1.523  0.020  1.523
 1QY  C9   C10  single  1.523  0.020  1.523
 1QY  C9   C8   single  1.523  0.020  1.523
 1QY  C5   C6   single  1.523  0.020  1.523
 1QY  C11  C10  single  1.523  0.020  1.523
 1QY  C11  C12  single  1.523  0.020  1.523
 1QY  C14  H1   single  0.970  0.020  1.090
 1QY  C14  H2   single  0.970  0.020  1.090
 1QY  C14  H3   single  0.970  0.020  1.090
 1QY  C13  H4   single  0.970  0.020  1.090
 1QY  C13  H5   single  0.970  0.020  1.090
 1QY  C12  H6   single  0.970  0.020  1.090
 1QY  C12  H7   single  0.970  0.020  1.090
 1QY  C11  H8   single  0.970  0.020  1.090
 1QY  C11  H9   single  0.970  0.020  1.090
 1QY  C10  H10  single  0.970  0.020  1.090
 1QY  C10  H11  single  0.970  0.020  1.090
 1QY  C9   H12  single  0.970  0.020  1.090
 1QY  C9   H13  single  0.970  0.020  1.090
 1QY  C8   H14  single  0.970  0.020  1.090
 1QY  C8   H15  single  0.970  0.020  1.090
 1QY  C7   H16  single  0.970  0.020  1.090
 1QY  C7   H17  single  0.970  0.020  1.090
 1QY  C6   H18  single  0.970  0.020  1.090
 1QY  C6   H19  single  0.970  0.020  1.090
 1QY  C5   H20  single  0.970  0.020  1.090
 1QY  C5   H21  single  0.970  0.020  1.090
 1QY  C4   H22  single  0.970  0.020  1.090
 1QY  C4   H23  single  0.970  0.020  1.090
 1QY  C3   H24  single  0.970  0.020  1.090
 1QY  C3   H25  single  0.970  0.020  1.090
 1QY  C2   H26  single  0.970  0.020  1.090
 1QY  C2   H27  single  0.970  0.020  1.090
 1QY  C1   H28  single  0.970  0.020  1.090
 1QY  C1   H29  single  0.970  0.020  1.090
 1QY  C1H  H31  single  0.970  0.020  1.090
 1QY  C1H  H32  single  0.970  0.020  1.090
 1QY  C2H  H33  single  0.970  0.020  1.090
 1QY  C2H  H34  single  0.970  0.020  1.090
 1QY  C3H  H35  single  0.970  0.020  1.090
 1QY  C3H  H36  single  0.970  0.020  1.090
 1QY  P1   O3   deloc   1.507  0.020  1.507

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
 1QY  H3   C14  H2   107.40  3.000
 1QY  H3   C14  H1   107.61  3.000
 1QY  H2   C14  H1   107.63  3.000
 1QY  H3   C14  C13  111.22  3.000
 1QY  H2   C14  C13  111.18  3.000
 1QY  H1   C14  C13  111.60  3.000
 1QY  H5   C13  H4   105.96  3.000
 1QY  H5   C13  C12  109.27  3.000
 1QY  H4   C13  C12  109.23  3.000
 1QY  H5   C13  C14  109.57  3.000
 1QY  H4   C13  C14  109.54  3.000
 1QY  C12  C13  C14  113.03  3.000
 1QY  H7   C12  H6   105.92  3.000
 1QY  H7   C12  C11  109.39  3.000
 1QY  H6   C12  C11  109.41  3.000
 1QY  H7   C12  C13  109.28  3.000
 1QY  H6   C12  C13  109.34  3.000
 1QY  C11  C12  C13  113.24  3.000
 1QY  H9   C11  H8   105.89  3.000
 1QY  H9   C11  C10  109.28  3.000
 1QY  H8   C11  C10  109.29  3.000
 1QY  H9   C11  C12  109.32  3.000
 1QY  H8   C11  C12  109.28  3.000
 1QY  C10  C11  C12  113.50  3.000
 1QY  H11  C10  H10  105.95  3.000
 1QY  H11  C10  C9   109.40  3.000
 1QY  H10  C10  C9   109.38  3.000
 1QY  H11  C10  C11  109.36  3.000
 1QY  H10  C10  C11  109.40  3.000
 1QY  C9   C10  C11  113.10  3.000
 1QY  H13  C9   H12  105.87  3.000
 1QY  H13  C9   C8   109.23  3.000
 1QY  H12  C9   C8   109.29  3.000
 1QY  H13  C9   C10  109.27  3.000
 1QY  H12  C9   C10  109.27  3.000
 1QY  C8   C9   C10  113.62  3.000
 1QY  H15  C8   H14  105.97  3.000
 1QY  H15  C8   C7   109.45  3.000
 1QY  H14  C8   C7   109.38  3.000
 1QY  H15  C8   C9   109.42  3.000
 1QY  H14  C8   C9   109.41  3.000
 1QY  C7   C8   C9   112.98  3.000
 1QY  H17  C7   H16  105.86  3.000
 1QY  H17  C7   C6   109.18  3.000
 1QY  H16  C7   C6   109.30  3.000
 1QY  H17  C7   C8   109.22  3.000
 1QY  H16  C7   C8   109.27  3.000
 1QY  C6   C7   C8   113.72  3.000
 1QY  H19  C6   H18  105.98  3.000
 1QY  H19  C6   C5   109.49  3.000
 1QY  H18  C6   C5   109.38  3.000
 1QY  H19  C6   C7   109.48  3.000
 1QY  H18  C6   C7   109.41  3.000
 1QY  C5   C6   C7   112.88  3.000
 1QY  H21  C5   H20  105.86  3.000
 1QY  H21  C5   C4   109.15  3.000
 1QY  H20  C5   C4   109.33  3.000
 1QY  H21  C5   C6   109.18  3.000
 1QY  H20  C5   C6   109.28  3.000
 1QY  C4   C5   C6   113.75  3.000
 1QY  H23  C4   H22  106.02  3.000
 1QY  H23  C4   C3   109.49  3.000
 1QY  H22  C4   C3   109.37  3.000
 1QY  H23  C4   C5   109.56  3.000
 1QY  H22  C4   C5   109.43  3.000
 1QY  C3   C4   C5   112.75  3.000
 1QY  H25  C3   H24  105.90  3.000
 1QY  H25  C3   C2   109.32  3.000
 1QY  H24  C3   C2   109.58  3.000
 1QY  H25  C3   C4   109.09  3.000
 1QY  H24  C3   C4   109.21  3.000
 1QY  C2   C3   C4   113.46  3.000
 1QY  H27  C2   H26  106.74  3.000
 1QY  H27  C2   C1   109.53  3.000
 1QY  H26  C2   C1   109.46  3.000
 1QY  H27  C2   C3   109.81  3.000
 1QY  H26  C2   C3   109.52  3.000
 1QY  C1   C2   C3   111.65  3.000
 1QY  H29  C1   H28  106.65  3.000
 1QY  H29  C1   O1   110.38  3.000
 1QY  H28  C1   O1   111.43  3.000
 1QY  H29  C1   C2   109.57  3.000
 1QY  H28  C1   C2   109.05  3.000
 1QY  O1   C1   C2   109.70  3.000
 1QY  P1   O1   C1   117.98  3.000
 1QY  O3   P1   C1H  109.86  3.000
 1QY  O3   P1   O2   118.78  3.000
 1QY  C1H  P1   O2   110.31  3.000
 1QY  O3   P1   O1   109.09  3.000
 1QY  C1H  P1   O1    97.79  3.000
 1QY  O2   P1   O1   108.96  3.000
 1QY  H32  C1H  H31  106.94  3.000
 1QY  H32  C1H  C2H  109.85  3.000
 1QY  H31  C1H  C2H  109.90  3.000
 1QY  H32  C1H  P1   109.52  3.000
 1QY  H31  C1H  P1   109.31  3.000
 1QY  C2H  C1H  P1   111.22  3.000
 1QY  H34  C2H  H33  107.02  3.000
 1QY  H34  C2H  C3H  109.55  3.000
 1QY  H33  C2H  C3H  109.36  3.000
 1QY  H34  C2H  C1H  109.53  3.000
 1QY  H33  C2H  C1H  110.04  3.000
 1QY  C3H  C2H  C1H  111.25  3.000
 1QY  H36  C3H  H35  107.39  3.000
 1QY  H36  C3H  N1   105.37  3.000
 1QY  H35  C3H  N1   110.39  3.000
 1QY  H36  C3H  C2H  110.25  3.000
 1QY  H35  C3H  C2H  110.36  3.000
 1QY  N1   C3H  C2H  112.83  3.000
 1QY  N2   N1   C3H  116.49  3.000
 1QY  N3   N2   N1   174.56  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
 1QY  Var_01  C11  C12  C13  C14   179.81  30.0  3
 1QY  Var_02  C10  C11  C12  C13  -179.82  30.0  1
 1QY  Var_03  C9   C10  C11  C12   179.86  30.0  3
 1QY  Var_04  C8   C9   C10  C11   179.93  30.0  1
 1QY  Var_05  C7   C8   C9   C10  -179.92  30.0  3
 1QY  Var_06  C6   C7   C8   C9    179.62  30.0  1
 1QY  Var_07  C5   C6   C7   C8   -179.65  30.0  3
 1QY  Var_08  C4   C5   C6   C7    179.29  30.0  1
 1QY  Var_09  C3   C4   C5   C6   -179.45  30.0  1
 1QY  Var_10  C2   C3   C4   C5    178.83  30.0  1
 1QY  Var_11  C1   C2   C3   C4   -179.81  30.0  3
 1QY  Var_12  O1   C1   C2   C3    177.00  30.0  1
 1QY  Var_13  O2   P1   O1   C1     48.92  30.0  1
 1QY  Var_14  C2H  C1H  P1   O1    179.08  30.0  1
 1QY  Var_15  C3H  C2H  C1H  P1    178.54  30.0  2
 1QY  Var_16  N1   C3H  C2H  C1H   177.23  30.0  3
 1QY  Var_17  H1   C14  C13  C12  -179.77  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
 1QY  plan-1  C3H  0.020
 1QY  plan-1  N1   0.020
 1QY  plan-1  N2   0.020
 1QY  plan-1  N3   0.020

