# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 11:58:19 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-(4-{[(2-chloro-6-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-5-methyl-N-(oxetan-3-yl)thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(cc1n2cc(NC(=O)Nc3c(F)cccc3Cl)cn2)C(=O)NC4COC4
#
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
 X3S  X3S  4-(4-{[(2-chloro-6-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-5-methyl-N-(oxetan-3-yl)thiophene-2-carboxamide  ligand  47  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X3S
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
 X3S  C2   C   CR16  0  -0.243  17.3575  11.9945  35.1338
 X3S  C1   C   CR16  0  -0.238  17.4386  12.1227  36.5125
 X3S  C4   C   CR6   0   0.107  19.7808  11.9488  35.0051
 X3S  C5   C   CR6   0   0.570  19.8103  12.0752  36.3903
 X3S  C6   C   CR16  0  -0.420  18.6663  12.1677  37.1557
 X3S  C3   C   CR6   0  -0.052  18.5258  11.9167  34.3931
 X3S  C10  C   CR15  0  -0.101  20.4566   7.1679  33.6924
 X3S  C11  C   CR5   0   0.414  23.1042   5.7177  32.0478
 X3S  C12  C   CR5   0  -0.203  23.8363   6.0246  30.9296
 X3S  C13  C   CR5   0  -0.293  24.2471   3.7335  31.7898
 X3S  C14  C   CR15  0  -0.229  23.3326   4.4089  32.5412
 X3S  C15  C   C     0   0.557  24.8068   2.3754  31.8986
 X3S  C16  C   C     0  -0.185  24.9024   0.2827  33.0977
 X3S  C17  C   C     0  -0.147  24.5304  -0.3920  34.4203
 X3S  C18  C   C     0  -0.126  26.3438   0.1411  33.6051
 X3S  C19  C   CH3   0  -0.731  23.8466   7.2798  30.1262
 X3S  C7   C   C     0   0.670  21.5434  10.7350  33.7785
 X3S  C8   C   CR5   0   0.084  21.2329   8.3363  33.5543
 X3S  C9   C   CR15  0   0.009  22.3660   7.9261  32.8909
 X3S  F1   F   F     0  -0.292  21.0037  12.1067  36.9845
 X3S  N1   N   NH1   0  -0.731  20.9734  11.8779  34.2735
 X3S  N2   N   NH1   0  -0.761  20.8590   9.5861  34.0273
 X3S  N3   N   NR5   0  -0.402  22.2048   6.5940  32.6706
 X3S  N4   N   N     0  -0.265  21.0590   6.1282  33.1555
 X3S  N5   N   NH1   0  -0.669  24.3868   1.6120  32.9185
 X3S  O1   O   O     0  -0.498  22.5919  10.7646  33.1567
 X3S  O2   O   O     0  -0.484  25.6227   1.9829  31.0730
 X3S  O3   O   O     0  -0.504  25.9056  -0.5692  34.7705
 X3S  S1   S   S2    0   0.276  24.8315   4.6999  30.4932
 X3S  CL1  CL  CL    0  -0.083  18.4416  11.7652  32.6795
 X3S  H2   H   HCR6  0   0.289  16.3966  11.9618  34.6400
 X3S  H1   H   HCR6  0   0.285  16.5293  12.1888  37.0940
 X3S  H3   H   HCR6  0   0.293  18.7350  12.2661  38.2307
 X3S  H7   H   HCR5  0   0.275  19.4898   7.0670  34.1632
 X3S  H8   H   HCR5  0   0.285  22.8278   4.0151  33.4125
 X3S  H10  H   H     0   0.282  24.6925  -0.3274  32.2183
 X3S  H11  H   H     0   0.233  23.9916  -1.3378  34.3303
 X3S  H13  H   H     0   0.224  27.0094  -0.4556  32.9774
 X3S  H14  H   H     0   0.217  26.8312   1.0897  33.8480
 X3S  H16  H   HCH3  0   0.271  24.1484   7.0878  29.0979
 X3S  H17  H   HCH3  0   0.265  22.8562   7.7338  30.1043
 X3S  H15  H   HCH3  0   0.269  24.5393   8.0141  30.5408
 X3S  H6   H   HCR5  0   0.306  23.2555   8.4491  32.5934
 X3S  H4   H   HNH1  0   0.413  21.5349  12.7128  34.1913
 X3S  H5   H   HNH1  0   0.423  20.0222   9.6091  34.5899
 X3S  H9   H   HNH1  0   0.417  23.7599   1.9839  33.6140
 X3S  H12  H   H     0   0.221  23.9943   0.2516  35.1263

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
 X3S  C19  C12  single    1.490  0.020  1.490
 X3S  S1   C12  aromatic  1.713  0.020  1.713
 X3S  S1   C13  aromatic  1.719  0.020  1.719
 X3S  C12  C11  aromatic  1.371  0.020  1.371
 X3S  C13  C15  single    1.473  0.020  1.473
 X3S  C13  C14  aromatic  1.363  0.020  1.363
 X3S  C11  C14  aromatic  1.417  0.020  1.417
 X3S  C11  N3   single    1.402  0.020  1.402
 X3S  O2   C15  double    1.225  0.020  1.225
 X3S  C15  N5   single    1.341  0.020  1.341
 X3S  O1   C7   double    1.219  0.020  1.219
 X3S  N3   C9   aromatic  1.360  0.020  1.360
 X3S  N3   N4   aromatic  1.328  0.020  1.328
 X3S  C9   C8   aromatic  1.376  0.020  1.376
 X3S  N5   C16  single    1.437  0.020  1.437
 X3S  N4   C10  aromatic  1.316  0.020  1.316
 X3S  C8   C10  aromatic  1.410  0.020  1.410
 X3S  C8   N2   single    1.388  0.020  1.388
 X3S  C7   N2   single    1.360  0.020  1.360
 X3S  C7   N1   single    1.370  0.020  1.370
 X3S  C16  C17  single    1.531  0.020  1.531
 X3S  C16  C18  single    1.535  0.020  1.535
 X3S  CL1  C3   single    1.722  0.020  1.722
 X3S  N1   C4   single    1.401  0.020  1.401
 X3S  C17  O3   single    1.430  0.020  1.430
 X3S  C18  O3   single    1.433  0.020  1.433
 X3S  C4   C3   aromatic  1.397  0.020  1.397
 X3S  C4   C5   aromatic  1.391  0.020  1.391
 X3S  C3   C2   aromatic  1.386  0.020  1.386
 X3S  C5   F1   single    1.334  0.020  1.334
 X3S  C5   C6   aromatic  1.379  0.020  1.379
 X3S  C2   C1   aromatic  1.387  0.020  1.387
 X3S  C1   C6   aromatic  1.387  0.020  1.387
 X3S  C2   H2   single    0.930  0.020  1.080
 X3S  C1   H1   single    0.930  0.020  1.080
 X3S  C6   H3   single    0.930  0.020  1.080
 X3S  C10  H7   single    0.930  0.020  1.080
 X3S  C14  H8   single    0.930  0.020  1.080
 X3S  C16  H10  single    0.970  0.020  1.090
 X3S  C17  H12  single    0.970  0.020  1.090
 X3S  C17  H11  single    0.970  0.020  1.090
 X3S  C18  H13  single    0.970  0.020  1.090
 X3S  C18  H14  single    0.970  0.020  1.090
 X3S  C19  H16  single    0.970  0.020  1.090
 X3S  C19  H17  single    0.970  0.020  1.090
 X3S  C19  H15  single    0.970  0.020  1.090
 X3S  C9   H6   single    0.930  0.020  1.080
 X3S  N1   H4   single    0.860  0.020  1.020
 X3S  N2   H5   single    0.860  0.020  1.020
 X3S  N5   H9   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
 X3S  H2   C2   C3   120.25  3.000
 X3S  H2   C2   C1   120.59  3.000
 X3S  C3   C2   C1   119.16  3.000
 X3S  H1   C1   C6   119.54  3.000
 X3S  H1   C1   C2   119.40  3.000
 X3S  C6   C1   C2   121.05  3.000
 X3S  N1   C4   C3   122.34  3.000
 X3S  C3   C4   C5   117.22  3.000
 X3S  N1   C4   C5   120.43  3.000
 X3S  F1   C5   C6   119.56  3.000
 X3S  C6   C5   C4   122.75  3.000
 X3S  F1   C5   C4   117.69  3.000
 X3S  H3   C6   C5   120.32  3.000
 X3S  H3   C6   C1   121.34  3.000
 X3S  C5   C6   C1   118.34  3.000
 X3S  CL1  C3   C4   118.81  3.000
 X3S  C4   C3   C2   121.48  3.000
 X3S  CL1  C3   C2   119.71  3.000
 X3S  H7   C10  N4   120.91  3.000
 X3S  H7   C10  C8   127.82  3.000
 X3S  N4   C10  C8   111.27  3.000
 X3S  N3   C11  C14  121.74  3.000
 X3S  N3   C11  C12  124.40  3.000
 X3S  C14  C11  C12  113.86  3.000
 X3S  S1   C12  C19  120.65  3.000
 X3S  S1   C12  C11  110.16  3.000
 X3S  C19  C12  C11  129.18  3.000
 X3S  S1   C13  C15  116.41  3.000
 X3S  C15  C13  C14  132.16  3.000
 X3S  S1   C13  C14  111.43  3.000
 X3S  H8   C14  C13  125.25  3.000
 X3S  H8   C14  C11  122.80  3.000
 X3S  C13  C14  C11  111.95  3.000
 X3S  O2   C15  N5   122.58  3.000
 X3S  N5   C15  C13  117.51  3.000
 X3S  O2   C15  C13  119.91  3.000
 X3S  H10  C16  N5   110.35  3.000
 X3S  H10  C16  C18  113.31  3.000
 X3S  N5   C16  C18  117.62  3.000
 X3S  H10  C16  C17  113.78  3.000
 X3S  C18  C16  C17   84.37  3.000
 X3S  N5   C16  C17  115.36  3.000
 X3S  H11  C17  H12  108.68  3.000
 X3S  H11  C17  O3   112.79  3.000
 X3S  H12  C17  O3   112.68  3.000
 X3S  H11  C17  C16  115.50  3.000
 X3S  H12  C17  C16  114.63  3.000
 X3S  O3   C17  C16   91.86  3.000
 X3S  H14  C18  H13  109.26  3.000
 X3S  H14  C18  O3   112.67  3.000
 X3S  H13  C18  O3   112.51  3.000
 X3S  H14  C18  C16  114.33  3.000
 X3S  H13  C18  C16  115.64  3.000
 X3S  O3   C18  C16   91.57  3.000
 X3S  H15  C19  H17  107.71  3.000
 X3S  H15  C19  H16  107.55  3.000
 X3S  H17  C19  H16  107.84  3.000
 X3S  H15  C19  C12  111.49  3.000
 X3S  H17  C19  C12  110.82  3.000
 X3S  H16  C19  C12  111.26  3.000
 X3S  O1   C7   N2   123.12  3.000
 X3S  N2   C7   N1   115.42  3.000
 X3S  O1   C7   N1   121.46  3.000
 X3S  N2   C8   C9   130.91  3.000
 X3S  N2   C8   C10  124.38  3.000
 X3S  C9   C8   C10  104.70  3.000
 X3S  H6   C9   N3   122.03  3.000
 X3S  H6   C9   C8   132.12  3.000
 X3S  N3   C9   C8   105.82  3.000
 X3S  H4   N1   C7   115.42  3.000
 X3S  H4   N1   C4   118.30  3.000
 X3S  C7   N1   C4   125.82  3.000
 X3S  H5   N2   C8   115.74  3.000
 X3S  H5   N2   C7   120.01  3.000
 X3S  C8   N2   C7   124.25  3.000
 X3S  N4   N3   C9   112.74  3.000
 X3S  N4   N3   C11  119.76  3.000
 X3S  C9   N3   C11  127.47  3.000
 X3S  N3   N4   C10  105.47  3.000
 X3S  H9   N5   C16  118.59  3.000
 X3S  H9   N5   C15  120.64  3.000
 X3S  C16  N5   C15  120.59  3.000
 X3S  C18  O3   C17   91.92  3.000
 X3S  C13  S1   C12   92.58  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
 X3S  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 X3S  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 X3S  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 X3S  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 X3S  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 X3S  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 X3S  CONST_07  C11  N3   N4   C10   180.00   0.0  0
 X3S  CONST_08  C9   N3   N4   C10     0.00   0.0  0
 X3S  CONST_09  N3   C9   C8   C10     0.00   0.0  0
 X3S  CONST_10  C13  S1   C12  C11     0.00   0.0  0
 X3S  CONST_11  S1   C13  C14  C11     0.00   0.0  0
 X3S  CONST_12  C8   C9   N3   C11   180.00   0.0  0
 X3S  CONST_13  C14  C13  S1   C12     0.00   0.0  0
 X3S  CONST_14  C13  C14  C11  C12     0.00   0.0  0
 X3S  CONST_17  N3   C11  C14  C13   180.00   0.0  0
 X3S  CONST_18  S1   C12  C11  C14     0.00   0.0  0
 X3S  CONST_21  N4   N3   C9   C8      0.00   0.0  0
 X3S  CONST_22  N3   N4   C10  C8      0.00   0.0  0
 X3S  CONST_23  N4   C10  C8   C9      0.00   0.0  0
 X3S  CONST_24  S1   C12  C11  N3    180.00   0.0  0
 X3S  CONST_25  N1   C4   C3   C2    180.00   0.0  0
 X3S  CONST_26  CL1  C3   C2   C1    180.00   0.0  0
 X3S  CONST_27  F1   C5   C6   C1    180.00   0.0  0
 X3S  CONST_28  CL1  C3   C4   C5    180.00   0.0  0
 X3S  CONST_29  N1   C4   C5   C6    180.00   0.0  0
 X3S  CONST_30  F1   C5   C4   C3    180.00   0.0  0
 X3S  CONST_31  C15  C13  C14  C11   180.00   0.0  0
 X3S  CONST_32  C15  C13  S1   C12   180.00   0.0  0
 X3S  CONST_33  C19  C12  S1   C13   180.00   0.0  0
 X3S  CONST_34  C19  C12  C11  C14   180.00   0.0  0
 X3S  CONST_35  N3   C11  C12  C19     0.00   0.0  0
 X3S  CONST_36  N3   C9   C8   N2    180.00   0.0  0
 X3S  CONST_37  N4   C10  C8   N2    180.00   0.0  0
 X3S  CONST_38  H3   C6   C1   C2    180.00   0.0  0
 X3S  CONST_39  H2   C2   C3   C4    180.00   0.0  0
 X3S  CONST_40  H1   C1   C6   C5    180.00   0.0  0
 X3S  CONST_41  H6   C9   C8   C10   180.00   0.0  0
 X3S  CONST_42  H8   C14  C11  C12   180.00   0.0  0
 X3S  CONST_43  H7   C10  C8   C9    180.00   0.0  0
 X3S  CONST_44  C16  N5   C15  C13   180.00   0.0  0
 X3S  CONST_47  C7   N2   C8   C10   180.00   0.0  0
 X3S  CONST_48  C9   C8   N2   C7      0.00   0.0  0
 X3S  CONST_50  H5   N2   C8   C10     0.00   0.0  0
 X3S  CONST_51  O1   C7   N1   C4    180.00   0.0  0
 X3S  CONST_52  O2   C15  N5   C16     0.00   0.0  0
 X3S  CONST_53  O1   C7   N2   C8      0.00   0.0  0
 X3S  CONST_54  N2   C7   N1   C4      0.00   0.0  0
 X3S  CONST_55  N1   C7   N2   C8    180.00   0.0  0
 X3S  CONST_56  H9   N5   C15  C13     0.00   0.0  0
 X3S  Var_01    H13  C18  O3   C17  -122.80  30.0  1
 X3S  Var_02    H12  C17  O3   C18  -113.62  30.0  1
 X3S  Var_03    O2   C15  C13  C14   179.10  30.0  2
 X3S  Var_04    H16  C19  C12  C11  -154.05  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
 X3S  chir_01  C16  N5  C17  C18  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
 X3S  plan-1  C10  0.020
 X3S  plan-1  C11  0.020
 X3S  plan-1  C8   0.020
 X3S  plan-1  C9   0.020
 X3S  plan-1  N2   0.020
 X3S  plan-1  N3   0.020
 X3S  plan-1  N4   0.020
 X3S  plan-1  H7   0.020
 X3S  plan-1  H6   0.020
 X3S  plan-2  C11  0.020
 X3S  plan-2  C12  0.020
 X3S  plan-2  C13  0.020
 X3S  plan-2  C14  0.020
 X3S  plan-2  C15  0.020
 X3S  plan-2  C19  0.020
 X3S  plan-2  N3   0.020
 X3S  plan-2  S1   0.020
 X3S  plan-2  H8   0.020
 X3S  plan-3  C2   0.020
 X3S  plan-3  C1   0.020
 X3S  plan-3  C4   0.020
 X3S  plan-3  C5   0.020
 X3S  plan-3  C6   0.020
 X3S  plan-3  C3   0.020
 X3S  plan-3  F1   0.020
 X3S  plan-3  N1   0.020
 X3S  plan-3  CL1  0.020
 X3S  plan-3  H2   0.020
 X3S  plan-3  H1   0.020
 X3S  plan-3  H3   0.020
 X3S  plan-4  C4   0.020
 X3S  plan-4  C7   0.020
 X3S  plan-4  C8   0.020
 X3S  plan-4  N1   0.020
 X3S  plan-4  N2   0.020
 X3S  plan-4  O1   0.020
 X3S  plan-4  H4   0.020
 X3S  plan-4  H5   0.020
 X3S  plan-5  C13  0.020
 X3S  plan-5  C15  0.020
 X3S  plan-5  C16  0.020
 X3S  plan-5  N5   0.020
 X3S  plan-5  O2   0.020
 X3S  plan-5  H9   0.020

