# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 04:28:12 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: 4-(4-{[(2-chlorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(oxetan-3-yl)thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1NC(=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
 X3V  X3V  4-(4-{[(2-chlorophenyl)carbamoyl]amino}-1H-pyrazol-1-yl)-N-(oxetan-3-yl)thiophene-2-carboxamide  ligand  44  28  .  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_X3V
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
 X3V  C8   C   CR15  0  -0.523  23.6751   6.1650  30.7101
 X3V  C5   C   C     0   0.671  20.7232  10.7379  32.8975
 X3V  C6   C   CR15  0  -0.252  23.1837   4.4572  32.2029
 X3V  C4   C   CR5   0   0.453  22.9359   5.7933  31.7977
 X3V  C2   C   CR5   0   0.086  20.8736   8.3298  33.1774
 X3V  N1   N   N     0  -0.262  21.1301   6.0965  33.2857
 X3V  C18  C   C     0  -0.128  25.3001  -0.0920  33.9127
 X3V  C14  C   CR6   0  -0.076  17.8048  12.3956  34.0153
 X3V  C12  C   CR16  0  -0.256  17.1397  12.1765  36.3064
 X3V  C16  C   C     0  -0.205  24.7133   0.3190  32.5538
 X3V  C1   C   CR15  0   0.013  21.9197   7.9753  32.3587
 X3V  C10  C   CR16  0  -0.280  19.3831  11.6305  35.6465
 X3V  C11  C   CR16  0  -0.246  18.4118  11.7263  36.6299
 X3V  C13  C   CR16  0  -0.220  16.8354  12.5199  34.9980
 X3V  C17  C   C     0  -0.130  23.6619  -0.7566  32.8584
 X3V  C3   C   CR15  0  -0.092  20.4225   7.1115  33.7296
 X3V  C7   C   CR5   0  -0.292  24.1111   3.8498  31.4067
 X3V  C9   C   CR6   0   0.324  19.0922  11.9522  34.3226
 X3V  N2   N   NR5   0  -0.407  22.0292   6.6231  32.4623
 X3V  N4   N   NH1   0  -0.756  20.0793  11.8665  33.3291
 X3V  N5   N   NH1   0  -0.659  24.2559   1.6648  32.3929
 X3V  O1   O   O     0  -0.498  21.5977  10.7929  32.0488
 X3V  O3   O   O     0  -0.504  24.3968  -1.1987  34.0044
 X3V  S1   S   S2    0   0.287  24.6852   4.9005  30.1764
 X3V  H6   H   HCR5  0   0.319  23.6696   7.1118  30.1917
 X3V  H5   H   HCR5  0   0.289  22.6884   3.9941  33.0443
 X3V  H16  H   H     0   0.231  26.3487  -0.3989  33.9172
 X3V  H15  H   H     0   0.217  25.1410   0.6495  34.7030
 X3V  H9   H   HCR6  0   0.272  16.3798  12.2662  37.0708
 X3V  H12  H   H     0   0.288  25.3575   0.0663  31.7155
 X3V  H1   H   HCR5  0   0.304  22.5827   8.5576  31.7462
 X3V  H7   H   HCR6  0   0.287  20.3860  11.3106  35.8998
 X3V  H8   H   HCR6  0   0.270  18.6558  11.4671  37.6512
 X3V  H10  H   HCR6  0   0.284  15.8461  12.8720  34.7389
 X3V  H14  H   H     0   0.217  22.6785  -0.3500  33.1190
 X3V  H13  H   H     0   0.232  23.5332  -1.5399  32.1077
 X3V  H2   H   HCR5  0   0.279  19.6122   6.9593  34.4272
 X3V  H4   H   HNH1  0   0.407  20.2625  12.6891  32.7730
 X3V  H11  H   HNH1  0   0.416  23.5844   2.0028  33.0654
 X3V  C15  C   C     0   0.561  24.6914   2.4914  31.4257
 X3V  N3   N   NH1   0  -0.760  20.3234   9.5685  33.4693
 X3V  O2   O   O     0  -0.477  25.5200   2.1824  30.5808
 X3V  CL1  CL  CL    0  -0.102  17.4115  12.7962  32.3807
 X3V  H3   H   HNH1  0   0.423  19.5318   9.5616  34.0943

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
 X3V  S1   C8   aromatic  1.704  0.020  1.704
 X3V  S1   C7   aromatic  1.717  0.020  1.717
 X3V  C8   C4   aromatic  1.367  0.020  1.367
 X3V  O2   C15  double    1.223  0.020  1.223
 X3V  C7   C15  single    1.477  0.020  1.477
 X3V  C7   C6   aromatic  1.365  0.020  1.365
 X3V  C4   C6   aromatic  1.418  0.020  1.418
 X3V  C4   N2   single    1.397  0.020  1.397
 X3V  C15  N5   single    1.345  0.020  1.345
 X3V  N2   C1   aromatic  1.361  0.020  1.361
 X3V  N2   N1   aromatic  1.328  0.020  1.328
 X3V  O1   C5   double    1.220  0.020  1.220
 X3V  C1   C2   aromatic  1.375  0.020  1.375
 X3V  N5   C16  single    1.430  0.020  1.430
 X3V  N1   C3   aromatic  1.314  0.020  1.314
 X3V  C2   N3   single    1.386  0.020  1.386
 X3V  C2   C3   aromatic  1.412  0.020  1.412
 X3V  C5   N3   single    1.362  0.020  1.362
 X3V  C5   N4   single    1.369  0.020  1.369
 X3V  C16  C17  single    1.535  0.020  1.535
 X3V  C16  C18  single    1.536  0.020  1.536
 X3V  C17  O3   single    1.431  0.020  1.431
 X3V  CL1  C14  single    1.728  0.020  1.728
 X3V  N4   C9   single    1.403  0.020  1.403
 X3V  C18  O3   single    1.431  0.020  1.431
 X3V  C9   C14  aromatic  1.396  0.020  1.396
 X3V  C9   C10  aromatic  1.393  0.020  1.393
 X3V  C14  C13  aromatic  1.386  0.020  1.386
 X3V  C13  C12  aromatic  1.386  0.020  1.386
 X3V  C10  C11  aromatic  1.386  0.020  1.386
 X3V  C12  C11  aromatic  1.388  0.020  1.388
 X3V  C8   H6   single    0.930  0.020  1.080
 X3V  C6   H5   single    0.930  0.020  1.080
 X3V  N3   H3   single    0.860  0.020  1.020
 X3V  C18  H16  single    0.970  0.020  1.090
 X3V  C18  H15  single    0.970  0.020  1.090
 X3V  C12  H9   single    0.930  0.020  1.080
 X3V  C16  H12  single    0.970  0.020  1.090
 X3V  C1   H1   single    0.930  0.020  1.080
 X3V  C10  H7   single    0.930  0.020  1.080
 X3V  C11  H8   single    0.930  0.020  1.080
 X3V  C13  H10  single    0.930  0.020  1.080
 X3V  C17  H14  single    0.970  0.020  1.090
 X3V  C17  H13  single    0.970  0.020  1.090
 X3V  C3   H2   single    0.930  0.020  1.080
 X3V  N4   H4   single    0.860  0.020  1.020
 X3V  N5   H11  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
 X3V  H6   C8   S1   120.23  3.000
 X3V  H6   C8   C4   128.16  3.000
 X3V  S1   C8   C4   111.60  3.000
 X3V  O1   C5   N4   121.28  3.000
 X3V  N4   C5   N3   115.94  3.000
 X3V  O1   C5   N3   122.78  3.000
 X3V  H5   C6   C7   125.10  3.000
 X3V  H5   C6   C4   123.10  3.000
 X3V  C7   C6   C4   111.80  3.000
 X3V  N2   C4   C6   122.48  3.000
 X3V  N2   C4   C8   124.62  3.000
 X3V  C6   C4   C8   112.90  3.000
 X3V  C3   C2   C1   104.69  3.000
 X3V  C3   C2   N3   124.19  3.000
 X3V  C1   C2   N3   131.12  3.000
 X3V  N2   N1   C3   105.53  3.000
 X3V  H15  C18  H16  109.06  3.000
 X3V  H15  C18  O3   112.68  3.000
 X3V  H16  C18  O3   112.84  3.000
 X3V  H15  C18  C16  113.68  3.000
 X3V  H16  C18  C16  116.45  3.000
 X3V  O3   C18  C16   91.29  3.000
 X3V  CL1  C14  C9   119.45  3.000
 X3V  C9   C14  C13  121.16  3.000
 X3V  CL1  C14  C13  119.38  3.000
 X3V  H9   C12  C13  119.48  3.000
 X3V  H9   C12  C11  120.41  3.000
 X3V  C13  C12  C11  120.10  3.000
 X3V  H12  C16  N5   108.75  3.000
 X3V  H12  C16  C17  113.33  3.000
 X3V  N5   C16  C17  117.56  3.000
 X3V  H12  C16  C18  113.18  3.000
 X3V  C17  C16  C18   84.18  3.000
 X3V  N5   C16  C18  118.25  3.000
 X3V  H1   C1   N2   122.17  3.000
 X3V  H1   C1   C2   132.02  3.000
 X3V  N2   C1   C2   105.79  3.000
 X3V  H7   C10  C9   118.95  3.000
 X3V  H7   C10  C11  120.24  3.000
 X3V  C9   C10  C11  120.80  3.000
 X3V  H8   C11  C10  119.70  3.000
 X3V  H8   C11  C12  120.31  3.000
 X3V  C10  C11  C12  119.98  3.000
 X3V  H10  C13  C12  120.50  3.000
 X3V  H10  C13  C14  119.94  3.000
 X3V  C12  C13  C14  119.56  3.000
 X3V  H13  C17  H14  108.89  3.000
 X3V  H13  C17  O3   112.90  3.000
 X3V  H14  C17  O3   112.65  3.000
 X3V  H13  C17  C16  116.54  3.000
 X3V  H14  C17  C16  113.70  3.000
 X3V  O3   C17  C16   91.35  3.000
 X3V  H2   C3   N1   120.88  3.000
 X3V  H2   C3   C2   127.88  3.000
 X3V  N1   C3   C2   111.24  3.000
 X3V  S1   C7   C15  116.15  3.000
 X3V  C15  C7   C6   131.96  3.000
 X3V  S1   C7   C6   111.90  3.000
 X3V  N4   C9   C10  120.79  3.000
 X3V  C10  C9   C14  118.37  3.000
 X3V  N4   C9   C14  120.82  3.000
 X3V  C1   N2   N1   112.75  3.000
 X3V  N1   N2   C4   119.92  3.000
 X3V  C1   N2   C4   127.32  3.000
 X3V  H4   N4   C9   117.89  3.000
 X3V  H4   N4   C5   114.37  3.000
 X3V  C9   N4   C5   127.19  3.000
 X3V  H11  N5   C16  116.95  3.000
 X3V  H11  N5   C15  119.28  3.000
 X3V  C16  N5   C15  123.76  3.000
 X3V  C17  O3   C18   91.94  3.000
 X3V  C7   S1   C8    91.81  3.000
 X3V  O2   C15  N5   124.12  3.000
 X3V  N5   C15  C7   116.57  3.000
 X3V  O2   C15  C7   119.31  3.000
 X3V  H3   N3   C2   115.84  3.000
 X3V  H3   N3   C5   119.77  3.000
 X3V  C2   N3   C5   124.22  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
 X3V  CONST_01  C6   C7   S1   C8      0.00   0.0  0
 X3V  CONST_02  C7   C6   C4   C8      0.00   0.0  0
 X3V  CONST_05  S1   C8   C4   C6      0.00   0.0  0
 X3V  CONST_08  C7   S1   C8   C4      0.00   0.0  0
 X3V  CONST_09  S1   C7   C6   C4      0.00   0.0  0
 X3V  CONST_10  C2   C1   N2   C4    180.00   0.0  0
 X3V  CONST_11  C3   N1   N2   C4    180.00   0.0  0
 X3V  CONST_12  N1   N2   C1   C2      0.00   0.0  0
 X3V  CONST_13  N2   N1   C3   C2      0.00   0.0  0
 X3V  CONST_14  C1   C2   C3   N1      0.00   0.0  0
 X3V  CONST_15  C11  C10  C9   C14     0.00   0.0  0
 X3V  CONST_16  C11  C12  C13  C14     0.00   0.0  0
 X3V  CONST_17  C9   C14  C13  C12     0.00   0.0  0
 X3V  CONST_18  C9   C10  C11  C12     0.00   0.0  0
 X3V  CONST_19  C3   N1   N2   C1      0.00   0.0  0
 X3V  CONST_20  C13  C14  C9   C10     0.00   0.0  0
 X3V  CONST_21  C13  C12  C11  C10     0.00   0.0  0
 X3V  CONST_22  N2   C1   C2   C3      0.00   0.0  0
 X3V  CONST_23  N2   C4   C6   C7    180.00   0.0  0
 X3V  CONST_24  S1   C8   C4   N2    180.00   0.0  0
 X3V  CONST_25  C15  C7   S1   C8    180.00   0.0  0
 X3V  CONST_26  C15  C7   C6   C4    180.00   0.0  0
 X3V  CONST_27  N2   C1   C2   N3    180.00   0.0  0
 X3V  CONST_28  N1   C3   C2   N3    180.00   0.0  0
 X3V  CONST_29  CL1  C14  C13  C12   180.00   0.0  0
 X3V  CONST_30  CL1  C14  C9   C10   180.00   0.0  0
 X3V  CONST_31  N4   C9   C10  C11   180.00   0.0  0
 X3V  CONST_32  N4   C9   C14  C13   180.00   0.0  0
 X3V  CONST_33  H5   C6   C4   C8    180.00   0.0  0
 X3V  CONST_34  H6   C8   C4   C6    180.00   0.0  0
 X3V  CONST_35  H1   C1   N2   C4      0.00   0.0  0
 X3V  CONST_36  H7   C10  C9   C14   180.00   0.0  0
 X3V  CONST_37  H9   C12  C13  C14   180.00   0.0  0
 X3V  CONST_38  H2   C3   C2   C1    180.00   0.0  0
 X3V  CONST_39  H10  C13  C12  C11   180.00   0.0  0
 X3V  CONST_40  H8   C11  C12  C13   180.00   0.0  0
 X3V  CONST_41  C7   C15  N5   C16   180.00   0.0  0
 X3V  CONST_42  C1   C2   N3   C5      0.00   0.0  0
 X3V  CONST_43  C3   C2   N3   C5    180.00   0.0  0
 X3V  CONST_47  H3   N3   C2   C1    180.00   0.0  0
 X3V  CONST_48  O1   C5   N3   C2      0.00   0.0  0
 X3V  CONST_49  O2   C15  N5   C16     0.00   0.0  0
 X3V  CONST_50  O1   C5   N4   C9    180.00   0.0  0
 X3V  CONST_51  C9   N4   C5   N3      0.00   0.0  0
 X3V  CONST_52  N4   C5   N3   C2    180.00   0.0  0
 X3V  CONST_53  H11  N5   C15  C7      0.00   0.0  0
 X3V  Var_01    C16  C17  O3   C18     8.68  30.0  1
 X3V  Var_02    H16  C18  O3   C17  -128.21  30.0  1
 X3V  Var_03    O2   C15  C7   C6    179.67  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
 X3V  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
 X3V  plan-1  C4   0.020
 X3V  plan-1  C2   0.020
 X3V  plan-1  N1   0.020
 X3V  plan-1  C1   0.020
 X3V  plan-1  C3   0.020
 X3V  plan-1  N2   0.020
 X3V  plan-1  H1   0.020
 X3V  plan-1  H2   0.020
 X3V  plan-1  N3   0.020
 X3V  plan-2  C8   0.020
 X3V  plan-2  C6   0.020
 X3V  plan-2  C4   0.020
 X3V  plan-2  C7   0.020
 X3V  plan-2  N2   0.020
 X3V  plan-2  S1   0.020
 X3V  plan-2  H6   0.020
 X3V  plan-2  H5   0.020
 X3V  plan-2  C15  0.020
 X3V  plan-3  C14  0.020
 X3V  plan-3  C12  0.020
 X3V  plan-3  C10  0.020
 X3V  plan-3  C11  0.020
 X3V  plan-3  C13  0.020
 X3V  plan-3  C9   0.020
 X3V  plan-3  N4   0.020
 X3V  plan-3  H9   0.020
 X3V  plan-3  H7   0.020
 X3V  plan-3  H8   0.020
 X3V  plan-3  H10  0.020
 X3V  plan-3  CL1  0.020
 X3V  plan-4  C16  0.020
 X3V  plan-4  C7   0.020
 X3V  plan-4  N5   0.020
 X3V  plan-4  H11  0.020
 X3V  plan-4  C15  0.020
 X3V  plan-4  O2   0.020
 X3V  plan-5  C5   0.020
 X3V  plan-5  C2   0.020
 X3V  plan-5  C9   0.020
 X3V  plan-5  N4   0.020
 X3V  plan-5  O1   0.020
 X3V  plan-5  H4   0.020
 X3V  plan-5  N3   0.020
 X3V  plan-5  H3   0.020

