# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:05:31 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 2,4-difluoro-6-[(3S)-pyrazolidin-3-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1c(F)cc(F)cc1[C@H]2CCNN2
#
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
 S9M  S9M  2,4-difluoro-6-[(3S)-pyrazolidin-3-yl]phenol  ligand  24  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S9M
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
 S9M  C10   C  CH1   0  -0.147  -27.0807  101.1594  133.8087
 S9M  C02   C  CR6   0   0.158  -27.9838   99.7144  135.6633
 S9M  C03   C  CR6   0   0.481  -28.0514   99.4282  137.0244
 S9M  C05   C  CR16  0  -0.571  -27.4434  100.2057  137.9872
 S9M  C06   C  CR6   0   0.531  -26.7515  101.3227  137.5605
 S9M  C08   C  CR16  0  -0.487  -26.6551  101.6551  136.2268
 S9M  C09   C  CR6   0   0.028  -27.2582  100.8455  135.2692
 S9M  C11   C  CH2   0  -0.488  -26.0125  100.2903  133.1042
 S9M  C12   C  CH2   0  -0.315  -26.7165   99.8385  131.8083
 S9M  F07   F  F     0  -0.319  -26.1619  102.1071  138.4795
 S9M  N13   N  NH1   0  -0.443  -27.8984  100.6815  131.6778
 S9M  N14   N  NH1   0  -0.541  -28.2948  100.8414  133.0317
 S9M  O01   O  OH1   0  -0.646  -28.6048   98.9027  134.7954
 S9M  H101  H  HCH1  0   0.272  -26.8166  102.2176  133.6983
 S9M  H051  H  HCR6  0   0.300  -27.5188   99.9488  139.0357
 S9M  H081  H  HCR6  0   0.278  -26.1086  102.5395  135.9232
 S9M  H111  H  HCH2  0   0.259  -25.1215  100.8822  132.9012
 S9M  H112  H  HCH2  0   0.257  -25.7083   99.4396  133.7142
 S9M  H121  H  HCH2  0   0.255  -26.0931   99.9367  130.9214
 S9M  H122  H  HCH2  0   0.241  -27.0305   98.7961  131.8871
 S9M  H131  H  HNH1  0   0.351  -27.5912  101.5875  131.3258
 S9M  H141  H  HNH1  0   0.387  -28.9985  101.5677  133.0971
 S9M  H011  H  HOH1  0   0.473  -28.6798   99.4202  133.9460
 S9M  F04   F  F     0  -0.313  -28.7407   98.3428  137.4053

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
 S9M  C02  O01   single    1.341  0.020  1.341
 S9M  C03  C02   aromatic  1.393  0.020  1.393
 S9M  F04  C03   single    1.341  0.020  1.341
 S9M  C05  C03   aromatic  1.379  0.020  1.379
 S9M  C06  C05   aromatic  1.381  0.020  1.381
 S9M  F07  C06   single    1.344  0.020  1.344
 S9M  C08  C06   aromatic  1.378  0.020  1.378
 S9M  C09  C08   aromatic  1.391  0.020  1.391
 S9M  C10  C09   single    1.504  0.020  1.504
 S9M  C11  C10   single    1.547  0.020  1.547
 S9M  C12  C11   single    1.543  0.020  1.543
 S9M  N13  C12   single    1.458  0.020  1.458
 S9M  N14  N13   single    1.420  0.020  1.420
 S9M  C02  C09   aromatic  1.400  0.020  1.400
 S9M  C10  N14   single    1.476  0.020  1.476
 S9M  C10  H101  single    0.970  0.020  1.090
 S9M  C05  H051  single    0.930  0.020  1.080
 S9M  C08  H081  single    0.930  0.020  1.080
 S9M  C11  H111  single    0.970  0.020  1.090
 S9M  C11  H112  single    0.970  0.020  1.090
 S9M  C12  H121  single    0.970  0.020  1.090
 S9M  C12  H122  single    0.970  0.020  1.090
 S9M  N13  H131  single    0.890  0.020  1.040
 S9M  N14  H141  single    0.890  0.020  1.040
 S9M  O01  H011  single    0.850  0.020  0.980

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
 S9M  H101  C10  N14   110.67  3.000
 S9M  H101  C10  C11   109.28  3.000
 S9M  N14   C10  C11   101.96  3.000
 S9M  H101  C10  C09   109.13  3.000
 S9M  N14   C10  C09   111.65  3.000
 S9M  C11   C10  C09   113.98  3.000
 S9M  O01   C02  C09   123.14  3.000
 S9M  C09   C02  C03   117.79  3.000
 S9M  O01   C02  C03   119.07  3.000
 S9M  F04   C03  C05   119.00  3.000
 S9M  C05   C03  C02   123.04  3.000
 S9M  F04   C03  C02   117.97  3.000
 S9M  H051  C05  C06   121.74  3.000
 S9M  H051  C05  C03   120.79  3.000
 S9M  C06   C05  C03   117.46  3.000
 S9M  F07   C06  C08   119.36  3.000
 S9M  C08   C06  C05   121.94  3.000
 S9M  F07   C06  C05   118.71  3.000
 S9M  H081  C08  C09   120.06  3.000
 S9M  H081  C08  C06   120.24  3.000
 S9M  C09   C08  C06   119.70  3.000
 S9M  C08   C09  C02   120.05  3.000
 S9M  C02   C09  C10   120.19  3.000
 S9M  C08   C09  C10   119.71  3.000
 S9M  H112  C11  H111  107.47  3.000
 S9M  H112  C11  C12   111.65  3.000
 S9M  H111  C11  C12   112.09  3.000
 S9M  H112  C11  C10   112.11  3.000
 S9M  H111  C11  C10   110.16  3.000
 S9M  C12   C11  C10   103.42  3.000
 S9M  H122  C12  H121  108.05  3.000
 S9M  H122  C12  N13   109.00  3.000
 S9M  H121  C12  N13   109.83  3.000
 S9M  H122  C12  C11   110.51  3.000
 S9M  H121  C12  C11   113.37  3.000
 S9M  N13   C12  C11   106.01  3.000
 S9M  H131  N13  N14   108.26  3.000
 S9M  H131  N13  C12   107.49  3.000
 S9M  N14   N13  C12   101.90  3.000
 S9M  H141  N14  N13   109.64  3.000
 S9M  H141  N14  C10   112.51  3.000
 S9M  N13   N14  C10   107.25  3.000
 S9M  H011  O01  C02   105.78  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
 S9M  CONST_01  C06   C05  C03  C02    0.00   0.0  0
 S9M  CONST_02  C06   C08  C09  C02    0.00   0.0  0
 S9M  CONST_03  C08   C09  C02  C03    0.00   0.0  0
 S9M  CONST_04  C08   C06  C05  C03    0.00   0.0  0
 S9M  CONST_05  C09   C02  C03  C05    0.00   0.0  0
 S9M  CONST_06  C09   C08  C06  C05    0.00   0.0  0
 S9M  CONST_07  C06   C08  C09  C10  180.00   0.0  0
 S9M  CONST_08  C03   C02  C09  C10  180.00   0.0  0
 S9M  CONST_09  O01   C02  C09  C10    0.00   0.0  0
 S9M  CONST_10  F07   C06  C05  C03  180.00   0.0  0
 S9M  CONST_11  O01   C02  C03  C05  180.00   0.0  0
 S9M  CONST_12  F04   C03  C05  C06  180.00   0.0  0
 S9M  CONST_13  O01   C02  C09  C08  180.00   0.0  0
 S9M  CONST_14  F07   C06  C08  C09  180.00   0.0  0
 S9M  CONST_15  F04   C03  C02  C09  180.00   0.0  0
 S9M  CONST_16  H081  C08  C09  C10    0.00   0.0  0
 S9M  CONST_17  H051  C05  C03  C02  180.00   0.0  0
 S9M  Var_01    N13   C12  C11  C10   13.75  30.0  1
 S9M  Var_02    C12   N13  N14  C10   45.87  30.0  1
 S9M  Var_03    N14   N13  C12  C11  -35.72  30.0  1

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
 S9M  chir_01  C10  C09  C11  N14  negativ

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
 S9M  plan-1  C10   0.020
 S9M  plan-1  C02   0.020
 S9M  plan-1  C03   0.020
 S9M  plan-1  C05   0.020
 S9M  plan-1  C06   0.020
 S9M  plan-1  C08   0.020
 S9M  plan-1  C09   0.020
 S9M  plan-1  F07   0.020
 S9M  plan-1  O01   0.020
 S9M  plan-1  H051  0.020
 S9M  plan-1  H081  0.020
 S9M  plan-1  F04   0.020

