# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:56:12 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: N-[(4,4-difluoro-1-hydroxycyclohexyl)methyl]-6-fluoro-4-oxo-4H-1-benzopyran-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1(CCC(F)(F)CC1)CNC(=O)C2=CC(=O)c3cc(F)ccc3O2
#
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
 FYB  FYB  N-[(4,4-difluoro-1-hydroxycyclohexyl)methyl]-6-fluoro-4-oxo-4H-1-benzopyran-2-carboxamide  ligand  41  25  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FYB
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
 FYB  C2   C  CH2   0  -0.558   5.4968   0.3349   0.7389
 FYB  C1   C  CH2   0  -0.457   4.3885  -0.5774   1.2580
 FYB  C3   C  CT    0   0.756   5.4929   0.3866  -0.7695
 FYB  C13  C  CR6   0   0.558  -5.6246   1.5309   0.4835
 FYB  C10  C  CR6   0   0.465  -3.6300  -0.9997  -1.4163
 FYB  C8   C  CR6   0   0.259  -1.4721  -0.9849  -0.2940
 FYB  C9   C  CR16  0  -0.464  -2.2673  -1.4721  -1.2599
 FYB  C4   C  CH2   0  -0.547   4.1488   0.7599  -1.3459
 FYB  C5   C  CH2   0  -0.495   3.0542  -0.1636  -0.8172
 FYB  C7   C  C     0   0.549  -0.0541  -1.4567  -0.1158
 FYB  C15  C  CR16  0  -0.308  -3.4460   1.4237   1.4612
 FYB  C16  C  CR66  0   0.379  -3.1115   0.4544   0.5199
 FYB  C12  C  CR16  0  -0.460  -5.3070   0.5793  -0.4498
 FYB  C14  C  CR16  0  -0.402  -4.7124   1.9646   1.4418
 FYB  C11  C  CR66  0  -0.111  -4.0241   0.0244  -0.4380
 FYB  O2   O  O     0  -0.421  -4.3878  -1.4107  -2.2799
 FYB  O3   O  O     0  -0.470  -1.8577  -0.0516   0.5779
 FYB  O1   O  O     0  -0.460   0.3869  -2.3108  -0.8652
 FYB  C6   C  CH2   0  -0.286   1.9891  -1.2202   1.2222
 FYB  C    C  CT    0   0.205   3.0123  -0.1937   0.7137
 FYB  O    O  OH1   0  -0.678   2.7078   1.0880   1.2329
 FYB  F    F  F     0  -0.359   5.8774  -0.8385  -1.2665
 FYB  F1   F  F     0  -0.356   6.4518   1.2626  -1.2118
 FYB  H1   H  HCH2  0   0.256   5.3526   1.3494   1.1150
 FYB  H2   H  HCH2  0   0.268   6.4698  -0.0080   1.0978
 FYB  H3   H  HCH2  0   0.246   4.5970  -1.6143   0.9828
 FYB  H4   H  HCH2  0   0.256   4.3778  -0.5435   2.3500
 FYB  H5   H  HCR6  0   0.295  -1.8834  -2.2264  -1.9312
 FYB  H6   H  HCH2  0   0.253   3.9366   1.7949  -1.0701
 FYB  H7   H  HCH2  0   0.268   4.1851   0.7182  -2.4369
 FYB  H8   H  HCH2  0   0.256   2.0915   0.1640  -1.2190
 FYB  H9   H  HCH2  0   0.247   3.2071  -1.1791  -1.1893
 FYB  H10  H  HCR6  0   0.301  -2.7205   1.7456   2.1960
 FYB  H11  H  HCR6  0   0.295  -6.0317   0.2560  -1.1857
 FYB  H12  H  HCR6  0   0.302  -4.9967   2.7177   2.1645
 FYB  H13  H  HNH1  0   0.413   0.1569  -0.2147   1.4749
 FYB  H14  H  HCH2  0   0.269   2.0533  -1.2786   2.3106
 FYB  H15  H  HCH2  0   0.257   2.2182  -2.2091   0.8274
 FYB  H16  H  HOH1  0   0.447   1.9913   1.4734   0.7175
 FYB  N    N  NH1   0  -0.660   0.6256  -0.8797   0.8805
 FYB  F2   F  F     0  -0.307  -6.8514   2.0664   0.4846

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
 FYB  O2   C10  double    1.220  0.020  1.220
 FYB  C10  C11  single    1.470  0.020  1.470
 FYB  C10  C9   single    1.451  0.020  1.451
 FYB  F2   C13  single    1.339  0.020  1.339
 FYB  C12  C11  aromatic  1.398  0.020  1.398
 FYB  C12  C13  aromatic  1.370  0.020  1.370
 FYB  C11  C16  aromatic  1.391  0.020  1.391
 FYB  C9   C8   double    1.343  0.020  1.343
 FYB  C13  C14  aromatic  1.392  0.020  1.392
 FYB  C16  C15  aromatic  1.392  0.020  1.392
 FYB  C16  O3   single    1.353  0.020  1.353
 FYB  C8   O3   single    1.334  0.020  1.334
 FYB  C8   C7   single    1.505  0.020  1.505
 FYB  C14  C15  aromatic  1.377  0.020  1.377
 FYB  O1   C7   double    1.219  0.020  1.219
 FYB  C7   N    single    1.337  0.020  1.337
 FYB  N    C6   single    1.446  0.020  1.446
 FYB  C1   C2   single    1.526  0.020  1.526
 FYB  C1   C    single    1.529  0.020  1.529
 FYB  C2   C3   single    1.509  0.020  1.509
 FYB  F    C3   single    1.377  0.020  1.377
 FYB  C6   C    single    1.536  0.020  1.536
 FYB  C3   F1   single    1.372  0.020  1.372
 FYB  C3   C4   single    1.509  0.020  1.509
 FYB  C    O    single    1.416  0.020  1.416
 FYB  C    C5   single    1.532  0.020  1.532
 FYB  C5   C4   single    1.527  0.020  1.527
 FYB  C2   H1   single    0.970  0.020  1.090
 FYB  C2   H2   single    0.970  0.020  1.090
 FYB  C1   H3   single    0.970  0.020  1.090
 FYB  C1   H4   single    0.970  0.020  1.090
 FYB  C9   H5   single    0.930  0.020  1.080
 FYB  C4   H6   single    0.970  0.020  1.090
 FYB  C4   H7   single    0.970  0.020  1.090
 FYB  C5   H8   single    0.970  0.020  1.090
 FYB  C5   H9   single    0.970  0.020  1.090
 FYB  C15  H10  single    0.930  0.020  1.080
 FYB  C12  H11  single    0.930  0.020  1.080
 FYB  C14  H12  single    0.930  0.020  1.080
 FYB  N    H13  single    0.860  0.020  1.020
 FYB  C6   H14  single    0.970  0.020  1.090
 FYB  C6   H15  single    0.970  0.020  1.090
 FYB  O    H16  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
 FYB  H2   C2   H1   107.23  3.000
 FYB  H2   C2   C3   109.96  3.000
 FYB  H1   C2   C3   108.19  3.000
 FYB  H2   C2   C1   110.33  3.000
 FYB  H1   C2   C1   110.02  3.000
 FYB  C3   C2   C1   111.01  3.000
 FYB  H4   C1   H3   106.44  3.000
 FYB  H4   C1   C    109.83  3.000
 FYB  H3   C1   C    108.68  3.000
 FYB  H4   C1   C2   109.18  3.000
 FYB  H3   C1   C2   110.05  3.000
 FYB  C    C1   C2   112.49  3.000
 FYB  F1   C3   F    104.86  3.000
 FYB  F1   C3   C4   109.96  3.000
 FYB  F    C3   C4   109.32  3.000
 FYB  C4   C3   C2   113.11  3.000
 FYB  F1   C3   C2   110.01  3.000
 FYB  F    C3   C2   109.24  3.000
 FYB  C14  C13  C12  122.23  3.000
 FYB  C14  C13  F2   118.38  3.000
 FYB  C12  C13  F2   119.39  3.000
 FYB  O2   C10  C11  122.62  3.000
 FYB  C11  C10  C9   114.01  3.000
 FYB  O2   C10  C9   123.36  3.000
 FYB  O3   C8   C7   114.47  3.000
 FYB  C7   C8   C9   121.97  3.000
 FYB  O3   C8   C9   123.56  3.000
 FYB  H5   C9   C8   119.34  3.000
 FYB  H5   C9   C10  119.61  3.000
 FYB  C8   C9   C10  121.05  3.000
 FYB  H7   C4   H6   107.15  3.000
 FYB  H7   C4   C5   110.28  3.000
 FYB  H6   C4   C5   110.27  3.000
 FYB  H7   C4   C3   110.02  3.000
 FYB  H6   C4   C3   108.12  3.000
 FYB  C5   C4   C3   110.89  3.000
 FYB  H9   C5   H8   106.06  3.000
 FYB  H9   C5   C    109.03  3.000
 FYB  H8   C5   C    110.43  3.000
 FYB  H9   C5   C4   110.12  3.000
 FYB  H8   C5   C4   108.83  3.000
 FYB  C    C5   C4   112.19  3.000
 FYB  N    C7   O1   125.22  3.000
 FYB  N    C7   C8   115.59  3.000
 FYB  O1   C7   C8   119.20  3.000
 FYB  H10  C15  C14  120.63  3.000
 FYB  H10  C15  C16  120.36  3.000
 FYB  C14  C15  C16  119.01  3.000
 FYB  O3   C16  C11  121.44  3.000
 FYB  O3   C16  C15  117.00  3.000
 FYB  C11  C16  C15  121.55  3.000
 FYB  H11  C12  C11  120.11  3.000
 FYB  H11  C12  C13  121.03  3.000
 FYB  C11  C12  C13  118.86  3.000
 FYB  H12  C14  C15  120.37  3.000
 FYB  H12  C14  C13  120.30  3.000
 FYB  C15  C14  C13  119.33  3.000
 FYB  C12  C11  C16  119.02  3.000
 FYB  C16  C11  C10  119.84  3.000
 FYB  C12  C11  C10  121.13  3.000
 FYB  C16  O3   C8   120.09  3.000
 FYB  H15  C6   H14  107.48  3.000
 FYB  H15  C6   C    110.29  3.000
 FYB  H14  C6   C    109.06  3.000
 FYB  H15  C6   N    109.05  3.000
 FYB  H14  C6   N    107.67  3.000
 FYB  C    C6   N    113.11  3.000
 FYB  O    C    C6   109.89  3.000
 FYB  O    C    C5   110.77  3.000
 FYB  C6   C    C5   111.24  3.000
 FYB  C5   C    C1   109.64  3.000
 FYB  O    C    C1   106.87  3.000
 FYB  C6   C    C1   108.30  3.000
 FYB  H16  O    C    109.02  3.000
 FYB  H13  N    C6   117.04  3.000
 FYB  H13  N    C7   119.21  3.000
 FYB  C6   N    C7   123.62  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
 FYB  CONST_01  C16  C11  C12  C13     0.00   0.0  0
 FYB  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 FYB  CONST_03  C12  C11  C16  C15     0.00   0.0  0
 FYB  CONST_04  C12  C13  C14  C15     0.00   0.0  0
 FYB  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 FYB  CONST_06  C11  C16  C15  C14     0.00   0.0  0
 FYB  CONST_07  F2   C13  C14  C15   180.00   0.0  0
 FYB  CONST_08  C11  C12  C13  F2    180.00   0.0  0
 FYB  CONST_09  H10  C15  C14  C13   180.00   0.0  0
 FYB  CONST_10  H11  C12  C11  C10     0.00   0.0  0
 FYB  CONST_11  H12  C14  C15  C16   180.00   0.0  0
 FYB  CONST_12  C6   N    C7   C8    180.00   0.0  0
 FYB  CONST_13  H13  N    C7   C8      0.00   0.0  0
 FYB  CONST_14  C6   N    C7   O1      0.00   0.0  0
 FYB  Var_01    C5   C4   C3   C2    -54.01  30.0  1
 FYB  Var_02    C4   C3   C2   C1     53.60  30.0  1
 FYB  Var_03    C    C1   C2   C3    -54.26  30.0  1
 FYB  Var_04    C    C5   C4   C3     54.95  30.0  1
 FYB  Var_05    O3   C8   C9   C10    -0.02  30.0  1
 FYB  Var_06    C11  C10  C9   C8     -0.16  30.0  1
 FYB  Var_07    C11  C16  O3   C8     -0.07  30.0  1
 FYB  Var_08    C12  C11  C10  C9   -179.75  30.0  1
 FYB  Var_09    O1   C7   C8   C9     -0.34  30.0  2
 FYB  Var_10    C    C6   N    C7    102.30  30.0  3

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
 FYB  chir_01  C  C1  O  C5  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
 FYB  plan-1  C8   0.020
 FYB  plan-1  C7   0.020
 FYB  plan-1  O1   0.020
 FYB  plan-1  C6   0.020
 FYB  plan-1  H13  0.020
 FYB  plan-1  N    0.020
 FYB  plan-2  C13  0.020
 FYB  plan-2  C10  0.020
 FYB  plan-2  C15  0.020
 FYB  plan-2  C16  0.020
 FYB  plan-2  C12  0.020
 FYB  plan-2  C14  0.020
 FYB  plan-2  C11  0.020
 FYB  plan-2  O3   0.020
 FYB  plan-2  H10  0.020
 FYB  plan-2  H11  0.020
 FYB  plan-2  H12  0.020
 FYB  plan-2  F2   0.020
 FYB  plan-3  C10  0.020
 FYB  plan-3  C9   0.020
 FYB  plan-3  C11  0.020
 FYB  plan-3  O2   0.020

