# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 20:32:29 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 1-[(3S)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-[(4-fluorophenyl)methyl]-5-methyl-1H-pyrazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1n(ncc1C(=O)NCc2ccc(F)cc2)[C@H]3CC[S](=O)(=O)C3
#
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
 LH7  LH7  1-[(3S)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-[(4-fluorophenyl)methyl]-5-methyl-1H-pyrazole-4-carboxamide  ligand  42  24  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LH7
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
 LH7  N1   N  N     0  -0.276  -1.3196   0.8423   0.5719
 LH7  N3   N  NH1   0  -0.648   2.4398  -0.9541  -0.1131
 LH7  C4   C  CR15  0  -0.034  -0.0554   0.4958   0.5626
 LH7  C5   C  CH1   0  -0.096  -3.4355  -0.2439   0.2475
 LH7  C6   C  CH2   0  -0.468  -4.0740   0.0469   1.6099
 LH7  C7   C  CH2   0  -0.617  -5.5537   0.2361   1.3256
 LH7  C8   C  CH2   0  -0.610  -3.9435   0.8079  -0.7454
 LH7  C10  C  CH2   0  -0.316   3.7479  -1.5634  -0.2379
 LH7  C13  C  CR16  0  -0.396   5.9592   1.2836   0.9526
 LH7  C15  C  CR16  0  -0.397   6.6985   0.6086  -1.2480
 LH7  C11  C  CR6   0   0.054   4.8241  -0.5134  -0.2051
 LH7  C12  C  CR16  0  -0.265   4.9681   0.3161   0.9059
 LH7  C14  C  CR6   0   0.515   6.8096   1.4105  -0.1309
 LH7  C16  C  CR16  0  -0.288   5.6953  -0.3523  -1.2758
 LH7  C2   C  CR5   0   0.492  -1.1950  -1.3527   0.1346
 LH7  C3   C  CR5   0  -0.362   0.0984  -0.8804   0.2955
 LH7  C9   C  C     0   0.494   1.3435  -1.6616   0.2241
 LH7  F1   F  F     0  -0.316   7.7729   2.3457  -0.0926
 LH7  N2   N  NR5   0  -0.350  -1.9934  -0.2794   0.2999
 LH7  O2   O  OS    0  -0.675  -6.6281   0.9165  -1.0582
 LH7  O3   O  O     0  -0.497   1.3861  -2.8618   0.4695
 LH7  S1   S  S     0   1.224  -5.5747   1.3052  -0.1253
 LH7  H1   H  HNH1  0   0.404   2.3222  -0.0304  -0.4981
 LH7  H2   H  HCR5  0   0.269   0.7091   1.2304   0.7701
 LH7  H3   H  HCH1  0   0.318  -3.7689  -1.2272  -0.0845
 LH7  H4   H  HCH2  0   0.297  -3.9138  -0.7782   2.3026
 LH7  H5   H  HCH2  0   0.277  -3.6431   0.9490   2.0481
 LH7  H6   H  HCH2  0   0.311  -6.0371  -0.7036   1.0558
 LH7  H7   H  HCH2  0   0.327  -6.1127   0.7205   2.1244
 LH7  H8   H  HCH2  0   0.321  -3.3123   1.6954  -0.7475
 LH7  H9   H  HCH2  0   0.327  -4.0479   0.4265  -1.7591
 LH7  H10  H  HCH2  0   0.262   3.8833  -2.2646   0.5871
 LH7  H11  H  HCH2  0   0.255   3.8203  -2.1452  -1.1612
 LH7  H12  H  HCR6  0   0.281   6.0711   1.9254   1.8165
 LH7  H13  H  HCR6  0   0.281   7.3748   0.7312  -2.0837
 LH7  H14  H  HCH3  0   0.267  -2.3235  -3.1041   0.6311
 LH7  H15  H  HCH3  0   0.265  -2.3409  -2.6899  -1.0814
 LH7  H16  H  HCH3  0   0.280  -0.8997  -3.3959  -0.3564
 LH7  H17  H  HCR6  0   0.266   4.2998   0.2074   1.7515
 LH7  H18  H  HCR6  0   0.267   5.5965  -0.9838  -2.1499
 LH7  C1   C  CH3   0  -0.762  -1.7191  -2.7057  -0.1856
 LH7  O1   O  OS    0  -0.682  -5.5115   2.6982   0.3138

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
 LH7  O1   S1   double    1.462  0.020  1.462
 LH7  S1   O2   double    1.460  0.020  1.460
 LH7  S1   C7   single    1.802  0.020  1.802
 LH7  S1   C8   single    1.815  0.020  1.815
 LH7  C7   C6   single    1.519  0.020  1.519
 LH7  C8   C5   single    1.533  0.020  1.533
 LH7  C6   C5   single    1.532  0.020  1.532
 LH7  C5   N2   single    1.444  0.020  1.444
 LH7  N1   N2   aromatic  1.336  0.020  1.336
 LH7  N1   C4   aromatic  1.311  0.020  1.311
 LH7  N2   C2   aromatic  1.348  0.020  1.348
 LH7  C4   C3   aromatic  1.410  0.020  1.410
 LH7  C2   C1   single    1.486  0.020  1.486
 LH7  C2   C3   aromatic  1.386  0.020  1.386
 LH7  C3   C9   single    1.472  0.020  1.472
 LH7  N3   C9   single    1.348  0.020  1.348
 LH7  N3   C10  single    1.448  0.020  1.448
 LH7  C9   O3   double    1.226  0.020  1.226
 LH7  C10  C11  single    1.504  0.020  1.504
 LH7  C11  C12  aromatic  1.394  0.020  1.394
 LH7  C11  C16  aromatic  1.390  0.020  1.390
 LH7  C12  C13  aromatic  1.386  0.020  1.386
 LH7  C16  C15  aromatic  1.390  0.020  1.390
 LH7  C13  C14  aromatic  1.383  0.020  1.383
 LH7  C15  C14  aromatic  1.380  0.020  1.380
 LH7  C14  F1   single    1.343  0.020  1.343
 LH7  N3   H1   single    0.860  0.020  1.020
 LH7  C4   H2   single    0.930  0.020  1.080
 LH7  C5   H3   single    0.970  0.020  1.090
 LH7  C6   H4   single    0.970  0.020  1.090
 LH7  C6   H5   single    0.970  0.020  1.090
 LH7  C7   H6   single    0.970  0.020  1.090
 LH7  C7   H7   single    0.970  0.020  1.090
 LH7  C8   H8   single    0.970  0.020  1.090
 LH7  C8   H9   single    0.970  0.020  1.090
 LH7  C10  H10  single    0.970  0.020  1.090
 LH7  C10  H11  single    0.970  0.020  1.090
 LH7  C13  H12  single    0.930  0.020  1.080
 LH7  C15  H13  single    0.930  0.020  1.080
 LH7  C1   H14  single    0.970  0.020  1.090
 LH7  C1   H15  single    0.970  0.020  1.090
 LH7  C1   H16  single    0.970  0.020  1.090
 LH7  C12  H17  single    0.930  0.020  1.080
 LH7  C16  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
 LH7  N2   N1   C4   105.25  3.000
 LH7  H1   N3   C9   118.81  3.000
 LH7  H1   N3   C10  117.27  3.000
 LH7  C9   N3   C10  122.37  3.000
 LH7  H2   C4   C3   128.52  3.000
 LH7  H2   C4   N1   120.09  3.000
 LH7  C3   C4   N1   111.37  3.000
 LH7  H3   C5   N2   107.13  3.000
 LH7  H3   C5   C8   108.68  3.000
 LH7  N2   C5   C8   111.80  3.000
 LH7  H3   C5   C6   108.33  3.000
 LH7  N2   C5   C6   112.87  3.000
 LH7  C8   C5   C6   107.91  3.000
 LH7  H5   C6   H4   108.22  3.000
 LH7  H5   C6   C7   110.91  3.000
 LH7  H4   C6   C7   110.90  3.000
 LH7  H5   C6   C5   110.44  3.000
 LH7  H4   C6   C5   111.12  3.000
 LH7  C7   C6   C5   105.26  3.000
 LH7  H7   C7   H6   109.71  3.000
 LH7  H7   C7   S1   108.71  3.000
 LH7  H6   C7   S1   107.87  3.000
 LH7  H7   C7   C6   114.73  3.000
 LH7  H6   C7   C6   111.76  3.000
 LH7  S1   C7   C6   103.65  3.000
 LH7  H9   C8   H8   109.85  3.000
 LH7  H9   C8   S1   109.16  3.000
 LH7  H8   C8   S1   107.35  3.000
 LH7  H9   C8   C5   113.25  3.000
 LH7  H8   C8   C5   111.61  3.000
 LH7  S1   C8   C5   105.34  3.000
 LH7  H11  C10  H10  106.75  3.000
 LH7  H11  C10  C11  110.02  3.000
 LH7  H10  C10  C11  110.08  3.000
 LH7  H11  C10  N3   110.88  3.000
 LH7  H10  C10  N3   108.50  3.000
 LH7  C11  C10  N3   110.53  3.000
 LH7  H12  C13  C14  120.49  3.000
 LH7  H12  C13  C12  120.99  3.000
 LH7  C14  C13  C12  118.51  3.000
 LH7  H13  C15  C16  120.94  3.000
 LH7  H13  C15  C14  120.62  3.000
 LH7  C16  C15  C14  118.44  3.000
 LH7  C16  C11  C12  118.71  3.000
 LH7  C16  C11  C10  120.85  3.000
 LH7  C12  C11  C10  120.45  3.000
 LH7  H17  C12  C11  119.91  3.000
 LH7  H17  C12  C13  119.02  3.000
 LH7  C11  C12  C13  121.07  3.000
 LH7  F1   C14  C15  119.04  3.000
 LH7  F1   C14  C13  118.85  3.000
 LH7  C15  C14  C13  122.11  3.000
 LH7  H18  C16  C11  119.81  3.000
 LH7  H18  C16  C15  119.03  3.000
 LH7  C11  C16  C15  121.16  3.000
 LH7  N2   C2   C3   105.49  3.000
 LH7  C3   C2   C1   131.63  3.000
 LH7  N2   C2   C1   122.86  3.000
 LH7  C9   C3   C2   127.08  3.000
 LH7  C9   C3   C4   128.28  3.000
 LH7  C2   C3   C4   104.64  3.000
 LH7  O3   C9   C3   122.65  3.000
 LH7  O3   C9   N3   122.40  3.000
 LH7  C3   C9   N3   114.94  3.000
 LH7  C2   N2   C5   127.36  3.000
 LH7  C2   N2   N1   113.25  3.000
 LH7  C5   N2   N1   119.37  3.000
 LH7  O2   S1   O1   118.48  3.000
 LH7  O2   S1   C8   110.94  3.000
 LH7  O1   S1   C8   108.96  3.000
 LH7  C8   S1   C7    95.86  3.000
 LH7  O2   S1   C7   111.40  3.000
 LH7  O1   S1   C7   108.84  3.000
 LH7  H16  C1   H15  108.10  3.000
 LH7  H16  C1   H14  107.69  3.000
 LH7  H15  C1   H14  107.72  3.000
 LH7  H16  C1   C2   110.29  3.000
 LH7  H15  C1   C2   111.40  3.000
 LH7  H14  C1   C2   111.49  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
 LH7  CONST_01  C3   C2   N2   N1      0.00   0.0  0
 LH7  CONST_02  C2   C3   C4   N1      0.00   0.0  0
 LH7  CONST_03  C2   N2   N1   C4      0.00   0.0  0
 LH7  CONST_04  N2   C2   C3   C4      0.00   0.0  0
 LH7  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 LH7  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 LH7  CONST_07  C12  C11  C16  C15     0.00   0.0  0
 LH7  CONST_08  C12  C13  C14  C15     0.00   0.0  0
 LH7  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 LH7  CONST_10  C14  C15  C16  C11     0.00   0.0  0
 LH7  CONST_11  N2   N1   C4   C3      0.00   0.0  0
 LH7  CONST_12  C5   N2   N1   C4    180.00   0.0  0
 LH7  CONST_13  C3   C2   N2   C5    180.00   0.0  0
 LH7  CONST_14  C1   C2   N2   N1    180.00   0.0  0
 LH7  CONST_15  C9   C3   C4   N1    180.00   0.0  0
 LH7  CONST_16  C1   C2   C3   C4    180.00   0.0  0
 LH7  CONST_17  C1   C2   N2   C5      0.00   0.0  0
 LH7  CONST_18  C13  C12  C11  C10   180.00   0.0  0
 LH7  CONST_19  C15  C16  C11  C10   180.00   0.0  0
 LH7  CONST_20  F1   C14  C13  C12   180.00   0.0  0
 LH7  CONST_21  F1   C14  C15  C16   180.00   0.0  0
 LH7  CONST_22  N2   C2   C3   C9    180.00   0.0  0
 LH7  CONST_23  H13  C15  C14  C13   180.00   0.0  0
 LH7  CONST_24  H12  C13  C14  C15   180.00   0.0  0
 LH7  CONST_25  H18  C16  C11  C12   180.00   0.0  0
 LH7  CONST_26  H17  C12  C13  C14   180.00   0.0  0
 LH7  CONST_27  H2   C4   C3   C2    180.00   0.0  0
 LH7  CONST_28  C3   C9   N3   C10   180.00   0.0  0
 LH7  CONST_29  H1   N3   C9   C3      0.00   0.0  0
 LH7  CONST_30  O3   C9   N3   C10     0.00   0.0  0
 LH7  Var_01    C7   S1   C8   C5      0.93  30.0  1
 LH7  Var_02    S1   C7   C6   C5    -45.22  30.0  1
 LH7  Var_03    C8   S1   C7   C6     25.82  30.0  1
 LH7  Var_04    C4   C3   C9   N3    -26.42  30.0  2
 LH7  Var_05    C12  C11  C10  N3     60.02  30.0  2
 LH7  Var_06    H14  C1   C2   C3    116.54  30.0  2
 LH7  Var_07    C9   N3   C10  C11  -162.77  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
 LH7  chir_01  C5  C8  C6  N2  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
 LH7  plan-1  N1   0.020
 LH7  plan-1  C4   0.020
 LH7  plan-1  C5   0.020
 LH7  plan-1  C2   0.020
 LH7  plan-1  C3   0.020
 LH7  plan-1  C9   0.020
 LH7  plan-1  N2   0.020
 LH7  plan-1  H2   0.020
 LH7  plan-1  C1   0.020
 LH7  plan-2  C10  0.020
 LH7  plan-2  C13  0.020
 LH7  plan-2  C15  0.020
 LH7  plan-2  C11  0.020
 LH7  plan-2  C12  0.020
 LH7  plan-2  C14  0.020
 LH7  plan-2  C16  0.020
 LH7  plan-2  F1   0.020
 LH7  plan-2  H12  0.020
 LH7  plan-2  H13  0.020
 LH7  plan-2  H17  0.020
 LH7  plan-2  H18  0.020
 LH7  plan-3  N3   0.020
 LH7  plan-3  C10  0.020
 LH7  plan-3  C3   0.020
 LH7  plan-3  C9   0.020
 LH7  plan-3  O3   0.020
 LH7  plan-3  H1   0.020

