# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:35:21 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2E)-2-[(4S)-4-(4-chlorophenyl)cyclohexylidene]-3,4-dihydroxynaphthalen-1(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(O)[C](=[C@@]2CC[CH](CC2)c3ccc(Cl)cc3)C(=O)c4ccccc14
#
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
 AFI  AFI  (2E)-2-[(4S)-4-(4-chlorophenyl)cyclohexylidene]-3,4-dihydroxynaphthalen-1(2H)-one  ligand  45  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_AFI
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
 AFI  O1    O   O     0  -0.397  -0.6230  -2.4691   2.7401
 AFI  O2    O   OH1   0  -0.652   1.6497   2.0168   4.5583
 AFI  C1    C   CR6   0   0.315  -0.2672  -1.3128   2.8719
 AFI  C2    C   CR6   0  -0.216   0.9086  -0.7153   2.1767
 AFI  C3    C   CR6   0   0.264   1.6107   0.3057   2.9667
 AFI  C4    C   CR6   0   0.165   0.9634   1.0288   3.9044
 AFI  C5    C   CR16  0  -0.322  -1.1551   1.6195   5.0680
 AFI  C6    C   CR16  0  -0.234  -2.4669   1.3152   5.3916
 AFI  C7    C   CR16  0  -0.264  -3.0725   0.1641   4.8969
 AFI  C8    C   CR16  0  -0.271  -2.3501  -0.6879   4.0793
 AFI  C9    C   CR66  0  -0.088  -1.0368  -0.3853   3.7308
 AFI  C10   C   CR66  0   0.069  -0.4238   0.7766   4.2271
 AFI  O6    O   OH1   0  -0.619   2.9263   0.4620   2.7419
 AFI  C11   C   CH2   0  -0.520   2.2113  -0.2701   0.0535
 AFI  C12   C   CH2   0  -0.413   1.5840   0.2643  -1.2374
 AFI  C13   C   CH1   0  -0.356   0.9428  -0.8434  -2.0697
 AFI  C14   C   CH2   0  -0.412  -0.0762  -1.5870  -1.2111
 AFI  C15   C   CH2   0  -0.524   0.5370  -2.1087   0.0894
 AFI  C16   C   C     0   0.181   1.2093  -1.0248   0.8864
 AFI  CL    CL  CL    0  -0.136  -1.4688   1.2366  -7.1908
 AFI  C17   C   CR6   0   0.216   0.3376  -0.3189  -3.3458
 AFI  C18   C   CR16  0  -0.345   0.8136  -0.7403  -4.5837
 AFI  C19   C   CR16  0  -0.192   0.2682  -0.2702  -5.7709
 AFI  C20   C   CR6   0  -0.062  -0.7745   0.6389  -5.7167
 AFI  C21   C   CR16  0  -0.194  -1.2721   1.0804  -4.5000
 AFI  C22   C   CR16  0  -0.327  -0.7122   0.5994  -3.3266
 AFI  H2    H   HOH1  0   0.475   1.6558   1.8408   5.5077
 AFI  H5    H   HCR6  0   0.258  -0.7028   2.5173   5.4678
 AFI  HA    H   HCR6  0   0.265  -3.0237   1.9824   6.0367
 AFI  H7    H   HCR6  0   0.261  -4.0986  -0.0645   5.1511
 AFI  H8    H   HCR6  0   0.264  -2.8100  -1.5897   3.6963
 AFI  H6    H   HOH1  0   0.472   3.2599   1.1667   3.3148
 AFI  H111  H   HCH2  0   0.276   2.6653   0.5559   0.5863
 AFI  H112  H   HCH2  0   0.252   3.0199  -0.9626  -0.2088
 AFI  H121  H   HCH2  0   0.232   0.8330   1.0205  -0.9889
 AFI  H122  H   HCH2  0   0.249   2.3595   0.7714  -1.8154
 AFI  H13   H   HCH1  0   0.244   1.7333  -1.5526  -2.3412
 AFI  H141  H   HCH2  0   0.232  -0.9124  -0.9236  -0.9698
 AFI  H142  H   HCH2  0   0.248  -0.4941  -2.4303  -1.7645
 AFI  H151  H   HCH2  0   0.254   1.3158  -2.8422  -0.1542
 AFI  H152  H   HCH2  0   0.281  -0.2124  -2.6469   0.6562
 AFI  H18   H   HCR6  0   0.259   1.6287  -1.4524  -4.6298
 AFI  H19   H   HCR6  0   0.277   0.6545  -0.6104  -6.7223
 AFI  H21   H   HCR6  0   0.277  -2.0864   1.7914  -4.4647
 AFI  H22   H   HCR6  0   0.259  -1.1108   0.9552  -2.3840

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
 AFI  O1   C1    double    1.217  0.020  1.217
 AFI  O2   C4    single    1.369  0.020  1.369
 AFI  O2   H2    single    0.850  0.020  0.980
 AFI  C1   C2    single    1.491  0.020  1.491
 AFI  C1   C9    single    1.480  0.020  1.480
 AFI  C2   C3    single    1.470  0.020  1.470
 AFI  C2   C16   double    1.361  0.020  1.361
 AFI  C3   C4    double    1.350  0.020  1.350
 AFI  C3   O6    single    1.344  0.020  1.344
 AFI  C4   C10   single    1.446  0.020  1.446
 AFI  C5   C6    aromatic  1.385  0.020  1.385
 AFI  C5   C10   aromatic  1.397  0.020  1.397
 AFI  C5   H5    single    0.930  0.020  1.080
 AFI  C6   C7    aromatic  1.392  0.020  1.392
 AFI  C6   HA    single    0.930  0.020  1.080
 AFI  C7   C8    aromatic  1.384  0.020  1.384
 AFI  C7   H7    single    0.930  0.020  1.080
 AFI  C8   C9    aromatic  1.392  0.020  1.392
 AFI  C8   H8    single    0.930  0.020  1.080
 AFI  C9   C10   aromatic  1.404  0.020  1.404
 AFI  O6   H6    single    0.850  0.020  0.980
 AFI  C11  C12   single    1.531  0.020  1.531
 AFI  C11  C16   single    1.506  0.020  1.506
 AFI  C11  H111  single    0.970  0.020  1.090
 AFI  C11  H112  single    0.970  0.020  1.090
 AFI  C12  C13   single    1.527  0.020  1.527
 AFI  C12  H121  single    0.970  0.020  1.090
 AFI  C12  H122  single    0.970  0.020  1.090
 AFI  C13  C14   single    1.526  0.020  1.526
 AFI  C13  C17   single    1.507  0.020  1.507
 AFI  C13  H13   single    0.970  0.020  1.090
 AFI  C14  C15   single    1.530  0.020  1.530
 AFI  C14  H141  single    0.970  0.020  1.090
 AFI  C14  H142  single    0.970  0.020  1.090
 AFI  C15  C16   single    1.504  0.020  1.504
 AFI  C15  H151  single    0.970  0.020  1.090
 AFI  C15  H152  single    0.970  0.020  1.090
 AFI  CL   C20   single    1.736  0.020  1.736
 AFI  C17  C18   aromatic  1.392  0.020  1.392
 AFI  C17  C22   aromatic  1.395  0.020  1.395
 AFI  C18  C19   aromatic  1.389  0.020  1.389
 AFI  C18  H18   single    0.930  0.020  1.080
 AFI  C19  C20   aromatic  1.384  0.020  1.384
 AFI  C19  H19   single    0.930  0.020  1.080
 AFI  C20  C21   aromatic  1.387  0.020  1.387
 AFI  C21  C22   aromatic  1.386  0.020  1.386
 AFI  C21  H21   single    0.930  0.020  1.080
 AFI  C22  H22   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
 AFI  H2    O2   C4    109.95  3.000
 AFI  C9    C1   C2    115.44  3.000
 AFI  C9    C1   O1    120.42  3.000
 AFI  C2    C1   O1    124.11  3.000
 AFI  C16   C2   C3    124.21  3.000
 AFI  C16   C2   C1    121.69  3.000
 AFI  C3    C2   C1    113.86  3.000
 AFI  O6    C3   C4    121.57  3.000
 AFI  O6    C3   C2    117.30  3.000
 AFI  C4    C3   C2    121.11  3.000
 AFI  C10   C4   C3    121.44  3.000
 AFI  C10   C4   O2    120.00  3.000
 AFI  C3    C4   O2    118.56  3.000
 AFI  H5    C5   C10   120.27  3.000
 AFI  H5    C5   C6    119.47  3.000
 AFI  C10   C5   C6    120.26  3.000
 AFI  HA    C6   C7    119.86  3.000
 AFI  HA    C6   C5    119.42  3.000
 AFI  C7    C6   C5    120.72  3.000
 AFI  H7    C7   C8    120.25  3.000
 AFI  H7    C7   C6    120.28  3.000
 AFI  C8    C7   C6    119.47  3.000
 AFI  H8    C8   C9    119.57  3.000
 AFI  H8    C8   C7    120.01  3.000
 AFI  C9    C8   C7    120.42  3.000
 AFI  C10   C9   C8    120.22  3.000
 AFI  C10   C9   C1    119.77  3.000
 AFI  C8    C9   C1    119.98  3.000
 AFI  C9    C10  C5    118.90  3.000
 AFI  C9    C10  C4    118.95  3.000
 AFI  C5    C10  C4    122.08  3.000
 AFI  H6    O6   C3    108.86  3.000
 AFI  H112  C11  H111  106.87  3.000
 AFI  H112  C11  C16   107.85  3.000
 AFI  H111  C11  C16   112.90  3.000
 AFI  H112  C11  C12   108.71  3.000
 AFI  H111  C11  C12   108.68  3.000
 AFI  C16   C11  C12   111.63  3.000
 AFI  H122  C12  H121  106.66  3.000
 AFI  H122  C12  C13   110.28  3.000
 AFI  H121  C12  C13   109.69  3.000
 AFI  H122  C12  C11   108.50  3.000
 AFI  H121  C12  C11   109.32  3.000
 AFI  C13   C12  C11   112.23  3.000
 AFI  H13   C13  C17   107.77  3.000
 AFI  H13   C13  C14   107.80  3.000
 AFI  C17   C13  C14   112.21  3.000
 AFI  H13   C13  C12   107.55  3.000
 AFI  C17   C13  C12   112.20  3.000
 AFI  C14   C13  C12   109.10  3.000
 AFI  H142  C14  H141  106.71  3.000
 AFI  H142  C14  C15   108.72  3.000
 AFI  H141  C14  C15   109.00  3.000
 AFI  H142  C14  C13   110.29  3.000
 AFI  H141  C14  C13   109.82  3.000
 AFI  C15   C14  C13   112.14  3.000
 AFI  H152  C15  H151  105.97  3.000
 AFI  H152  C15  C16   112.97  3.000
 AFI  H151  C15  C16   106.39  3.000
 AFI  H152  C15  C14   109.70  3.000
 AFI  H151  C15  C14   108.89  3.000
 AFI  C16   C15  C14   112.58  3.000
 AFI  C15   C16  C11   111.44  3.000
 AFI  C15   C16  C2    124.59  3.000
 AFI  C11   C16  C2    123.90  3.000
 AFI  C22   C17  C18   117.97  3.000
 AFI  C22   C17  C13   121.32  3.000
 AFI  C18   C17  C13   120.71  3.000
 AFI  H18   C18  C19   118.79  3.000
 AFI  H18   C18  C17   119.63  3.000
 AFI  C19   C18  C17   121.58  3.000
 AFI  H19   C19  C20   120.66  3.000
 AFI  H19   C19  C18   120.35  3.000
 AFI  C20   C19  C18   118.99  3.000
 AFI  C21   C20  C19   120.91  3.000
 AFI  C21   C20  CL    119.47  3.000
 AFI  C19   C20  CL    119.61  3.000
 AFI  H21   C21  C22   120.30  3.000
 AFI  H21   C21  C20   120.54  3.000
 AFI  C22   C21  C20   119.16  3.000
 AFI  H22   C22  C21   118.29  3.000
 AFI  H22   C22  C17   120.33  3.000
 AFI  C21   C22  C17   121.38  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
 AFI  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 AFI  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 AFI  CONST_03  C9   C10  C5   C6      0.00   0.0  0
 AFI  CONST_04  C9   C8   C7   C6      0.00   0.0  0
 AFI  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 AFI  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 AFI  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 AFI  CONST_08  C20  C21  C22  C17     0.00   0.0  0
 AFI  CONST_09  C21  C22  C17  C18     0.00   0.0  0
 AFI  CONST_10  C21  C20  C19  C18     0.00   0.0  0
 AFI  CONST_11  C22  C17  C18  C19     0.00   0.0  0
 AFI  CONST_12  C22  C21  C20  C19     0.00   0.0  0
 AFI  CONST_13  C19  C18  C17  C13   180.00   0.0  0
 AFI  CONST_14  C21  C22  C17  C13   180.00   0.0  0
 AFI  CONST_15  C18  C19  C20  CL    180.00   0.0  0
 AFI  CONST_16  C22  C21  C20  CL    180.00   0.0  0
 AFI  CONST_17  H8   C8   C9   C1      0.00   0.0  0
 AFI  CONST_18  H5   C5   C10  C4      0.00   0.0  0
 AFI  CONST_19  H7   C7   C6   C5    180.00   0.0  0
 AFI  CONST_20  HA   C6   C7   C8    180.00   0.0  0
 AFI  CONST_21  H18  C18  C17  C13     0.00   0.0  0
 AFI  CONST_22  H22  C22  C17  C13     0.00   0.0  0
 AFI  CONST_23  H19  C19  C18  C17   180.00   0.0  0
 AFI  CONST_24  H21  C21  C22  C17   180.00   0.0  0
 AFI  Var_01    C11  C16  C2   C1    167.91  30.0  2
 AFI  Var_02    C12  C11  C16  C2   -123.32  30.0  1
 AFI  Var_03    C14  C15  C16  C2    123.74  30.0  1
 AFI  Var_04    C16  C11  C12  C13   -56.01  30.0  1
 AFI  Var_05    C16  C15  C14  C13    54.54  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
 AFI  chir_01  C13  C12  C14  C17  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
 AFI  plan-1  C13  0.020
 AFI  plan-1  CL   0.020
 AFI  plan-1  C17  0.020
 AFI  plan-1  C18  0.020
 AFI  plan-1  C19  0.020
 AFI  plan-1  C20  0.020
 AFI  plan-1  C21  0.020
 AFI  plan-1  C22  0.020
 AFI  plan-1  H18  0.020
 AFI  plan-1  H19  0.020
 AFI  plan-1  H21  0.020
 AFI  plan-1  H22  0.020
 AFI  plan-2  O1   0.020
 AFI  plan-2  O2   0.020
 AFI  plan-2  C1   0.020
 AFI  plan-2  C2   0.020
 AFI  plan-2  C3   0.020
 AFI  plan-2  C4   0.020
 AFI  plan-2  C5   0.020
 AFI  plan-2  C6   0.020
 AFI  plan-2  C7   0.020
 AFI  plan-2  C8   0.020
 AFI  plan-2  C9   0.020
 AFI  plan-2  C10  0.020
 AFI  plan-2  O6   0.020
 AFI  plan-2  C16  0.020
 AFI  plan-2  H5   0.020
 AFI  plan-2  HA   0.020
 AFI  plan-2  H7   0.020
 AFI  plan-2  H8   0.020

