# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:27:49 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-chloro-4-{[(1R,3Z,7S,7aS)-7-hydroxy-1-(trifluoromethyl)tetrahydro-1H-pyrrolo[1,2-c][1,3]oxazol-3-ylidene]amino}-3-methylbenzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Cl)c(ccc1N=C2O[C@H]([C@@H]3[C@@H](O)CCN23)C(F)(F)F)C#N
#
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
 LGB  LGB  2-chloro-4-{[(1R,3Z,7S,7aS)-7-hydroxy-1-(trifluoromethyl)tetrahydro-1H-pyrrolo[1,2-c][1,3]oxazol-3-ylidene]amino}-3-methylbenzonitrile  ligand  37  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LGB
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
 LGB  C1    C   CH2   0  -0.290   2.8880  -2.2723   0.7339
 LGB  N2    N   NT    0  -0.477   2.3952  -0.8901   0.7624
 LGB  C3    C   CH1   0  -0.190   3.3642   0.0090   0.1689
 LGB  C4    C   CH1   0   0.072   4.0338  -0.8661  -0.8872
 LGB  C5    C   CH2   0  -0.524   4.1563  -2.1951  -0.1324
 LGB  C6    C   C     0   0.715   1.1530  -0.5768   0.3187
 LGB  O7    O   O2    0  -0.467   1.1623   0.6174  -0.3079
 LGB  C8    C   CH1   0  -0.199   2.4775   1.1514  -0.3204
 LGB  N9    N   N     0  -0.523   0.1206  -1.2927   0.4788
 LGB  C10   C   CR6   0   0.213  -1.0938  -0.9888  -0.1046
 LGB  C11   C   CR6   0   0.122  -2.2388  -0.9172   0.7150
 LGB  C12   C   CR6   0  -0.126  -3.4588  -0.6796   0.0983
 LGB  C13   C   CR6   0   0.079  -3.5817  -0.5257  -1.2847
 LGB  C14   C   CR16  0  -0.281  -2.4391  -0.6156  -2.0776
 LGB  C15   C   CR16  0  -0.271  -1.2144  -0.8426  -1.4921
 LGB  C16   C   CH3   0  -0.724  -2.1410  -1.0803   2.2005
 LGB  CL17  CL  CL    0  -0.090  -4.8863  -0.5580   1.0619
 LGB  O18   O   OH1   0  -0.657   5.2350  -0.2854  -1.2981
 LGB  C19   C   CSP   0   0.045  -4.8473  -0.2897  -1.8874
 LGB  N20   N   NS    0  -0.248  -5.8610  -0.1012  -2.4030
 LGB  C21   C   CT    0   1.019   2.4931   2.3595   0.6015
 LGB  F22   F   F     0  -0.300   3.7108   2.9058   0.6282
 LGB  F23   F   F     0  -0.298   1.6331   3.2936   0.1946
 LGB  F24   F   F     0  -0.301   2.1629   2.0318   1.8541
 LGB  H1    H   HCH2  0   0.265   3.1016  -2.6288   1.7401
 LGB  H1A   H   HCH2  0   0.259   2.1233  -2.9172   0.3020
 LGB  H3    H   HCH1  0   0.302   4.1163   0.3344   0.8940
 LGB  H4    H   HCH1  0   0.223   3.3392  -0.9909  -1.7316
 LGB  H5    H   HCH2  0   0.254   5.0502  -2.1657   0.4944
 LGB  H5A   H   HCH2  0   0.272   4.2430  -3.0494  -0.8027
 LGB  H8    H   HCH1  0   0.333   2.7278   1.4798  -1.3329
 LGB  H14   H   HCR6  0   0.286  -2.5209  -0.5093  -3.1504
 LGB  H15   H   HCR6  0   0.272  -0.3378  -0.9292  -2.1195
 LGB  H16   H   HCH3  0   0.257  -2.4091  -0.1571   2.7165
 LGB  H16A  H   HCH3  0   0.253  -2.8143  -1.8589   2.5601
 LGB  H16B  H   HCH3  0   0.262  -1.1296  -1.3454   2.4939
 LGB  HO18  H   HOH1  0   0.463   5.5974  -0.8069  -2.0211

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
 LGB  C5   C1    single    1.538  0.020  1.538
 LGB  C1   N2    single    1.468  0.020  1.468
 LGB  C1   H1    single    0.970  0.020  1.090
 LGB  C1   H1A   single    0.970  0.020  1.090
 LGB  C6   N2    single    1.356  0.020  1.356
 LGB  C3   N2    single    1.449  0.020  1.449
 LGB  C4   C3    single    1.526  0.020  1.526
 LGB  C3   C8    single    1.527  0.020  1.527
 LGB  C3   H3    single    0.970  0.020  1.090
 LGB  C5   C4    single    1.533  0.020  1.533
 LGB  C4   O18   single    1.396  0.020  1.396
 LGB  C4   H4    single    0.970  0.020  1.090
 LGB  C5   H5    single    0.970  0.020  1.090
 LGB  C5   H5A   single    0.970  0.020  1.090
 LGB  N9   C6    double    1.267  0.020  1.267
 LGB  C6   O7    single    1.349  0.020  1.349
 LGB  O7   C8    single    1.420  0.020  1.420
 LGB  C8   C21   single    1.520  0.020  1.520
 LGB  C8   H8    single    0.970  0.020  1.090
 LGB  C10  N9    single    1.381  0.020  1.381
 LGB  C15  C10   aromatic  1.400  0.020  1.400
 LGB  C10  C11   aromatic  1.410  0.020  1.410
 LGB  C12  C11   aromatic  1.387  0.020  1.387
 LGB  C11  C16   single    1.498  0.020  1.498
 LGB  C13  C12   aromatic  1.397  0.020  1.397
 LGB  C12  CL17  single    1.727  0.020  1.727
 LGB  C14  C13   aromatic  1.394  0.020  1.394
 LGB  C19  C13   single    1.422  0.020  1.422
 LGB  C14  C15   aromatic  1.376  0.020  1.376
 LGB  C14  H14   single    0.930  0.020  1.080
 LGB  C15  H15   single    0.930  0.020  1.080
 LGB  C16  H16   single    0.970  0.020  1.090
 LGB  C16  H16A  single    0.970  0.020  1.090
 LGB  C16  H16B  single    0.970  0.020  1.090
 LGB  O18  HO18  single    0.850  0.020  0.980
 LGB  N20  C19   triple    1.153  0.020  1.153
 LGB  C21  F22   single    1.335  0.020  1.335
 LGB  C21  F24   single    1.336  0.020  1.336
 LGB  C21  F23   single    1.333  0.020  1.333

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
 LGB  H1A   C1   H1    108.07  3.000
 LGB  H1A   C1   C5    112.66  3.000
 LGB  H1    C1   C5    112.04  3.000
 LGB  H1A   C1   N2    109.24  3.000
 LGB  H1    C1   N2    110.87  3.000
 LGB  C5    C1   N2    103.92  3.000
 LGB  C6    N2   C3    109.60  3.000
 LGB  C3    N2   C1    110.60  3.000
 LGB  C6    N2   C1    121.26  3.000
 LGB  H3    C3   C8    112.89  3.000
 LGB  H3    C3   C4    109.12  3.000
 LGB  C8    C3   C4    117.52  3.000
 LGB  H3    C3   N2    111.89  3.000
 LGB  C8    C3   N2    101.95  3.000
 LGB  C4    C3   N2    102.77  3.000
 LGB  H4    C4   O18   111.37  3.000
 LGB  H4    C4   C5    109.26  3.000
 LGB  O18   C4   C5    115.89  3.000
 LGB  H4    C4   C3    108.61  3.000
 LGB  O18   C4   C3    110.04  3.000
 LGB  C5    C4   C3    101.04  3.000
 LGB  H5A   C5   H5    108.01  3.000
 LGB  H5A   C5   C4    112.54  3.000
 LGB  H5    C5   C4    108.94  3.000
 LGB  H5A   C5   C1    111.90  3.000
 LGB  H5    C5   C1    110.68  3.000
 LGB  C4    C5   C1    104.77  3.000
 LGB  N9    C6   O7    124.39  3.000
 LGB  O7    C6   N2    110.51  3.000
 LGB  N9    C6   N2    125.09  3.000
 LGB  C8    O7   C6    110.09  3.000
 LGB  H8    C8   C21   108.70  3.000
 LGB  H8    C8   O7    109.46  3.000
 LGB  C21   C8   O7    107.65  3.000
 LGB  H8    C8   C3    112.86  3.000
 LGB  C21   C8   C3    113.23  3.000
 LGB  O7    C8   C3    104.70  3.000
 LGB  C10   N9   C6    122.61  3.000
 LGB  C15   C10  C11   120.05  3.000
 LGB  C11   C10  N9    118.67  3.000
 LGB  C15   C10  N9    121.14  3.000
 LGB  C16   C11  C12   121.13  3.000
 LGB  C16   C11  C10   121.20  3.000
 LGB  C12   C11  C10   117.67  3.000
 LGB  CL17  C12  C13   118.16  3.000
 LGB  CL17  C12  C11   119.41  3.000
 LGB  C13   C12  C11   122.43  3.000
 LGB  C19   C13  C14   119.96  3.000
 LGB  C19   C13  C12   121.09  3.000
 LGB  C14   C13  C12   118.94  3.000
 LGB  H14   C14  C15   120.37  3.000
 LGB  H14   C14  C13   119.75  3.000
 LGB  C15   C14  C13   119.88  3.000
 LGB  H15   C15  C14   119.19  3.000
 LGB  H15   C15  C10   119.78  3.000
 LGB  C14   C15  C10   121.02  3.000
 LGB  H16B  C16  H16A  108.17  3.000
 LGB  H16B  C16  H16   107.92  3.000
 LGB  H16A  C16  H16   107.24  3.000
 LGB  H16B  C16  C11   110.82  3.000
 LGB  H16A  C16  C11   111.38  3.000
 LGB  H16   C16  C11   111.15  3.000
 LGB  HO18  O18  C4    108.65  3.000
 LGB  N20   C19  C13   180.00  3.000
 LGB  F24   C21  F23   107.37  3.000
 LGB  F23   C21  F22   107.93  3.000
 LGB  F24   C21  F22   107.88  3.000
 LGB  F23   C21  C8    111.42  3.000
 LGB  F24   C21  C8    111.79  3.000
 LGB  F22   C21  C8    110.29  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
 LGB  CONST_01  C13   C14  C15  C10     0.00   0.0  0
 LGB  CONST_02  C13   C12  C11  C10     0.00   0.0  0
 LGB  CONST_03  C14   C15  C10  C11     0.00   0.0  0
 LGB  CONST_04  C14   C13  C12  C11     0.00   0.0  0
 LGB  CONST_05  C15   C10  C11  C12     0.00   0.0  0
 LGB  CONST_06  C15   C14  C13  C12     0.00   0.0  0
 LGB  CONST_08  O7    C6   N2   C3      0.00   0.0  0
 LGB  CONST_09  C14   C15  C10  N9    180.00   0.0  0
 LGB  CONST_10  C12   C11  C10  N9    180.00   0.0  0
 LGB  CONST_11  CL17  C12  C11  C10   180.00   0.0  0
 LGB  CONST_12  C19   C13  C12  C11   180.00   0.0  0
 LGB  CONST_13  C16   C11  C12  C13   180.00   0.0  0
 LGB  CONST_14  CL17  C12  C13  C14   180.00   0.0  0
 LGB  CONST_15  C16   C11  C10  C15   180.00   0.0  0
 LGB  CONST_16  C19   C13  C14  C15   180.00   0.0  0
 LGB  CONST_18  C10   N9   C6   N2    180.00   0.0  0
 LGB  CONST_19  N9    C6   N2   C3    180.00   0.0  0
 LGB  CONST_20  C10   N9   C6   O7      0.00   0.0  0
 LGB  CONST_21  H14   C14  C15  C10   180.00   0.0  0
 LGB  CONST_22  H15   C15  C10  C11   180.00   0.0  0
 LGB  Var_01    C4    C5   C1   N2    -17.55  30.0  1
 LGB  Var_02    C5    C1   N2   C3     -8.73  30.0  1
 LGB  Var_03    C15   C10  N9   C6     56.99  30.0  2
 LGB  Var_04    N9    C6   O7   C8   -179.72  30.0  1
 LGB  Var_05    H16   C16  C11  C10   114.47  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
 LGB  chir_01  C3  N2   C4  C8   negativ
 LGB  chir_02  C4  O18  C3  C5   positiv
 LGB  chir_03  C8  O7   C3  C21  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
 LGB  plan-1  N9    0.020
 LGB  plan-1  C10   0.020
 LGB  plan-1  C11   0.020
 LGB  plan-1  C12   0.020
 LGB  plan-1  C13   0.020
 LGB  plan-1  C14   0.020
 LGB  plan-1  C15   0.020
 LGB  plan-1  C16   0.020
 LGB  plan-1  CL17  0.020
 LGB  plan-1  C19   0.020
 LGB  plan-1  N20   0.020
 LGB  plan-1  H14   0.020
 LGB  plan-1  H15   0.020
 LGB  plan-2  C1    0.020
 LGB  plan-2  N2    0.020
 LGB  plan-2  C3    0.020
 LGB  plan-2  C6    0.020
 LGB  plan-2  O7    0.020
 LGB  plan-2  N9    0.020
 LGB  plan-2  C10   0.020

