# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 04:05:28 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-[2-[5-methyl-3-(trifluoromethyl)pyrazol-1-yl]ethanoylamino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(nn1CC(=O)Nc2sc3CCCCc3c2C(N)=O)C(F)(F)F
#
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
 8SR  8SR  2-[2-[5-methyl-3-(trifluoromethyl)pyrazol-1-yl]ethanoylamino]-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxamide  ligand  43  26  .  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_8SR
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
 8SR  C4   C  CR5   0  -0.277   3.6930  -1.4189   0.2932
 8SR  C5   C  CR5   0   0.006  -4.5106   0.1269  -0.0576
 8SR  C6   C  CR5   0   0.443  -3.4092   0.9387   1.6552
 8SR  C7   C  CR5   0   0.094   1.9678   0.3153  -0.0200
 8SR  C8   C  C     0   0.505   3.3480   2.0302  -1.1517
 8SR  C10  C  CH2   0  -0.555   5.6712  -0.2042  -0.5999
 8SR  C13  C  CH2   0  -0.446   5.8199  -2.6458  -0.0132
 8SR  C15  C  CH2   0  -0.455  -1.4697   1.7239   0.2982
 8SR  C1   C  CR15  0  -0.563  -4.5696   0.2721   1.3352
 8SR  C2   C  CR5   0  -0.109   3.1985   0.7124  -0.4993
 8SR  C3   C  CR5   0   0.223   4.2017  -0.3032  -0.2912
 8SR  C9   C  C     0   0.552  -0.3926   0.6557   0.3811
 8SR  C11  C  CH2   0  -0.474   4.4469  -2.6595   0.6527
 8SR  C12  C  CH2   0  -0.442   6.4716  -1.2778   0.1325
 8SR  C14  C  CH3   0  -0.749  -2.8685   1.3687   2.9691
 8SR  C16  C  CT    0   1.066  -5.5261  -0.4824  -0.9522
 8SR  N17  N  N     0  -0.287  -3.4185   0.6577  -0.5641
 8SR  N18  N  NR5   0  -0.310  -2.7720   1.1555   0.4812
 8SR  N19  N  NH2   0  -0.813   4.4329   2.2354  -1.9096
 8SR  N20  N  NH1   0  -0.720   0.8199   1.0726  -0.0423
 8SR  O21  O  O     0  -0.517   2.4937   2.9119  -1.0140
 8SR  O22  O  O     0  -0.440  -0.6025  -0.4598   0.8122
 8SR  F23  F  F     0  -0.316  -6.4275   0.4155  -1.3794
 8SR  F24  F  F     0  -0.309  -4.9754  -1.0245  -2.0410
 8SR  F25  F  F     0  -0.309  -6.2104  -1.4425  -0.3197
 8SR  S26  S  S2    0   0.254   2.0021  -1.2790   0.6238
 8SR  H1   H  HCH2  0   0.245   5.8373  -0.3186  -1.6779
 8SR  H2   H  HCH2  0   0.260   6.0503   0.7832  -0.3270
 8SR  H3   H  HCH2  0   0.242   6.4477  -3.4212   0.4288
 8SR  H4   H  HCH2  0   0.228   5.7156  -2.8881  -1.0749
 8SR  H5   H  HCH2  0   0.324  -1.2885   2.4755   1.0686
 8SR  H6   H  HCH2  0   0.324  -1.4401   2.2362  -0.6634
 8SR  H7   H  HCR5  0   0.281  -5.3370  -0.0572   2.0157
 8SR  H8   H  HCH2  0   0.249   4.5604  -2.7264   1.7394
 8SR  H9   H  HCH2  0   0.255   3.8888  -3.5488   0.3493
 8SR  H10  H  HCH2  0   0.242   7.4907  -1.2950  -0.2568
 8SR  H11  H  HCH2  0   0.228   6.5444  -1.0190   1.1932
 8SR  H12  H  HCH3  0   0.265  -2.6435   2.4359   2.9875
 8SR  H13  H  HCH3  0   0.274  -3.5980   1.1686   3.7502
 8SR  H14  H  HCH3  0   0.264  -1.9529   0.8317   3.2208
 8SR  H15  H  HNH2  0   0.421   5.0608   1.4977  -2.1738
 8SR  H16  H  HNH2  0   0.408   4.5220   3.1069  -2.4075
 8SR  H17  H  HNH1  0   0.440   0.9697   2.0225  -0.3812

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
 8SR  C14  C6   single    1.484  0.020  1.484
 8SR  C15  C9   single    1.519  0.020  1.519
 8SR  C15  N18  single    1.433  0.020  1.433
 8SR  O21  C8   double    1.235  0.020  1.235
 8SR  N19  C8   single    1.339  0.020  1.339
 8SR  C8   C2   single    1.478  0.020  1.478
 8SR  N20  C9   single    1.350  0.020  1.350
 8SR  N20  C7   single    1.375  0.020  1.375
 8SR  C9   O22  double    1.214  0.020  1.214
 8SR  C6   N18  aromatic  1.353  0.020  1.353
 8SR  C6   C1   aromatic  1.376  0.020  1.376
 8SR  N18  N17  aromatic  1.326  0.020  1.326
 8SR  C7   C2   aromatic  1.379  0.020  1.379
 8SR  C7   S26  aromatic  1.720  0.020  1.720
 8SR  C2   C3   aromatic  1.443  0.020  1.443
 8SR  C1   C5   aromatic  1.402  0.020  1.402
 8SR  N17  C5   aromatic  1.316  0.020  1.316
 8SR  C3   C10  single    1.505  0.020  1.505
 8SR  C3   C4   aromatic  1.358  0.020  1.358
 8SR  S26  C4   aromatic  1.729  0.020  1.729
 8SR  C10  C12  single    1.526  0.020  1.526
 8SR  C5   C16  single    1.484  0.020  1.484
 8SR  C4   C11  single    1.496  0.020  1.496
 8SR  F24  C16  single    1.335  0.020  1.335
 8SR  C13  C12  single    1.522  0.020  1.522
 8SR  C13  C11  single    1.526  0.020  1.526
 8SR  C16  F23  single    1.342  0.020  1.342
 8SR  C16  F25  single    1.338  0.020  1.338
 8SR  C10  H1   single    0.970  0.020  1.090
 8SR  C10  H2   single    0.970  0.020  1.090
 8SR  C13  H3   single    0.970  0.020  1.090
 8SR  C13  H4   single    0.970  0.020  1.090
 8SR  C15  H5   single    0.970  0.020  1.090
 8SR  C15  H6   single    0.970  0.020  1.090
 8SR  C1   H7   single    0.930  0.020  1.080
 8SR  C11  H8   single    0.970  0.020  1.090
 8SR  C11  H9   single    0.970  0.020  1.090
 8SR  C12  H10  single    0.970  0.020  1.090
 8SR  C12  H11  single    0.970  0.020  1.090
 8SR  C14  H12  single    0.970  0.020  1.090
 8SR  C14  H13  single    0.970  0.020  1.090
 8SR  C14  H14  single    0.970  0.020  1.090
 8SR  N19  H15  single    0.860  0.020  1.020
 8SR  N19  H16  single    0.860  0.020  1.020
 8SR  N20  H17  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
 8SR  S26  C4   C11  120.95  3.000
 8SR  C11  C4   C3   126.58  3.000
 8SR  S26  C4   C3   112.47  3.000
 8SR  N17  C5   C16  120.10  3.000
 8SR  C16  C5   C1   127.78  3.000
 8SR  N17  C5   C1   112.07  3.000
 8SR  N18  C6   C14  123.37  3.000
 8SR  N18  C6   C1   105.84  3.000
 8SR  C14  C6   C1   130.79  3.000
 8SR  S26  C7   N20  122.22  3.000
 8SR  S26  C7   C2   112.29  3.000
 8SR  N20  C7   C2   125.49  3.000
 8SR  O21  C8   N19  120.93  3.000
 8SR  N19  C8   C2   117.93  3.000
 8SR  O21  C8   C2   121.14  3.000
 8SR  H2   C10  H1   106.69  3.000
 8SR  H2   C10  C12  109.51  3.000
 8SR  H1   C10  C12  108.59  3.000
 8SR  H2   C10  C3   110.32  3.000
 8SR  H1   C10  C3   110.04  3.000
 8SR  C12  C10  C3   111.55  3.000
 8SR  H4   C13  H3   106.89  3.000
 8SR  H4   C13  C12  109.43  3.000
 8SR  H3   C13  C12  110.71  3.000
 8SR  H4   C13  C11  109.61  3.000
 8SR  H3   C13  C11  109.54  3.000
 8SR  C12  C13  C11  110.57  3.000
 8SR  H6   C15  H5   107.14  3.000
 8SR  H6   C15  N18  108.90  3.000
 8SR  H5   C15  N18  109.50  3.000
 8SR  H6   C15  C9   111.07  3.000
 8SR  H5   C15  C9   109.14  3.000
 8SR  N18  C15  C9   111.01  3.000
 8SR  H7   C1   C6   127.01  3.000
 8SR  H7   C1   C5   128.76  3.000
 8SR  C6   C1   C5   104.23  3.000
 8SR  C3   C2   C8   128.39  3.000
 8SR  C3   C2   C7   111.57  3.000
 8SR  C8   C2   C7   120.03  3.000
 8SR  C2   C3   C10  127.09  3.000
 8SR  C10  C3   C4   120.54  3.000
 8SR  C2   C3   C4   112.32  3.000
 8SR  O22  C9   N20  123.39  3.000
 8SR  O22  C9   C15  122.87  3.000
 8SR  N20  C9   C15  113.73  3.000
 8SR  H9   C11  H8   106.20  3.000
 8SR  H9   C11  C13  110.22  3.000
 8SR  H8   C11  C13  109.90  3.000
 8SR  H9   C11  C4   110.54  3.000
 8SR  H8   C11  C4   109.97  3.000
 8SR  C13  C11  C4   109.95  3.000
 8SR  H11  C12  H10  106.70  3.000
 8SR  H11  C12  C13  109.50  3.000
 8SR  H10  C12  C13  110.58  3.000
 8SR  H11  C12  C10  109.49  3.000
 8SR  H10  C12  C10  109.25  3.000
 8SR  C13  C12  C10  111.21  3.000
 8SR  H14  C14  H13  107.86  3.000
 8SR  H14  C14  H12  107.73  3.000
 8SR  H13  C14  H12  107.84  3.000
 8SR  H14  C14  C6   111.55  3.000
 8SR  H13  C14  C6   109.77  3.000
 8SR  H12  C14  C6   111.93  3.000
 8SR  F25  C16  F24  107.76  3.000
 8SR  F25  C16  F23  106.68  3.000
 8SR  F24  C16  F23  106.81  3.000
 8SR  F25  C16  C5   111.07  3.000
 8SR  F23  C16  C5   112.14  3.000
 8SR  F24  C16  C5   112.08  3.000
 8SR  N18  N17  C5   104.64  3.000
 8SR  N17  N18  C15  119.43  3.000
 8SR  N17  N18  C6   113.22  3.000
 8SR  C15  N18  C6   127.04  3.000
 8SR  H16  N19  H15  116.75  3.000
 8SR  H16  N19  C8   118.93  3.000
 8SR  H15  N19  C8   122.88  3.000
 8SR  H17  N20  C9   121.59  3.000
 8SR  H17  N20  C7   113.31  3.000
 8SR  C9   N20  C7   125.05  3.000
 8SR  C7   S26  C4    91.31  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
 8SR  CONST_01  C7   C2   C3   C4      0.00   0.0  0
 8SR  CONST_02  C2   C7   S26  C4      0.00   0.0  0
 8SR  CONST_03  N18  C6   C1   C5      0.00   0.0  0
 8SR  CONST_04  C6   N18  N17  C5      0.00   0.0  0
 8SR  CONST_05  N17  C5   C1   C6      0.00   0.0  0
 8SR  CONST_06  C3   C4   S26  C7      0.00   0.0  0
 8SR  CONST_07  N17  N18  C6   C1      0.00   0.0  0
 8SR  CONST_08  N18  N17  C5   C1      0.00   0.0  0
 8SR  CONST_09  S26  C4   C3   C2      0.00   0.0  0
 8SR  CONST_10  S26  C7   C2   C3      0.00   0.0  0
 8SR  CONST_11  C8   C2   C3   C4    180.00   0.0  0
 8SR  CONST_12  N20  C7   S26  C4    180.00   0.0  0
 8SR  CONST_13  C14  C6   C1   C5    180.00   0.0  0
 8SR  CONST_14  C15  N18  N17  C5    180.00   0.0  0
 8SR  CONST_15  C16  C5   C1   C6    180.00   0.0  0
 8SR  CONST_16  S26  C7   C2   C8    180.00   0.0  0
 8SR  CONST_17  C10  C3   C2   C8      0.00   0.0  0
 8SR  CONST_18  C1   C6   N18  C15   180.00   0.0  0
 8SR  CONST_19  N20  C7   C2   C3    180.00   0.0  0
 8SR  CONST_20  N17  N18  C6   C14   180.00   0.0  0
 8SR  CONST_21  N18  N17  C5   C16   180.00   0.0  0
 8SR  CONST_22  H7   C1   C5   N17   180.00   0.0  0
 8SR  CONST_23  C9   N20  C7   C2    180.00   0.0  0
 8SR  CONST_24  S26  C7   N20  C9      0.00   0.0  0
 8SR  CONST_25  H17  N20  C7   C2      0.00   0.0  0
 8SR  CONST_26  C15  C9   N20  C7    180.00   0.0  0
 8SR  CONST_27  O22  C9   N20  C7      0.00   0.0  0
 8SR  CONST_28  H15  N19  C8   C2      0.00   0.0  0
 8SR  CONST_29  H16  N19  C8   C2    180.00   0.0  0
 8SR  Var_01    C12  C10  C3   C4    -14.83  30.0  1
 8SR  Var_02    C12  C13  C11  C4     44.60  30.0  1
 8SR  Var_03    C11  C13  C12  C10   -63.95  30.0  1
 8SR  Var_04    C3   C10  C12  C13    47.09  30.0  1
 8SR  Var_05    C3   C4   C11  C13   -13.01  30.0  1
 8SR  Var_06    C9   C15  N18  C6     86.76  30.0  2
 8SR  Var_07    O21  C8   C2   C7     16.88  30.0  2
 8SR  Var_08    F24  C16  C5   C1   -150.83  30.0  2
 8SR  Var_09    H12  C14  C6   C1   -125.51  30.0  2
 8SR  Var_10    N20  C9   C15  N18   167.56  30.0  3

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
 8SR  plan-1  C5   0.020
 8SR  plan-1  C6   0.020
 8SR  plan-1  C15  0.020
 8SR  plan-1  C1   0.020
 8SR  plan-1  C14  0.020
 8SR  plan-1  C16  0.020
 8SR  plan-1  N17  0.020
 8SR  plan-1  N18  0.020
 8SR  plan-1  H7   0.020
 8SR  plan-2  C4   0.020
 8SR  plan-2  C7   0.020
 8SR  plan-2  C8   0.020
 8SR  plan-2  C10  0.020
 8SR  plan-2  C2   0.020
 8SR  plan-2  C3   0.020
 8SR  plan-2  C11  0.020
 8SR  plan-2  N20  0.020
 8SR  plan-2  S26  0.020
 8SR  plan-3  C8   0.020
 8SR  plan-3  C2   0.020
 8SR  plan-3  N19  0.020
 8SR  plan-3  O21  0.020
 8SR  plan-3  H15  0.020
 8SR  plan-3  H16  0.020
 8SR  plan-4  C7   0.020
 8SR  plan-4  C15  0.020
 8SR  plan-4  C9   0.020
 8SR  plan-4  N20  0.020
 8SR  plan-4  O22  0.020
 8SR  plan-4  H17  0.020

