# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:25:31 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (5S)-5-({4-[2-(5-ethylpyridin-2-yl)-2-oxoethoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc(nc1)C(=O)COc2ccc(C[C@@H]3SC(=O)NC3=O)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
 LO7  LO7  (5S)-5-({4-[2-(5-ethylpyridin-2-yl)-2-oxoethoxy]phenyl}methyl)-1,3-thiazolidine-2,4-dione  ligand  44  26  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LO7
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
 LO7  C13  C  CR6   0   0.378   0.0875   1.5209   0.1380
 LO7  C15  C  CR16  0  -0.285   1.8193   0.1922   1.1437
 LO7  C17  C  CR16  0  -0.279   2.3868   2.2260   0.0349
 LO7  C20  C  CR15  0  -0.552   4.9800   0.3307  -0.2105
 LO7  C21  C  CR5   0   0.623   6.4479   0.0686   0.0679
 LO7  C24  C  CR5   0   0.403   5.8277  -2.0703  -0.7136
 LO7  C01  C  CH3   0  -0.657  -8.0464  -3.0595  -0.4632
 LO7  C03  C  CR6   0   0.053  -6.8569  -1.0066   0.3281
 LO7  C04  C  CR16  0  -0.104  -5.5686  -1.2735   0.7963
 LO7  C06  C  CR6   0   0.124  -4.7024   0.5963  -0.1746
 LO7  C07  C  CR16  0  -0.266  -5.9396   0.9654  -0.6861
 LO7  C08  C  CR16  0  -0.200  -7.0261   0.1462  -0.4291
 LO7  C09  C  C     0   0.327  -3.4963   1.4307  -0.4264
 LO7  C14  C  CR16  0  -0.363   0.4738   0.3911   0.8501
 LO7  C16  C  CR6   0   0.089   2.7937   1.0959   0.7461
 LO7  C18  C  CR16  0  -0.332   1.0566   2.4418  -0.2670
 LO7  C19  C  CH2   0  -0.498   4.2478   0.8484   1.0302
 LO7  N05  N  N     0  -0.419  -4.5242  -0.5028   0.5536
 LO7  N23  N  NR15  0  -0.658   6.7940  -1.2177  -0.2365
 LO7  O10  O  O     0  -0.369  -3.5560   2.4616  -1.0514
 LO7  O12  O  O2    0  -0.470  -1.1851   1.8142  -0.2032
 LO7  O25  O  O     0  -0.401   5.9994  -3.2199  -1.0127
 LO7  S26  S  S2    0   0.085   4.2787  -1.2320  -0.8201
 LO7  H1   H  HCR6  0   0.257   2.1050  -0.6928   1.6992
 LO7  H2   H  HCR6  0   0.256   3.1231   2.9537  -0.2872
 LO7  H3   H  HCR5  0   0.354   4.9206   1.0705  -1.0130
 LO7  H4   H  HCH3  0   0.239  -8.8817  -3.7325  -0.2701
 LO7  H5   H  HCH3  0   0.231  -8.1752  -2.6417  -1.4622
 LO7  H6   H  HCH3  0   0.230  -7.1314  -3.6528  -0.4639
 LO7  H7   H  HCH2  0   0.252  -8.9285  -1.4066   0.6061
 LO7  H8   H  HCH2  0   0.252  -7.8669  -2.4035   1.5817
 LO7  H9   H  HCR6  0   0.265  -5.3875  -2.1582   1.3993
 LO7  H10  H  HCR6  0   0.279  -6.0505   1.8681  -1.2707
 LO7  H11  H  HCR6  0   0.273  -8.0052   0.4062  -0.8129
 LO7  H12  H  HCH2  0   0.268  -2.2948   0.7855   1.2242
 LO7  H13  H  HCH2  0   0.267  -2.0077  -0.0934  -0.2727
 LO7  H14  H  HCR6  0   0.282  -0.2454  -0.3431   1.1864
 LO7  H15  H  HCR6  0   0.264   0.7558   3.3253  -0.8162
 LO7  H16  H  HCH2  0   0.279   4.3580   0.1282   1.8432
 LO7  H17  H  HCH2  0   0.283   4.7378   1.7732   1.3414
 LO7  H18  H  HNR5  0   0.440   7.7427  -1.5505  -0.1067
 LO7  O22  O  O     0  -0.411   7.2056   0.8950   0.5093
 LO7  C11  C  CH2   0  -0.278  -2.1951   0.9059   0.1386
 LO7  C02  C  CH2   0  -0.510  -7.9854  -1.9560   0.5927

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
 LO7  C15  C14  aromatic  1.391  0.020  1.391
 LO7  C15  C16  aromatic  1.387  0.020  1.387
 LO7  C14  C13  aromatic  1.390  0.020  1.390
 LO7  O22  C21  double    1.205  0.020  1.205
 LO7  C19  C16  single    1.502  0.020  1.502
 LO7  C19  C20  single    1.531  0.020  1.531
 LO7  C16  C17  aromatic  1.396  0.020  1.396
 LO7  C11  C09  single    1.513  0.020  1.513
 LO7  C11  O12  single    1.401  0.020  1.401
 LO7  O10  C09  double    1.207  0.020  1.207
 LO7  C21  C20  single    1.517  0.020  1.517
 LO7  C21  N23  single    1.366  0.020  1.366
 LO7  C09  C06  single    1.488  0.020  1.488
 LO7  N05  C04  aromatic  1.320  0.020  1.320
 LO7  N05  C06  aromatic  1.330  0.020  1.330
 LO7  C13  O12  single    1.350  0.020  1.350
 LO7  C13  C18  aromatic  1.397  0.020  1.397
 LO7  C04  C03  aromatic  1.396  0.020  1.396
 LO7  C20  S26  single    1.818  0.020  1.818
 LO7  C06  C07  aromatic  1.389  0.020  1.389
 LO7  C17  C18  aromatic  1.381  0.020  1.381
 LO7  C03  C02  single    1.498  0.020  1.498
 LO7  C03  C08  aromatic  1.390  0.020  1.390
 LO7  N23  C24  single    1.374  0.020  1.374
 LO7  C07  C08  aromatic  1.385  0.020  1.385
 LO7  C02  C01  single    1.529  0.020  1.529
 LO7  S26  C24  single    1.765  0.020  1.765
 LO7  C24  O25  double    1.200  0.020  1.200
 LO7  C15  H1   single    0.930  0.020  1.080
 LO7  C17  H2   single    0.930  0.020  1.080
 LO7  C20  H3   single    0.970  0.020  1.090
 LO7  C01  H4   single    0.970  0.020  1.090
 LO7  C01  H5   single    0.970  0.020  1.090
 LO7  C01  H6   single    0.970  0.020  1.090
 LO7  C02  H7   single    0.970  0.020  1.090
 LO7  C02  H8   single    0.970  0.020  1.090
 LO7  C04  H9   single    0.930  0.020  1.080
 LO7  C07  H10  single    0.930  0.020  1.080
 LO7  C08  H11  single    0.930  0.020  1.080
 LO7  C11  H12  single    0.970  0.020  1.090
 LO7  C11  H13  single    0.970  0.020  1.090
 LO7  C14  H14  single    0.930  0.020  1.080
 LO7  C18  H15  single    0.930  0.020  1.080
 LO7  C19  H16  single    0.970  0.020  1.090
 LO7  C19  H17  single    0.970  0.020  1.090
 LO7  N23  H18  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
 LO7  O12  C13  C18  115.94  3.000
 LO7  C18  C13  C14  119.44  3.000
 LO7  O12  C13  C14  124.62  3.000
 LO7  H1   C15  C16  119.59  3.000
 LO7  H1   C15  C14  118.69  3.000
 LO7  C16  C15  C14  121.71  3.000
 LO7  H2   C17  C18  118.97  3.000
 LO7  H2   C17  C16  119.79  3.000
 LO7  C18  C17  C16  121.24  3.000
 LO7  H3   C20  S26  108.34  3.000
 LO7  H3   C20  C19  109.89  3.000
 LO7  S26  C20  C19  112.20  3.000
 LO7  H3   C20  C21  107.72  3.000
 LO7  S26  C20  C21  106.64  3.000
 LO7  C19  C20  C21  111.87  3.000
 LO7  O22  C21  N23  124.61  3.000
 LO7  N23  C21  C20  111.52  3.000
 LO7  O22  C21  C20  123.86  3.000
 LO7  S26  C24  O25  124.44  3.000
 LO7  O25  C24  N23  125.47  3.000
 LO7  S26  C24  N23  110.09  3.000
 LO7  H6   C01  H5   107.88  3.000
 LO7  H6   C01  H4   107.90  3.000
 LO7  H5   C01  H4   107.97  3.000
 LO7  H6   C01  C02  111.08  3.000
 LO7  H5   C01  C02  111.16  3.000
 LO7  H4   C01  C02  110.73  3.000
 LO7  C08  C03  C04  116.98  3.000
 LO7  C08  C03  C02  122.02  3.000
 LO7  C04  C03  C02  120.96  3.000
 LO7  H9   C04  N05  116.47  3.000
 LO7  H9   C04  C03  119.72  3.000
 LO7  N05  C04  C03  123.81  3.000
 LO7  N05  C06  C09  116.57  3.000
 LO7  N05  C06  C07  122.72  3.000
 LO7  C09  C06  C07  120.71  3.000
 LO7  H10  C07  C08  120.92  3.000
 LO7  H10  C07  C06  120.83  3.000
 LO7  C08  C07  C06  118.25  3.000
 LO7  H11  C08  C07  120.09  3.000
 LO7  H11  C08  C03  120.14  3.000
 LO7  C07  C08  C03  119.76  3.000
 LO7  O10  C09  C11  122.17  3.000
 LO7  O10  C09  C06  121.77  3.000
 LO7  C11  C09  C06  116.07  3.000
 LO7  H14  C14  C15  118.72  3.000
 LO7  H14  C14  C13  121.75  3.000
 LO7  C15  C14  C13  119.53  3.000
 LO7  C19  C16  C17  120.79  3.000
 LO7  C17  C16  C15  117.95  3.000
 LO7  C19  C16  C15  121.23  3.000
 LO7  H15  C18  C17  120.39  3.000
 LO7  H15  C18  C13  119.49  3.000
 LO7  C17  C18  C13  120.12  3.000
 LO7  H17  C19  H16  107.53  3.000
 LO7  H17  C19  C16  110.41  3.000
 LO7  H16  C19  C16  110.32  3.000
 LO7  H17  C19  C20  107.62  3.000
 LO7  H16  C19  C20  109.41  3.000
 LO7  C16  C19  C20  111.44  3.000
 LO7  C06  N05  C04  118.48  3.000
 LO7  H18  N23  C24  119.93  3.000
 LO7  H18  N23  C21  121.16  3.000
 LO7  C24  N23  C21  118.90  3.000
 LO7  C11  O12  C13  118.50  3.000
 LO7  C24  S26  C20   92.84  3.000
 LO7  H13  C11  H12  106.66  3.000
 LO7  H13  C11  O12  112.09  3.000
 LO7  H12  C11  O12  112.23  3.000
 LO7  H13  C11  C09  108.85  3.000
 LO7  H12  C11  C09  109.25  3.000
 LO7  O12  C11  C09  107.71  3.000
 LO7  H8   C02  H7   106.80  3.000
 LO7  H8   C02  C03  109.75  3.000
 LO7  H7   C02  C03  109.51  3.000
 LO7  H8   C02  C01  109.52  3.000
 LO7  H7   C02  C01  109.71  3.000
 LO7  C03  C02  C01  111.44  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
 LO7  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 LO7  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 LO7  CONST_03  C18  C13  C14  C15     0.00   0.0  0
 LO7  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 LO7  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 LO7  CONST_06  C14  C13  C18  C17     0.00   0.0  0
 LO7  CONST_07  C06  N05  C04  C03     0.00   0.0  0
 LO7  CONST_08  C06  C07  C08  C03     0.00   0.0  0
 LO7  CONST_09  C07  C06  N05  C04     0.00   0.0  0
 LO7  CONST_10  C07  C08  C03  C04     0.00   0.0  0
 LO7  CONST_11  N05  C04  C03  C08     0.00   0.0  0
 LO7  CONST_12  N05  C06  C07  C08     0.00   0.0  0
 LO7  CONST_13  C24  N23  C21  C20     0.00   0.0  0
 LO7  CONST_14  O12  C13  C14  C15   180.00   0.0  0
 LO7  CONST_15  O12  C13  C18  C17   180.00   0.0  0
 LO7  CONST_16  N05  C04  C03  C02   180.00   0.0  0
 LO7  CONST_17  C07  C08  C03  C02   180.00   0.0  0
 LO7  CONST_18  C09  C06  N05  C04   180.00   0.0  0
 LO7  CONST_19  C09  C06  C07  C08   180.00   0.0  0
 LO7  CONST_20  C19  C16  C15  C14   180.00   0.0  0
 LO7  CONST_21  C19  C16  C17  C18   180.00   0.0  0
 LO7  CONST_22  O22  C21  N23  C24   180.00   0.0  0
 LO7  CONST_23  H1   C15  C14  C13   180.00   0.0  0
 LO7  CONST_24  H2   C17  C18  C13   180.00   0.0  0
 LO7  CONST_25  H10  C07  C08  C03   180.00   0.0  0
 LO7  CONST_26  H11  C08  C03  C04   180.00   0.0  0
 LO7  CONST_27  H9   C04  N05  C06   180.00   0.0  0
 LO7  CONST_28  H15  C18  C13  C14   180.00   0.0  0
 LO7  CONST_29  H14  C14  C15  C16   180.00   0.0  0
 LO7  CONST_30  H18  N23  C21  C20   180.00   0.0  0
 LO7  Var_01    N23  C24  S26  C20     0.55  30.0  1
 LO7  Var_02    S26  C24  N23  C21    -0.00  30.0  1
 LO7  Var_03    C20  C19  C16  C15   101.49  30.0  2
 LO7  Var_04    C04  C03  C02  C01   -85.86  30.0  2
 LO7  Var_05    C11  C09  C06  C07  -177.94  30.0  2
 LO7  Var_06    C14  C13  O12  C11    -2.18  30.0  2
 LO7  Var_07    C09  C11  O12  C13  -176.68  30.0  1
 LO7  Var_08    O12  C11  C09  C06   179.71  30.0  2
 LO7  Var_09    H4   C01  C02  C03  -178.97  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
 LO7  chir_01  C20  C19  C21  S26  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
 LO7  plan-1  C13  0.020
 LO7  plan-1  C15  0.020
 LO7  plan-1  C17  0.020
 LO7  plan-1  C14  0.020
 LO7  plan-1  C16  0.020
 LO7  plan-1  C18  0.020
 LO7  plan-1  C19  0.020
 LO7  plan-1  O12  0.020
 LO7  plan-1  H1   0.020
 LO7  plan-1  H2   0.020
 LO7  plan-1  H14  0.020
 LO7  plan-1  H15  0.020
 LO7  plan-2  C03  0.020
 LO7  plan-2  C04  0.020
 LO7  plan-2  C06  0.020
 LO7  plan-2  C07  0.020
 LO7  plan-2  C08  0.020
 LO7  plan-2  C09  0.020
 LO7  plan-2  N05  0.020
 LO7  plan-2  H9   0.020
 LO7  plan-2  H10  0.020
 LO7  plan-2  H11  0.020
 LO7  plan-2  C02  0.020
 LO7  plan-3  C20  0.020
 LO7  plan-3  C21  0.020
 LO7  plan-3  C24  0.020
 LO7  plan-3  N23  0.020
 LO7  plan-3  H18  0.020
 LO7  plan-3  O22  0.020
 LO7  plan-4  C24  0.020
 LO7  plan-4  N23  0.020
 LO7  plan-4  O25  0.020
 LO7  plan-4  S26  0.020
 LO7  plan-5  C06  0.020
 LO7  plan-5  C09  0.020
 LO7  plan-5  O10  0.020
 LO7  plan-5  C11  0.020

