# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 02:46:46 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: 4-(4-{[(2-chloro-6-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(oxetan-3-yl)thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(Cl)c1NC(=O)Nc2cnn(c2)c3csc(c3)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
 X3Y  X3Y  4-(4-{[(2-chloro-6-fluorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(oxetan-3-yl)thiophene-2-carboxamide  ligand  44  29  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_X3Y
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
 X3Y  C4   C   CR5   0   0.457  22.8588   5.9144  32.2181
 X3Y  C5   C   C     0   0.673  20.3642  10.7805  33.0186
 X3Y  C6   C   CR15  0  -0.255  22.9935   4.5380  32.5331
 X3Y  N1   N   N     0  -0.262  21.0735   6.2163  33.7291
 X3Y  C2   C   CR5   0   0.085  20.6588   8.4100  33.4539
 X3Y  C1   C   CR15  0   0.015  21.6955   8.0594  32.6223
 X3Y  C10  C   CR6   0   0.564  19.2077  11.9605  35.7800
 X3Y  C11  C   CR16  0  -0.416  18.3589  12.0799  36.8601
 X3Y  C12  C   CR16  0  -0.241  17.0041  12.2484  36.6171
 X3Y  C13  C   CR16  0  -0.241  16.5095  12.2863  35.3220
 X3Y  C14  C   CR6   0  -0.062  17.3877  12.1468  34.2591
 X3Y  C15  C   C     0   0.560  24.4865   2.5577  31.7711
 X3Y  C16  C   C     0  -0.204  24.3017   0.3225  32.7513
 X3Y  C17  C   C     0  -0.131  23.1603  -0.6859  32.9373
 X3Y  C18  C   C     0  -0.129  24.7964  -0.2291  34.0964
 X3Y  C3   C   CR15  0  -0.088  20.3123   7.2139  34.1187
 X3Y  C7   C   CR5   0  -0.292  23.9893   3.9477  31.8105
 X3Y  C8   C   CR15  0  -0.528  23.7503   6.3310  31.2694
 X3Y  C9   C   CR6   0   0.133  18.7588  11.9846  34.4625
 X3Y  N2   N   NR5   0  -0.410  21.9045   6.7311  32.8301
 X3Y  N4   N   NH1   0  -0.737  19.6625  11.8928  33.3974
 X3Y  N5   N   NH1   0  -0.659  23.9562   1.7073  32.6676
 X3Y  O1   O   O     0  -0.495  21.2202  10.8321  32.1523
 X3Y  O2   O   O     0  -0.477  25.3356   2.2469  30.9478
 X3Y  O3   O   O     0  -0.504  23.8257  -1.2805  34.0558
 X3Y  S1   S   S2    0   0.287  24.7556   5.0570  30.7490
 X3Y  CL1  CL  CL    0  -0.085  16.7898  12.1733  32.6443
 X3Y  H1   H   HCR5  0   0.290  22.3687   4.0341  33.2562
 X3Y  H3   H   HCR5  0   0.305  22.2802   8.6321  31.9271
 X3Y  H4   H   HCR6  0   0.293  18.7521  12.0541  37.8675
 X3Y  H5   H   HCR6  0   0.285  16.3222  12.3517  37.4500
 X3Y  H6   H   HCR6  0   0.289  15.4518  12.4159  35.1410
 X3Y  H7   H   H     0   0.287  24.9602   0.0749  31.9227
 X3Y  H8   H   H     0   0.216  22.2069  -0.2210  33.2128
 X3Y  H9   H   H     0   0.233  22.9879  -1.3904  32.1205
 X3Y  H10  H   H     0   0.232  25.8237  -0.5995  34.1265
 X3Y  H11  H   H     0   0.216  24.6386   0.4573  34.9354
 X3Y  H12  H   HCR5  0   0.279  19.5395   7.0656  34.8585
 X3Y  H13  H   HCR5  0   0.319  23.8668   7.3181  30.8490
 X3Y  H14  H   HNH1  0   0.412  19.8148  12.7145  32.8305
 X3Y  H15  H   HNH1  0   0.416  23.2887   2.0544  33.3393
 X3Y  N3   N   NH1   0  -0.761  20.0360   9.6299  33.6686
 X3Y  F1   F   F     0  -0.294  20.5165  11.8078  35.9879
 X3Y  H2   H   HNH1  0   0.423  19.2406   9.6130  34.2887

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
 X3Y  S1   C8   aromatic  1.704  0.020  1.704
 X3Y  S1   C7   aromatic  1.716  0.020  1.716
 X3Y  C8   C4   aromatic  1.367  0.020  1.367
 X3Y  C7   C15  single    1.477  0.020  1.477
 X3Y  C7   C6   aromatic  1.365  0.020  1.365
 X3Y  O2   C15  double    1.223  0.020  1.223
 X3Y  C4   N2   single    1.397  0.020  1.397
 X3Y  C4   C6   aromatic  1.418  0.020  1.418
 X3Y  C15  N5   single    1.345  0.020  1.345
 X3Y  N2   C1   aromatic  1.361  0.020  1.361
 X3Y  N2   N1   aromatic  1.328  0.020  1.328
 X3Y  O1   C5   double    1.219  0.020  1.219
 X3Y  C1   C2   aromatic  1.374  0.020  1.374
 X3Y  N1   C3   aromatic  1.314  0.020  1.314
 X3Y  N5   C16  single    1.430  0.020  1.430
 X3Y  C2   C3   aromatic  1.412  0.020  1.412
 X3Y  C2   N3   single    1.386  0.020  1.386
 X3Y  C17  C16  single    1.534  0.020  1.534
 X3Y  C17  O3   single    1.431  0.020  1.431
 X3Y  C5   N3   single    1.362  0.020  1.362
 X3Y  C5   N4   single    1.369  0.020  1.369
 X3Y  CL1  C14  single    1.722  0.020  1.722
 X3Y  C16  C18  single    1.536  0.020  1.536
 X3Y  N4   C9   single    1.400  0.020  1.400
 X3Y  C14  C9   aromatic  1.396  0.020  1.396
 X3Y  C14  C13  aromatic  1.386  0.020  1.386
 X3Y  C18  O3   single    1.431  0.020  1.431
 X3Y  C9   C10  aromatic  1.392  0.020  1.392
 X3Y  C13  C12  aromatic  1.387  0.020  1.387
 X3Y  C10  F1   single    1.334  0.020  1.334
 X3Y  C10  C11  aromatic  1.379  0.020  1.379
 X3Y  C12  C11  aromatic  1.387  0.020  1.387
 X3Y  C6   H1   single    0.930  0.020  1.080
 X3Y  N3   H2   single    0.860  0.020  1.020
 X3Y  C1   H3   single    0.930  0.020  1.080
 X3Y  C11  H4   single    0.930  0.020  1.080
 X3Y  C12  H5   single    0.930  0.020  1.080
 X3Y  C13  H6   single    0.930  0.020  1.080
 X3Y  C16  H7   single    0.970  0.020  1.090
 X3Y  C17  H8   single    0.970  0.020  1.090
 X3Y  C17  H9   single    0.970  0.020  1.090
 X3Y  C18  H10  single    0.970  0.020  1.090
 X3Y  C18  H11  single    0.970  0.020  1.090
 X3Y  C3   H12  single    0.930  0.020  1.080
 X3Y  C8   H13  single    0.930  0.020  1.080
 X3Y  N4   H14  single    0.860  0.020  1.020
 X3Y  N5   H15  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
 X3Y  N2   C4   C8   124.84  3.000
 X3Y  N2   C4   C6   122.33  3.000
 X3Y  C8   C4   C6   112.83  3.000
 X3Y  O1   C5   N4   121.49  3.000
 X3Y  N4   C5   N3   115.53  3.000
 X3Y  O1   C5   N3   122.97  3.000
 X3Y  H1   C6   C7   125.08  3.000
 X3Y  H1   C6   C4   123.12  3.000
 X3Y  C7   C6   C4   111.80  3.000
 X3Y  N2   N1   C3   105.60  3.000
 X3Y  C3   C2   C1   104.71  3.000
 X3Y  C3   C2   N3   124.22  3.000
 X3Y  C1   C2   N3   131.06  3.000
 X3Y  H3   C1   N2   122.40  3.000
 X3Y  H3   C1   C2   131.79  3.000
 X3Y  N2   C1   C2   105.81  3.000
 X3Y  F1   C10  C9   117.77  3.000
 X3Y  F1   C10  C11  119.46  3.000
 X3Y  C9   C10  C11  122.77  3.000
 X3Y  H4   C11  C12  121.41  3.000
 X3Y  H4   C11  C10  120.24  3.000
 X3Y  C12  C11  C10  118.34  3.000
 X3Y  H5   C12  C13  119.46  3.000
 X3Y  H5   C12  C11  119.52  3.000
 X3Y  C13  C12  C11  121.02  3.000
 X3Y  H6   C13  C14  120.25  3.000
 X3Y  H6   C13  C12  120.57  3.000
 X3Y  C14  C13  C12  119.18  3.000
 X3Y  CL1  C14  C9   118.65  3.000
 X3Y  C9   C14  C13  121.50  3.000
 X3Y  CL1  C14  C13  119.84  3.000
 X3Y  O2   C15  N5   124.20  3.000
 X3Y  N5   C15  C7   116.41  3.000
 X3Y  O2   C15  C7   119.40  3.000
 X3Y  H7   C16  N5   108.81  3.000
 X3Y  H7   C16  C18  113.00  3.000
 X3Y  N5   C16  C18  118.49  3.000
 X3Y  H7   C16  C17  113.17  3.000
 X3Y  C18  C16  C17   84.11  3.000
 X3Y  N5   C16  C17  117.64  3.000
 X3Y  H9   C17  H8   108.92  3.000
 X3Y  H9   C17  O3   112.95  3.000
 X3Y  H8   C17  O3   112.61  3.000
 X3Y  H9   C17  C16  116.78  3.000
 X3Y  H8   C17  C16  113.51  3.000
 X3Y  O3   C17  C16   91.26  3.000
 X3Y  H11  C18  H10  109.07  3.000
 X3Y  H11  C18  O3   112.60  3.000
 X3Y  H10  C18  O3   112.92  3.000
 X3Y  H11  C18  C16  113.54  3.000
 X3Y  H10  C18  C16  116.67  3.000
 X3Y  O3   C18  C16   91.18  3.000
 X3Y  H12  C3   C2   127.92  3.000
 X3Y  H12  C3   N1   120.89  3.000
 X3Y  C2   C3   N1   111.19  3.000
 X3Y  S1   C7   C15  116.21  3.000
 X3Y  C15  C7   C6   131.83  3.000
 X3Y  S1   C7   C6   111.95  3.000
 X3Y  H13  C8   S1   120.07  3.000
 X3Y  H13  C8   C4   128.29  3.000
 X3Y  S1   C8   C4   111.64  3.000
 X3Y  N4   C9   C14  122.07  3.000
 X3Y  C14  C9   C10  117.18  3.000
 X3Y  N4   C9   C10  120.72  3.000
 X3Y  C1   N2   N1   112.68  3.000
 X3Y  N1   N2   C4   119.82  3.000
 X3Y  C1   N2   C4   127.50  3.000
 X3Y  H14  N4   C9   118.11  3.000
 X3Y  H14  N4   C5   115.38  3.000
 X3Y  C9   N4   C5   126.51  3.000
 X3Y  H15  N5   C16  117.02  3.000
 X3Y  H15  N5   C15  119.17  3.000
 X3Y  C16  N5   C15  123.80  3.000
 X3Y  C18  O3   C17   91.85  3.000
 X3Y  C8   S1   C7    91.77  3.000
 X3Y  H2   N3   C2   115.76  3.000
 X3Y  H2   N3   C5   119.84  3.000
 X3Y  C2   N3   C5   124.15  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
 X3Y  CONST_01  C7   S1   C8   C4      0.00   0.0  0
 X3Y  CONST_02  C2   C1   N2   C4    180.00   0.0  0
 X3Y  CONST_03  C3   N1   N2   C4    180.00   0.0  0
 X3Y  CONST_04  S1   C7   C6   C4      0.00   0.0  0
 X3Y  CONST_05  C8   S1   C7   C6      0.00   0.0  0
 X3Y  CONST_06  S1   C8   C4   C6      0.00   0.0  0
 X3Y  CONST_07  C1   N2   C4   C6    180.00   0.0  0
 X3Y  CONST_08  N1   N2   C4   C6      0.00   0.0  0
 X3Y  CONST_09  C8   C4   N2   N1    180.00   0.0  0
 X3Y  CONST_10  C2   C1   N2   N1      0.00   0.0  0
 X3Y  CONST_11  C1   C2   C3   N1      0.00   0.0  0
 X3Y  CONST_12  N2   N1   C3   C2      0.00   0.0  0
 X3Y  CONST_13  C8   C4   N2   C1      0.00   0.0  0
 X3Y  CONST_14  C3   N1   N2   C1      0.00   0.0  0
 X3Y  CONST_15  C13  C14  C9   C10     0.00   0.0  0
 X3Y  CONST_16  C13  C12  C11  C10     0.00   0.0  0
 X3Y  CONST_17  C14  C9   C10  C11     0.00   0.0  0
 X3Y  CONST_18  C14  C13  C12  C11     0.00   0.0  0
 X3Y  CONST_19  C9   C14  C13  C12     0.00   0.0  0
 X3Y  CONST_20  C9   C10  C11  C12     0.00   0.0  0
 X3Y  CONST_21  N2   C1   C2   C3      0.00   0.0  0
 X3Y  CONST_22  C8   C4   C6   C7      0.00   0.0  0
 X3Y  CONST_23  N2   C4   C6   C7    180.00   0.0  0
 X3Y  CONST_24  S1   C8   C4   N2    180.00   0.0  0
 X3Y  CONST_25  C15  C7   C6   C4    180.00   0.0  0
 X3Y  CONST_26  N3   C2   C3   N1    180.00   0.0  0
 X3Y  CONST_27  N2   C1   C2   N3    180.00   0.0  0
 X3Y  CONST_28  CL1  C14  C9   C10   180.00   0.0  0
 X3Y  CONST_29  N4   C9   C10  C11   180.00   0.0  0
 X3Y  CONST_30  CL1  C14  C13  C12   180.00   0.0  0
 X3Y  CONST_31  F1   C10  C11  C12   180.00   0.0  0
 X3Y  CONST_32  N4   C9   C14  C13   180.00   0.0  0
 X3Y  CONST_33  F1   C10  C9   C14   180.00   0.0  0
 X3Y  CONST_34  C8   S1   C7   C15   180.00   0.0  0
 X3Y  CONST_35  H3   C1   N2   C4      0.00   0.0  0
 X3Y  CONST_36  H13  C8   C4   C6    180.00   0.0  0
 X3Y  CONST_37  H12  C3   C2   C1    180.00   0.0  0
 X3Y  CONST_38  H5   C12  C11  C10   180.00   0.0  0
 X3Y  CONST_39  H6   C13  C12  C11   180.00   0.0  0
 X3Y  CONST_40  H4   C11  C12  C13   180.00   0.0  0
 X3Y  CONST_41  H1   C6   C4   C8    180.00   0.0  0
 X3Y  CONST_42  C7   C15  N5   C16   180.00   0.0  0
 X3Y  CONST_43  C1   C2   N3   C5      0.00   0.0  0
 X3Y  CONST_44  C3   C2   N3   C5    180.00   0.0  0
 X3Y  CONST_47  H2   N3   C2   C1    180.00   0.0  0
 X3Y  CONST_49  O1   C5   N3   C2      0.00   0.0  0
 X3Y  CONST_50  O2   C15  N5   C16     0.00   0.0  0
 X3Y  CONST_51  O1   C5   N4   C9    180.00   0.0  0
 X3Y  CONST_52  C9   N4   C5   N3      0.00   0.0  0
 X3Y  CONST_53  N4   C5   N3   C2    180.00   0.0  0
 X3Y  CONST_54  H15  N5   C15  C7      0.00   0.0  0
 X3Y  Var_01    H10  C18  O3   C17  -129.63  30.0  1
 X3Y  Var_02    H8   C17  O3   C18  -106.29  30.0  1
 X3Y  Var_03    O2   C15  C7   C6    174.10  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
 X3Y  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
 X3Y  plan-1  C4   0.020
 X3Y  plan-1  N1   0.020
 X3Y  plan-1  C2   0.020
 X3Y  plan-1  C1   0.020
 X3Y  plan-1  C3   0.020
 X3Y  plan-1  N2   0.020
 X3Y  plan-1  H3   0.020
 X3Y  plan-1  H12  0.020
 X3Y  plan-1  N3   0.020
 X3Y  plan-2  C4   0.020
 X3Y  plan-2  C6   0.020
 X3Y  plan-2  C15  0.020
 X3Y  plan-2  C7   0.020
 X3Y  plan-2  C8   0.020
 X3Y  plan-2  N2   0.020
 X3Y  plan-2  S1   0.020
 X3Y  plan-2  H1   0.020
 X3Y  plan-2  H13  0.020
 X3Y  plan-3  C10  0.020
 X3Y  plan-3  C11  0.020
 X3Y  plan-3  C12  0.020
 X3Y  plan-3  C13  0.020
 X3Y  plan-3  C14  0.020
 X3Y  plan-3  C9   0.020
 X3Y  plan-3  N4   0.020
 X3Y  plan-3  CL1  0.020
 X3Y  plan-3  H4   0.020
 X3Y  plan-3  H5   0.020
 X3Y  plan-3  H6   0.020
 X3Y  plan-3  F1   0.020
 X3Y  plan-4  C15  0.020
 X3Y  plan-4  C16  0.020
 X3Y  plan-4  C7   0.020
 X3Y  plan-4  N5   0.020
 X3Y  plan-4  O2   0.020
 X3Y  plan-4  H15  0.020
 X3Y  plan-5  C5   0.020
 X3Y  plan-5  C2   0.020
 X3Y  plan-5  C9   0.020
 X3Y  plan-5  N4   0.020
 X3Y  plan-5  O1   0.020
 X3Y  plan-5  H14  0.020
 X3Y  plan-5  N3   0.020
 X3Y  plan-5  H2   0.020

