# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:50:54 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: dodecyl hydrogen (S)-(3-azidopropyl)phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCO[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
 1QX  1QX  'dodecyl hydrogen (S)-(3-azidopropyl)phosphonate'  ligand  54  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1QX
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
 1QX  C12  C  CH3    0  -0.662  12.5406  -0.8742  -0.3934
 1QX  C11  C  CH2    0  -0.419  11.3301   0.0467  -0.3246
 1QX  C10  C  CH2    0  -0.406  10.0136  -0.7153  -0.2312
 1QX  C9   C  CH2    0  -0.412   8.7930   0.1940  -0.1631
 1QX  C8   C  CH2    0  -0.412   7.4782  -0.5686  -0.0575
 1QX  C7   C  CH2    0  -0.412   6.2591   0.3429   0.0091
 1QX  C6   C  CH2    0  -0.412   4.9421  -0.4157   0.1145
 1QX  C5   C  CH2    0  -0.412   3.7266   0.5010   0.1759
 1QX  C4   C  CH2    0  -0.412   2.4060  -0.2533   0.2636
 1QX  C3   C  CH2    0  -0.428   1.1969   0.6723   0.3160
 1QX  C2   C  CH2    0  -0.461  -0.1257  -0.0839   0.3666
 1QX  C1   C  CH2    0  -0.153  -1.3003   0.8687   0.4091
 1QX  O1   O  O2     0  -0.599  -2.5170   0.1031   0.4393
 1QX  P1   P  P      0   1.388  -3.9256   0.8077   0.1344
 1QX  O2   O  O      0  -0.718  -4.1998   2.0538   0.8896
 1QX  C1H  C  CH2    0  -0.755  -5.0732  -0.5543   0.3977
 1QX  C2H  C  CH2    0  -0.450  -6.5103  -0.1651   0.0587
 1QX  C3H  C  CH2    0  -0.295  -7.4497  -1.3357   0.3185
 1QX  N1   N  N      0  -0.361  -8.8537  -0.9942   0.0660
 1QX  N2   N  N      1   0.355  -9.1892  -0.9091  -1.1004
 1QX  N3   N  N     -1  -0.225  -9.5991  -0.8096  -2.1432
 1QX  H1   H  HCH3   0   0.225  13.4733  -0.3119  -0.4506
 1QX  H2   H  HCH3   0   0.215  12.5958  -1.5163   0.4879
 1QX  H3   H  HCH3   0   0.216  12.4912  -1.5227  -1.2701
 1QX  H4   H  HCH2   0   0.210  11.4232   0.7126   0.5392
 1QX  H5   H  HCH2   0   0.210  11.3116   0.6962  -1.2055
 1QX  H6   H  HCH2   0   0.206   9.9199  -1.3851  -1.0936
 1QX  H7   H  HCH2   0   0.205  10.0335  -1.3635   0.6525
 1QX  H8   H  HCH2   0   0.206   8.8911   0.8679   0.6956
 1QX  H9   H  HCH2   0   0.206   8.7700   0.8372  -1.0501
 1QX  H10  H  HCH2   0   0.206   7.3796  -1.2438  -0.9150
 1QX  H11  H  HCH2   0   0.206   7.5008  -1.2102   0.8307
 1QX  H12  H  HCH2   0   0.206   6.3589   1.0184   0.8663
 1QX  H13  H  HCH2   0   0.206   6.2378   0.9846  -0.8791
 1QX  H14  H  HCH2   0   0.207   4.8428  -1.0916  -0.7424
 1QX  H15  H  HCH2   0   0.207   4.9602  -1.0560   1.0036
 1QX  H16  H  HCH2   0   0.208   3.8209   1.1710   1.0378
 1QX  H17  H  HCH2   0   0.208   3.7161   1.1472  -0.7090
 1QX  H18  H  HCH2   0   0.210   2.3121  -0.9230  -0.5982
 1QX  H19  H  HCH2   0   0.211   2.4100  -0.8975   1.1497
 1QX  H20  H  HCH2   0   0.218   1.2801   1.3279   1.1895
 1QX  H21  H  HCH2   0   0.217   1.2081   1.3296  -0.5602
 1QX  H22  H  HCH2   0   0.229  -0.2133  -0.7300  -0.5119
 1QX  H23  H  HCH2   0   0.230  -0.1476  -0.7338   1.2466
 1QX  H24  H  HCH2   0   0.233  -1.2502   1.5034   1.2973
 1QX  H25  H  HCH2   0   0.225  -1.2829   1.5211  -0.4692
 1QX  H27  H  HCH2   0   0.290  -4.7511  -1.4115  -0.1996
 1QX  H28  H  HCH2   0   0.293  -4.9954  -0.8521   1.4466
 1QX  H29  H  HCH2   0   0.256  -6.8244   0.6899   0.6603
 1QX  H30  H  HCH2   0   0.247  -6.5795   0.1354  -0.9897
 1QX  H31  H  HCH2   0   0.254  -7.1496  -2.2048  -0.2747
 1QX  H32  H  HCH2   0   0.261  -7.4048  -1.6264   1.3664
 1QX  O3   O  OH1    0  -0.753  -3.9358   1.1415  -1.4423
 1QX  H26  H  HOH1   0   0.489  -3.7562   0.3931  -2.0264

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
 1QX  C12  C11  single  1.522  0.020  1.522
 1QX  C11  C10  single  1.524  0.020  1.524
 1QX  C10  C9   single  1.524  0.020  1.524
 1QX  C9   C8   single  1.524  0.020  1.524
 1QX  C7   C8   single  1.524  0.020  1.524
 1QX  C7   C6   single  1.524  0.020  1.524
 1QX  C1   C2   single  1.513  0.020  1.513
 1QX  C1   O1   single  1.438  0.020  1.438
 1QX  O2   P1   double  1.483  0.020  1.483
 1QX  C2   C3   single  1.524  0.020  1.524
 1QX  C5   C6   single  1.524  0.020  1.524
 1QX  C5   C4   single  1.523  0.020  1.523
 1QX  N3   N2   double  1.125  0.020  1.125
 1QX  O1   P1   single  1.604  0.020  1.604
 1QX  C3   C4   single  1.524  0.020  1.524
 1QX  P1   C1H  single  1.800  0.020  1.800
 1QX  N2   N1   double  1.217  0.020  1.217
 1QX  C1H  C2H  single  1.527  0.020  1.527
 1QX  N1   C3H  single  1.467  0.020  1.467
 1QX  C2H  C3H  single  1.523  0.020  1.523
 1QX  C12  H1   single  0.970  0.020  1.090
 1QX  C12  H2   single  0.970  0.020  1.090
 1QX  C12  H3   single  0.970  0.020  1.090
 1QX  C11  H4   single  0.970  0.020  1.090
 1QX  C11  H5   single  0.970  0.020  1.090
 1QX  C10  H6   single  0.970  0.020  1.090
 1QX  C10  H7   single  0.970  0.020  1.090
 1QX  C9   H8   single  0.970  0.020  1.090
 1QX  C9   H9   single  0.970  0.020  1.090
 1QX  C8   H10  single  0.970  0.020  1.090
 1QX  C8   H11  single  0.970  0.020  1.090
 1QX  C7   H12  single  0.970  0.020  1.090
 1QX  C7   H13  single  0.970  0.020  1.090
 1QX  C6   H14  single  0.970  0.020  1.090
 1QX  C6   H15  single  0.970  0.020  1.090
 1QX  C5   H16  single  0.970  0.020  1.090
 1QX  C5   H17  single  0.970  0.020  1.090
 1QX  C4   H18  single  0.970  0.020  1.090
 1QX  C4   H19  single  0.970  0.020  1.090
 1QX  C3   H20  single  0.970  0.020  1.090
 1QX  C3   H21  single  0.970  0.020  1.090
 1QX  C2   H22  single  0.970  0.020  1.090
 1QX  C2   H23  single  0.970  0.020  1.090
 1QX  C1   H24  single  0.970  0.020  1.090
 1QX  C1   H25  single  0.970  0.020  1.090
 1QX  C1H  H27  single  0.970  0.020  1.090
 1QX  C1H  H28  single  0.970  0.020  1.090
 1QX  C2H  H29  single  0.970  0.020  1.090
 1QX  C2H  H30  single  0.970  0.020  1.090
 1QX  C3H  H31  single  0.970  0.020  1.090
 1QX  C3H  H32  single  0.970  0.020  1.090
 1QX  P1   O3   single  1.612  0.020  1.612
 1QX  O3   H26  single  0.850  0.020  0.980

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
 1QX  H3   C12  H2   107.53  3.000
 1QX  H3   C12  H1   107.63  3.000
 1QX  H2   C12  H1   107.60  3.000
 1QX  H3   C12  C11  111.08  3.000
 1QX  H2   C12  C11  111.07  3.000
 1QX  H1   C12  C11  111.74  3.000
 1QX  H5   C11  H4   105.99  3.000
 1QX  H5   C11  C10  109.36  3.000
 1QX  H4   C11  C10  109.22  3.000
 1QX  H5   C11  C12  109.63  3.000
 1QX  H4   C11  C12  109.63  3.000
 1QX  C10  C11  C12  112.78  3.000
 1QX  H7   C10  H6   105.94  3.000
 1QX  H7   C10  C9   109.36  3.000
 1QX  H6   C10  C9   109.36  3.000
 1QX  H7   C10  C11  109.23  3.000
 1QX  H6   C10  C11  109.34  3.000
 1QX  C9   C10  C11  113.35  3.000
 1QX  H9   C9   H8   105.97  3.000
 1QX  H9   C9   C8   109.37  3.000
 1QX  H8   C9   C8   109.31  3.000
 1QX  H9   C9   C10  109.33  3.000
 1QX  H8   C9   C10  109.29  3.000
 1QX  C8   C9   C10  113.31  3.000
 1QX  H11  C8   H10  105.98  3.000
 1QX  H11  C8   C7   109.35  3.000
 1QX  H10  C8   C7   109.32  3.000
 1QX  H11  C8   C9   109.35  3.000
 1QX  H10  C8   C9   109.38  3.000
 1QX  C7   C8   C9   113.20  3.000
 1QX  H13  C7   H12  105.95  3.000
 1QX  H13  C7   C6   109.32  3.000
 1QX  H12  C7   C6   109.37  3.000
 1QX  H13  C7   C8   109.29  3.000
 1QX  H12  C7   C8   109.27  3.000
 1QX  C6   C7   C8   113.38  3.000
 1QX  H15  C6   H14  105.99  3.000
 1QX  H15  C6   C5   109.39  3.000
 1QX  H14  C6   C5   109.29  3.000
 1QX  H15  C6   C7   109.43  3.000
 1QX  H14  C6   C7   109.35  3.000
 1QX  C5   C6   C7   113.13  3.000
 1QX  H17  C5   H16  105.99  3.000
 1QX  H17  C5   C4   109.28  3.000
 1QX  H16  C5   C4   109.40  3.000
 1QX  H17  C5   C6   109.26  3.000
 1QX  H16  C5   C6   109.33  3.000
 1QX  C4   C5   C6   113.33  3.000
 1QX  H19  C4   H18  106.09  3.000
 1QX  H19  C4   C3   109.41  3.000
 1QX  H18  C4   C3   109.30  3.000
 1QX  H19  C4   C5   109.54  3.000
 1QX  H18  C4   C5   109.37  3.000
 1QX  C3   C4   C5   112.90  3.000
 1QX  H21  C3   H20  106.14  3.000
 1QX  H21  C3   C2   109.46  3.000
 1QX  H20  C3   C2   109.66  3.000
 1QX  H21  C3   C4   109.20  3.000
 1QX  H20  C3   C4   109.32  3.000
 1QX  C2   C3   C4   112.85  3.000
 1QX  H23  C2   H22  107.06  3.000
 1QX  H23  C2   C1   109.63  3.000
 1QX  H22  C2   C1   109.41  3.000
 1QX  H23  C2   C3   109.80  3.000
 1QX  H22  C2   C3   109.62  3.000
 1QX  C1   C2   C3   111.23  3.000
 1QX  H25  C1   H24  107.78  3.000
 1QX  H25  C1   O1   110.34  3.000
 1QX  H24  C1   O1   109.33  3.000
 1QX  H25  C1   C2   109.91  3.000
 1QX  H24  C1   C2   110.67  3.000
 1QX  O1   C1   C2   108.80  3.000
 1QX  P1   O1   C1   120.34  3.000
 1QX  O3   P1   C1H  107.20  3.000
 1QX  O3   P1   O2   108.85  3.000
 1QX  C1H  P1   O2   116.32  3.000
 1QX  O3   P1   O1   106.41  3.000
 1QX  C1H  P1   O1   101.52  3.000
 1QX  O2   P1   O1   115.76  3.000
 1QX  H28  C1H  H27  106.84  3.000
 1QX  H28  C1H  C2H  110.45  3.000
 1QX  H27  C1H  C2H  110.84  3.000
 1QX  H28  C1H  P1   107.52  3.000
 1QX  H27  C1H  P1   108.99  3.000
 1QX  C2H  C1H  P1   112.00  3.000
 1QX  H30  C2H  H29  107.16  3.000
 1QX  H30  C2H  C3H  109.63  3.000
 1QX  H29  C2H  C3H  109.30  3.000
 1QX  H30  C2H  C1H  110.04  3.000
 1QX  H29  C2H  C1H  110.37  3.000
 1QX  C3H  C2H  C1H  110.28  3.000
 1QX  H32  C3H  H31  107.37  3.000
 1QX  H32  C3H  N1   105.51  3.000
 1QX  H31  C3H  N1   110.74  3.000
 1QX  H32  C3H  C2H  110.12  3.000
 1QX  H31  C3H  C2H  110.41  3.000
 1QX  N1   C3H  C2H  112.46  3.000
 1QX  N2   N1   C3H  116.45  3.000
 1QX  N3   N2   N1   174.51  3.000
 1QX  H26  O3   P1   115.45  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
 1QX  Var_01  C9   C10  C11  C12  -179.94  30.0  3
 1QX  Var_02  C8   C9   C10  C11  -179.50  30.0  3
 1QX  Var_03  C7   C8   C9   C10  -179.95  30.0  3
 1QX  Var_04  C6   C7   C8   C9    179.99  30.0  1
 1QX  Var_05  C5   C6   C7   C8   -179.80  30.0  3
 1QX  Var_06  C4   C5   C6   C7    179.27  30.0  1
 1QX  Var_07  C3   C4   C5   C6   -179.65  30.0  3
 1QX  Var_08  C2   C3   C4   C5    178.48  30.0  1
 1QX  Var_09  C1   C2   C3   C4   -179.65  30.0  1
 1QX  Var_10  O1   C1   C2   C3    179.31  30.0  1
 1QX  Var_11  O2   P1   O1   C1    -49.97  30.0  3
 1QX  Var_12  C2H  C1H  P1   O1   -175.51  30.0  3
 1QX  Var_13  C3H  C2H  C1H  P1   -179.00  30.0  3
 1QX  Var_14  N1   C3H  C2H  C1H   177.40  30.0  3
 1QX  Var_15  H1   C12  C11  C10  -179.48  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 1QX  chir_01  P1  O1  C1H  O3  both

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
 1QX  plan-1  C3H  0.020
 1QX  plan-1  N1   0.020
 1QX  plan-1  N2   0.020
 1QX  plan-1  N3   0.020

