# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 11:09:20 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: (5S)-5-{[4-(2-{5-[(1S)-1-hydroxyethyl]pyridin-2-yl}ethoxy)phenyl]methyl}-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)c1ccc(CCOc2ccc(C[C@@H]3SC(=O)NC3=O)cc2)nc1
#
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
 GFV  GFV  (5S)-5-{[4-(2-{5-[(1S)-1-hydroxyethyl]pyridin-2-yl}ethoxy)phenyl]methyl}-1,3-thiazolidine-2,4-dione  ligand  46  26  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GFV
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
 GFV  C10  C  CH2   0  -0.169   2.0900  -0.9815  -0.3758
 GFV  C13  C  CR16  0  -0.334  -1.3579  -1.9599  -1.0006
 GFV  C15  C  CR6   0   0.086  -2.8021  -0.0244  -1.1680
 GFV  C17  C  CR16  0  -0.366  -0.4229   0.2448  -0.7726
 GFV  C20  C  CR5   0   0.623  -6.1287   1.6335  -0.1332
 GFV  C01  C  CH3   0  -0.690   7.5806   2.5561   1.2204
 GFV  C02  C  CH1   0  -0.007   8.0068   1.1846   0.7070
 GFV  C03  C  CR6   0   0.002   6.7999   0.3142   0.4759
 GFV  C04  C  CR16  0  -0.109   6.1114   0.3058  -0.7329
 GFV  C06  C  CR6   0   0.236   4.5309  -1.1658   0.0284
 GFV  C07  C  CR16  0  -0.331   5.1459  -1.2264   1.2736
 GFV  C08  C  CR16  0  -0.188   6.2920  -0.4813   1.4937
 GFV  C09  C  CH2   0  -0.525   3.2701  -1.9314  -0.2571
 GFV  C12  C  CR6   0   0.376  -0.2498  -1.1378  -0.7935
 GFV  C14  C  CR16  0  -0.281  -2.6120  -1.4050  -1.1821
 GFV  C16  C  CR16  0  -0.282  -1.6899   0.7821  -0.9602
 GFV  C19  C  CR15  0  -0.552  -4.7400   1.0418   0.0139
 GFV  C23  C  CR5   0   0.403  -6.6035  -0.0444   1.4576
 GFV  N05  N  N     0  -0.419   5.0160  -0.4096  -0.9535
 GFV  N22  N  NR15  0  -0.658  -7.0314   0.9992   0.6729
 GFV  O11  O  O2    0  -0.477   0.9339  -1.7603  -0.6294
 GFV  O24  O  O     0  -0.401  -7.2937  -0.6841   2.2028
 GFV  O26  O  OH1   0  -0.668   8.7246   1.2778  -0.5033
 GFV  S25  S  S2    0   0.085  -4.8785  -0.3204   1.2106
 GFV  H1   H  HCH2  0   0.230   1.9705  -0.4080   0.5509
 GFV  H2   H  HCH2  0   0.229   2.2661  -0.2704  -1.1895
 GFV  H3   H  HCR6  0   0.262  -1.2288  -3.0349  -1.0191
 GFV  H4   H  HCR6  0   0.279   0.4089   0.9183  -0.6180
 GFV  H5   H  HCH3  0   0.237   7.0268   2.4656   2.1552
 GFV  H6   H  HCH3  0   0.239   8.4508   3.1869   1.4148
 GFV  H7   H  HCH3  0   0.233   6.9416   3.0620   0.4944
 GFV  H8   H  HCH1  0   0.220   8.6214   0.7061   1.4827
 GFV  H9   H  HCR6  0   0.259   6.4616   0.9038  -1.5670
 GFV  H10  H  HCR6  0   0.266   4.7342  -1.8524   2.0545
 GFV  H11  H  HCR6  0   0.265   6.7895  -0.5209   2.4559
 GFV  H12  H  HCH2  0   0.257   3.0856  -2.6510   0.5424
 GFV  H13  H  HCH2  0   0.260   3.3811  -2.4907  -1.1894
 GFV  H14  H  HCR6  0   0.254  -3.4603  -2.0604  -1.3392
 GFV  H15  H  HCR6  0   0.257  -1.8019   1.8604  -0.9444
 GFV  H18  H  HCR5  0   0.353  -4.0927   1.8110   0.4429
 GFV  H19  H  HNR5  0   0.440  -8.0063   1.2756   0.6874
 GFV  H20  H  HOH1  0   0.455   9.4337   1.9171  -0.3821
 GFV  C18  C  CH2   0  -0.497  -4.1716   0.5734  -1.3277
 GFV  O21  O  O     0  -0.411  -6.3964   2.5439  -0.8757
 GFV  H16  H  HCH2  0   0.282  -4.1341   1.4392  -1.9923
 GFV  H17  H  HCH2  0   0.278  -4.8517  -0.1522  -1.7779

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
 GFV  O26  C02  single    1.410  0.020  1.410
 GFV  C02  C03  single    1.506  0.020  1.506
 GFV  C02  C01  single    1.525  0.020  1.525
 GFV  C08  C03  aromatic  1.388  0.020  1.388
 GFV  C08  C07  aromatic  1.385  0.020  1.385
 GFV  C03  C04  aromatic  1.391  0.020  1.391
 GFV  C07  C06  aromatic  1.390  0.020  1.390
 GFV  C04  N05  aromatic  1.327  0.020  1.327
 GFV  C06  N05  aromatic  1.331  0.020  1.331
 GFV  C06  C09  single    1.502  0.020  1.502
 GFV  C09  C10  single    1.520  0.020  1.520
 GFV  C10  O11  single    1.417  0.020  1.417
 GFV  O11  C12  single    1.347  0.020  1.347
 GFV  C12  C13  aromatic  1.395  0.020  1.395
 GFV  C12  C17  aromatic  1.394  0.020  1.394
 GFV  C13  C14  aromatic  1.383  0.020  1.383
 GFV  C17  C16  aromatic  1.389  0.020  1.389
 GFV  C14  C15  aromatic  1.394  0.020  1.394
 GFV  C16  C15  aromatic  1.389  0.020  1.389
 GFV  C15  C18  single    1.503  0.020  1.503
 GFV  S25  C19  single    1.818  0.020  1.818
 GFV  S25  C23  single    1.764  0.020  1.764
 GFV  C18  C19  single    1.531  0.020  1.531
 GFV  C19  C20  single    1.517  0.020  1.517
 GFV  C23  O24  double    1.200  0.020  1.200
 GFV  C23  N22  single    1.374  0.020  1.374
 GFV  C20  N22  single    1.366  0.020  1.366
 GFV  C20  O21  double    1.205  0.020  1.205
 GFV  C10  H1   single    0.970  0.020  1.090
 GFV  C10  H2   single    0.970  0.020  1.090
 GFV  C13  H3   single    0.930  0.020  1.080
 GFV  C17  H4   single    0.930  0.020  1.080
 GFV  C01  H5   single    0.970  0.020  1.090
 GFV  C01  H6   single    0.970  0.020  1.090
 GFV  C01  H7   single    0.970  0.020  1.090
 GFV  C02  H8   single    0.970  0.020  1.090
 GFV  C04  H9   single    0.930  0.020  1.080
 GFV  C07  H10  single    0.930  0.020  1.080
 GFV  C08  H11  single    0.930  0.020  1.080
 GFV  C09  H12  single    0.970  0.020  1.090
 GFV  C09  H13  single    0.970  0.020  1.090
 GFV  C14  H14  single    0.930  0.020  1.080
 GFV  C16  H15  single    0.930  0.020  1.080
 GFV  C18  H16  single    0.970  0.020  1.090
 GFV  C18  H17  single    0.970  0.020  1.090
 GFV  C19  H18  single    0.970  0.020  1.090
 GFV  N22  H19  single    0.860  0.020  1.020
 GFV  O26  H20  single    0.850  0.020  0.980

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
 GFV  H2   C10  H1   107.81  3.000
 GFV  H2   C10  O11  110.81  3.000
 GFV  H1   C10  O11  110.48  3.000
 GFV  H2   C10  C09  109.82  3.000
 GFV  H1   C10  C09  110.22  3.000
 GFV  O11  C10  C09  107.70  3.000
 GFV  H3   C13  C14  120.27  3.000
 GFV  H3   C13  C12  119.52  3.000
 GFV  C14  C13  C12  120.21  3.000
 GFV  C18  C15  C16  120.96  3.000
 GFV  C18  C15  C14  121.15  3.000
 GFV  C16  C15  C14  117.86  3.000
 GFV  H4   C17  C16  118.69  3.000
 GFV  H4   C17  C12  121.63  3.000
 GFV  C16  C17  C12  119.68  3.000
 GFV  O21  C20  N22  124.58  3.000
 GFV  O21  C20  C19  123.91  3.000
 GFV  N22  C20  C19  111.50  3.000
 GFV  H7   C01  H6   108.49  3.000
 GFV  H7   C01  H5   108.15  3.000
 GFV  H6   C01  H5   107.46  3.000
 GFV  H7   C01  C02  110.89  3.000
 GFV  H6   C01  C02  110.89  3.000
 GFV  H5   C01  C02  110.85  3.000
 GFV  H8   C02  O26  110.47  3.000
 GFV  H8   C02  C03  107.75  3.000
 GFV  O26  C02  C03  108.32  3.000
 GFV  H8   C02  C01  108.07  3.000
 GFV  C03  C02  C01  110.33  3.000
 GFV  O26  C02  C01  111.82  3.000
 GFV  C08  C03  C04  116.91  3.000
 GFV  C04  C03  C02  122.24  3.000
 GFV  C08  C03  C02  120.79  3.000
 GFV  H9   C04  N05  115.85  3.000
 GFV  H9   C04  C03  120.34  3.000
 GFV  N05  C04  C03  123.80  3.000
 GFV  N05  C06  C09  117.08  3.000
 GFV  C09  C06  C07  121.28  3.000
 GFV  N05  C06  C07  121.63  3.000
 GFV  H10  C07  C08  120.76  3.000
 GFV  H10  C07  C06  120.22  3.000
 GFV  C08  C07  C06  119.02  3.000
 GFV  H11  C08  C07  120.09  3.000
 GFV  H11  C08  C03  120.26  3.000
 GFV  C07  C08  C03  119.65  3.000
 GFV  H13  C09  H12  107.74  3.000
 GFV  H13  C09  C06  109.73  3.000
 GFV  H12  C09  C06  109.80  3.000
 GFV  H13  C09  C10  109.40  3.000
 GFV  H12  C09  C10  109.76  3.000
 GFV  C06  C09  C10  110.37  3.000
 GFV  O11  C12  C17  124.45  3.000
 GFV  C17  C12  C13  119.22  3.000
 GFV  O11  C12  C13  116.33  3.000
 GFV  H14  C14  C15  119.59  3.000
 GFV  H14  C14  C13  119.09  3.000
 GFV  C15  C14  C13  121.31  3.000
 GFV  H15  C16  C17  118.49  3.000
 GFV  H15  C16  C15  119.78  3.000
 GFV  C17  C16  C15  121.73  3.000
 GFV  H18  C19  S25  108.30  3.000
 GFV  H18  C19  C18  109.84  3.000
 GFV  S25  C19  C18  112.08  3.000
 GFV  H18  C19  C20  107.80  3.000
 GFV  C18  C19  C20  111.99  3.000
 GFV  S25  C19  C20  106.64  3.000
 GFV  S25  C23  O24  124.45  3.000
 GFV  O24  C23  N22  125.47  3.000
 GFV  S25  C23  N22  110.08  3.000
 GFV  C06  N05  C04  118.99  3.000
 GFV  H19  N22  C23  119.90  3.000
 GFV  H19  N22  C20  121.15  3.000
 GFV  C23  N22  C20  118.93  3.000
 GFV  C12  O11  C10  118.99  3.000
 GFV  H20  O26  C02  108.10  3.000
 GFV  C23  S25  C19   92.83  3.000
 GFV  H17  C18  H16  107.30  3.000
 GFV  H17  C18  C19  109.48  3.000
 GFV  H16  C18  C19  107.67  3.000
 GFV  H17  C18  C15  110.32  3.000
 GFV  H16  C18  C15  110.41  3.000
 GFV  C19  C18  C15  111.53  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
 GFV  CONST_01  C16  C17  C12  C13     0.00   0.0  0
 GFV  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 GFV  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 GFV  CONST_04  C12  C17  C16  C15     0.00   0.0  0
 GFV  CONST_05  C14  C13  C12  C17     0.00   0.0  0
 GFV  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 GFV  CONST_07  C06  C07  C08  C03     0.00   0.0  0
 GFV  CONST_08  C06  N05  C04  C03     0.00   0.0  0
 GFV  CONST_09  C07  C08  C03  C04     0.00   0.0  0
 GFV  CONST_10  C07  C06  N05  C04     0.00   0.0  0
 GFV  CONST_11  N05  C04  C03  C08     0.00   0.0  0
 GFV  CONST_12  N05  C06  C07  C08     0.00   0.0  0
 GFV  CONST_13  C23  N22  C20  C19     0.00   0.0  0
 GFV  CONST_14  C18  C15  C14  C13   180.00   0.0  0
 GFV  CONST_15  C18  C15  C16  C17   180.00   0.0  0
 GFV  CONST_16  C07  C08  C03  C02   180.00   0.0  0
 GFV  CONST_17  N05  C04  C03  C02   180.00   0.0  0
 GFV  CONST_18  C09  C06  N05  C04   180.00   0.0  0
 GFV  CONST_19  C09  C06  C07  C08   180.00   0.0  0
 GFV  CONST_20  O11  C12  C13  C14   180.00   0.0  0
 GFV  CONST_21  O11  C12  C17  C16   180.00   0.0  0
 GFV  CONST_22  O21  C20  N22  C23   180.00   0.0  0
 GFV  CONST_23  H4   C17  C12  C13   180.00   0.0  0
 GFV  CONST_24  H3   C13  C14  C15   180.00   0.0  0
 GFV  CONST_25  H10  C07  C08  C03   180.00   0.0  0
 GFV  CONST_26  H11  C08  C03  C04   180.00   0.0  0
 GFV  CONST_27  H9   C04  N05  C06   180.00   0.0  0
 GFV  CONST_28  H14  C14  C13  C12   180.00   0.0  0
 GFV  CONST_29  H15  C16  C17  C12   180.00   0.0  0
 GFV  CONST_30  H19  N22  C20  C19   180.00   0.0  0
 GFV  Var_01    S25  C23  N22  C20     0.04  30.0  1
 GFV  Var_02    N22  C23  S25  C19     0.56  30.0  1
 GFV  Var_03    C19  C18  C15  C14   102.53  30.0  2
 GFV  Var_04    C07  C06  C09  C10   108.94  30.0  2
 GFV  Var_05    C13  C12  O11  C10  -178.15  30.0  2
 GFV  Var_06    O11  C10  C09  C06  -179.37  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
 GFV  chir_01  C02  O26  C03  C01  positiv
 GFV  chir_02  C19  S25  C18  C20  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
 GFV  plan-1  C02  0.020
 GFV  plan-1  C03  0.020
 GFV  plan-1  C04  0.020
 GFV  plan-1  C06  0.020
 GFV  plan-1  C07  0.020
 GFV  plan-1  C08  0.020
 GFV  plan-1  C09  0.020
 GFV  plan-1  N05  0.020
 GFV  plan-1  H9   0.020
 GFV  plan-1  H10  0.020
 GFV  plan-1  H11  0.020
 GFV  plan-2  C13  0.020
 GFV  plan-2  C15  0.020
 GFV  plan-2  C17  0.020
 GFV  plan-2  C12  0.020
 GFV  plan-2  C14  0.020
 GFV  plan-2  C16  0.020
 GFV  plan-2  O11  0.020
 GFV  plan-2  H3   0.020
 GFV  plan-2  H4   0.020
 GFV  plan-2  H14  0.020
 GFV  plan-2  H15  0.020
 GFV  plan-2  C18  0.020
 GFV  plan-3  C23  0.020
 GFV  plan-3  N22  0.020
 GFV  plan-3  O24  0.020
 GFV  plan-3  S25  0.020
 GFV  plan-4  C20  0.020
 GFV  plan-4  C19  0.020
 GFV  plan-4  C23  0.020
 GFV  plan-4  N22  0.020
 GFV  plan-4  H19  0.020
 GFV  plan-4  O21  0.020

