# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:51:31 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-cyclopropyl-1-[3-(1,3-thiazol-2-yl)benzyl]-3-[4-(trifluoromethoxy)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)Oc1ccc(NC(=O)N(Cc2cccc(c2)c3sccn3)C4CC4)cc1
#
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
 31W  31W  1-cyclopropyl-1-[3-(1,3-thiazol-2-yl)benzyl]-3-[4-(trifluoromethoxy)phenyl]urea  ligand  48  30  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_31W
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
 31W  C2   C  CH2   0  -0.497  -1.6932   4.2182   0.7289
 31W  C3   C  CH2   0  -0.499  -2.9669   4.0321  -0.0261
 31W  C5   C  CR6   0   0.157  -3.1563   0.2017  -0.2657
 31W  C7   C  CR6   0   0.125  -4.3575  -1.8907  -0.0034
 31W  C9   C  CR15  0  -0.012  -5.9403  -5.0666  -0.6487
 31W  C10  C  CR15  0  -0.502  -5.7304  -4.9182  -1.9825
 31W  C11  C  CR16  0  -0.302  -4.4616  -1.6552   1.3684
 31W  C12  C  CR16  0  -0.224  -3.9164  -0.5040   1.9102
 31W  C13  C  CR16  0  -0.302  -3.2691   0.4216   1.1020
 31W  C15  C  CR16  0  -0.302   2.3467   0.7399   1.0085
 31W  C18  C  CT    0   1.071   6.7776   0.7167   0.6373
 31W  C20  C  CR16  0  -0.349   2.9634   2.9508   0.2917
 31W  O1   O  O     0  -0.508  -0.1547   0.2535  -0.3696
 31W  C    C  C     0   0.746  -0.3170   1.4595  -0.2723
 31W  N2   N  NH1   0  -0.795   0.6716   2.3177   0.1354
 31W  C14  C  CR6   0   0.387   1.9811   1.9732   0.4661
 31W  C19  C  CR16  0  -0.289   4.2818   2.7075   0.6330
 31W  C17  C  CR6   0   0.293   4.6267   1.4709   1.1488
 31W  O    O  O2    0  -0.523   5.9412   1.2341   1.5433
 31W  F2   F  F     0  -0.278   7.9638   0.5875   1.2112
 31W  F1   F  F     0  -0.300   6.3904  -0.4843   0.2017
 31W  F    F  F     0  -0.300   6.9163   1.4899  -0.4420
 31W  C16  C  CR16  0  -0.292   3.6695   0.4917   1.3414
 31W  N    N  NT    0  -0.509  -1.5168   2.0469  -0.5663
 31W  C1   C  CH1   0  -0.159  -1.6965   3.4673  -0.5742
 31W  C4   C  CH2   0  -0.353  -2.5123   1.2021  -1.1940
 31W  C6   C  CR16  0  -0.394  -3.6996  -0.9579  -0.8029
 31W  C8   C  CR5   0   0.018  -4.9317  -3.1120  -0.5699
 31W  S    S  S2    0   0.230  -4.9322  -3.4337  -2.2738
 31W  N1   N  N     0  -0.394  -5.4897  -4.0493   0.1344
 31W  H1   H  HCH2  0   0.270  -1.2309   5.1965   0.7457
 31W  H2   H  HCH2  0   0.269  -1.5610   3.6398   1.6346
 31W  H3   H  HCH2  0   0.263  -3.6977   3.3447   0.3817
 31W  H4   H  HCH2  0   0.271  -3.3937   4.8799  -0.5445
 31W  H5   H  HCR5  0   0.274  -6.4267  -5.9178  -0.1946
 31W  H6   H  HCR5  0   0.311  -5.9965  -5.5871  -2.7850
 31W  H7   H  HCR6  0   0.259  -4.9655  -2.3722   2.0019
 31W  H8   H  HCR6  0   0.261  -3.9955  -0.3238   2.9743
 31W  H9   H  HCR6  0   0.250  -2.8419   1.3107   1.5478
 31W  H10  H  HCR6  0   0.280   1.6118  -0.0281   1.1856
 31W  H11  H  HCR6  0   0.279   2.6938   3.9156  -0.1201
 31W  H12  H  HNH1  0   0.433   0.5054   3.3061   0.0301
 31W  H13  H  HCR6  0   0.281   5.0257   3.4820   0.5024
 31W  H14  H  HCR6  0   0.280   3.9407  -0.4620   1.7747
 31W  H15  H  HCH1  0   0.283  -1.2786   3.9835  -1.4357
 31W  H16  H  HCH2  0   0.264  -2.0910   0.6761  -2.0543
 31W  H17  H  HCH2  0   0.283  -3.2858   1.8598  -1.5926
 31W  H18  H  HCR6  0   0.247  -3.5934  -1.1300  -1.8693

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
 31W  C19  C20  aromatic  1.383  0.020  1.383
 31W  C19  C17  aromatic  1.384  0.020  1.384
 31W  C20  C14  aromatic  1.397  0.020  1.397
 31W  F2   C18  single    1.324  0.020  1.324
 31W  C2   C1   single    1.504  0.020  1.504
 31W  C2   C3   single    1.492  0.020  1.492
 31W  C1   C3   single    1.494  0.020  1.494
 31W  C1   N    single    1.432  0.020  1.432
 31W  C17  O    single    1.393  0.020  1.393
 31W  C17  C16  aromatic  1.383  0.020  1.383
 31W  C14  N2   single    1.394  0.020  1.394
 31W  C14  C15  aromatic  1.396  0.020  1.396
 31W  O    C18  single    1.337  0.020  1.337
 31W  N2   C    single    1.371  0.020  1.371
 31W  C18  F    single    1.335  0.020  1.335
 31W  C18  F1   single    1.335  0.020  1.335
 31W  N    C    single    1.368  0.020  1.368
 31W  N    C4   single    1.449  0.020  1.449
 31W  C    O1   double    1.221  0.020  1.221
 31W  C16  C15  aromatic  1.386  0.020  1.386
 31W  C4   C5   single    1.509  0.020  1.509
 31W  C5   C13  aromatic  1.390  0.020  1.390
 31W  C5   C6   aromatic  1.389  0.020  1.389
 31W  C13  C12  aromatic  1.389  0.020  1.389
 31W  C6   C7   aromatic  1.394  0.020  1.394
 31W  C12  C11  aromatic  1.384  0.020  1.384
 31W  C7   C11  aromatic  1.396  0.020  1.396
 31W  C7   C8   single    1.464  0.020  1.464
 31W  S    C8   aromatic  1.734  0.020  1.734
 31W  S    C10  aromatic  1.711  0.020  1.711
 31W  C8   N1   aromatic  1.298  0.020  1.298
 31W  C10  C9   aromatic  1.358  0.020  1.358
 31W  N1   C9   aromatic  1.361  0.020  1.361
 31W  C2   H1   single    0.970  0.020  1.090
 31W  C2   H2   single    0.970  0.020  1.090
 31W  C3   H3   single    0.970  0.020  1.090
 31W  C3   H4   single    0.970  0.020  1.090
 31W  C9   H5   single    0.930  0.020  1.080
 31W  C10  H6   single    0.930  0.020  1.080
 31W  C11  H7   single    0.930  0.020  1.080
 31W  C12  H8   single    0.930  0.020  1.080
 31W  C13  H9   single    0.930  0.020  1.080
 31W  C15  H10  single    0.930  0.020  1.080
 31W  C20  H11  single    0.930  0.020  1.080
 31W  N2   H12  single    0.860  0.020  1.020
 31W  C19  H13  single    0.930  0.020  1.080
 31W  C16  H14  single    0.930  0.020  1.080
 31W  C1   H15  single    0.970  0.020  1.090
 31W  C4   H16  single    0.970  0.020  1.090
 31W  C4   H17  single    0.970  0.020  1.090
 31W  C6   H18  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
 31W  H2   C2   H1   114.70  3.000
 31W  H2   C2   C1   117.28  3.000
 31W  H1   C2   C1   117.76  3.000
 31W  H2   C2   C3   117.44  3.000
 31W  H1   C2   C3   119.03  3.000
 31W  C1   C2   C3    59.83  3.000
 31W  H4   C3   H3   114.32  3.000
 31W  H4   C3   C1   117.12  3.000
 31W  H3   C3   C1   118.16  3.000
 31W  H4   C3   C2   118.79  3.000
 31W  H3   C3   C2   117.68  3.000
 31W  C1   C3   C2    60.47  3.000
 31W  C6   C5   C4   118.85  3.000
 31W  C6   C5   C13  118.75  3.000
 31W  C4   C5   C13  122.35  3.000
 31W  C8   C7   C6   121.44  3.000
 31W  C8   C7   C11  119.47  3.000
 31W  C6   C7   C11  119.08  3.000
 31W  H5   C9   N1   119.75  3.000
 31W  H5   C9   C10  124.64  3.000
 31W  N1   C9   C10  115.61  3.000
 31W  H6   C10  S    121.79  3.000
 31W  H6   C10  C9   128.68  3.000
 31W  S    C10  C9   109.53  3.000
 31W  H7   C11  C12  120.38  3.000
 31W  H7   C11  C7   119.90  3.000
 31W  C12  C11  C7   119.72  3.000
 31W  H8   C12  C13  119.69  3.000
 31W  H8   C12  C11  119.64  3.000
 31W  C13  C12  C11  120.67  3.000
 31W  H9   C13  C12  119.45  3.000
 31W  H9   C13  C5   120.21  3.000
 31W  C12  C13  C5   120.33  3.000
 31W  H10  C15  C16  118.92  3.000
 31W  H10  C15  C14  120.99  3.000
 31W  C16  C15  C14  120.09  3.000
 31W  F    C18  F1   106.70  3.000
 31W  F1   C18  F2   108.27  3.000
 31W  F    C18  F2   108.29  3.000
 31W  F1   C18  O    112.81  3.000
 31W  F    C18  O    112.88  3.000
 31W  F2   C18  O    107.73  3.000
 31W  H11  C20  C19  119.19  3.000
 31W  H11  C20  C14  119.72  3.000
 31W  C19  C20  C14  121.09  3.000
 31W  N    C    N2   115.31  3.000
 31W  N    C    O1   121.58  3.000
 31W  N2   C    O1   123.10  3.000
 31W  H12  N2   C14  114.97  3.000
 31W  H12  N2   C    117.63  3.000
 31W  C14  N2   C    126.39  3.000
 31W  N2   C14  C20  117.27  3.000
 31W  N2   C14  C15  123.82  3.000
 31W  C20  C14  C15  118.86  3.000
 31W  H13  C19  C17  120.90  3.000
 31W  H13  C19  C20  119.98  3.000
 31W  C17  C19  C20  119.13  3.000
 31W  C16  C17  O    119.57  3.000
 31W  C16  C17  C19  120.82  3.000
 31W  O    C17  C19  119.53  3.000
 31W  C17  O    C18  117.66  3.000
 31W  H14  C16  C17  120.42  3.000
 31W  H14  C16  C15  119.54  3.000
 31W  C17  C16  C15  120.02  3.000
 31W  C4   N    C1   119.33  3.000
 31W  C4   N    C    116.45  3.000
 31W  C1   N    C    122.50  3.000
 31W  H15  C1   N    115.27  3.000
 31W  H15  C1   C3   115.96  3.000
 31W  N    C1   C3   118.66  3.000
 31W  H15  C1   C2   116.64  3.000
 31W  N    C1   C2   119.36  3.000
 31W  C3   C1   C2    59.70  3.000
 31W  H17  C4   H16  106.02  3.000
 31W  H17  C4   N    107.10  3.000
 31W  H16  C4   N    110.91  3.000
 31W  H17  C4   C5   108.77  3.000
 31W  H16  C4   C5   109.25  3.000
 31W  N    C4   C5   114.41  3.000
 31W  H18  C6   C7   120.25  3.000
 31W  H18  C6   C5   118.31  3.000
 31W  C7   C6   C5   121.45  3.000
 31W  N1   C8   S    113.51  3.000
 31W  N1   C8   C7   124.13  3.000
 31W  S    C8   C7   122.36  3.000
 31W  C8   S    C10   89.64  3.000
 31W  C8   N1   C9   111.71  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
 31W  CONST_01  C11  C12  C13  C5      0.00   0.0  0
 31W  CONST_02  C11  C7   C6   C5      0.00   0.0  0
 31W  CONST_03  C8   C7   C6   C5    180.00   0.0  0
 31W  CONST_04  C13  C5   C6   C7      0.00   0.0  0
 31W  CONST_05  C13  C12  C11  C7      0.00   0.0  0
 31W  CONST_06  C10  S    C8   C7    180.00   0.0  0
 31W  CONST_07  C9   N1   C8   C7    180.00   0.0  0
 31W  CONST_08  C8   S    C10  C9      0.00   0.0  0
 31W  CONST_09  S    C8   N1   C9      0.00   0.0  0
 31W  CONST_10  N1   C8   S    C10     0.00   0.0  0
 31W  CONST_11  C8   N1   C9   C10     0.00   0.0  0
 31W  CONST_12  S    C8   C7   C11   180.00   0.0  0
 31W  CONST_13  N1   C8   C7   C11     0.00   0.0  0
 31W  CONST_14  C6   C5   C13  C12     0.00   0.0  0
 31W  CONST_15  C6   C7   C11  C12     0.00   0.0  0
 31W  CONST_16  C8   C7   C11  C12   180.00   0.0  0
 31W  CONST_17  C19  C20  C14  C15     0.00   0.0  0
 31W  CONST_18  C19  C17  C16  C15     0.00   0.0  0
 31W  CONST_19  C16  C17  C19  C20     0.00   0.0  0
 31W  CONST_20  C16  C15  C14  C20     0.00   0.0  0
 31W  CONST_21  C17  C19  C20  C14     0.00   0.0  0
 31W  CONST_22  C17  C16  C15  C14     0.00   0.0  0
 31W  CONST_23  S    C8   C7   C6      0.00   0.0  0
 31W  CONST_24  N1   C8   C7   C6    180.00   0.0  0
 31W  CONST_25  N1   C9   C10  S       0.00   0.0  0
 31W  CONST_26  C4   C5   C6   C7    180.00   0.0  0
 31W  CONST_27  C4   C5   C13  C12   180.00   0.0  0
 31W  CONST_28  O    C17  C16  C15   180.00   0.0  0
 31W  CONST_29  O    C17  C19  C20   180.00   0.0  0
 31W  CONST_30  C19  C20  C14  N2    180.00   0.0  0
 31W  CONST_31  C16  C15  C14  N2    180.00   0.0  0
 31W  CONST_32  H8   C12  C13  C5    180.00   0.0  0
 31W  CONST_33  H9   C13  C12  C11   180.00   0.0  0
 31W  CONST_34  H18  C6   C7   C11   180.00   0.0  0
 31W  CONST_35  H7   C11  C12  C13   180.00   0.0  0
 31W  CONST_36  H11  C20  C14  C15   180.00   0.0  0
 31W  CONST_37  H10  C15  C14  C20   180.00   0.0  0
 31W  CONST_38  H13  C19  C20  C14   180.00   0.0  0
 31W  CONST_39  H14  C16  C15  C14   180.00   0.0  0
 31W  CONST_40  H6   C10  S    C8    180.00   0.0  0
 31W  CONST_41  H5   C9   N1   C8    180.00   0.0  0
 31W  CONST_45  C14  N2   C    O1      0.00   0.0  0
 31W  CONST_46  C1   N    C    O1    180.00   0.0  0
 31W  CONST_47  N    C    N2   C14   180.00   0.0  0
 31W  CONST_48  C1   N    C    N2      0.00   0.0  0
 31W  CONST_49  C4   N    C    O1      0.00   0.0  0
 31W  CONST_50  C4   N    C    N2    180.00   0.0  0
 31W  Var_01    N    C1   C3   C2    109.13  30.0  1
 31W  Var_02    C    N    C1   C2    -71.17  30.0  3
 31W  Var_03    C1   N    C4   C5   -120.67  30.0  2
 31W  Var_04    N    C4   C5   C13    27.23  30.0  3
 31W  Var_05    C19  C17  O    C18   -91.51  30.0  3
 31W  Var_06    F2   C18  O    C17   179.36  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
 31W  chir_01  C1  C2  C3  N  both

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
 31W  plan-1  C7   0.020
 31W  plan-1  C9   0.020
 31W  plan-1  C10  0.020
 31W  plan-1  C8   0.020
 31W  plan-1  S    0.020
 31W  plan-1  N1   0.020
 31W  plan-1  H5   0.020
 31W  plan-1  H6   0.020
 31W  plan-2  C5   0.020
 31W  plan-2  C7   0.020
 31W  plan-2  C11  0.020
 31W  plan-2  C12  0.020
 31W  plan-2  C13  0.020
 31W  plan-2  C4   0.020
 31W  plan-2  C6   0.020
 31W  plan-2  C8   0.020
 31W  plan-2  H7   0.020
 31W  plan-2  H8   0.020
 31W  plan-2  H9   0.020
 31W  plan-2  H18  0.020
 31W  plan-3  C15  0.020
 31W  plan-3  C20  0.020
 31W  plan-3  N2   0.020
 31W  plan-3  C14  0.020
 31W  plan-3  C19  0.020
 31W  plan-3  C17  0.020
 31W  plan-3  O    0.020
 31W  plan-3  C16  0.020
 31W  plan-3  H10  0.020
 31W  plan-3  H11  0.020
 31W  plan-3  H13  0.020
 31W  plan-3  H14  0.020
 31W  plan-4  O1   0.020
 31W  plan-4  C    0.020
 31W  plan-4  N2   0.020
 31W  plan-4  C14  0.020
 31W  plan-4  N    0.020
 31W  plan-4  C1   0.020
 31W  plan-4  C4   0.020
 31W  plan-4  H12  0.020

