# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 03:35:45 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  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_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  -0.226   1.0313  -2.9219   1.3847
 AY5  C2   C   CR16   0  -0.328  -0.2132  -2.3108   1.3270
 AY5  C3   C   CR16   0  -0.309  -2.5319  -0.4055   1.4934
 AY5  C7   C   CR16   0  -0.314  -3.5753   0.3989  -0.9332
 AY5  C8   C   CR16   0  -0.325   5.3874  -1.3797  -1.0588
 AY5  C9   C   CR16   0  -0.198   6.5532  -1.0171  -0.3989
 AY5  C10  C   CR16   0  -0.403   0.5532  -0.9432  -0.4824
 AY5  C11  C   CR16   0  -0.234   4.1472   0.1667   0.2817
 AY5  C12  C   CR6    0   0.063  -1.7906  -0.6463   0.3323
 AY5  C13  C   CR6    0   0.118  -0.4732  -1.3067   0.3936
 AY5  C14  C   CR6    0   0.138  -4.3139   0.6374   0.2225
 AY5  C15  C   CR6    0   0.120   1.8002  -1.5493  -0.4326
 AY5  C16  C   CR6    0   0.061   4.1733  -0.7988  -0.7201
 AY5  C19  C   CH1    0  -0.060   2.8766  -1.1583  -1.4237
 AY5  C20  C   CH1    0  -0.329  -5.6573   1.2904   0.1944
 AY5  C4   C   CR16   0  -0.300  -2.3393  -0.2305  -0.8800
 AY5  C5   C   CR16   0  -0.304   2.0398  -2.5444   0.5122
 AY5  C6   C   CR16   0  -0.282  -3.7642   0.2179   1.4353
 AY5  C17  C   CR6    0  -0.020   6.5206  -0.0576   0.5980
 AY5  C18  C   CR6    0   0.021   5.3085   0.5392   0.9340
 AY5  O22  O   OH1    0  -0.644   3.0474  -2.1422  -2.4132
 AY5  O23  O   OH1    0  -0.713  -5.8818   2.0198  -0.9931
 AY5  P26  P   P      0   1.156  -7.0838   0.0195   0.3020
 AY5  CL1  CL  CL     0  -0.100   7.9742   0.3844   1.4099
 AY5  CL2  CL  CL     0  -0.098   5.2379   1.7435   2.1651
 AY5  H1   H   HCR6   0   0.258   1.2111  -3.6996   2.1155
 AY5  H2   H   HCR6   0   0.253  -0.9930  -2.6297   2.0072
 AY5  H3   H   HCR6   0   0.242  -2.1289  -0.6888   2.4585
 AY5  H4   H   HCR6   0   0.234  -3.9670   0.7089  -1.8929
 AY5  H5   H   HCR6   0   0.267   5.4445  -2.1231  -1.8414
 AY5  H6   H   HCR6   0   0.288   7.4930  -1.4827  -0.6630
 AY5  H7   H   HCR6   0   0.252   0.3866  -0.1511  -1.2038
 AY5  H8   H   HCR6   0   0.279   3.2120   0.6347   0.5636
 AY5  H9   H   HCH1   0   0.275   2.5380  -0.2636  -1.9561
 AY5  H10  H   HCH1   0   0.195  -5.7294   1.9615   1.0612
 AY5  H11  H   HCR6   0   0.240  -1.8037  -0.4131  -1.8045
 AY5  H12  H   HCR6   0   0.256   3.0127  -3.0183   0.5817
 AY5  H13  H   HCR6   0   0.231  -4.3036   0.4017   2.3573
 AY5  H14  H   HOH1   0   0.454   3.1507  -3.0025  -1.9907
 AY5  H15  H   HOH1   0   0.426  -6.5447   1.4385  -1.4454
 AY5  O21  O   O      0  -0.863  -6.5068  -1.3204   0.7386
 AY5  O24  O   OP    -1  -0.888  -8.1109   0.6168   1.2623
 AY5  O25  O   OP    -1  -0.890  -7.5221   0.0731  -1.1858

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    1.724  0.020  1.724
 AY5  CL1  C17  single    1.723  0.020  1.723
 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  1.392  0.020  1.392
 AY5  C9   C8   aromatic  1.388  0.020  1.388
 AY5  O22  C19  single    1.406  0.020  1.406
 AY5  C16  C8   aromatic  1.388  0.020  1.388
 AY5  C16  C19  single    1.518  0.020  1.518
 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  1.397  0.020  1.397
 AY5  C5   C1   aromatic  1.386  0.020  1.386
 AY5  C4   C7   aromatic  1.388  0.020  1.388
 AY5  C4   C12  aromatic  1.394  0.020  1.394
 AY5  O23  C20  single    1.412  0.020  1.412
 AY5  C7   C14  aromatic  1.392  0.020  1.392
 AY5  C13  C12  single    1.475  0.020  1.475
 AY5  C13  C2   aromatic  1.395  0.020  1.395
 AY5  C12  C3   aromatic  1.398  0.020  1.398
 AY5  C14  C20  single    1.494  0.020  1.494
 AY5  C14  C6   aromatic  1.396  0.020  1.396
 AY5  O21  P26  deloc     1.523  0.020  1.523
 AY5  C1   C2   aromatic  1.388  0.020  1.388
 AY5  C3   C6   aromatic  1.382  0.020  1.382
 AY5  C20  P26  single    1.914  0.020  1.914
 AY5  P26  O24  deloc     1.528  0.020  1.528
 AY5  P26  O25  deloc     1.552  0.020  1.552
 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

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   120.00  3.000
 AY5  H1   C1   C2   119.57  3.000
 AY5  C5   C1   C2   120.43  3.000
 AY5  H2   C2   C13  119.87  3.000
 AY5  H2   C2   C1   119.34  3.000
 AY5  C13  C2   C1   120.79  3.000
 AY5  H3   C3   C6   119.15  3.000
 AY5  H3   C3   C12  119.82  3.000
 AY5  C6   C3   C12  121.02  3.000
 AY5  H4   C7   C4   119.09  3.000
 AY5  H4   C7   C14  119.69  3.000
 AY5  C4   C7   C14  121.22  3.000
 AY5  H5   C8   C16  120.72  3.000
 AY5  H5   C8   C9   118.66  3.000
 AY5  C16  C8   C9   120.63  3.000
 AY5  H6   C9   C17  119.65  3.000
 AY5  H6   C9   C8   120.09  3.000
 AY5  C17  C9   C8   120.25  3.000
 AY5  H7   C10  C15  118.76  3.000
 AY5  H7   C10  C13  119.62  3.000
 AY5  C15  C10  C13  121.60  3.000
 AY5  H8   C11  C18  119.07  3.000
 AY5  H8   C11  C16  120.22  3.000
 AY5  C18  C11  C16  120.71  3.000
 AY5  C4   C12  C13  121.41  3.000
 AY5  C13  C12  C3   121.07  3.000
 AY5  C4   C12  C3   117.52  3.000
 AY5  C12  C13  C10  120.90  3.000
 AY5  C12  C13  C2   121.09  3.000
 AY5  C10  C13  C2   118.01  3.000
 AY5  C6   C14  C20  120.11  3.000
 AY5  C6   C14  C7   117.44  3.000
 AY5  C20  C14  C7   122.43  3.000
 AY5  C5   C15  C19  120.40  3.000
 AY5  C5   C15  C10  119.41  3.000
 AY5  C19  C15  C10  120.17  3.000
 AY5  C19  C16  C11  118.80  3.000
 AY5  C19  C16  C8   122.34  3.000
 AY5  C11  C16  C8   118.85  3.000
 AY5  H9   C19  O22  105.50  3.000
 AY5  H9   C19  C16  107.22  3.000
 AY5  O22  C19  C16  112.84  3.000
 AY5  H9   C19  C15  108.02  3.000
 AY5  C16  C19  C15  111.39  3.000
 AY5  O22  C19  C15  111.49  3.000
 AY5  H10  C20  P26  108.20  3.000
 AY5  H10  C20  O23  109.73  3.000
 AY5  P26  C20  O23  105.78  3.000
 AY5  H10  C20  C14  108.13  3.000
 AY5  P26  C20  C14  112.27  3.000
 AY5  O23  C20  C14  112.62  3.000
 AY5  H11  C4   C12  119.80  3.000
 AY5  H11  C4   C7   118.93  3.000
 AY5  C12  C4   C7   121.26  3.000
 AY5  H12  C5   C15  120.66  3.000
 AY5  H12  C5   C1   119.57  3.000
 AY5  C15  C5   C1   119.76  3.000
 AY5  H13  C6   C14  119.48  3.000
 AY5  H13  C6   C3   118.97  3.000
 AY5  C14  C6   C3   121.54  3.000
 AY5  CL1  C17  C18  120.72  3.000
 AY5  C18  C17  C9   119.44  3.000
 AY5  CL1  C17  C9   119.83  3.000
 AY5  CL2  C18  C17  120.50  3.000
 AY5  C17  C18  C11  120.11  3.000
 AY5  CL2  C18  C11  119.38  3.000
 AY5  H14  O22  C19  109.22  3.000
 AY5  H15  O23  C20  100.79  3.000
 AY5  O25  P26  O24  113.53  3.000
 AY5  O25  P26  O21  114.34  3.000
 AY5  O24  P26  O21  114.75  3.000
 AY5  O25  P26  C20   97.68  3.000
 AY5  O24  P26  C20  106.07  3.000
 AY5  O21  P26  C20  108.55  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

