# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:52:06 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: [(~{S})-[4-[3-[(~{S})-(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
 AY5  AY5  '[(~{S})-[4-[3-[(~{S})-(3,4-dichlorophenyl)-oxidanyl-methyl]phenyl]phenyl]-oxidanyl-methyl]phosphonic acid'  ligand  45  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 OK
;

data_comp_AY5
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
 AY5  C1   C   CR16  0  -0.225   1.3007  -2.5949   2.0086
 AY5  C2   C   CR16  0  -0.321   0.0093  -2.0882   1.9609
 AY5  C3   C   CR16  0  -0.294  -2.8839  -1.5202   1.3125
 AY5  C7   C   CR16  0  -0.296  -3.3113   0.9607   0.1650
 AY5  C8   C   CR16  0  -0.324   5.2086  -1.4461  -1.2881
 AY5  C9   C   CR16  0  -0.198   6.3874  -0.8241  -0.9020
 AY5  C10  C   CR16  0  -0.395   0.4510  -1.2025  -0.2227
 AY5  C11  C   CR16  0  -0.233   3.9463   0.3080  -0.2600
 AY5  C12  C   CR6   0   0.077  -1.7965  -0.8205   0.7898
 AY5  C13  C   CR6   0   0.113  -0.4315  -1.3794   0.8450
 AY5  C14  C   CR6   0   0.086  -4.3925   0.2617   0.6946
 AY5  C15  C   CR6   0   0.121   1.7440  -1.7032  -0.1824
 AY5  C16  C   CR6   0   0.060   3.9781  -0.8917  -0.9639
 AY5  C19  C   CH1   0  -0.061   2.6661  -1.5392  -1.3727
 AY5  C20  C   CH1   0  -0.309  -5.7943   0.8132   0.6359
 AY5  C4   C   CR16  0  -0.292  -2.0334   0.4289   0.2165
 AY5  C5   C   CR16  0  -0.298   2.1691  -2.4003   0.9465
 AY5  C6   C   CR16  0  -0.278  -4.1610  -0.9857   1.2643
 AY5  C17  C   CR6   0  -0.020   6.3497   0.3675  -0.1992
 AY5  C18  C   CR6   0   0.021   5.1193   0.9367   0.1174
 AY5  O22  O   OH1   0  -0.643   2.8472  -2.7505  -2.0611
 AY5  O23  O   OH1   0  -0.644  -5.9188   2.1673   0.9834
 AY5  P26  P   P     0   1.353  -6.4988   0.4693  -1.0242
 AY5  CL1  CL  CL    0  -0.099   7.8203   1.1290   0.2740
 AY5  CL2  CL  CL    0  -0.098   5.0402   2.4240   0.9844
 AY5  H1   H   HCR6  0   0.262   1.6338  -3.1318   2.8870
 AY5  H2   H   HCR6  0   0.259  -0.6482  -2.2244   2.8104
 AY5  H3   H   HCR6  0   0.259  -2.7384  -2.4999   1.7498
 AY5  H4   H   HCR6  0   0.253  -3.4395   1.9322  -0.2973
 AY5  H5   H   HCR6  0   0.267   5.2683  -2.3687  -1.8482
 AY5  H6   H   HCR6  0   0.288   7.3417  -1.2686  -1.1496
 AY5  H7   H   HCR6  0   0.258   0.1174  -0.6779  -1.1110
 AY5  H8   H   HCR6  0   0.279   2.9986   0.7622   0.0016
 AY5  H9   H   HCH1  0   0.277   2.1801  -0.8682  -2.0883
 AY5  H10  H   HCH1  0   0.303  -6.4147   0.2529   1.3415
 AY5  H11  H   HCR6  0   0.260  -1.2086   1.0065  -0.1817
 AY5  H12  H   HCR6  0   0.260   3.1817  -2.7830   1.0091
 AY5  H13  H   HCR6  0   0.261  -4.9871  -1.5493   1.6806
 AY5  H14  H   HOH1  0   0.455   3.1129  -3.4354  -1.4370
 AY5  H15  H   HOH1  0   0.461  -5.2723   2.6984   0.5077
 AY5  H16  H   HOH1  0   0.498  -8.5914   0.7853  -1.5777
 AY5  H17  H   HOH1  0   0.493  -6.0520   2.3842  -2.0454
 AY5  O21  O   O     0  -0.700  -6.3546  -0.9335  -1.4746
 AY5  O24  O   OH1   0  -0.744  -7.9924   1.0294  -0.8580
 AY5  O25  O   OH1   0  -0.749  -5.7491   1.4673  -2.0413

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
 AY5  CL2  C18  single    1.723  0.020  1.723
 AY5  CL1  C17  single    1.722  0.020  1.722
 AY5  C18  C17  aromatic  1.392  0.020  1.392
 AY5  C18  C11  aromatic  1.383  0.020  1.383
 AY5  C17  C9   aromatic  1.384  0.020  1.384
 AY5  C11  C16  aromatic  1.391  0.020  1.391
 AY5  C9   C8   aromatic  1.388  0.020  1.388
 AY5  O22  C19  single    1.405  0.020  1.405
 AY5  C16  C8   aromatic  1.388  0.020  1.388
 AY5  C16  C19  single    1.519  0.020  1.519
 AY5  C19  C15  single    1.515  0.020  1.515
 AY5  C15  C10  aromatic  1.387  0.020  1.387
 AY5  C15  C5   aromatic  1.393  0.020  1.393
 AY5  C10  C13  aromatic  1.396  0.020  1.396
 AY5  C5   C1   aromatic  1.386  0.020  1.386
 AY5  C4   C7   aromatic  1.385  0.020  1.385
 AY5  C4   C12  aromatic  1.395  0.020  1.395
 AY5  O23  C20  single    1.404  0.020  1.404
 AY5  C7   C14  aromatic  1.392  0.020  1.392
 AY5  C13  C12  single    1.476  0.020  1.476
 AY5  C13  C2   aromatic  1.394  0.020  1.394
 AY5  C12  C3   aromatic  1.395  0.020  1.395
 AY5  C14  C20  single    1.508  0.020  1.508
 AY5  C14  C6   aromatic  1.391  0.020  1.391
 AY5  O21  P26  double    1.480  0.020  1.480
 AY5  C1   C2   aromatic  1.388  0.020  1.388
 AY5  C3   C6   aromatic  1.385  0.020  1.385
 AY5  C20  P26  single    1.836  0.020  1.836
 AY5  P26  O24  single    1.604  0.020  1.604
 AY5  P26  O25  single    1.610  0.020  1.610
 AY5  C1   H1   single    0.930  0.020  1.080
 AY5  C2   H2   single    0.930  0.020  1.080
 AY5  C3   H3   single    0.930  0.020  1.080
 AY5  C7   H4   single    0.930  0.020  1.080
 AY5  C8   H5   single    0.930  0.020  1.080
 AY5  C9   H6   single    0.930  0.020  1.080
 AY5  C10  H7   single    0.930  0.020  1.080
 AY5  C11  H8   single    0.930  0.020  1.080
 AY5  C19  H9   single    0.970  0.020  1.090
 AY5  C20  H10  single    0.970  0.020  1.090
 AY5  C4   H11  single    0.930  0.020  1.080
 AY5  C5   H12  single    0.930  0.020  1.080
 AY5  C6   H13  single    0.930  0.020  1.080
 AY5  O22  H14  single    0.850  0.020  0.980
 AY5  O23  H15  single    0.850  0.020  0.980
 AY5  O24  H16  single    0.850  0.020  0.980
 AY5  O25  H17  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
 AY5  H1   C1   C5   119.93  3.000
 AY5  H1   C1   C2   119.70  3.000
 AY5  C5   C1   C2   120.37  3.000
 AY5  H2   C2   C13  120.01  3.000
 AY5  H2   C2   C1   119.48  3.000
 AY5  C13  C2   C1   120.49  3.000
 AY5  H3   C3   C6   119.15  3.000
 AY5  H3   C3   C12  120.03  3.000
 AY5  C6   C3   C12  120.81  3.000
 AY5  H4   C7   C4   117.99  3.000
 AY5  H4   C7   C14  121.38  3.000
 AY5  C4   C7   C14  120.64  3.000
 AY5  H5   C8   C16  120.73  3.000
 AY5  H5   C8   C9   118.67  3.000
 AY5  C16  C8   C9   120.60  3.000
 AY5  H6   C9   C17  119.62  3.000
 AY5  H6   C9   C8   120.11  3.000
 AY5  C17  C9   C8   120.27  3.000
 AY5  H7   C10  C15  119.04  3.000
 AY5  H7   C10  C13  119.55  3.000
 AY5  C15  C10  C13  121.41  3.000
 AY5  H8   C11  C18  119.05  3.000
 AY5  H8   C11  C16  120.25  3.000
 AY5  C18  C11  C16  120.70  3.000
 AY5  C4   C12  C13  120.77  3.000
 AY5  C13  C12  C3   121.14  3.000
 AY5  C4   C12  C3   118.09  3.000
 AY5  C12  C13  C10  120.52  3.000
 AY5  C12  C13  C2   121.00  3.000
 AY5  C10  C13  C2   118.47  3.000
 AY5  C6   C14  C20  119.93  3.000
 AY5  C6   C14  C7   118.48  3.000
 AY5  C20  C14  C7   121.58  3.000
 AY5  C5   C15  C19  120.34  3.000
 AY5  C5   C15  C10  119.25  3.000
 AY5  C19  C15  C10  120.37  3.000
 AY5  C19  C16  C11  118.94  3.000
 AY5  C19  C16  C8   122.18  3.000
 AY5  C11  C16  C8   118.87  3.000
 AY5  H9   C19  O22  105.39  3.000
 AY5  H9   C19  C16  107.34  3.000
 AY5  O22  C19  C16  112.83  3.000
 AY5  H9   C19  C15  108.05  3.000
 AY5  C16  C19  C15  111.13  3.000
 AY5  O22  C19  C15  111.73  3.000
 AY5  H10  C20  P26  105.65  3.000
 AY5  H10  C20  O23  106.51  3.000
 AY5  P26  C20  O23  111.75  3.000
 AY5  H10  C20  C14  108.35  3.000
 AY5  P26  C20  C14  108.88  3.000
 AY5  O23  C20  C14  115.20  3.000
 AY5  H11  C4   C12  119.97  3.000
 AY5  H11  C4   C7   118.97  3.000
 AY5  C12  C4   C7   121.06  3.000
 AY5  H12  C5   C15  120.55  3.000
 AY5  H12  C5   C1   119.44  3.000
 AY5  C15  C5   C1   120.00  3.000
 AY5  H13  C6   C14  119.81  3.000
 AY5  H13  C6   C3   119.27  3.000
 AY5  C14  C6   C3   120.92  3.000
 AY5  CL1  C17  C18  120.75  3.000
 AY5  C18  C17  C9   119.45  3.000
 AY5  CL1  C17  C9   119.80  3.000
 AY5  CL2  C18  C17  120.52  3.000
 AY5  C17  C18  C11  120.10  3.000
 AY5  CL2  C18  C11  119.38  3.000
 AY5  H14  O22  C19  109.33  3.000
 AY5  H15  O23  C20  110.51  3.000
 AY5  O25  P26  O24  106.42  3.000
 AY5  O25  P26  O21  110.48  3.000
 AY5  O24  P26  O21  116.94  3.000
 AY5  O25  P26  C20  106.05  3.000
 AY5  O24  P26  C20  101.44  3.000
 AY5  O21  P26  C20  114.53  3.000
 AY5  H16  O24  P26  114.29  3.000
 AY5  H17  O25  P26  116.43  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
 AY5  CONST_01  C10  C15  C5   C1     0.00  0.0  0
 AY5  CONST_02  C10  C13  C2   C1     0.00  0.0  0
 AY5  CONST_03  C12  C13  C2   C1   180.00  0.0  0
 AY5  CONST_04  C15  C10  C13  C2     0.00  0.0  0
 AY5  CONST_07  C15  C5   C1   C2     0.00  0.0  0
 AY5  CONST_08  C7   C4   C12  C3     0.00  0.0  0
 AY5  CONST_10  C7   C14  C6   C3     0.00  0.0  0
 AY5  CONST_11  C13  C12  C4   C7   180.00  0.0  0
 AY5  CONST_12  C18  C17  C9   C8     0.00  0.0  0
 AY5  CONST_13  C18  C11  C16  C8     0.00  0.0  0
 AY5  CONST_14  C11  C18  C17  C9     0.00  0.0  0
 AY5  CONST_15  C11  C16  C8   C9     0.00  0.0  0
 AY5  CONST_17  C14  C7   C4   C12    0.00  0.0  0
 AY5  CONST_18  C15  C10  C13  C12  180.00  0.0  0
 AY5  CONST_19  C14  C6   C3   C12    0.00  0.0  0
 AY5  CONST_20  C5   C15  C10  C13    0.00  0.0  0
 AY5  CONST_21  C6   C3   C12  C13  180.00  0.0  0
 AY5  CONST_22  C5   C1   C2   C13    0.00  0.0  0
 AY5  CONST_23  C17  C18  C11  C16    0.00  0.0  0
 AY5  CONST_24  C17  C9   C8   C16    0.00  0.0  0
 AY5  CONST_25  C6   C14  C7   C4     0.00  0.0  0
 AY5  CONST_26  C6   C3   C12  C4     0.00  0.0  0
 AY5  CONST_27  C19  C15  C5   C1   180.00  0.0  0
 AY5  CONST_28  C20  C14  C6   C3   180.00  0.0  0
 AY5  CONST_29  CL1  C17  C9   C8   180.00  0.0  0
 AY5  CONST_30  CL2  C18  C17  C9   180.00  0.0  0
 AY5  CONST_31  C19  C16  C8   C9   180.00  0.0  0
 AY5  CONST_32  CL1  C17  C18  C11  180.00  0.0  0
 AY5  CONST_33  C19  C15  C10  C13  180.00  0.0  0
 AY5  CONST_34  CL2  C18  C11  C16  180.00  0.0  0
 AY5  CONST_35  C18  C11  C16  C19  180.00  0.0  0
 AY5  CONST_36  C4   C7   C14  C20  180.00  0.0  0
 AY5  CONST_37  H7   C10  C13  C2   180.00  0.0  0
 AY5  CONST_38  H12  C5   C1   C2   180.00  0.0  0
 AY5  CONST_39  H11  C4   C12  C3   180.00  0.0  0
 AY5  CONST_40  H13  C6   C14  C7   180.00  0.0  0
 AY5  CONST_41  H8   C11  C16  C8   180.00  0.0  0
 AY5  CONST_42  H2   C2   C13  C10  180.00  0.0  0
 AY5  CONST_43  H5   C8   C16  C11  180.00  0.0  0
 AY5  CONST_44  H4   C7   C4   C12  180.00  0.0  0
 AY5  CONST_45  H3   C3   C12  C13    0.00  0.0  0
 AY5  CONST_46  H1   C1   C2   C13  180.00  0.0  0
 AY5  CONST_47  H6   C9   C8   C16  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
 AY5  chir_01  C19  O22  C16  C15  positiv
 AY5  chir_02  C20  O23  C14  P26  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
 AY5  plan-1  C1   0.020
 AY5  plan-1  C2   0.020
 AY5  plan-1  C10  0.020
 AY5  plan-1  C12  0.020
 AY5  plan-1  C13  0.020
 AY5  plan-1  C15  0.020
 AY5  plan-1  C19  0.020
 AY5  plan-1  C5   0.020
 AY5  plan-1  H1   0.020
 AY5  plan-1  H2   0.020
 AY5  plan-1  H7   0.020
 AY5  plan-1  H12  0.020
 AY5  plan-2  C3   0.020
 AY5  plan-2  C7   0.020
 AY5  plan-2  C12  0.020
 AY5  plan-2  C13  0.020
 AY5  plan-2  C14  0.020
 AY5  plan-2  C20  0.020
 AY5  plan-2  C4   0.020
 AY5  plan-2  C6   0.020
 AY5  plan-2  H3   0.020
 AY5  plan-2  H4   0.020
 AY5  plan-2  H11  0.020
 AY5  plan-2  H13  0.020
 AY5  plan-3  C8   0.020
 AY5  plan-3  C9   0.020
 AY5  plan-3  C11  0.020
 AY5  plan-3  C16  0.020
 AY5  plan-3  C19  0.020
 AY5  plan-3  C17  0.020
 AY5  plan-3  C18  0.020
 AY5  plan-3  CL1  0.020
 AY5  plan-3  CL2  0.020
 AY5  plan-3  H5   0.020
 AY5  plan-3  H6   0.020
 AY5  plan-3  H8   0.020

