# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:33:45 2021
#   Inital geometry file: a 74 line input string
#   Ligand name: (2R,5S)-5-(4-chlorophenyl)oxolane-2-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NNC(=O)[C@@H]1CC[C@@H](O1)c2ccc(Cl)cc2
#
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
 S4Y  S4Y  (2R,5S)-5-(4-chlorophenyl)oxolane-2-carbohydrazide  ligand  29  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S4Y
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
 S4Y  C10   C   CR16  0  -0.324   -8.8888  80.5659  143.8629
 S4Y  C15   C   CR16  0  -0.320   -8.9456  82.9596  143.8422
 S4Y  C03   C   C     0   0.506  -12.1695  78.7009  145.5511
 S4Y  C05   C   CH1   0  -0.056  -12.2354  80.1771  145.9322
 S4Y  C06   C   CH2   0  -0.511  -13.0995  80.9723  144.9389
 S4Y  C07   C   CH2   0  -0.480  -12.0575  81.4880  143.9573
 S4Y  C08   C   CH1   0   0.015  -10.8741  81.7525  144.8820
 S4Y  C09   C   CR6   0   0.110   -9.5377  81.7523  144.1952
 S4Y  C11   C   CR16  0  -0.197   -7.6778  80.5849  143.1882
 S4Y  C12   C   CR6   0  -0.055   -7.1125  81.8029  142.8406
 S4Y  C14   C   CR16  0  -0.197   -7.7370  82.9966  143.1610
 S4Y  N01   N   NH2   0  -0.639  -14.3402  78.4991  146.5328
 S4Y  N02   N   NH1   0  -0.496  -13.2404  77.9602  145.8884
 S4Y  O04   O   O     0  -0.480  -11.2194  78.2126  144.9592
 S4Y  O16   O   O2    0  -0.499  -10.9398  80.7330  145.8659
 S4Y  CL13  CL  CL    0  -0.135   -5.5958  81.8312  141.9982
 S4Y  H101  H   HCR6  0   0.279   -9.3323  79.6159  144.1295
 S4Y  H151  H   HCR6  0   0.261   -9.4292  83.8939  144.1015
 S4Y  H051  H   HCH1  0   0.263  -12.6201  80.2733  146.9496
 S4Y  H062  H   HCH2  0   0.262  -13.8761  80.3749  144.4646
 S4Y  H061  H   HCH2  0   0.259  -13.5887  81.8005  145.4542
 S4Y  H072  H   HCH2  0   0.248  -11.8080  80.7271  143.2138
 S4Y  H071  H   HCH2  0   0.260  -12.3719  82.3868  143.4283
 S4Y  H081  H   HCH1  0   0.229  -11.0149  82.7323  145.3610
 S4Y  H111  H   HCR6  0   0.276   -7.1798  79.6578  142.9379
 S4Y  H141  H   HCR6  0   0.278   -7.2883  83.9443  142.8958
 S4Y  H012  H   HNH2  0   0.375  -15.1548  78.4183  145.9377
 S4Y  H011  H   HNH2  0   0.378  -14.5215  77.9755  147.3789
 S4Y  H021  H   HNH1  0   0.390  -13.2470  76.9867  145.6111

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
 S4Y  N02   N01   single    1.384  0.020  1.384
 S4Y  C03   N02   single    1.345  0.020  1.345
 S4Y  O04   C03   double    1.221  0.020  1.221
 S4Y  C05   C03   single    1.526  0.020  1.526
 S4Y  C06   C05   single    1.538  0.020  1.538
 S4Y  C07   C06   single    1.522  0.020  1.522
 S4Y  C08   C07   single    1.525  0.020  1.525
 S4Y  C10   C09   aromatic  1.393  0.020  1.393
 S4Y  C11   C10   aromatic  1.386  0.020  1.386
 S4Y  C12   C11   aromatic  1.387  0.020  1.387
 S4Y  CL13  C12   single    1.735  0.020  1.735
 S4Y  C14   C12   aromatic  1.385  0.020  1.385
 S4Y  C15   C14   aromatic  1.388  0.020  1.388
 S4Y  C09   C08   single    1.503  0.020  1.503
 S4Y  O16   C08   single    1.418  0.020  1.418
 S4Y  C05   O16   single    1.411  0.020  1.411
 S4Y  C09   C15   aromatic  1.390  0.020  1.390
 S4Y  C10   H101  single    0.930  0.020  1.080
 S4Y  C15   H151  single    0.930  0.020  1.080
 S4Y  C05   H051  single    0.970  0.020  1.090
 S4Y  C06   H062  single    0.970  0.020  1.090
 S4Y  C06   H061  single    0.970  0.020  1.090
 S4Y  C07   H072  single    0.970  0.020  1.090
 S4Y  C07   H071  single    0.970  0.020  1.090
 S4Y  C08   H081  single    0.970  0.020  1.090
 S4Y  C11   H111  single    0.930  0.020  1.080
 S4Y  C14   H141  single    0.930  0.020  1.080
 S4Y  N01   H012  single    0.890  0.020  1.040
 S4Y  N01   H011  single    0.890  0.020  1.040
 S4Y  N02   H021  single    0.860  0.020  1.020

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
 S4Y  H101  C10  C11   119.34  3.000
 S4Y  H101  C10  C09   119.89  3.000
 S4Y  C11   C10  C09   120.77  3.000
 S4Y  H151  C15  C14   118.89  3.000
 S4Y  H151  C15  C09   119.87  3.000
 S4Y  C14   C15  C09   121.25  3.000
 S4Y  O04   C03  N02   121.39  3.000
 S4Y  O04   C03  C05   122.78  3.000
 S4Y  N02   C03  C05   115.83  3.000
 S4Y  H051  C05  O16   109.42  3.000
 S4Y  H051  C05  C06   110.99  3.000
 S4Y  O16   C05  C06   106.37  3.000
 S4Y  H051  C05  C03   109.46  3.000
 S4Y  O16   C05  C03   109.25  3.000
 S4Y  C06   C05  C03   111.29  3.000
 S4Y  H061  C06  H062  107.61  3.000
 S4Y  H061  C06  C07   110.76  3.000
 S4Y  H062  C06  C07   113.17  3.000
 S4Y  H061  C06  C05   109.83  3.000
 S4Y  H062  C06  C05   113.48  3.000
 S4Y  C07   C06  C05   101.95  3.000
 S4Y  H071  C07  H072  108.06  3.000
 S4Y  H071  C07  C08   112.04  3.000
 S4Y  H072  C07  C08   110.86  3.000
 S4Y  H071  C07  C06   113.29  3.000
 S4Y  H072  C07  C06   111.06  3.000
 S4Y  C08   C07  C06   101.48  3.000
 S4Y  H081  C08  O16   109.41  3.000
 S4Y  H081  C08  C09   108.25  3.000
 S4Y  O16   C08  C09   110.98  3.000
 S4Y  H081  C08  C07   108.62  3.000
 S4Y  O16   C08  C07   105.07  3.000
 S4Y  C09   C08  C07   114.40  3.000
 S4Y  C08   C09  C15   119.65  3.000
 S4Y  C15   C09  C10   118.74  3.000
 S4Y  C08   C09  C10   121.58  3.000
 S4Y  H111  C11  C12   120.46  3.000
 S4Y  H111  C11  C10   120.20  3.000
 S4Y  C12   C11  C10   119.34  3.000
 S4Y  CL13  C12  C14   119.50  3.000
 S4Y  C14   C12  C11   121.01  3.000
 S4Y  CL13  C12  C11   119.49  3.000
 S4Y  H141  C14  C12   120.77  3.000
 S4Y  H141  C14  C15   120.33  3.000
 S4Y  C12   C14  C15   118.90  3.000
 S4Y  H011  N01  H012  107.84  3.000
 S4Y  H011  N01  N02   109.29  3.000
 S4Y  H012  N01  N02   109.56  3.000
 S4Y  H021  N02  N01   119.79  3.000
 S4Y  H021  N02  C03   117.78  3.000
 S4Y  N01   N02  C03   122.35  3.000
 S4Y  C08   O16  C05   110.99  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
 S4Y  CONST_01  C14   C15  C09  C10    0.00   0.0  0
 S4Y  CONST_02  C14   C12  C11  C10    0.00   0.0  0
 S4Y  CONST_03  C11   C12  C14  C15    0.00   0.0  0
 S4Y  CONST_04  C11   C10  C09  C15    0.00   0.0  0
 S4Y  CONST_05  C12   C11  C10  C09    0.00   0.0  0
 S4Y  CONST_06  C12   C14  C15  C09    0.00   0.0  0
 S4Y  CONST_07  C11   C10  C09  C08  180.00   0.0  0
 S4Y  CONST_08  C14   C15  C09  C08  180.00   0.0  0
 S4Y  CONST_09  CL13  C12  C11  C10  180.00   0.0  0
 S4Y  CONST_10  CL13  C12  C14  C15  180.00   0.0  0
 S4Y  CONST_11  H151  C15  C09  C10  180.00   0.0  0
 S4Y  CONST_12  H101  C10  C09  C15  180.00   0.0  0
 S4Y  CONST_13  H111  C11  C10  C09  180.00   0.0  0
 S4Y  CONST_14  H141  C14  C15  C09  180.00   0.0  0
 S4Y  CONST_15  N01   N02  C03  C05    0.00   0.0  0
 S4Y  CONST_16  H021  N02  C03  C05  180.00   0.0  0
 S4Y  CONST_17  O04   C03  N02  N01  180.00   0.0  0
 S4Y  Var_01    C08   C07  C06  C05  -35.65  30.0  1
 S4Y  Var_02    H012  N01  N02  C03  116.74  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
 S4Y  chir_01  C05  C03  C06  O16  positiv
 S4Y  chir_02  C08  O16  C07  C09  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
 S4Y  plan-1  C10   0.020
 S4Y  plan-1  C15   0.020
 S4Y  plan-1  C08   0.020
 S4Y  plan-1  C09   0.020
 S4Y  plan-1  C11   0.020
 S4Y  plan-1  C12   0.020
 S4Y  plan-1  C14   0.020
 S4Y  plan-1  CL13  0.020
 S4Y  plan-1  H101  0.020
 S4Y  plan-1  H151  0.020
 S4Y  plan-1  H111  0.020
 S4Y  plan-1  H141  0.020
 S4Y  plan-2  C03   0.020
 S4Y  plan-2  C05   0.020
 S4Y  plan-2  N01   0.020
 S4Y  plan-2  N02   0.020
 S4Y  plan-2  O04   0.020
 S4Y  plan-2  H021  0.020

