# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 01:28:51 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (2R)-2-[4-(2,4-dichlorophenoxy)phenoxy]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Oc1ccc(Oc2ccc(Cl)cc2Cl)cc1)C(O)=O
#
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
 D1L  D1L  '(2R)-2-[4-(2,4-dichlorophenoxy)phenoxy]propanoic acid'  ligand  33  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D1L
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
 D1L  O1A   O   OH1   0  -0.590   0.4230   0.3584   7.0682
 D1L  C1    C   C     0   0.537  -0.0858  -0.4401   6.1426
 D1L  O1B   O   O     0  -0.423  -0.7763  -1.3950   6.3736
 D1L  C2    C   CH1   0  -0.106   0.3296   0.0197   4.7567
 D1L  C2A   C   CH3   0  -0.686   1.8428  -0.0529   4.5812
 D1L  O2    O   O2    0  -0.475  -0.3453  -0.8262   3.8545
 D1L  C3    C   CR6   0   0.397  -0.5406  -0.4335   2.5778
 D1L  C4    C   CR16  0  -0.346  -1.1548  -1.3719   1.7463
 D1L  C5    C   CR16  0  -0.282  -1.4219  -1.0708   0.4240
 D1L  C6    C   CR16  0  -0.374  -0.1940   0.8120   2.0616
 D1L  C7    C   CR16  0  -0.288  -0.4636   1.1110   0.7310
 D1L  C8    C   CR6   0   0.277  -1.0761   0.1753  -0.0794
 D1L  O8    O   O2    0  -0.499  -1.3850   0.4977  -1.3834
 D1L  C9    C   CR6   0   0.449  -0.5235   0.1531  -2.3637
 D1L  C10   C   CR16  0  -0.354   0.7233  -0.4208  -2.1505
 D1L  C11   C   CR16  0  -0.197   1.5477  -0.7336  -3.2211
 D1L  C12   C   CR6   0  -0.066   1.1242  -0.4710  -4.5116
 D1L  CL12  CL  CL    0  -0.122   2.1480  -0.8575  -5.8529
 D1L  C13   C   CR16  0  -0.167  -0.1160   0.1009  -4.7493
 D1L  C14   C   CR6   0  -0.142  -0.9298   0.4077  -3.6742
 D1L  CL14  CL  CL    0  -0.093  -2.4761   1.1202  -3.9491
 D1L  H1A   H   HOH1  0   0.490   0.1669   0.0546   7.9524
 D1L  H2    H   HCH1  0   0.279  -0.0079   1.0580   4.6492
 D1L  H2A1  H   HCH3  0   0.251   2.2111  -1.0595   4.7796
 D1L  H2A2  H   HCH3  0   0.258   2.1250   0.2190   3.5651
 D1L  H2A3  H   HCH3  0   0.256   2.3418   0.6403   5.2552
 D1L  H4    H   HCR6  0   0.275  -1.4293  -2.3396   2.1464
 D1L  H5    H   HCR6  0   0.281  -1.9058  -1.8040  -0.2090
 D1L  H6    H   HCR6  0   0.289   0.2860   1.5711   2.6638
 D1L  H7    H   HCR6  0   0.281  -0.1919   2.0821   0.3374
 D1L  H10   H   HCR6  0   0.299   1.0681  -0.6301  -1.1470
 D1L  H11   H   HCR6  0   0.291   2.5150  -1.1796  -3.0362
 D1L  H13   H   HCR6  0   0.303  -0.4507   0.3055  -5.7567

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
 D1L  O1A  C1    single    1.324  0.020  1.324
 D1L  O1A  H1A   single    0.850  0.020  0.980
 D1L  C1   O1B   double    1.201  0.020  1.201
 D1L  C1   C2    single    1.518  0.020  1.518
 D1L  C2   C2A   single    1.525  0.020  1.525
 D1L  C2   O2    single    1.409  0.020  1.409
 D1L  C2   H2    single    0.970  0.020  1.090
 D1L  C2A  H2A1  single    0.970  0.020  1.090
 D1L  C2A  H2A2  single    0.970  0.020  1.090
 D1L  C2A  H2A3  single    0.970  0.020  1.090
 D1L  O2   C3    single    1.350  0.020  1.350
 D1L  C3   C4    aromatic  1.396  0.020  1.396
 D1L  C3   C6    aromatic  1.392  0.020  1.392
 D1L  C4   C5    aromatic  1.382  0.020  1.382
 D1L  C4   H4    single    0.930  0.020  1.080
 D1L  C5   C8    aromatic  1.388  0.020  1.388
 D1L  C5   H5    single    0.930  0.020  1.080
 D1L  C6   C7    aromatic  1.390  0.020  1.390
 D1L  C6   H6    single    0.930  0.020  1.080
 D1L  C7   C8    aromatic  1.381  0.020  1.381
 D1L  C7   H7    single    0.930  0.020  1.080
 D1L  C8   O8    single    1.378  0.020  1.378
 D1L  O8   C9    single    1.350  0.020  1.350
 D1L  C9   C10   aromatic  1.389  0.020  1.389
 D1L  C9   C14   aromatic  1.395  0.020  1.395
 D1L  C10  C11   aromatic  1.387  0.020  1.387
 D1L  C10  H10   single    0.930  0.020  1.080
 D1L  C11  C12   aromatic  1.383  0.020  1.383
 D1L  C11  H11   single    0.930  0.020  1.080
 D1L  C12  CL12  single    1.731  0.020  1.731
 D1L  C12  C13   aromatic  1.386  0.020  1.386
 D1L  C13  C14   aromatic  1.383  0.020  1.383
 D1L  C13  H13   single    0.930  0.020  1.080
 D1L  C14  CL14  single    1.725  0.020  1.725

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
 D1L  H1A   O1A  C1    110.31  3.000
 D1L  C2    C1   O1B   125.02  3.000
 D1L  C2    C1   O1A   110.51  3.000
 D1L  O1B   C1   O1A   124.47  3.000
 D1L  H2    C2   O2    110.99  3.000
 D1L  H2    C2   C2A   109.82  3.000
 D1L  O2    C2   C2A   111.90  3.000
 D1L  H2    C2   C1    106.98  3.000
 D1L  O2    C2   C1    105.76  3.000
 D1L  C2A   C2   C1    111.23  3.000
 D1L  H2A3  C2A  H2A2  107.46  3.000
 D1L  H2A3  C2A  H2A1  108.70  3.000
 D1L  H2A2  C2A  H2A1  108.23  3.000
 D1L  H2A3  C2A  C2    110.69  3.000
 D1L  H2A2  C2A  C2    110.65  3.000
 D1L  H2A1  C2A  C2    110.99  3.000
 D1L  C3    O2   C2    120.01  3.000
 D1L  C6    C3   C4    119.34  3.000
 D1L  C6    C3   O2    125.10  3.000
 D1L  C4    C3   O2    115.55  3.000
 D1L  H4    C4   C5    119.95  3.000
 D1L  H4    C4   C3    119.49  3.000
 D1L  C5    C4   C3    120.56  3.000
 D1L  H5    C5   C8    120.49  3.000
 D1L  H5    C5   C4    119.88  3.000
 D1L  C8    C5   C4    119.63  3.000
 D1L  H6    C6   C7    117.92  3.000
 D1L  H6    C6   C3    122.15  3.000
 D1L  C7    C6   C3    119.94  3.000
 D1L  H7    C7   C8    120.38  3.000
 D1L  H7    C7   C6    119.49  3.000
 D1L  C8    C7   C6    120.13  3.000
 D1L  O8    C8   C7    119.74  3.000
 D1L  O8    C8   C5    119.83  3.000
 D1L  C7    C8   C5    120.40  3.000
 D1L  C9    O8   C8    118.97  3.000
 D1L  C14   C9   C10   118.74  3.000
 D1L  C14   C9   O8    116.72  3.000
 D1L  C10   C9   O8    124.54  3.000
 D1L  H10   C10  C11   118.89  3.000
 D1L  H10   C10  C9    120.57  3.000
 D1L  C11   C10  C9    120.55  3.000
 D1L  H11   C11  C12   120.79  3.000
 D1L  H11   C11  C10   119.52  3.000
 D1L  C12   C11  C10   119.69  3.000
 D1L  C13   C12  CL12  119.23  3.000
 D1L  C13   C12  C11   120.81  3.000
 D1L  CL12  C12  C11   119.96  3.000
 D1L  H13   C13  C14   120.02  3.000
 D1L  H13   C13  C12   120.99  3.000
 D1L  C14   C13  C12   118.99  3.000
 D1L  CL14  C14  C13   119.69  3.000
 D1L  CL14  C14  C9    119.09  3.000
 D1L  C13   C14  C9    121.22  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
 D1L  CONST_01  C8    C5   C4   C3      0.00   0.0  0
 D1L  CONST_02  C8    C7   C6   C3      0.00   0.0  0
 D1L  CONST_03  C7    C6   C3   C4      0.00   0.0  0
 D1L  CONST_04  C7    C8   C5   C4      0.00   0.0  0
 D1L  CONST_05  C6    C3   C4   C5      0.00   0.0  0
 D1L  CONST_06  C6    C7   C8   C5      0.00   0.0  0
 D1L  CONST_07  C12   C11  C10  C9      0.00   0.0  0
 D1L  CONST_08  C12   C13  C14  C9      0.00   0.0  0
 D1L  CONST_09  C13   C14  C9   C10     0.00   0.0  0
 D1L  CONST_10  C13   C12  C11  C10     0.00   0.0  0
 D1L  CONST_11  C14   C9   C10  C11     0.00   0.0  0
 D1L  CONST_12  C14   C13  C12  C11     0.00   0.0  0
 D1L  CONST_13  C5    C4   C3   O2    180.00   0.0  0
 D1L  CONST_14  C7    C6   C3   O2    180.00   0.0  0
 D1L  CONST_15  O8    C8   C5   C4    180.00   0.0  0
 D1L  CONST_16  O8    C8   C7   C6    180.00   0.0  0
 D1L  CONST_17  C11   C10  C9   O8    180.00   0.0  0
 D1L  CONST_18  C13   C14  C9   O8    180.00   0.0  0
 D1L  CONST_19  CL14  C14  C9   C10   180.00   0.0  0
 D1L  CONST_20  CL12  C12  C11  C10   180.00   0.0  0
 D1L  CONST_21  CL14  C14  C13  C12   180.00   0.0  0
 D1L  CONST_22  C14   C13  C12  CL12  180.00   0.0  0
 D1L  CONST_23  H5    C5   C4   C3    180.00   0.0  0
 D1L  CONST_24  H7    C7   C6   C3    180.00   0.0  0
 D1L  CONST_25  H6    C6   C3   C4    180.00   0.0  0
 D1L  CONST_26  H4    C4   C3   C6    180.00   0.0  0
 D1L  CONST_27  H11   C11  C10  C9    180.00   0.0  0
 D1L  CONST_28  H13   C13  C14  C9    180.00   0.0  0
 D1L  CONST_29  H10   C10  C11  C12   180.00   0.0  0
 D1L  CONST_30  H1A   O1A  C1   O1B     0.00   0.0  0
 D1L  Var_01    C10   C9   O8   C8     -5.31  30.0  2
 D1L  Var_02    C4    C3   O2   C2    176.68  30.0  2

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
 D1L  chir_01  C2  C1  C2A  O2  negativ

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
 D1L  plan-1  O2    0.020
 D1L  plan-1  C3    0.020
 D1L  plan-1  C4    0.020
 D1L  plan-1  C5    0.020
 D1L  plan-1  C6    0.020
 D1L  plan-1  C7    0.020
 D1L  plan-1  C8    0.020
 D1L  plan-1  O8    0.020
 D1L  plan-1  H4    0.020
 D1L  plan-1  H5    0.020
 D1L  plan-1  H6    0.020
 D1L  plan-1  H7    0.020
 D1L  plan-2  O8    0.020
 D1L  plan-2  C9    0.020
 D1L  plan-2  C10   0.020
 D1L  plan-2  C11   0.020
 D1L  plan-2  C12   0.020
 D1L  plan-2  CL12  0.020
 D1L  plan-2  C13   0.020
 D1L  plan-2  C14   0.020
 D1L  plan-2  CL14  0.020
 D1L  plan-2  H10   0.020
 D1L  plan-2  H11   0.020
 D1L  plan-2  H13   0.020
 D1L  plan-3  O1A   0.020
 D1L  plan-3  C1    0.020
 D1L  plan-3  O1B   0.020
 D1L  plan-3  C2    0.020
 D1L  plan-3  H1A   0.020

