# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:58:34 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](CO)N1[C@@H]([C@@H](O[C@@H](CC(O)=O)C1=O)c2cccc(Cl)c2)c3ccc(Cl)cc3
#
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
 1MY  1MY  '{(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid'  ligand  53  30  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1MY
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
 1MY  C20  C   CR16  0  -0.258   0.2825  -2.4532  -1.2391
 1MY  C19  C   CR6   0  -0.025  -0.3824  -3.6679  -1.2592
 1MY  CL2  CL  CL    0  -0.129  -0.3800  -4.6080  -2.7163
 1MY  C18  C   CR16  0  -0.224  -1.0410  -4.1483  -0.1388
 1MY  C17  C   CR16  0  -0.242  -1.0257  -3.3826   1.0179
 1MY  C16  C   CR16  0  -0.270  -0.3712  -2.1602   1.0547
 1MY  C10  C   CR6   0   0.067   0.2859  -1.6906  -0.0768
 1MY  C6   C   CH1   0   0.002   0.9566  -0.3467  -0.1101
 1MY  O1   O   O2    0  -0.478   1.3201   0.0290   1.1880
 1MY  C7   C   CH1   0  -0.111   2.0975   1.1992   1.2333
 1MY  C21  C   CH2   0  -0.599   3.5809   0.8586   1.1016
 1MY  C22  C   C     0   0.558   4.0199  -0.0832   2.1911
 1MY  O5   O   OH1   0  -0.588   4.9778  -0.9041   1.7831
 1MY  O4   O   O     0  -0.442   3.5836  -0.0777   3.3146
 1MY  C8   C   C     0   0.536   1.7398   2.2704   0.2035
 1MY  O2   O   O     0  -0.490   2.3634   3.3213   0.2450
 1MY  N1   N   NT    0  -0.469   0.7803   2.0006  -0.7040
 1MY  C1   C   CH1   0  -0.139   0.5341   2.9577  -1.7906
 1MY  C3   C   CH2   0  -0.430   1.1023   2.4498  -3.1182
 1MY  C4   C   CH3   0  -0.667   2.5964   2.1633  -3.0753
 1MY  C2   C   CH2   0  -0.166  -0.9217   3.3891  -1.9051
 1MY  O3   O   OH1   0  -0.661  -1.7009   2.4017  -2.5412
 1MY  C5   C   CH1   0  -0.205   0.0471   0.7424  -0.6987
 1MY  C9   C   CR6   0   0.193  -1.2715   0.8203   0.0338
 1MY  C11  C   CR16  0  -0.282  -2.3543   0.0874  -0.4410
 1MY  C12  C   CR16  0  -0.202  -3.5648   0.0711   0.2310
 1MY  C13  C   CR6   0  -0.055  -3.6940   0.8088   1.3975
 1MY  CL1  CL  CL    0  -0.133  -5.2052   0.8029   2.2486
 1MY  C14  C   CR16  0  -0.198  -2.6368   1.5559   1.8886
 1MY  C15  C   CR16  0  -0.306  -1.4306   1.5557   1.2017
 1MY  H1   H   HCR6  0   0.274   0.7968  -2.1019  -2.1256
 1MY  H2   H   HCR6  0   0.280  -1.5545  -5.0997  -0.1651
 1MY  H3   H   HCR6  0   0.268  -1.5369  -3.7460   1.8994
 1MY  H4   H   HCR6  0   0.261  -0.3848  -1.5751   1.9634
 1MY  H5   H   HCH1  0   0.259   1.8391  -0.4169  -0.7648
 1MY  H6   H   HCH1  0   0.303   1.9224   1.6449   2.2165
 1MY  H7   H   HCH2  0   0.282   3.8126   0.4412   0.1191
 1MY  H8   H   HCH2  0   0.313   4.1784   1.7689   1.1950
 1MY  H9   H   HOH1  0   0.482   5.2664  -1.4673   2.5173
 1MY  H10  H   HCH1  0   0.272   1.0800   3.8591  -1.5138
 1MY  H11  H   HCH2  0   0.232   0.5657   1.5586  -3.4515
 1MY  H12  H   HCH2  0   0.240   0.9033   3.2184  -3.8700
 1MY  H13  H   HCH3  0   0.226   3.1637   3.0386  -2.7571
 1MY  H14  H   HCH3  0   0.213   2.8366   1.3475  -2.3914
 1MY  H15  H   HCH3  0   0.240   2.9584   1.8706  -4.0607
 1MY  H16  H   HCH2  0   0.230  -1.3037   3.6331  -0.9086
 1MY  H17  H   HCH2  0   0.216  -0.9297   4.3198  -2.4876
 1MY  H18  H   HOH1  0   0.459  -2.6028   2.4648  -2.2177
 1MY  H19  H   HCH1  0   0.292  -0.1503   0.4704  -1.7374
 1MY  H20  H   HCR6  0   0.260  -2.2568  -0.4881  -1.3531
 1MY  H21  H   HCR6  0   0.277  -4.3957  -0.5041  -0.1537
 1MY  H22  H   HCR6  0   0.279  -2.7451   2.1364   2.7946
 1MY  H23  H   HCR6  0   0.256  -0.6242   2.1585   1.5979

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
 1MY  O4   C22  double    1.205  0.020  1.205
 1MY  O5   C22  single    1.326  0.020  1.326
 1MY  C22  C21  single    1.506  0.020  1.506
 1MY  CL2  C19  single    1.734  0.020  1.734
 1MY  C21  C7   single    1.528  0.020  1.528
 1MY  C19  C20  aromatic  1.385  0.020  1.385
 1MY  C19  C18  aromatic  1.386  0.020  1.386
 1MY  O1   C7   single    1.406  0.020  1.406
 1MY  O1   C6   single    1.399  0.020  1.399
 1MY  C20  C10  aromatic  1.390  0.020  1.390
 1MY  C7   C8   single    1.528  0.020  1.528
 1MY  C18  C17  aromatic  1.387  0.020  1.387
 1MY  C10  C6   single    1.502  0.020  1.502
 1MY  C10  C16  aromatic  1.390  0.020  1.390
 1MY  C17  C16  aromatic  1.387  0.020  1.387
 1MY  C6   C5   single    1.536  0.020  1.536
 1MY  C15  C14  aromatic  1.388  0.020  1.388
 1MY  C15  C9   aromatic  1.389  0.020  1.389
 1MY  C14  C13  aromatic  1.385  0.020  1.385
 1MY  C8   O2   double    1.223  0.020  1.223
 1MY  C8   N1   single    1.348  0.020  1.348
 1MY  C5   C9   single    1.510  0.020  1.510
 1MY  C5   N1   single    1.456  0.020  1.456
 1MY  C9   C11  aromatic  1.391  0.020  1.391
 1MY  C13  CL1  single    1.734  0.020  1.734
 1MY  C13  C12  aromatic  1.386  0.020  1.386
 1MY  N1   C1   single    1.469  0.020  1.469
 1MY  C11  C12  aromatic  1.385  0.020  1.385
 1MY  C4   C3   single    1.522  0.020  1.522
 1MY  C1   C3   single    1.531  0.020  1.531
 1MY  C1   C2   single    1.523  0.020  1.523
 1MY  O3   C2   single    1.410  0.020  1.410
 1MY  C20  H1   single    0.930  0.020  1.080
 1MY  C18  H2   single    0.930  0.020  1.080
 1MY  C17  H3   single    0.930  0.020  1.080
 1MY  C16  H4   single    0.930  0.020  1.080
 1MY  C6   H5   single    0.970  0.020  1.090
 1MY  C7   H6   single    0.970  0.020  1.090
 1MY  C21  H7   single    0.970  0.020  1.090
 1MY  C21  H8   single    0.970  0.020  1.090
 1MY  O5   H9   single    0.850  0.020  0.980
 1MY  C1   H10  single    0.970  0.020  1.090
 1MY  C3   H11  single    0.970  0.020  1.090
 1MY  C3   H12  single    0.970  0.020  1.090
 1MY  C4   H13  single    0.970  0.020  1.090
 1MY  C4   H14  single    0.970  0.020  1.090
 1MY  C4   H15  single    0.970  0.020  1.090
 1MY  C2   H16  single    0.970  0.020  1.090
 1MY  C2   H17  single    0.970  0.020  1.090
 1MY  O3   H18  single    0.850  0.020  0.980
 1MY  C5   H19  single    0.970  0.020  1.090
 1MY  C11  H20  single    0.930  0.020  1.080
 1MY  C12  H21  single    0.930  0.020  1.080
 1MY  C14  H22  single    0.930  0.020  1.080
 1MY  C15  H23  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
 1MY  H1   C20  C10  120.34  3.000
 1MY  H1   C20  C19  120.03  3.000
 1MY  C10  C20  C19  119.64  3.000
 1MY  C18  C19  CL2  119.48  3.000
 1MY  C18  C19  C20  121.37  3.000
 1MY  CL2  C19  C20  119.15  3.000
 1MY  H2   C18  C17  120.74  3.000
 1MY  H2   C18  C19  120.73  3.000
 1MY  C17  C18  C19  118.53  3.000
 1MY  H3   C17  C16  119.82  3.000
 1MY  H3   C17  C18  119.27  3.000
 1MY  C16  C17  C18  120.91  3.000
 1MY  H4   C16  C10  120.49  3.000
 1MY  H4   C16  C17  119.57  3.000
 1MY  C10  C16  C17  119.94  3.000
 1MY  C6   C10  C16  122.09  3.000
 1MY  C16  C10  C20  119.61  3.000
 1MY  C6   C10  C20  118.25  3.000
 1MY  H5   C6   C5   106.97  3.000
 1MY  H5   C6   O1   111.13  3.000
 1MY  C5   C6   O1   108.59  3.000
 1MY  H5   C6   C10  108.30  3.000
 1MY  C5   C6   C10  112.23  3.000
 1MY  O1   C6   C10  109.60  3.000
 1MY  C7   O1   C6   113.39  3.000
 1MY  H6   C7   C8   106.42  3.000
 1MY  H6   C7   C21  108.89  3.000
 1MY  C8   C7   C21  108.99  3.000
 1MY  H6   C7   O1   106.24  3.000
 1MY  C8   C7   O1   115.62  3.000
 1MY  C21  C7   O1   110.40  3.000
 1MY  H8   C21  H7   106.21  3.000
 1MY  H8   C21  C22  107.44  3.000
 1MY  H7   C21  C22  110.49  3.000
 1MY  H8   C21  C7   109.74  3.000
 1MY  H7   C21  C7   111.63  3.000
 1MY  C22  C21  C7   111.11  3.000
 1MY  O4   C22  O5   123.45  3.000
 1MY  O5   C22  C21  112.04  3.000
 1MY  O4   C22  C21  124.48  3.000
 1MY  H9   O5   C22  109.98  3.000
 1MY  N1   C8   O2   123.91  3.000
 1MY  N1   C8   C7   118.68  3.000
 1MY  O2   C8   C7   117.40  3.000
 1MY  C5   N1   C1   118.77  3.000
 1MY  C1   N1   C8   119.14  3.000
 1MY  C5   N1   C8   121.93  3.000
 1MY  H10  C1   C2   105.29  3.000
 1MY  H10  C1   C3   107.99  3.000
 1MY  C2   C1   C3   112.56  3.000
 1MY  H10  C1   N1   105.50  3.000
 1MY  C2   C1   N1   113.61  3.000
 1MY  C3   C1   N1   111.30  3.000
 1MY  H12  C3   H11  105.92  3.000
 1MY  H12  C3   C4   109.30  3.000
 1MY  H11  C3   C4   109.71  3.000
 1MY  H12  C3   C1   107.19  3.000
 1MY  H11  C3   C1   110.66  3.000
 1MY  C4   C3   C1   113.73  3.000
 1MY  H15  C4   H14  107.02  3.000
 1MY  H15  C4   H13  107.85  3.000
 1MY  H14  C4   H13  107.61  3.000
 1MY  H15  C4   C3   110.56  3.000
 1MY  H14  C4   C3   111.99  3.000
 1MY  H13  C4   C3   111.58  3.000
 1MY  H17  C2   H16  106.94  3.000
 1MY  H17  C2   O3   110.51  3.000
 1MY  H16  C2   O3   111.96  3.000
 1MY  H17  C2   C1   106.68  3.000
 1MY  H16  C2   C1   109.17  3.000
 1MY  O3   C2   C1   111.35  3.000
 1MY  H18  O3   C2   108.73  3.000
 1MY  H19  C5   C9   108.45  3.000
 1MY  H19  C5   N1   107.63  3.000
 1MY  C9   C5   N1   113.38  3.000
 1MY  H19  C5   C6   107.15  3.000
 1MY  N1   C5   C6   108.41  3.000
 1MY  C9   C5   C6   111.57  3.000
 1MY  C15  C9   C11  118.47  3.000
 1MY  C11  C9   C5   119.13  3.000
 1MY  C15  C9   C5   122.34  3.000
 1MY  H20  C11  C12  118.77  3.000
 1MY  H20  C11  C9   119.83  3.000
 1MY  C12  C11  C9   121.40  3.000
 1MY  H21  C12  C13  120.72  3.000
 1MY  H21  C12  C11  120.35  3.000
 1MY  C13  C12  C11  118.93  3.000
 1MY  C14  C13  CL1  119.54  3.000
 1MY  CL1  C13  C12  119.50  3.000
 1MY  C14  C13  C12  120.96  3.000
 1MY  H22  C14  C15  120.11  3.000
 1MY  H22  C14  C13  120.69  3.000
 1MY  C15  C14  C13  119.20  3.000
 1MY  H23  C15  C14  117.80  3.000
 1MY  H23  C15  C9   121.16  3.000
 1MY  C14  C15  C9   121.04  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
 1MY  CONST_01  C17  C18  C19  C20    0.00   0.0  0
 1MY  CONST_02  C17  C16  C10  C20    0.00   0.0  0
 1MY  CONST_03  C16  C10  C20  C19    0.00   0.0  0
 1MY  CONST_04  C16  C17  C18  C19    0.00   0.0  0
 1MY  CONST_05  C10  C20  C19  C18    0.00   0.0  0
 1MY  CONST_06  C10  C16  C17  C18    0.00   0.0  0
 1MY  CONST_07  C13  C14  C15  C9     0.00   0.0  0
 1MY  CONST_08  C13  C12  C11  C9     0.00   0.0  0
 1MY  CONST_09  C14  C15  C9   C11    0.00   0.0  0
 1MY  CONST_10  C14  C13  C12  C11    0.00   0.0  0
 1MY  CONST_11  C15  C14  C13  C12    0.00   0.0  0
 1MY  CONST_12  C15  C9   C11  C12    0.00   0.0  0
 1MY  CONST_13  C6   C10  C20  C19  180.00   0.0  0
 1MY  CONST_14  C6   C10  C16  C17  180.00   0.0  0
 1MY  CONST_15  C14  C15  C9   C5   180.00   0.0  0
 1MY  CONST_16  C12  C11  C9   C5   180.00   0.0  0
 1MY  CONST_17  C5   N1   C8   C7     0.00   0.0  0
 1MY  CONST_18  C10  C20  C19  CL2  180.00   0.0  0
 1MY  CONST_19  C17  C18  C19  CL2  180.00   0.0  0
 1MY  CONST_20  CL1  C13  C12  C11  180.00   0.0  0
 1MY  CONST_21  C15  C14  C13  CL1  180.00   0.0  0
 1MY  CONST_22  C1   N1   C8   C7   180.00   0.0  0
 1MY  CONST_23  C5   N1   C8   O2   180.00   0.0  0
 1MY  CONST_24  H2   C18  C19  C20  180.00   0.0  0
 1MY  CONST_25  H4   C16  C10  C20  180.00   0.0  0
 1MY  CONST_26  H3   C17  C18  C19  180.00   0.0  0
 1MY  CONST_27  H1   C20  C19  C18  180.00   0.0  0
 1MY  CONST_28  H23  C15  C9   C5     0.00   0.0  0
 1MY  CONST_29  H20  C11  C9   C5     0.00   0.0  0
 1MY  CONST_30  H22  C14  C15  C9   180.00   0.0  0
 1MY  CONST_31  H21  C12  C11  C9   180.00   0.0  0
 1MY  CONST_32  C1   N1   C8   O2     0.00   0.0  0
 1MY  CONST_33  H9   O5   C22  C21  180.00   0.0  0
 1MY  Var_01    O4   C22  C21  C7   -34.09  30.0  1
 1MY  Var_02    H13  C4   C3   C1   -56.14  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
 1MY  chir_01  C6  O1  C10  C5   negativ
 1MY  chir_02  C7  O1  C8   C21  positiv
 1MY  chir_03  C1  N1  C3   C2   negativ
 1MY  chir_04  C5  N1  C9   C6   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
 1MY  plan-1  C20  0.020
 1MY  plan-1  C19  0.020
 1MY  plan-1  CL2  0.020
 1MY  plan-1  C18  0.020
 1MY  plan-1  C17  0.020
 1MY  plan-1  C16  0.020
 1MY  plan-1  C10  0.020
 1MY  plan-1  C6   0.020
 1MY  plan-1  H1   0.020
 1MY  plan-1  H2   0.020
 1MY  plan-1  H3   0.020
 1MY  plan-1  H4   0.020
 1MY  plan-2  C5   0.020
 1MY  plan-2  C9   0.020
 1MY  plan-2  C11  0.020
 1MY  plan-2  C12  0.020
 1MY  plan-2  C13  0.020
 1MY  plan-2  CL1  0.020
 1MY  plan-2  C14  0.020
 1MY  plan-2  C15  0.020
 1MY  plan-2  H20  0.020
 1MY  plan-2  H21  0.020
 1MY  plan-2  H22  0.020
 1MY  plan-2  H23  0.020
 1MY  plan-3  C21  0.020
 1MY  plan-3  C22  0.020
 1MY  plan-3  O5   0.020
 1MY  plan-3  O4   0.020
 1MY  plan-3  H9   0.020
 1MY  plan-4  C7   0.020
 1MY  plan-4  C8   0.020
 1MY  plan-4  O2   0.020
 1MY  plan-4  N1   0.020
 1MY  plan-4  C1   0.020
 1MY  plan-4  C5   0.020

