# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:21:09 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-phenyl-pyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@]1(CCN(C1=O)c2ccccc2)C(=O)NCc3cc(F)cc(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
 HZW  HZW  (3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-phenyl-pyrrolidine-3-carboxamide  ligand  41  25  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HZW
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
 HZW  C1   C   CR6   0   0.044  -3.0406   0.9358   0.2906
 HZW  C2   C   CH2   0  -0.299  -2.3302   2.2614   0.4741
 HZW  O5   O   O     0  -0.494   0.0182   1.3659   1.7347
 HZW  C7   C   C     0   0.604   1.8977   0.4112  -0.2347
 HZW  C9   C   CH2   0  -0.288   3.7430   1.7631   0.2589
 HZW  C10  C   CH2   0  -0.473   2.4931   2.5692   0.5897
 HZW  C11  C   CR6   0   0.359   4.0782  -0.6949  -0.0650
 HZW  C14  C   CR16  0  -0.335   5.4069  -0.5102  -0.4461
 HZW  C15  C   CR16  0  -0.284   6.2686  -1.5937  -0.5233
 HZW  C16  C   CR16  0  -0.249   5.8187  -2.8729  -0.2381
 HZW  C19  C   CR16  0  -0.266  -2.4308  -0.1691  -0.2882
 HZW  C20  C   CR6   0  -0.028  -3.1422  -1.3552  -0.4038
 HZW  C21  C   CR16  0  -0.411  -4.4460  -1.4781   0.0434
 HZW  C22  C   CR6   0   0.652  -5.0229  -0.3567   0.6103
 HZW  N3   N   NH1   0  -0.672  -0.9950   2.3121  -0.0502
 HZW  C4   C   C     0   0.566   0.0677   1.8421   0.6146
 HZW  C6   C   CT    0  -0.064   1.3858   1.8529  -0.1540
 HZW  N8   N   NT    0  -0.584   3.2255   0.4175   0.0364
 HZW  O13  O   OH1   0  -0.587   1.3008   2.3541  -1.4643
 HZW  C17  C   CR16  0  -0.252   4.4961  -3.0552   0.1375
 HZW  C18  C   CR16  0  -0.261   3.6278  -1.9804   0.2349
 HZW  C23  C   CR16  0  -0.448  -4.3537   0.8392   0.7441
 HZW  CL1  CL  CL    0  -0.082  -2.3765  -2.7254  -1.1257
 HZW  F25  F   F     0  -0.341  -6.2846  -0.4428   1.0440
 HZW  H1   H   HCH2  0   0.289  -2.9079   3.0458  -0.0146
 HZW  H2   H   HCH2  0   0.276  -2.3098   2.5087   1.5364
 HZW  H3   H   HCH2  0   0.205   4.2395   2.1409  -0.6379
 HZW  H4   H   HCH2  0   0.294   2.3119   2.5462   1.6624
 HZW  H5   H   HCR6  0   0.282   5.7863   0.4748  -0.6763
 HZW  H6   H   HCR6  0   0.240   7.2987  -1.4290  -0.8084
 HZW  H7   H   HCR6  0   0.264   6.4907  -3.7168  -0.3091
 HZW  H8   H   HCR6  0   0.279  -1.4193  -0.1173  -0.6649
 HZW  H9   H   HCR6  0   0.296  -4.9974  -2.4024  -0.0418
 HZW  H10  H   HNH1  0   0.392  -0.8570   2.7064  -0.9618
 HZW  H11  H   HOH1  0   0.375   0.8895   1.6950  -2.0331
 HZW  H12  H   HCR6  0   0.244   4.1297  -4.0451   0.3718
 HZW  H13  H   HCR6  0   0.296   2.6121  -2.1535   0.5534
 HZW  H14  H   HCR6  0   0.282  -4.8481   1.6880   1.1999
 HZW  H15  H   HCH2  0   0.298   2.5803   3.6095   0.2832
 HZW  H16  H   HCH2  0   0.269   4.4623   1.7612   1.0766
 HZW  O12  O   O     0  -0.390   1.2093  -0.5218  -0.5797

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
 HZW  C23  C1   aromatic  1.393  0.020  1.393
 HZW  C23  C22  aromatic  1.377  0.020  1.377
 HZW  F25  C22  single    1.337  0.020  1.337
 HZW  C2   C1   single    1.515  0.020  1.515
 HZW  C2   N3   single    1.435  0.020  1.435
 HZW  C1   C19  aromatic  1.388  0.020  1.388
 HZW  C22  C21  aromatic  1.383  0.020  1.383
 HZW  O5   C4   double    1.218  0.020  1.218
 HZW  C19  C20  aromatic  1.388  0.020  1.388
 HZW  C21  C20  aromatic  1.384  0.020  1.384
 HZW  C20  CL1  single    1.728  0.020  1.728
 HZW  C4   N3   single    1.339  0.020  1.339
 HZW  C4   C6   single    1.526  0.020  1.526
 HZW  O12  C7   double    1.210  0.020  1.210
 HZW  O13  C6   single    1.405  0.020  1.405
 HZW  C6   C7   single    1.532  0.020  1.532
 HZW  C6   C10  single    1.514  0.020  1.514
 HZW  C7   N8   single    1.355  0.020  1.355
 HZW  C10  C9   single    1.524  0.020  1.524
 HZW  N8   C11  single    1.405  0.020  1.405
 HZW  N8   C9   single    1.459  0.020  1.459
 HZW  C14  C11  aromatic  1.394  0.020  1.394
 HZW  C14  C15  aromatic  1.387  0.020  1.387
 HZW  C11  C18  aromatic  1.395  0.020  1.395
 HZW  C15  C16  aromatic  1.386  0.020  1.386
 HZW  C18  C17  aromatic  1.385  0.020  1.385
 HZW  C16  C17  aromatic  1.387  0.020  1.387
 HZW  C2   H1   single    0.970  0.020  1.090
 HZW  C2   H2   single    0.970  0.020  1.090
 HZW  C9   H3   single    0.970  0.020  1.090
 HZW  C10  H4   single    0.970  0.020  1.090
 HZW  C14  H5   single    0.930  0.020  1.080
 HZW  C15  H6   single    0.930  0.020  1.080
 HZW  C16  H7   single    0.930  0.020  1.080
 HZW  C19  H8   single    0.930  0.020  1.080
 HZW  C21  H9   single    0.930  0.020  1.080
 HZW  N3   H10  single    0.860  0.020  1.020
 HZW  O13  H11  single    0.850  0.020  0.980
 HZW  C17  H12  single    0.930  0.020  1.080
 HZW  C18  H13  single    0.930  0.020  1.080
 HZW  C23  H14  single    0.930  0.020  1.080
 HZW  C10  H15  single    0.970  0.020  1.090
 HZW  C9   H16  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
 HZW  C23  C1   C19  119.65  3.000
 HZW  C19  C1   C2   122.74  3.000
 HZW  C23  C1   C2   117.61  3.000
 HZW  H2   C2   H1   106.46  3.000
 HZW  H2   C2   N3   109.29  3.000
 HZW  H1   C2   N3   107.69  3.000
 HZW  H2   C2   C1   108.96  3.000
 HZW  H1   C2   C1   109.07  3.000
 HZW  N3   C2   C1   115.01  3.000
 HZW  O12  C7   N8   128.18  3.000
 HZW  N8   C7   C6   108.21  3.000
 HZW  O12  C7   C6   123.41  3.000
 HZW  H16  C9   H3   108.47  3.000
 HZW  H16  C9   N8   110.32  3.000
 HZW  H3   C9   N8   110.80  3.000
 HZW  H16  C9   C10  112.31  3.000
 HZW  H3   C9   C10  111.59  3.000
 HZW  N8   C9   C10  103.31  3.000
 HZW  H15  C10  H4   108.14  3.000
 HZW  H15  C10  C6   111.88  3.000
 HZW  H4   C10  C6   110.63  3.000
 HZW  H15  C10  C9   112.27  3.000
 HZW  H4   C10  C9   109.84  3.000
 HZW  C6   C10  C9   104.06  3.000
 HZW  C18  C11  N8   121.21  3.000
 HZW  C18  C11  C14  119.24  3.000
 HZW  N8   C11  C14  119.54  3.000
 HZW  H5   C14  C15  118.84  3.000
 HZW  H5   C14  C11  120.90  3.000
 HZW  C15  C14  C11  120.26  3.000
 HZW  H6   C15  C16  120.28  3.000
 HZW  H6   C15  C14  119.19  3.000
 HZW  C16  C15  C14  120.53  3.000
 HZW  H7   C16  C17  120.52  3.000
 HZW  H7   C16  C15  120.35  3.000
 HZW  C17  C16  C15  119.13  3.000
 HZW  H8   C19  C20  119.45  3.000
 HZW  H8   C19  C1   121.22  3.000
 HZW  C20  C19  C1   119.32  3.000
 HZW  CL1  C20  C21  118.82  3.000
 HZW  CL1  C20  C19  119.04  3.000
 HZW  C21  C20  C19  122.14  3.000
 HZW  H9   C21  C22  120.90  3.000
 HZW  H9   C21  C20  122.12  3.000
 HZW  C22  C21  C20  116.97  3.000
 HZW  F25  C22  C23  118.89  3.000
 HZW  F25  C22  C21  118.33  3.000
 HZW  C23  C22  C21  122.78  3.000
 HZW  H10  N3   C4   118.70  3.000
 HZW  H10  N3   C2   118.30  3.000
 HZW  C4   N3   C2   123.00  3.000
 HZW  C6   C4   N3   115.67  3.000
 HZW  C6   C4   O5   120.07  3.000
 HZW  N3   C4   O5   124.17  3.000
 HZW  O13  C6   C4   114.83  3.000
 HZW  O13  C6   C10  109.48  3.000
 HZW  C4   C6   C10  112.81  3.000
 HZW  C10  C6   C7   103.10  3.000
 HZW  O13  C6   C7   107.86  3.000
 HZW  C4   C6   C7   107.97  3.000
 HZW  C11  N8   C9   121.73  3.000
 HZW  C9   N8   C7   112.48  3.000
 HZW  C11  N8   C7   125.20  3.000
 HZW  H11  O13  C6   109.42  3.000
 HZW  H12  C17  C18  118.86  3.000
 HZW  H12  C17  C16  120.15  3.000
 HZW  C18  C17  C16  120.98  3.000
 HZW  H13  C18  C17  119.12  3.000
 HZW  H13  C18  C11  121.04  3.000
 HZW  C17  C18  C11  119.85  3.000
 HZW  H14  C23  C22  119.98  3.000
 HZW  H14  C23  C1   120.88  3.000
 HZW  C22  C23  C1   119.14  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
 HZW  CONST_01  C21  C22  C23  C1     0.00   0.0  0
 HZW  CONST_02  C21  C20  C19  C1     0.00   0.0  0
 HZW  CONST_03  C16  C15  C14  C11    0.00   0.0  0
 HZW  CONST_04  C16  C17  C18  C11    0.00   0.0  0
 HZW  CONST_05  C17  C18  C11  C14    0.00   0.0  0
 HZW  CONST_06  C17  C16  C15  C14    0.00   0.0  0
 HZW  CONST_07  C18  C11  C14  C15    0.00   0.0  0
 HZW  CONST_08  C18  C17  C16  C15    0.00   0.0  0
 HZW  CONST_09  C22  C23  C1   C19    0.00   0.0  0
 HZW  CONST_10  C22  C21  C20  C19    0.00   0.0  0
 HZW  CONST_11  C23  C1   C19  C20    0.00   0.0  0
 HZW  CONST_12  C23  C22  C21  C20    0.00   0.0  0
 HZW  CONST_13  N8   C11  C14  C15  180.00   0.0  0
 HZW  CONST_14  C17  C18  C11  N8   180.00   0.0  0
 HZW  CONST_15  C6   C7   N8   C9     0.00   0.0  0
 HZW  CONST_16  C6   C7   N8   C11  180.00   0.0  0
 HZW  CONST_17  F25  C22  C23  C1   180.00   0.0  0
 HZW  CONST_18  CL1  C20  C19  C1   180.00   0.0  0
 HZW  CONST_19  C22  C23  C1   C2   180.00   0.0  0
 HZW  CONST_20  C20  C19  C1   C2   180.00   0.0  0
 HZW  CONST_21  F25  C22  C21  C20  180.00   0.0  0
 HZW  CONST_22  CL1  C20  C21  C22  180.00   0.0  0
 HZW  CONST_23  O12  C7   N8   C9   180.00   0.0  0
 HZW  CONST_24  O12  C7   N8   C11    0.00   0.0  0
 HZW  CONST_25  H6   C15  C14  C11  180.00   0.0  0
 HZW  CONST_26  H12  C17  C18  C11  180.00   0.0  0
 HZW  CONST_27  H13  C18  C11  C14  180.00   0.0  0
 HZW  CONST_28  H7   C16  C15  C14  180.00   0.0  0
 HZW  CONST_29  H5   C14  C15  C16  180.00   0.0  0
 HZW  CONST_30  H14  C23  C1   C19  180.00   0.0  0
 HZW  CONST_31  H9   C21  C20  C19  180.00   0.0  0
 HZW  CONST_32  H8   C19  C20  C21  180.00   0.0  0
 HZW  CONST_33  C6   C4   N3   C2   180.00   0.0  0
 HZW  CONST_34  H10  N3   C4   C6     0.00   0.0  0
 HZW  CONST_35  O5   C4   N3   C2     0.00   0.0  0
 HZW  Var_01    C14  C11  N8   C7   146.85  30.0  2
 HZW  Var_02    C10  C9   N8   C7    19.83  30.0  1
 HZW  Var_03    N8   C9   C10  C6   -28.86  30.0  1
 HZW  Var_04    N3   C2   C1   C19    2.70  30.0  2
 HZW  Var_05    C4   N3   C2   C1   -82.05  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
 HZW  chir_01  C6  O13  C7  C10  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
 HZW  plan-1  C11  0.020
 HZW  plan-1  C14  0.020
 HZW  plan-1  C15  0.020
 HZW  plan-1  C16  0.020
 HZW  plan-1  N8   0.020
 HZW  plan-1  C17  0.020
 HZW  plan-1  C18  0.020
 HZW  plan-1  H5   0.020
 HZW  plan-1  H6   0.020
 HZW  plan-1  H7   0.020
 HZW  plan-1  H12  0.020
 HZW  plan-1  H13  0.020
 HZW  plan-2  C1   0.020
 HZW  plan-2  C2   0.020
 HZW  plan-2  C19  0.020
 HZW  plan-2  C20  0.020
 HZW  plan-2  C21  0.020
 HZW  plan-2  C22  0.020
 HZW  plan-2  C23  0.020
 HZW  plan-2  CL1  0.020
 HZW  plan-2  F25  0.020
 HZW  plan-2  H8   0.020
 HZW  plan-2  H9   0.020
 HZW  plan-2  H14  0.020
 HZW  plan-3  C2   0.020
 HZW  plan-3  O5   0.020
 HZW  plan-3  N3   0.020
 HZW  plan-3  C4   0.020
 HZW  plan-3  C6   0.020
 HZW  plan-3  H10  0.020
 HZW  plan-4  C7   0.020
 HZW  plan-4  C9   0.020
 HZW  plan-4  C11  0.020
 HZW  plan-4  C6   0.020
 HZW  plan-4  N8   0.020
 HZW  plan-4  O12  0.020

