# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:26:49 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: [(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-(cyclopropylmethyl)-2-oxopiperidin-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H]1C[C@@H]([C@H](N(CC2CC2)C1=O)c3ccc(Cl)cc3)c4cccc(Cl)c4
#
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
 13Q  13Q  '[(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-(cyclopropylmethyl)-2-oxopiperidin-3-yl]acetic acid'  ligand  51  29  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_13Q
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
 13Q  C1   C   CR16   0  -0.301   1.6152   1.6020   0.3615
 13Q  C2   C   CR16   0  -0.197   2.3483   2.6186  -0.2356
 13Q  C3   C   CR6    0  -0.053   1.8253   3.2582  -1.3459
 13Q  C4   C   CR16   0  -0.199   0.5898   2.8984  -1.8656
 13Q  C5   C   CR16   0  -0.290  -0.1232   1.8778  -1.2588
 13Q  C6   C   CR6    0   0.117   0.3784   1.2209  -0.1394
 13Q  C7   C   CH1    0  -0.074  -0.3724   0.0603   0.4721
 13Q  N1   N   NT     0  -0.485  -1.7712   0.4059   0.7242
 13Q  C8   C   C      0   0.569  -2.8345  -0.4193   0.5310
 13Q  O2   O   O      0  -0.613  -5.2472  -2.2907  -1.3494
 13Q  C9   C   CH1    0  -0.364  -2.6209  -1.7177  -0.2136
 13Q  C10  C   CH2    0  -0.429  -1.2033  -2.2433  -0.0496
 13Q  C11  C   CH1    0  -0.387  -0.2117  -1.1626  -0.4458
 13Q  C12  C   CR6    0   0.197   1.2221  -1.6254  -0.4430
 13Q  C13  C   CR16   0  -0.302   2.0255  -1.4421  -1.5629
 13Q  C14  C   CR16   0  -0.282   1.7689  -2.2295   0.6866
 13Q  C15  C   CR6    0  -0.022   3.0916  -2.6387   0.6747
 13Q  O3   O   OC    -1  -0.617  -4.9455  -0.5222  -2.6692
 13Q  C16  C   CR16   0  -0.233   3.8968  -2.4632  -0.4399
 13Q  C17  C   CR16   0  -0.243   3.3490  -1.8586  -1.5613
 13Q  C18  C   CH2    0  -0.325  -1.9928   1.5975   1.5400
 13Q  C19  C   CH1    0  -0.242  -1.9088   1.3273   3.0195
 13Q  C20  C   CH2    0  -0.492  -1.5987   2.4622   3.9458
 13Q  C21  C   CH2    0  -0.487  -0.5871   1.3787   3.7260
 13Q  C22  C   CH2    0  -0.571  -3.0236  -1.5240  -1.6832
 13Q  C23  C   C      0   0.416  -4.5445  -1.4260  -1.9100
 13Q  CL1  CL  CL     0  -0.132   2.7267   4.5346  -2.0989
 13Q  CL2  CL  CL     0  -0.133   3.7567  -3.3904   2.0911
 13Q  H1   H   HCR6   0   0.258   2.0235   1.0970   1.2288
 13Q  H2   H   HCR6   0   0.280   3.3119   2.9046   0.1633
 13Q  H3   H   HCR6   0   0.279   0.1886   3.4065  -2.7321
 13Q  H4   H   HCR6   0   0.263  -1.0898   1.6012  -1.6643
 13Q  H5   H   HCH1   0   0.263   0.0956  -0.1759   1.4361
 13Q  H6   H   HCH1   0   0.266  -3.3175  -2.4379   0.2196
 13Q  H8   H   HCH2   0   0.245  -1.0354  -2.5569   0.9855
 13Q  H7   H   HCH2   0   0.253  -1.0654  -3.1280  -0.6752
 13Q  H9   H   HCH1   0   0.279  -0.4498  -0.8479  -1.4664
 13Q  H10  H   HCR6   0   0.254   1.6136  -0.9661  -2.4441
 13Q  H11  H   HCR6   0   0.274   1.1668  -2.3805   1.5740
 13Q  H12  H   HCR6   0   0.278   4.9277  -2.7895  -0.4349
 13Q  H13  H   HCR6   0   0.267   3.9645  -1.7122  -2.4390
 13Q  H15  H   HCH2   0   0.252  -1.2496   2.3480   1.2652
 13Q  H14  H   HCH2   0   0.263  -2.9640   2.0167   1.2846
 13Q  H16  H   HCH1   0   0.259  -2.6181   0.5959   3.3912
 13Q  H18  H   HCH2   0   0.245  -1.3991   3.4336   3.5087
 13Q  H17  H   HCH2   0   0.253  -2.1159   2.5020   4.8956
 13Q  H20  H   HCH2   0   0.252  -0.4069   0.6708   4.5252
 13Q  H19  H   HCH2   0   0.239   0.2955   1.6296   3.1492
 13Q  H22  H   HCH2   0   0.215  -2.5226  -0.6546  -2.1152
 13Q  H21  H   HCH2   0   0.242  -2.6594  -2.3952  -2.2406
 13Q  O1   O   O      0  -0.503  -3.9548  -0.1033   0.9119

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
 13Q  CL1  C3   single    1.735  0.020  1.735
 13Q  C3   C4   aromatic  1.388  0.020  1.388
 13Q  C3   C2   aromatic  1.384  0.020  1.384
 13Q  C4   C5   aromatic  1.385  0.020  1.385
 13Q  C20  C21  single    1.499  0.020  1.499
 13Q  C20  C19  single    1.497  0.020  1.497
 13Q  C21  C19  single    1.500  0.020  1.500
 13Q  C2   C1   aromatic  1.388  0.020  1.388
 13Q  C5   C6   aromatic  1.391  0.020  1.391
 13Q  C1   C6   aromatic  1.388  0.020  1.388
 13Q  C19  C18  single    1.506  0.020  1.506
 13Q  C6   C7   single    1.511  0.020  1.511
 13Q  CL2  C15  single    1.736  0.020  1.736
 13Q  C18  N1   single    1.461  0.020  1.461
 13Q  C15  C14  aromatic  1.385  0.020  1.385
 13Q  C15  C16  aromatic  1.386  0.020  1.386
 13Q  C7   N1   single    1.463  0.020  1.463
 13Q  C7   C11  single    1.538  0.020  1.538
 13Q  N1   C8   single    1.360  0.020  1.360
 13Q  C14  C12  aromatic  1.393  0.020  1.393
 13Q  C16  C17  aromatic  1.387  0.020  1.387
 13Q  C12  C11  single    1.507  0.020  1.507
 13Q  C12  C13  aromatic  1.390  0.020  1.390
 13Q  C11  C10  single    1.519  0.020  1.519
 13Q  C17  C13  aromatic  1.387  0.020  1.387
 13Q  C8   O1   double    1.225  0.020  1.225
 13Q  C8   C9   single    1.512  0.020  1.512
 13Q  C10  C9   single    1.521  0.020  1.521
 13Q  C9   C22  single    1.536  0.020  1.536
 13Q  C22  C23  single    1.541  0.020  1.541
 13Q  C23  O3   deloc     1.247  0.020  1.247
 13Q  C23  O2   deloc     1.247  0.020  1.247
 13Q  C1   H1   single    0.930  0.020  1.080
 13Q  C2   H2   single    0.930  0.020  1.080
 13Q  C4   H3   single    0.930  0.020  1.080
 13Q  C5   H4   single    0.930  0.020  1.080
 13Q  C7   H5   single    0.970  0.020  1.090
 13Q  C9   H6   single    0.970  0.020  1.090
 13Q  C10  H8   single    0.970  0.020  1.090
 13Q  C10  H7   single    0.970  0.020  1.090
 13Q  C11  H9   single    0.970  0.020  1.090
 13Q  C13  H10  single    0.930  0.020  1.080
 13Q  C14  H11  single    0.930  0.020  1.080
 13Q  C16  H12  single    0.930  0.020  1.080
 13Q  C17  H13  single    0.930  0.020  1.080
 13Q  C18  H15  single    0.970  0.020  1.090
 13Q  C18  H14  single    0.970  0.020  1.090
 13Q  C19  H16  single    0.970  0.020  1.090
 13Q  C20  H18  single    0.970  0.020  1.090
 13Q  C20  H17  single    0.970  0.020  1.090
 13Q  C21  H20  single    0.970  0.020  1.090
 13Q  C21  H19  single    0.970  0.020  1.090
 13Q  C22  H22  single    0.970  0.020  1.090
 13Q  C22  H21  single    0.970  0.020  1.090

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
 13Q  H1   C1   C6   119.79  3.000
 13Q  H1   C1   C2   119.12  3.000
 13Q  C6   C1   C2   121.09  3.000
 13Q  H2   C2   C3   120.69  3.000
 13Q  H2   C2   C1   120.37  3.000
 13Q  C3   C2   C1   118.95  3.000
 13Q  CL1  C3   C4   119.40  3.000
 13Q  C4   C3   C2   121.13  3.000
 13Q  CL1  C3   C2   119.47  3.000
 13Q  H3   C4   C5   120.41  3.000
 13Q  H3   C4   C3   120.56  3.000
 13Q  C5   C4   C3   119.04  3.000
 13Q  H4   C5   C6   120.13  3.000
 13Q  H4   C5   C4   118.89  3.000
 13Q  C6   C5   C4   120.98  3.000
 13Q  C7   C6   C5   120.59  3.000
 13Q  C7   C6   C1   120.50  3.000
 13Q  C5   C6   C1   118.82  3.000
 13Q  H5   C7   C11  107.98  3.000
 13Q  H5   C7   N1   107.90  3.000
 13Q  C11  C7   N1   113.00  3.000
 13Q  H5   C7   C6   107.99  3.000
 13Q  C11  C7   C6   108.50  3.000
 13Q  N1   C7   C6   111.31  3.000
 13Q  C18  N1   C8   117.11  3.000
 13Q  C8   N1   C7   125.45  3.000
 13Q  C18  N1   C7   115.71  3.000
 13Q  C9   C8   O1   120.26  3.000
 13Q  C9   C8   N1   118.73  3.000
 13Q  O1   C8   N1   120.97  3.000
 13Q  H6   C9   C22  107.19  3.000
 13Q  H6   C9   C10  108.90  3.000
 13Q  C22  C9   C10  113.02  3.000
 13Q  H6   C9   C8   106.32  3.000
 13Q  C22  C9   C8   109.02  3.000
 13Q  C10  C9   C8   112.05  3.000
 13Q  H7   C10  H8   106.87  3.000
 13Q  H7   C10  C11  110.15  3.000
 13Q  H8   C10  C11  110.50  3.000
 13Q  H7   C10  C9   109.63  3.000
 13Q  H8   C10  C9   110.12  3.000
 13Q  C11  C10  C9   109.53  3.000
 13Q  H9   C11  C12  107.29  3.000
 13Q  H9   C11  C10  107.80  3.000
 13Q  C12  C11  C10  113.71  3.000
 13Q  H9   C11  C7   107.78  3.000
 13Q  C10  C11  C7   109.99  3.000
 13Q  C12  C11  C7   110.04  3.000
 13Q  C14  C12  C13  118.92  3.000
 13Q  C13  C12  C11  120.52  3.000
 13Q  C14  C12  C11  120.55  3.000
 13Q  H10  C13  C17  119.72  3.000
 13Q  H10  C13  C12  119.57  3.000
 13Q  C17  C13  C12  120.71  3.000
 13Q  H11  C14  C15  119.80  3.000
 13Q  H11  C14  C12  120.45  3.000
 13Q  C15  C14  C12  119.75  3.000
 13Q  CL2  C15  C16  119.23  3.000
 13Q  C16  C15  C14  121.63  3.000
 13Q  CL2  C15  C14  119.14  3.000
 13Q  H12  C16  C17  120.80  3.000
 13Q  H12  C16  C15  120.78  3.000
 13Q  C17  C16  C15  118.42  3.000
 13Q  H13  C17  C16  119.35  3.000
 13Q  H13  C17  C13  120.08  3.000
 13Q  C16  C17  C13  120.57  3.000
 13Q  H14  C18  H15  106.49  3.000
 13Q  H14  C18  C19  110.45  3.000
 13Q  H15  C18  C19  109.43  3.000
 13Q  H14  C18  N1   108.57  3.000
 13Q  H15  C18  N1   108.48  3.000
 13Q  C19  C18  N1   113.19  3.000
 13Q  H16  C19  C21  115.98  3.000
 13Q  H16  C19  C20  115.76  3.000
 13Q  C21  C19  C20   60.01  3.000
 13Q  H16  C19  C18  114.91  3.000
 13Q  C21  C19  C18  120.38  3.000
 13Q  C20  C19  C18  118.90  3.000
 13Q  H17  C20  H18  114.14  3.000
 13Q  H17  C20  C21  118.55  3.000
 13Q  H18  C20  C21  117.68  3.000
 13Q  H17  C20  C19  118.16  3.000
 13Q  H18  C20  C19  117.90  3.000
 13Q  C21  C20  C19   60.07  3.000
 13Q  H19  C21  H20  114.12  3.000
 13Q  H19  C21  C20  117.41  3.000
 13Q  H20  C21  C20  118.48  3.000
 13Q  H19  C21  C19  118.36  3.000
 13Q  H20  C21  C19  118.17  3.000
 13Q  C20  C21  C19   59.92  3.000
 13Q  H21  C22  H22  106.20  3.000
 13Q  H21  C22  C23  107.67  3.000
 13Q  H22  C22  C23  110.11  3.000
 13Q  H21  C22  C9   107.41  3.000
 13Q  H22  C22  C9   111.01  3.000
 13Q  C23  C22  C9   114.05  3.000
 13Q  C22  C23  O3   116.95  3.000
 13Q  O3   C23  O2   126.52  3.000
 13Q  C22  C23  O2   116.48  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
 13Q  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 13Q  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 13Q  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 13Q  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 13Q  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 13Q  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 13Q  CONST_07  C16  C15  C14  C12     0.00   0.0  0
 13Q  CONST_08  C16  C17  C13  C12     0.00   0.0  0
 13Q  CONST_09  C15  C14  C12  C13     0.00   0.0  0
 13Q  CONST_10  C15  C16  C17  C13     0.00   0.0  0
 13Q  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 13Q  CONST_12  C17  C13  C12  C14     0.00   0.0  0
 13Q  CONST_13  C7   C6   C1   C2    180.00   0.0  0
 13Q  CONST_14  C7   C6   C5   C4    180.00   0.0  0
 13Q  CONST_15  C15  C14  C12  C11   180.00   0.0  0
 13Q  CONST_16  C17  C13  C12  C11   180.00   0.0  0
 13Q  CONST_17  C9   C8   N1   C7      0.00   0.0  0
 13Q  CONST_18  CL1  C3   C2   C1    180.00   0.0  0
 13Q  CONST_19  CL1  C3   C4   C5    180.00   0.0  0
 13Q  CONST_20  CL2  C15  C14  C12   180.00   0.0  0
 13Q  CONST_21  CL2  C15  C16  C17   180.00   0.0  0
 13Q  CONST_22  O1   C8   N1   C7    180.00   0.0  0
 13Q  CONST_23  C18  N1   C8   C9    180.00   0.0  0
 13Q  CONST_24  H4   C5   C6   C1    180.00   0.0  0
 13Q  CONST_25  H3   C4   C3   C2    180.00   0.0  0
 13Q  CONST_26  H1   C1   C2   C3    180.00   0.0  0
 13Q  CONST_27  H2   C2   C3   C4    180.00   0.0  0
 13Q  CONST_28  H11  C14  C12  C11     0.00   0.0  0
 13Q  CONST_29  H10  C13  C12  C11     0.00   0.0  0
 13Q  CONST_30  H13  C17  C13  C12   180.00   0.0  0
 13Q  CONST_31  H12  C16  C17  C13   180.00   0.0  0
 13Q  CONST_32  C18  N1   C8   O1      0.00   0.0  0
 13Q  Var_01    C19  C18  N1   C7    -83.26  30.0  1
 13Q  Var_02    C20  C19  C18  N1    157.20  30.0  2
 13Q  Var_03    C21  C20  C19  C18  -110.39  30.0  1
 13Q  Var_04    H20  C21  C20  C19  -107.85  30.0  1
 13Q  Var_05    C9   C22  C23  O2    -47.57  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
 13Q  chir_01  C7   C6   N1   C11  negativ
 13Q  chir_02  C9   C22  C10  C8   negativ
 13Q  chir_03  C11  C7   C12  C10  negativ
 13Q  chir_04  C19  C20  C21  C18  both

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
 13Q  plan-1  C1   0.020
 13Q  plan-1  C2   0.020
 13Q  plan-1  C3   0.020
 13Q  plan-1  C4   0.020
 13Q  plan-1  C5   0.020
 13Q  plan-1  C6   0.020
 13Q  plan-1  C7   0.020
 13Q  plan-1  CL1  0.020
 13Q  plan-1  H1   0.020
 13Q  plan-1  H2   0.020
 13Q  plan-1  H3   0.020
 13Q  plan-1  H4   0.020
 13Q  plan-2  C7   0.020
 13Q  plan-2  N1   0.020
 13Q  plan-2  C8   0.020
 13Q  plan-2  C9   0.020
 13Q  plan-2  C18  0.020
 13Q  plan-2  O1   0.020
 13Q  plan-3  C11  0.020
 13Q  plan-3  C12  0.020
 13Q  plan-3  C13  0.020
 13Q  plan-3  C14  0.020
 13Q  plan-3  C15  0.020
 13Q  plan-3  C16  0.020
 13Q  plan-3  C17  0.020
 13Q  plan-3  CL2  0.020
 13Q  plan-3  H10  0.020
 13Q  plan-3  H11  0.020
 13Q  plan-3  H12  0.020
 13Q  plan-3  H13  0.020
 13Q  plan-4  O2   0.020
 13Q  plan-4  O3   0.020
 13Q  plan-4  C22  0.020
 13Q  plan-4  C23  0.020

