# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:28:24 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: {2-methyl-4-[({5-[4-(trifluoromethyl)phenyl]-1,3,4-thiadiazol-2-yl}methyl)sulfanyl]phenoxy}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(SCc2sc(nn2)c3ccc(cc3)C(F)(F)F)ccc1OCC(O)=O
#
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
 9RF  9RF  '{2-methyl-4-[({5-[4-(trifluoromethyl)phenyl]-1,3,4-thiadiazol-2-yl}methyl)sulfanyl]phenoxy}acetic acid'  ligand  43  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9RF
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
 9RF  C10   C  CR5    0   0.032  -2.8818   0.6421   0.2477
 9RF  C13   C  CR16   0  -0.260  -5.2540   1.0640   0.7771
 9RF  C15   C  CR6    0  -0.198  -6.9904  -0.3941  -0.0177
 9RF  C20   C  CR16   0  -0.261  -6.0422  -1.1847  -0.6495
 9RF  C21   C  CR16   0  -0.303  -4.6999  -0.8497  -0.5685
 9RF  C22   C  CR16   0  -0.233   4.0953   0.0520   1.4515
 9RF  C24   C  CR6    0   0.365   6.0393  -0.3192   0.0738
 9RF  C26   C  CH2    0  -0.335   8.2199   0.3646   0.7183
 9RF  C02   C  CR6    0  -0.001   5.2374  -0.9409  -0.9020
 9RF  C03   C  CR16   0  -0.259   3.8767  -1.0452  -0.6703
 9RF  C04   C  CR6    0  -0.156   3.2919  -0.5514   0.4966
 9RF  C06   C  CH2    0  -0.619   0.9484   0.8348   0.0242
 9RF  C07   C  CR5    0   0.092  -0.5224   0.9085   0.1948
 9RF  C12   C  CR6    0   0.112  -4.2920   0.2739   0.1441
 9RF  C14   C  CR16   0  -0.247  -6.5915   0.7322   0.6973
 9RF  C23   C  CR16   0  -0.377   5.4629   0.1712   1.2446
 9RF  C27   C  C      0   0.383   9.6648   0.3571   0.1926
 9RF  F17   F  F      0  -0.310  -9.1999   0.3171  -0.3742
 9RF  F18   F  F      0  -0.300  -8.7209  -1.7012  -0.9469
 9RF  F19   F  F      0  -0.312  -8.8767  -1.1776   1.1346
 9RF  N08   N  N      0  -0.220  -1.1273   1.8215   0.8844
 9RF  N09   N  N      0  -0.263  -2.4587   1.6736   0.9099
 9RF  O28   O  O      0  -0.587   9.8852  -0.1383  -0.9207
 9RF  O29   O  OC    -1  -0.623  10.4799   0.8739   0.9819
 9RF  S05   S  S2     0   0.002   1.5541  -0.7239   0.7740
 9RF  S11   S  S2     0   0.242  -1.5991  -0.2502  -0.4878
 9RF  H131  H  HCR6   0   0.276  -4.9540   1.9417   1.3321
 9RF  H201  H  HCR6   0   0.282  -6.3260  -2.0652  -1.2085
 9RF  H211  H  HCR6   0   0.270  -3.9806  -1.4831  -1.0729
 9RF  H221  H  HCR6   0   0.269   3.6612   0.4358   2.3657
 9RF  H262  H  HCH2   0   0.230   8.1864  -0.1605   1.6807
 9RF  H261  H  HCH2   0   0.230   7.9144   1.4008   0.9077
 9RF  H012  H  HCH3   0   0.244   6.6172  -2.2274  -1.9463
 9RF  H013  H  HCH3   0   0.241   5.0990  -1.9375  -2.7917
 9RF  H011  H  HCH3   0   0.244   6.3413  -0.6887  -2.7366
 9RF  H031  H  HCR6   0   0.259   3.2536  -1.5254  -1.4159
 9RF  H062  H  HCH2   0   0.312   1.2203   0.8546  -1.0315
 9RF  H061  H  HCH2   0   0.312   1.4022   1.6885   0.5250
 9RF  H141  H  HCR6   0   0.284  -7.3168   1.3606   1.1976
 9RF  H231  H  HCR6   0   0.281   6.0608   0.6497   2.0079
 9RF  C01   C  CH3    0  -0.708   5.8552  -1.4761  -2.1587
 9RF  C16   C  CT     0   1.055  -8.4455  -0.7436  -0.0588
 9RF  O25   O  O2     0  -0.443   7.3445  -0.2477  -0.2107

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
 9RF  O28  C27   deloc     1.238  0.020  1.238
 9RF  O29  C27   deloc     1.247  0.020  1.247
 9RF  C27  C26   single    1.538  0.020  1.538
 9RF  C22  C23   aromatic  1.388  0.020  1.388
 9RF  C22  C04   aromatic  1.386  0.020  1.386
 9RF  C23  C24   aromatic  1.394  0.020  1.394
 9RF  S05  C04   single    1.768  0.020  1.768
 9RF  S05  C06   single    1.833  0.020  1.833
 9RF  C04  C03   aromatic  1.396  0.020  1.396
 9RF  C06  C07   single    1.483  0.020  1.483
 9RF  C26  O25   single    1.416  0.020  1.416
 9RF  C24  O25   single    1.338  0.020  1.338
 9RF  C24  C02   aromatic  1.408  0.020  1.408
 9RF  C03  C02   aromatic  1.384  0.020  1.384
 9RF  C02  C01   single    1.499  0.020  1.499
 9RF  C07  N08   aromatic  1.294  0.020  1.294
 9RF  C07  S11   aromatic  1.723  0.020  1.723
 9RF  N08  N09   aromatic  1.340  0.020  1.340
 9RF  S11  C10   aromatic  1.727  0.020  1.727
 9RF  N09  C10   aromatic  1.297  0.020  1.297
 9RF  C10  C12   single    1.461  0.020  1.461
 9RF  C12  C13   aromatic  1.397  0.020  1.397
 9RF  C12  C21   aromatic  1.392  0.020  1.392
 9RF  C13  C14   aromatic  1.380  0.020  1.380
 9RF  C21  C20   aromatic  1.386  0.020  1.386
 9RF  C14  C15   aromatic  1.392  0.020  1.392
 9RF  C20  C15   aromatic  1.387  0.020  1.387
 9RF  C15  C16   single    1.497  0.020  1.497
 9RF  C16  F19   single    1.341  0.020  1.341
 9RF  C16  F18   single    1.335  0.020  1.335
 9RF  C16  F17   single    1.339  0.020  1.339
 9RF  C13  H131  single    0.930  0.020  1.080
 9RF  C20  H201  single    0.930  0.020  1.080
 9RF  C21  H211  single    0.930  0.020  1.080
 9RF  C22  H221  single    0.930  0.020  1.080
 9RF  C26  H262  single    0.970  0.020  1.090
 9RF  C26  H261  single    0.970  0.020  1.090
 9RF  C01  H012  single    0.970  0.020  1.090
 9RF  C01  H013  single    0.970  0.020  1.090
 9RF  C01  H011  single    0.970  0.020  1.090
 9RF  C03  H031  single    0.930  0.020  1.080
 9RF  C06  H062  single    0.970  0.020  1.090
 9RF  C06  H061  single    0.970  0.020  1.090
 9RF  C14  H141  single    0.930  0.020  1.080
 9RF  C23  H231  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
 9RF  S11   C10  N09   112.72  3.000
 9RF  N09   C10  C12   123.47  3.000
 9RF  S11   C10  C12   123.81  3.000
 9RF  H131  C13  C14   119.59  3.000
 9RF  H131  C13  C12   120.07  3.000
 9RF  C14   C13  C12   120.34  3.000
 9RF  C16   C15  C14   118.77  3.000
 9RF  C16   C15  C20   121.26  3.000
 9RF  C14   C15  C20   119.95  3.000
 9RF  H201  C20  C21   118.78  3.000
 9RF  H201  C20  C15   121.36  3.000
 9RF  C21   C20  C15   119.85  3.000
 9RF  H211  C21  C12   121.07  3.000
 9RF  H211  C21  C20   118.33  3.000
 9RF  C12   C21  C20   120.60  3.000
 9RF  H221  C22  C23   119.38  3.000
 9RF  H221  C22  C04   120.25  3.000
 9RF  C23   C22  C04   120.38  3.000
 9RF  O25   C24  C23   124.28  3.000
 9RF  O25   C24  C02   115.59  3.000
 9RF  C23   C24  C02   120.13  3.000
 9RF  H261  C26  H262  106.99  3.000
 9RF  H261  C26  O25   110.47  3.000
 9RF  H262  C26  O25   110.48  3.000
 9RF  H261  C26  C27   108.99  3.000
 9RF  H262  C26  C27   109.05  3.000
 9RF  O25   C26  C27   110.77  3.000
 9RF  C03   C02  C01   121.23  3.000
 9RF  C01   C02  C24   120.27  3.000
 9RF  C03   C02  C24   118.50  3.000
 9RF  H031  C03  C04   119.41  3.000
 9RF  H031  C03  C02   118.90  3.000
 9RF  C04   C03  C02   121.68  3.000
 9RF  S05   C04  C03   120.56  3.000
 9RF  C03   C04  C22   119.15  3.000
 9RF  S05   C04  C22   120.27  3.000
 9RF  H061  C06  H062  109.10  3.000
 9RF  H061  C06  S05   109.94  3.000
 9RF  H062  C06  S05   109.22  3.000
 9RF  H061  C06  C07   108.76  3.000
 9RF  H062  C06  C07   110.97  3.000
 9RF  S05   C06  C07   108.85  3.000
 9RF  S11   C07  N08   113.17  3.000
 9RF  S11   C07  C06   122.75  3.000
 9RF  N08   C07  C06   124.06  3.000
 9RF  C21   C12  C13   119.15  3.000
 9RF  C21   C12  C10   121.51  3.000
 9RF  C13   C12  C10   119.34  3.000
 9RF  H141  C14  C15   121.00  3.000
 9RF  H141  C14  C13   118.88  3.000
 9RF  C15   C14  C13   120.11  3.000
 9RF  H231  C23  C24   121.33  3.000
 9RF  H231  C23  C22   118.52  3.000
 9RF  C24   C23  C22   120.15  3.000
 9RF  O29   C27  O28   128.22  3.000
 9RF  O29   C27  C26   113.32  3.000
 9RF  O28   C27  C26   118.46  3.000
 9RF  N09   N08  C07   113.37  3.000
 9RF  N08   N09  C10   113.72  3.000
 9RF  C06   S05  C04   100.23  3.000
 9RF  C07   S11  C10    87.02  3.000
 9RF  H011  C01  H013  107.90  3.000
 9RF  H011  C01  H012  106.80  3.000
 9RF  H013  C01  H012  107.84  3.000
 9RF  H011  C01  C02   111.71  3.000
 9RF  H013  C01  C02   110.64  3.000
 9RF  H012  C01  C02   111.74  3.000
 9RF  F19   C16  F18   107.07  3.000
 9RF  F18   C16  F17   107.17  3.000
 9RF  F19   C16  F17   106.55  3.000
 9RF  F17   C16  C15   111.66  3.000
 9RF  F18   C16  C15   112.73  3.000
 9RF  F19   C16  C15   111.33  3.000
 9RF  C26   O25  C24   119.14  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
 9RF  CONST_01  N08   C07  S11  C10     0.00   0.0  0
 9RF  CONST_02  C07   N08  N09  C10     0.00   0.0  0
 9RF  CONST_03  C14   C13  C12  C10   180.00   0.0  0
 9RF  CONST_04  C20   C21  C12  C10   180.00   0.0  0
 9RF  CONST_05  S11   C10  C12  C13   180.00   0.0  0
 9RF  CONST_06  N09   C10  C12  C13     0.00   0.0  0
 9RF  CONST_07  C20   C21  C12  C13     0.00   0.0  0
 9RF  CONST_08  C20   C15  C14  C13     0.00   0.0  0
 9RF  CONST_09  C12   C13  C14  C15     0.00   0.0  0
 9RF  CONST_10  C12   C21  C20  C15     0.00   0.0  0
 9RF  CONST_11  S11   C10  C12  C21     0.00   0.0  0
 9RF  CONST_12  N09   C10  C12  C21   180.00   0.0  0
 9RF  CONST_13  C14   C13  C12  C21     0.00   0.0  0
 9RF  CONST_14  C14   C15  C20  C21     0.00   0.0  0
 9RF  CONST_15  C02   C24  C23  C22     0.00   0.0  0
 9RF  CONST_16  C02   C03  C04  C22     0.00   0.0  0
 9RF  CONST_17  C04   C22  C23  C24     0.00   0.0  0
 9RF  CONST_18  C04   C03  C02  C24     0.00   0.0  0
 9RF  CONST_19  C23   C22  C04  C03     0.00   0.0  0
 9RF  CONST_20  C23   C24  C02  C03     0.00   0.0  0
 9RF  CONST_21  N09   C10  S11  C07     0.00   0.0  0
 9RF  CONST_22  C12   C10  S11  C07   180.00   0.0  0
 9RF  CONST_23  N08   N09  C10  C12   180.00   0.0  0
 9RF  CONST_24  S11   C10  N09  N08     0.00   0.0  0
 9RF  CONST_25  S11   C07  N08  N09     0.00   0.0  0
 9RF  CONST_26  C06   C07  S11  C10   180.00   0.0  0
 9RF  CONST_27  C16   C15  C14  C13   180.00   0.0  0
 9RF  CONST_28  C16   C15  C20  C21   180.00   0.0  0
 9RF  CONST_29  O25   C24  C23  C22   180.00   0.0  0
 9RF  CONST_30  C23   C24  C02  C01   180.00   0.0  0
 9RF  CONST_31  C04   C03  C02  C01   180.00   0.0  0
 9RF  CONST_32  S05   C04  C03  C02   180.00   0.0  0
 9RF  CONST_33  O25   C24  C02  C03   180.00   0.0  0
 9RF  CONST_34  N09   N08  C07  C06   180.00   0.0  0
 9RF  CONST_35  S05   C04  C22  C23   180.00   0.0  0
 9RF  CONST_36  H131  C13  C12  C10     0.00   0.0  0
 9RF  CONST_37  H211  C21  C12  C10     0.00   0.0  0
 9RF  CONST_38  H141  C14  C15  C20   180.00   0.0  0
 9RF  CONST_39  H031  C03  C04  C22   180.00   0.0  0
 9RF  CONST_40  H221  C22  C23  C24   180.00   0.0  0
 9RF  CONST_41  H231  C23  C24  C02   180.00   0.0  0
 9RF  CONST_42  H201  C20  C21  C12   180.00   0.0  0
 9RF  Var_01    F19   C16  C15  C20   108.45  30.0  2
 9RF  Var_02    C23   C24  O25  C26    -0.21  30.0  2
 9RF  Var_03    C07   C06  S05  C04  -178.17  30.0  3
 9RF  Var_04    S05   C06  C07  N08   116.96  30.0  2
 9RF  Var_05    H012  C01  C02  C24    58.82  30.0  2
 9RF  Var_06    C27   C26  O25  C24  -179.31  30.0  1
 9RF  Var_07    O28   C27  C26  O25     0.78  30.0  2

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
 9RF  plan-1  C10   0.020
 9RF  plan-1  C06   0.020
 9RF  plan-1  C07   0.020
 9RF  plan-1  C12   0.020
 9RF  plan-1  N08   0.020
 9RF  plan-1  N09   0.020
 9RF  plan-1  S11   0.020
 9RF  plan-2  C22   0.020
 9RF  plan-2  C24   0.020
 9RF  plan-2  C02   0.020
 9RF  plan-2  C03   0.020
 9RF  plan-2  C04   0.020
 9RF  plan-2  C23   0.020
 9RF  plan-2  S05   0.020
 9RF  plan-2  H221  0.020
 9RF  plan-2  H031  0.020
 9RF  plan-2  H231  0.020
 9RF  plan-2  C01   0.020
 9RF  plan-2  O25   0.020
 9RF  plan-3  C10   0.020
 9RF  plan-3  C13   0.020
 9RF  plan-3  C15   0.020
 9RF  plan-3  C20   0.020
 9RF  plan-3  C21   0.020
 9RF  plan-3  C12   0.020
 9RF  plan-3  C14   0.020
 9RF  plan-3  H131  0.020
 9RF  plan-3  H201  0.020
 9RF  plan-3  H211  0.020
 9RF  plan-3  H141  0.020
 9RF  plan-3  C16   0.020
 9RF  plan-4  C26   0.020
 9RF  plan-4  C27   0.020
 9RF  plan-4  O28   0.020
 9RF  plan-4  O29   0.020

