# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 05:53:27 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: [(~{S})-[4-[3-[(~{R})-(3,4-dichlorophenyl)-oxidanyl-methyl]phenyl]phenyl]-oxidanyl-methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](c1cccc(c1)c2ccc(cc2)[C@@H](O)[P](O)(O)=O)c3ccc(Cl)c(Cl)c3
#
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
 AXK  AXK  '[(~{S})-[4-[3-[(~{R})-(3,4-dichlorophenyl)-oxidanyl-methyl]phenyl]phenyl]-oxidanyl-methyl]phosphonic acid'  ligand  43  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AXK
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
 AXK  C2   C   CR16   0  -0.281  -4.2384   1.5924   0.4640
 AXK  C4   C   CR16   0  -0.312  -3.4810  -0.0419  -1.0954
 AXK  C5   C   CR16   0  -0.310  -2.9299   1.8999   0.7889
 AXK  C6   C   CR6    0   0.064  -1.8607   1.2376   0.1774
 AXK  C8   C   CR6    0   0.123  -0.4627   1.5778   0.5038
 AXK  C9   C   CR16   0  -0.301   2.1964   2.2490   1.0936
 AXK  C10  C   CR6    0   0.118   1.8487   1.8587  -0.1973
 AXK  C11  C   CR16   0  -0.332  -0.0916   1.9628   1.7919
 AXK  C12  C   CR16   0  -0.224   1.2248   2.2985   2.0800
 AXK  C1   C   CR6    0   0.132  -4.5453   0.6228  -0.4924
 AXK  C3   C   CR16   0  -0.299  -2.1664   0.2582  -0.7663
 AXK  C7   C   CR16   0  -0.405   0.5300   1.5366  -0.4803
 AXK  C13  C   CH1    0  -0.326  -5.9694   0.3088  -0.8167
 AXK  P14  P   P      0   1.155  -6.7665  -0.8602   0.4652
 AXK  O15  O   OP    -1  -0.863  -5.9614  -0.7846   1.7560
 AXK  O16  O   OP    -1  -0.888  -8.2207  -0.4073   0.5888
 AXK  O17  O   O      0  -0.890  -6.5959  -2.1838  -0.3243
 AXK  O18  O   OH1    0  -0.712  -6.1091  -0.3435  -2.0623
 AXK  C19  C   CH1    0  -0.064   2.8969   1.7947  -1.2905
 AXK  O20  O   OH1    0  -0.653   3.6561   2.9706  -1.3703
 AXK  C21  C   CR6    0   0.094   3.8307   0.6348  -1.0314
 AXK  C22  C   CR6    0  -0.019   5.4791  -1.5543  -0.5068
 AXK  C23  C   CR16   0  -0.201   4.1927  -1.7508  -0.9897
 AXK  C24  C   CR16   0  -0.280   3.3793  -0.6638  -1.2493
 AXK  C25  C   CR16   0  -0.285   5.1178   0.8282  -0.5523
 AXK  C26  C   CR6    0   0.027   5.9369  -0.2620  -0.2903
 AXK  CL7  CL  CL     0  -0.100   7.5320   0.0127   0.3032
 AXK  CL8  CL  CL     0  -0.100   6.4864  -2.9153  -0.1895
 AXK  H1   H   HCR6   0   0.231  -5.0412   2.1379   0.9461
 AXK  H2   H   HCR6   0   0.234  -3.6723  -0.8008  -1.8424
 AXK  H3   H   HCR6   0   0.241  -2.7381   2.6839   1.5119
 AXK  H4   H   HCR6   0   0.255   3.2208   2.5071   1.3325
 AXK  H5   H   HCR6   0   0.253  -0.8295   1.9847   2.5837
 AXK  H6   H   HCR6   0   0.257   1.4942   2.5910   3.0866
 AXK  H7   H   HCR6   0   0.238  -1.3682  -0.2953  -1.2468
 AXK  H8   H   HCR6   0   0.250   0.2623   1.2723  -1.4971
 AXK  H9   H   HCH1   0   0.197  -6.5358   1.2493  -0.8291
 AXK  H12  H   HOH1   0   0.424  -6.2663  -1.2738  -1.7702
 AXK  H13  H   HCH1   0   0.250   2.3800   1.5961  -2.2403
 AXK  H14  H   HOH1   0   0.462   3.0552   3.7143  -1.4830
 AXK  H15  H   HCR6   0   0.289   3.8330  -2.7553  -1.1649
 AXK  H16  H   HCR6   0   0.267   2.3780  -0.8367  -1.6248
 AXK  H17  H   HCR6   0   0.284   5.5007   1.8235  -0.3761

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
 AXK  CL7  C26  single    1.724  0.020  1.724
 AXK  CL8  C22  single    1.723  0.020  1.723
 AXK  C26  C22  aromatic  1.388  0.020  1.388
 AXK  C26  C25  aromatic  1.389  0.020  1.389
 AXK  C22  C23  aromatic  1.388  0.020  1.388
 AXK  C25  C21  aromatic  1.387  0.020  1.387
 AXK  C23  C24  aromatic  1.382  0.020  1.382
 AXK  C21  C24  aromatic  1.392  0.020  1.392
 AXK  C21  C19  single    1.511  0.020  1.511
 AXK  O20  C19  single    1.402  0.020  1.402
 AXK  C19  C10  single    1.516  0.020  1.516
 AXK  C10  C7   aromatic  1.387  0.020  1.387
 AXK  C10  C9   aromatic  1.393  0.020  1.393
 AXK  C7   C8   aromatic  1.398  0.020  1.398
 AXK  C9   C12  aromatic  1.385  0.020  1.385
 AXK  C3   C4   aromatic  1.388  0.020  1.388
 AXK  C3   C6   aromatic  1.394  0.020  1.394
 AXK  O18  C13  single    1.413  0.020  1.413
 AXK  C4   C1   aromatic  1.392  0.020  1.392
 AXK  C8   C6   single    1.475  0.020  1.475
 AXK  C8   C11  aromatic  1.395  0.020  1.395
 AXK  C6   C5   aromatic  1.398  0.020  1.398
 AXK  C12  C11  aromatic  1.389  0.020  1.389
 AXK  C1   C13  single    1.494  0.020  1.494
 AXK  C1   C2   aromatic  1.396  0.020  1.396
 AXK  C13  P14  single    1.909  0.020  1.909
 AXK  O17  P14  deloc     1.551  0.020  1.551
 AXK  C5   C2   aromatic  1.383  0.020  1.383
 AXK  P14  O15  deloc     1.523  0.020  1.523
 AXK  P14  O16  deloc     1.528  0.020  1.528
 AXK  C2   H1   single    0.930  0.020  1.080
 AXK  C4   H2   single    0.930  0.020  1.080
 AXK  C5   H3   single    0.930  0.020  1.080
 AXK  C9   H4   single    0.930  0.020  1.080
 AXK  C11  H5   single    0.930  0.020  1.080
 AXK  C12  H6   single    0.930  0.020  1.080
 AXK  C3   H7   single    0.930  0.020  1.080
 AXK  C7   H8   single    0.930  0.020  1.080
 AXK  C13  H9   single    0.970  0.020  1.090
 AXK  O18  H12  single    0.850  0.020  0.980
 AXK  C19  H13  single    0.970  0.020  1.090
 AXK  O20  H14  single    0.850  0.020  0.980
 AXK  C23  H15  single    0.930  0.020  1.080
 AXK  C24  H16  single    0.930  0.020  1.080
 AXK  C25  H17  single    0.930  0.020  1.080

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
 AXK  H1   C2   C1   119.44  3.000
 AXK  H1   C2   C5   118.98  3.000
 AXK  C1   C2   C5   121.56  3.000
 AXK  H2   C4   C3   118.87  3.000
 AXK  H2   C4   C1   119.91  3.000
 AXK  C3   C4   C1   121.21  3.000
 AXK  H3   C5   C6   119.93  3.000
 AXK  H3   C5   C2   119.02  3.000
 AXK  C6   C5   C2   121.03  3.000
 AXK  C3   C6   C8   121.30  3.000
 AXK  C8   C6   C5   121.24  3.000
 AXK  C3   C6   C5   117.45  3.000
 AXK  C7   C8   C11  117.98  3.000
 AXK  C11  C8   C6   121.34  3.000
 AXK  C7   C8   C6   120.68  3.000
 AXK  H4   C9   C12  119.86  3.000
 AXK  H4   C9   C10  120.49  3.000
 AXK  C12  C9   C10  119.65  3.000
 AXK  C19  C10  C7   120.04  3.000
 AXK  C7   C10  C9   119.45  3.000
 AXK  C19  C10  C9   120.50  3.000
 AXK  H5   C11  C12  119.31  3.000
 AXK  H5   C11  C8   119.98  3.000
 AXK  C12  C11  C8   120.70  3.000
 AXK  H6   C12  C11  119.62  3.000
 AXK  H6   C12  C9   119.81  3.000
 AXK  C11  C12  C9   120.56  3.000
 AXK  C13  C1   C4   122.30  3.000
 AXK  C13  C1   C2   120.29  3.000
 AXK  C4   C1   C2   117.40  3.000
 AXK  H7   C3   C6   119.83  3.000
 AXK  H7   C3   C4   118.82  3.000
 AXK  C6   C3   C4   121.34  3.000
 AXK  H8   C7   C10  118.87  3.000
 AXK  H8   C7   C8   119.46  3.000
 AXK  C10  C7   C8   121.65  3.000
 AXK  H9   C13  O18  109.54  3.000
 AXK  H9   C13  P14  108.46  3.000
 AXK  O18  C13  P14  105.54  3.000
 AXK  H9   C13  C1   108.31  3.000
 AXK  P14  C13  C1   112.39  3.000
 AXK  O18  C13  C1   112.50  3.000
 AXK  O17  P14  O16  113.51  3.000
 AXK  O16  P14  O15  114.82  3.000
 AXK  O17  P14  O15  114.56  3.000
 AXK  O16  P14  C13  105.67  3.000
 AXK  O15  P14  C13  108.54  3.000
 AXK  O17  P14  C13   97.75  3.000
 AXK  H12  O18  C13  100.94  3.000
 AXK  H13  C19  C21  107.46  3.000
 AXK  H13  C19  O20  110.92  3.000
 AXK  C21  C19  O20  108.60  3.000
 AXK  H13  C19  C10  107.78  3.000
 AXK  O20  C19  C10  112.34  3.000
 AXK  C21  C19  C10  109.63  3.000
 AXK  H14  O20  C19  108.46  3.000
 AXK  C25  C21  C24  119.02  3.000
 AXK  C24  C21  C19  119.26  3.000
 AXK  C25  C21  C19  121.71  3.000
 AXK  CL8  C22  C26  120.93  3.000
 AXK  C26  C22  C23  119.46  3.000
 AXK  CL8  C22  C23  119.61  3.000
 AXK  H15  C23  C24  120.29  3.000
 AXK  H15  C23  C22  119.75  3.000
 AXK  C24  C23  C22  119.96  3.000
 AXK  H16  C24  C23  118.92  3.000
 AXK  H16  C24  C21  120.19  3.000
 AXK  C23  C24  C21  120.89  3.000
 AXK  H17  C25  C26  118.90  3.000
 AXK  H17  C25  C21  120.89  3.000
 AXK  C26  C25  C21  120.21  3.000
 AXK  CL7  C26  C25  119.06  3.000
 AXK  C25  C26  C22  120.46  3.000
 AXK  CL7  C26  C22  120.48  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
 AXK  CONST_01  C3   C4   C1   C2     0.00  0.0  0
 AXK  CONST_02  C3   C6   C5   C2     0.00  0.0  0
 AXK  CONST_03  C8   C6   C5   C2   180.00  0.0  0
 AXK  CONST_04  C8   C6   C3   C4   180.00  0.0  0
 AXK  CONST_05  C5   C6   C3   C4     0.00  0.0  0
 AXK  CONST_06  C5   C2   C1   C4     0.00  0.0  0
 AXK  CONST_09  C1   C4   C3   C6     0.00  0.0  0
 AXK  CONST_10  C10  C7   C8   C6   180.00  0.0  0
 AXK  CONST_11  C12  C11  C8   C6   180.00  0.0  0
 AXK  CONST_12  C1   C2   C5   C6     0.00  0.0  0
 AXK  CONST_13  C9   C10  C7   C8     0.00  0.0  0
 AXK  CONST_14  C9   C12  C11  C8     0.00  0.0  0
 AXK  CONST_15  C11  C8   C7   C10    0.00  0.0  0
 AXK  CONST_16  C11  C12  C9   C10    0.00  0.0  0
 AXK  CONST_18  C7   C10  C9   C12    0.00  0.0  0
 AXK  CONST_19  C7   C8   C11  C12    0.00  0.0  0
 AXK  CONST_21  C22  C26  C25  C21    0.00  0.0  0
 AXK  CONST_22  C22  C23  C24  C21    0.00  0.0  0
 AXK  CONST_23  C25  C26  C22  C23    0.00  0.0  0
 AXK  CONST_24  C25  C21  C24  C23    0.00  0.0  0
 AXK  CONST_25  C26  C22  C23  C24    0.00  0.0  0
 AXK  CONST_26  C26  C25  C21  C24    0.00  0.0  0
 AXK  CONST_27  C13  C1   C2   C5   180.00  0.0  0
 AXK  CONST_28  C19  C10  C7   C8   180.00  0.0  0
 AXK  CONST_29  C19  C10  C9   C12  180.00  0.0  0
 AXK  CONST_30  C13  C1   C4   C3   180.00  0.0  0
 AXK  CONST_31  C26  C25  C21  C19  180.00  0.0  0
 AXK  CONST_32  C23  C24  C21  C19  180.00  0.0  0
 AXK  CONST_33  CL7  C26  C25  C21  180.00  0.0  0
 AXK  CONST_34  CL7  C26  C22  C23  180.00  0.0  0
 AXK  CONST_35  CL8  C22  C23  C24  180.00  0.0  0
 AXK  CONST_36  CL8  C22  C26  C25  180.00  0.0  0
 AXK  CONST_37  H2   C4   C1   C2   180.00  0.0  0
 AXK  CONST_38  H1   C2   C1   C4   180.00  0.0  0
 AXK  CONST_39  H7   C3   C6   C5   180.00  0.0  0
 AXK  CONST_40  H8   C7   C8   C6     0.00  0.0  0
 AXK  CONST_41  H5   C11  C8   C6     0.00  0.0  0
 AXK  CONST_42  H3   C5   C6   C8     0.00  0.0  0
 AXK  CONST_43  H6   C12  C11  C8   180.00  0.0  0
 AXK  CONST_44  H4   C9   C12  C11  180.00  0.0  0
 AXK  CONST_45  H15  C23  C24  C21  180.00  0.0  0
 AXK  CONST_46  H17  C25  C26  C22  180.00  0.0  0
 AXK  CONST_47  H16  C24  C23  C22  180.00  0.0  0

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
 AXK  chir_01  C13  O18  C1   P14  positiv
 AXK  chir_02  C19  C21  O20  C10  positiv

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
 AXK  plan-1  C6   0.020
 AXK  plan-1  C8   0.020
 AXK  plan-1  C9   0.020
 AXK  plan-1  C10  0.020
 AXK  plan-1  C11  0.020
 AXK  plan-1  C12  0.020
 AXK  plan-1  C7   0.020
 AXK  plan-1  C19  0.020
 AXK  plan-1  H4   0.020
 AXK  plan-1  H5   0.020
 AXK  plan-1  H6   0.020
 AXK  plan-1  H8   0.020
 AXK  plan-2  C2   0.020
 AXK  plan-2  C4   0.020
 AXK  plan-2  C5   0.020
 AXK  plan-2  C6   0.020
 AXK  plan-2  C8   0.020
 AXK  plan-2  C1   0.020
 AXK  plan-2  C3   0.020
 AXK  plan-2  C13  0.020
 AXK  plan-2  H1   0.020
 AXK  plan-2  H2   0.020
 AXK  plan-2  H3   0.020
 AXK  plan-2  H7   0.020
 AXK  plan-3  C19  0.020
 AXK  plan-3  C21  0.020
 AXK  plan-3  C22  0.020
 AXK  plan-3  C23  0.020
 AXK  plan-3  C24  0.020
 AXK  plan-3  C25  0.020
 AXK  plan-3  C26  0.020
 AXK  plan-3  CL7  0.020
 AXK  plan-3  CL8  0.020
 AXK  plan-3  H15  0.020
 AXK  plan-3  H16  0.020
 AXK  plan-3  H17  0.020

