# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:37:05 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (1R)-5'-[(2-chlorophenyl)sulfanyl]-4'-hydroxy-2,3-dihydrospiro[indene-1,2'-pyran]-6'(3'H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(Sc2ccccc2Cl)C(=O)O[C@]3(CCc4ccccc34)C1
#
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
 49C  49C  (1R)-5'-[(2-chlorophenyl)sulfanyl]-4'-hydroxy-2,3-dihydrospiro[indene-1,2'-pyran]-6'(3'H)-one  ligand  39  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_49C
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
 49C  C4   C   CR6   0   0.146   2.3448   0.3296   0.2569
 49C  C14  C   CR6   0   0.519   0.2348   0.8515  -0.9219
 49C  C5   C   CR6   0   0.109   3.7040  -0.2993   0.1126
 49C  C6   C   CR6   0   0.095   4.6929   0.6732   0.1665
 49C  C11  C   CR16  0  -0.260   5.3485  -1.9913  -0.2302
 49C  C7   C   CH2   0  -0.504   4.0894   2.0314   0.3838
 49C  C8   C   CH2   0  -0.473   2.6728   1.7028   0.8754
 49C  C9   C   CR16  0  -0.324   6.0255   0.3172   0.0198
 49C  C10  C   CR16  0  -0.251   6.3460  -1.0214  -0.1753
 49C  C12  C   CR16  0  -0.311   4.0126  -1.6344  -0.0913
 49C  C13  C   C     0  -0.560   1.6568   0.4502  -1.0977
 49C  C2   C   CR6   0   0.582   0.2393  -0.2673   1.2556
 49C  O3   O   O     0  -0.463   1.5555  -0.4789   1.1370
 49C  O15  O   OH1   0  -0.554  -0.3009   1.4808  -1.9388
 49C  C16  C   CR6   0  -0.538  -0.4191   0.5274   0.2225
 49C  S17  S   S2    0   0.098  -2.0698   1.0451   0.4800
 49C  C18  C   CR6   0  -0.031  -3.0216  -0.3772   0.0155
 49C  C19  C   CR16  0  -0.247  -2.4715  -1.5351  -0.5228
 49C  C20  C   CR16  0  -0.232  -3.2821  -2.6066  -0.8644
 49C  C21  C   CR16  0  -0.274  -4.6551  -2.5377  -0.6765
 49C  C22  C   CR16  0  -0.200  -5.2189  -1.3883  -0.1447
 49C  C23  C   CR6   0  -0.061  -4.4019  -0.3229   0.1960
 49C  CL   CL  CL    0  -0.115  -5.1148   1.1118   0.8561
 49C  H1   H   HCR6  0   0.258   5.6156  -3.0294  -0.3784
 49C  H2   H   HCH2  0   0.266   4.6460   2.6362   1.1001
 49C  H3   H   HCH2  0   0.259   4.0654   2.5972  -0.5523
 49C  H4   H   HCH2  0   0.259   1.9428   2.4740   0.6273
 49C  H5   H   HCH2  0   0.270   2.6839   1.5959   1.9619
 49C  H6   H   HCR6  0   0.254   6.8066   1.0658   0.0653
 49C  H7   H   HCR6  0   0.258   7.3827  -1.3138  -0.2824
 49C  H8   H   HCR6  0   0.255   3.2377  -2.3897  -0.1331
 49C  H9   H   H     0   0.305   2.1813   1.1799  -1.7177
 49C  H10  H   H     0   0.317   1.6845  -0.5007  -1.6418
 49C  H11  H   HOH1  0   0.487  -1.2325   1.6982  -1.7545
 49C  H12  H   HCR6  0   0.266  -1.4048  -1.6040  -0.6865
 49C  H13  H   HCR6  0   0.269  -2.8333  -3.4983  -1.2806
 49C  H14  H   HCR6  0   0.271  -5.2897  -3.3716  -0.9435
 49C  H15  H   HCR6  0   0.285  -6.2875  -1.3168   0.0064
 49C  O1   O   O     0  -0.429  -0.3453  -0.7727   2.1814

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
 49C  C22  C21  aromatic  1.386  0.020  1.386
 49C  C22  C23  aromatic  1.385  0.020  1.385
 49C  CL   C23  single    1.733  0.020  1.733
 49C  C21  C20  aromatic  1.388  0.020  1.388
 49C  C23  C18  aromatic  1.393  0.020  1.393
 49C  O15  C14  single    1.310  0.020  1.310
 49C  C20  C19  aromatic  1.386  0.020  1.386
 49C  C18  C19  aromatic  1.390  0.020  1.390
 49C  C18  S17  single    1.773  0.020  1.773
 49C  S17  C16  single    1.749  0.020  1.749
 49C  C14  C16  double    1.357  0.020  1.357
 49C  C14  C13  single    1.488  0.020  1.488
 49C  C16  C2   single    1.460  0.020  1.460
 49C  C13  C4   single    1.524  0.020  1.524
 49C  C2   O1   double    1.206  0.020  1.206
 49C  C2   O3   single    1.338  0.020  1.338
 49C  C8   C4   single    1.541  0.020  1.541
 49C  C8   C7   single    1.535  0.020  1.535
 49C  C4   O3   single    1.432  0.020  1.432
 49C  C4   C5   single    1.505  0.020  1.505
 49C  C7   C6   single    1.502  0.020  1.502
 49C  C5   C6   aromatic  1.388  0.020  1.388
 49C  C5   C12  aromatic  1.385  0.020  1.385
 49C  C6   C9   aromatic  1.387  0.020  1.387
 49C  C12  C11  aromatic  1.390  0.020  1.390
 49C  C9   C10  aromatic  1.390  0.020  1.390
 49C  C11  C10  aromatic  1.392  0.020  1.392
 49C  C11  H1   single    0.930  0.020  1.080
 49C  C7   H2   single    0.970  0.020  1.090
 49C  C7   H3   single    0.970  0.020  1.090
 49C  C8   H4   single    0.970  0.020  1.090
 49C  C8   H5   single    0.970  0.020  1.090
 49C  C9   H6   single    0.930  0.020  1.080
 49C  C10  H7   single    0.930  0.020  1.080
 49C  C12  H8   single    0.930  0.020  1.080
 49C  C13  H9   single    0.970  0.020  1.090
 49C  C13  H10  single    0.970  0.020  1.090
 49C  O15  H11  single    0.850  0.020  0.980
 49C  C19  H12  single    0.930  0.020  1.080
 49C  C20  H13  single    0.930  0.020  1.080
 49C  C21  H14  single    0.930  0.020  1.080
 49C  C22  H15  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
 49C  O3   C4   C13  110.00  3.000
 49C  O3   C4   C8   111.93  3.000
 49C  C13  C4   C8   112.47  3.000
 49C  O3   C4   C5   108.72  3.000
 49C  C8   C4   C5   102.63  3.000
 49C  C13  C4   C5   110.83  3.000
 49C  C16  C14  O15  124.89  3.000
 49C  C16  C14  C13  119.71  3.000
 49C  O15  C14  C13  115.37  3.000
 49C  C12  C5   C6   121.48  3.000
 49C  C12  C5   C4   128.18  3.000
 49C  C6   C5   C4   110.31  3.000
 49C  C9   C6   C7   129.30  3.000
 49C  C9   C6   C5   120.03  3.000
 49C  C7   C6   C5   110.66  3.000
 49C  H1   C11  C12  119.82  3.000
 49C  H1   C11  C10  119.79  3.000
 49C  C12  C11  C10  120.39  3.000
 49C  H3   C7   H2   106.65  3.000
 49C  H3   C7   C8   111.38  3.000
 49C  H2   C7   C8   112.30  3.000
 49C  H3   C7   C6   110.65  3.000
 49C  H2   C7   C6   113.05  3.000
 49C  C8   C7   C6   102.92  3.000
 49C  H5   C8   H4   107.61  3.000
 49C  H5   C8   C7   109.29  3.000
 49C  H4   C8   C7   113.17  3.000
 49C  H5   C8   C4   108.32  3.000
 49C  H4   C8   C4   113.35  3.000
 49C  C7   C8   C4   104.98  3.000
 49C  H6   C9   C10  120.35  3.000
 49C  H6   C9   C6   120.74  3.000
 49C  C10  C9   C6   118.91  3.000
 49C  H7   C10  C9   119.66  3.000
 49C  H7   C10  C11  119.60  3.000
 49C  C9   C10  C11  120.74  3.000
 49C  H8   C12  C11  120.32  3.000
 49C  H8   C12  C5   121.23  3.000
 49C  C11  C12  C5   118.45  3.000
 49C  H10  C13  H9   106.61  3.000
 49C  H10  C13  C14  108.47  3.000
 49C  H9   C13  C14  110.24  3.000
 49C  H10  C13  C4   111.18  3.000
 49C  H9   C13  C4   109.92  3.000
 49C  C14  C13  C4   110.35  3.000
 49C  C16  C2   O3   117.83  3.000
 49C  O3   C2   O1   118.59  3.000
 49C  C16  C2   O1   123.55  3.000
 49C  C2   O3   C4   120.48  3.000
 49C  H11  O15  C14  110.57  3.000
 49C  S17  C16  C2   118.85  3.000
 49C  C2   C16  C14  120.61  3.000
 49C  S17  C16  C14  120.54  3.000
 49C  C18  S17  C16  103.33  3.000
 49C  C23  C18  C19  118.34  3.000
 49C  C19  C18  S17  123.85  3.000
 49C  C23  C18  S17  117.81  3.000
 49C  H12  C19  C20  119.35  3.000
 49C  H12  C19  C18  120.13  3.000
 49C  C20  C19  C18  120.51  3.000
 49C  H13  C20  C21  120.24  3.000
 49C  H13  C20  C19  119.31  3.000
 49C  C21  C20  C19  120.45  3.000
 49C  H14  C21  C22  119.70  3.000
 49C  H14  C21  C20  120.60  3.000
 49C  C22  C21  C20  119.71  3.000
 49C  H15  C22  C23  119.84  3.000
 49C  H15  C22  C21  120.68  3.000
 49C  C23  C22  C21  119.48  3.000
 49C  CL   C23  C22  119.20  3.000
 49C  CL   C23  C18  119.30  3.000
 49C  C22  C23  C18  121.50  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
 49C  CONST_01  C10  C9   C6   C5     0.00   0.0  0
 49C  CONST_02  C10  C11  C12  C5     0.00   0.0  0
 49C  CONST_03  C11  C12  C5   C6     0.00   0.0  0
 49C  CONST_04  C11  C10  C9   C6     0.00   0.0  0
 49C  CONST_05  C12  C5   C6   C9     0.00   0.0  0
 49C  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 49C  CONST_07  C21  C22  C23  C18    0.00   0.0  0
 49C  CONST_08  C21  C20  C19  C18    0.00   0.0  0
 49C  CONST_09  C22  C21  C20  C19    0.00   0.0  0
 49C  CONST_10  C22  C23  C18  C19    0.00   0.0  0
 49C  CONST_11  C23  C22  C21  C20    0.00   0.0  0
 49C  CONST_12  C23  C18  C19  C20    0.00   0.0  0
 49C  CONST_13  C22  C23  C18  S17  180.00   0.0  0
 49C  CONST_14  C20  C19  C18  S17  180.00   0.0  0
 49C  CONST_15  CL   C23  C18  C19  180.00   0.0  0
 49C  CONST_16  CL   C23  C22  C21  180.00   0.0  0
 49C  CONST_17  H8   C12  C5   C4     0.00   0.0  0
 49C  CONST_18  H6   C9   C6   C5   180.00   0.0  0
 49C  CONST_19  H1   C11  C12  C5   180.00   0.0  0
 49C  CONST_20  H7   C10  C9   C6   180.00   0.0  0
 49C  CONST_21  H15  C22  C23  C18  180.00   0.0  0
 49C  CONST_22  H13  C20  C19  C18  180.00   0.0  0
 49C  CONST_23  H14  C21  C20  C19  180.00   0.0  0
 49C  CONST_24  H12  C19  C20  C21  180.00   0.0  0
 49C  Var_01    C16  C14  C13  C4   -27.37  30.0  1
 49C  Var_02    C6   C7   C8   C4   -27.40  30.0  1
 49C  Var_03    C16  C2   O3   C4    16.65  30.0  1
 49C  Var_04    O3   C2   C16  C14   10.47  30.0  1
 49C  Var_05    C8   C7   C6   C5    16.62  30.0  1
 49C  Var_06    C2   C16  C14  C13   -2.98  30.0  1
 49C  Var_07    C23  C18  S17  C16  175.61  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
 49C  chir_01  C4  C8  O3  C5  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
 49C  plan-1  S17  0.020
 49C  plan-1  C18  0.020
 49C  plan-1  C19  0.020
 49C  plan-1  C20  0.020
 49C  plan-1  C21  0.020
 49C  plan-1  C22  0.020
 49C  plan-1  C23  0.020
 49C  plan-1  CL   0.020
 49C  plan-1  H12  0.020
 49C  plan-1  H13  0.020
 49C  plan-1  H14  0.020
 49C  plan-1  H15  0.020
 49C  plan-2  C4   0.020
 49C  plan-2  C5   0.020
 49C  plan-2  C6   0.020
 49C  plan-2  C11  0.020
 49C  plan-2  C7   0.020
 49C  plan-2  C9   0.020
 49C  plan-2  C10  0.020
 49C  plan-2  C12  0.020
 49C  plan-2  H1   0.020
 49C  plan-2  H6   0.020
 49C  plan-2  H7   0.020
 49C  plan-2  H8   0.020
 49C  plan-3  C2   0.020
 49C  plan-3  O3   0.020
 49C  plan-3  C16  0.020
 49C  plan-3  O1   0.020

