# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:28:25 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2~{R})-1-(4-chloranyl-2-fluoranyl-phenyl)-2-cyclohexyl-3-ethanoyl-4-oxidanyl-2~{H}-pyrrol-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)C1=C(O)C(=O)N([C@@H]1C2CCCCC2)c3ccc(Cl)cc3F
#
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
 VT5  VT5  (2~{R})-1-(4-chloranyl-2-fluoranyl-phenyl)-2-cyclohexyl-3-ethanoyl-4-oxidanyl-2~{H}-pyrrol-5-one  ligand  43  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VT5
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
 VT5  C    C   CH3   0  -0.806  -3.8715   0.8039  -2.1456
 VT5  C1   C   C     0   0.366  -3.8906  -0.1943  -1.0191
 VT5  O    O   O     0  -0.402  -4.9389  -0.6576  -0.6100
 VT5  C2   C   CR5   0  -0.132  -2.6138  -0.6142  -0.4340
 VT5  C3   C   CR5   0   0.252  -2.4565  -1.6462   0.4152
 VT5  C4   C   CR5   0   0.475  -1.0108  -1.8669   0.6727
 VT5  O1   O   O     0  -0.454  -0.5420  -2.7743   1.3290
 VT5  N    N   NR5   0  -0.593  -0.3581  -0.8994  -0.0102
 VT5  C5   C   CR15  0  -0.116  -1.2639  -0.0145  -0.7411
 VT5  C6   C   CH1   0  -0.239  -1.1418   1.4661  -0.3347
 VT5  C11  C   CH2   0  -0.424  -1.3181   1.7097   1.1625
 VT5  C10  C   CH2   0  -0.429  -1.3309   3.2059   1.4665
 VT5  C9   C   CH2   0  -0.431  -0.0774   3.8954   0.9381
 VT5  C8   C   CH2   0  -0.432   0.1114   3.6291  -0.5517
 VT5  C7   C   CH2   0  -0.425   0.1399   2.1312  -0.8411
 VT5  C12  C   CR6   0   0.139   1.0374  -0.8967  -0.1602
 VT5  C13  C   CR16  0  -0.267   1.6246  -1.0101  -1.4147
 VT5  C14  C   CR16  0  -0.225   3.0003  -0.9924  -1.5668
 VT5  C15  C   CR6   0  -0.024   3.7992  -0.8815  -0.4391
 VT5  C16  C   CR16  0  -0.373   3.2482  -0.7781   0.8279
 VT5  C17  C   CR6   0   0.546   1.8730  -0.7828   0.9432
 VT5  F    F   F     0  -0.294   1.3351  -0.6499   2.1564
 VT5  CL   CL  CL    0  -0.106   5.5175  -0.8693  -0.6078
 VT5  O2   O   OH1   0  -0.566  -3.3533  -2.4508   0.9410
 VT5  H1   H   HCH3  0   0.281  -4.7112   0.6245  -2.8148
 VT5  H2   H   HCH3  0   0.277  -3.9882   1.8122  -1.7413
 VT5  H3   H   HCH3  0   0.258  -2.9478   0.7852  -2.7217
 VT5  H4   H   HCR5  0   0.286  -1.0539  -0.0994  -1.8145
 VT5  H5   H   HCH1  0   0.244  -1.9668   1.9732  -0.8490
 VT5  H6   H   HCH2  0   0.236  -2.2417   1.2486   1.5208
 VT5  H7   H   HCH2  0   0.218  -0.4974   1.2406   1.7136
 VT5  H8   H   HCH2  0   0.213  -2.2151   3.6597   1.0057
 VT5  H9   H   HCH2  0   0.230  -1.4268   3.3635   2.5433
 VT5  H10  H   HCH2  0   0.229  -0.1296   4.9702   1.1277
 VT5  H11  H   HCH2  0   0.210   0.7975   3.5237   1.4836
 VT5  H12  H   HCH2  0   0.213  -0.7107   4.0885  -1.1117
 VT5  H13  H   HCH2  0   0.231   1.0325   4.0958  -0.9081
 VT5  H14  H   HCH2  0   0.220   1.0165   1.6977  -0.3519
 VT5  H15  H   HCH2  0   0.235   0.2590   1.9529  -1.9137
 VT5  H16  H   HCR6  0   0.294   0.9960  -1.1105  -2.2900
 VT5  H17  H   HCR6  0   0.292   3.4395  -1.0777  -2.5506
 VT5  H18  H   HCR6  0   0.309   3.8669  -0.6849   1.7101
 VT5  H19  H   HOH1  0   0.485  -2.9074  -3.1349   1.4641

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
 VT5  CL   C15  single    1.727  0.020  1.727
 VT5  C16  C15  aromatic  1.385  0.020  1.385
 VT5  C16  C17  aromatic  1.380  0.020  1.380
 VT5  C15  C14  aromatic  1.387  0.020  1.387
 VT5  F    C17  single    1.334  0.020  1.334
 VT5  C17  C12  aromatic  1.389  0.020  1.389
 VT5  C8   C9   single    1.525  0.020  1.525
 VT5  C8   C7   single    1.526  0.020  1.526
 VT5  C14  C13  aromatic  1.384  0.020  1.384
 VT5  C9   C10  single    1.525  0.020  1.525
 VT5  C12  C13  aromatic  1.390  0.020  1.390
 VT5  C12  N    single    1.404  0.020  1.404
 VT5  C10  C11  single    1.527  0.020  1.527
 VT5  C7   C6   single    1.530  0.020  1.530
 VT5  O1   C4   double    1.214  0.020  1.214
 VT5  C6   C11  single    1.527  0.020  1.527
 VT5  C6   C5   single    1.540  0.020  1.540
 VT5  N    C4   single    1.352  0.020  1.352
 VT5  N    C5   single    1.462  0.020  1.462
 VT5  C4   C3   single    1.485  0.020  1.485
 VT5  C5   C2   single    1.509  0.020  1.509
 VT5  C3   C2   double    1.346  0.020  1.346
 VT5  C3   O2   single    1.315  0.020  1.315
 VT5  C2   C1   single    1.466  0.020  1.466
 VT5  C1   O    double    1.217  0.020  1.217
 VT5  C1   C    single    1.505  0.020  1.505
 VT5  C    H1   single    0.970  0.020  1.090
 VT5  C    H2   single    0.970  0.020  1.090
 VT5  C    H3   single    0.970  0.020  1.090
 VT5  C5   H4   single    0.970  0.020  1.090
 VT5  C6   H5   single    0.970  0.020  1.090
 VT5  C11  H6   single    0.970  0.020  1.090
 VT5  C11  H7   single    0.970  0.020  1.090
 VT5  C10  H8   single    0.970  0.020  1.090
 VT5  C10  H9   single    0.970  0.020  1.090
 VT5  C9   H10  single    0.970  0.020  1.090
 VT5  C9   H11  single    0.970  0.020  1.090
 VT5  C8   H12  single    0.970  0.020  1.090
 VT5  C8   H13  single    0.970  0.020  1.090
 VT5  C7   H14  single    0.970  0.020  1.090
 VT5  C7   H15  single    0.970  0.020  1.090
 VT5  C13  H16  single    0.930  0.020  1.080
 VT5  C14  H17  single    0.930  0.020  1.080
 VT5  C16  H18  single    0.930  0.020  1.080
 VT5  O2   H19  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
 VT5  H3   C    H2   107.59  3.000
 VT5  H3   C    H1   109.04  3.000
 VT5  H2   C    H1   107.28  3.000
 VT5  H3   C    C1   113.29  3.000
 VT5  H2   C    C1   109.49  3.000
 VT5  H1   C    C1   109.94  3.000
 VT5  C2   C1   O    120.47  3.000
 VT5  O    C1   C    120.99  3.000
 VT5  C2   C1   C    118.53  3.000
 VT5  C5   C2   C3   109.19  3.000
 VT5  C3   C2   C1   124.99  3.000
 VT5  C5   C2   C1   125.75  3.000
 VT5  O2   C3   C4   120.25  3.000
 VT5  O2   C3   C2   129.94  3.000
 VT5  C4   C3   C2   109.71  3.000
 VT5  N    C4   O1   128.42  3.000
 VT5  N    C4   C3   106.02  3.000
 VT5  O1   C4   C3   125.51  3.000
 VT5  C12  N    C5   124.16  3.000
 VT5  C5   N    C4   112.74  3.000
 VT5  C12  N    C4   122.36  3.000
 VT5  H4   C5   C6   108.50  3.000
 VT5  H4   C5   N    108.89  3.000
 VT5  C6   C5   N    113.63  3.000
 VT5  H4   C5   C2   109.86  3.000
 VT5  N    C5   C2   102.24  3.000
 VT5  C6   C5   C2   113.53  3.000
 VT5  H5   C6   C7   105.90  3.000
 VT5  H5   C6   C11  107.41  3.000
 VT5  C7   C6   C11  110.60  3.000
 VT5  H5   C6   C5   105.14  3.000
 VT5  C11  C6   C5   113.75  3.000
 VT5  C7   C6   C5   113.38  3.000
 VT5  H7   C11  H6   106.73  3.000
 VT5  H7   C11  C10  109.04  3.000
 VT5  H6   C11  C10  109.94  3.000
 VT5  H7   C11  C6   109.81  3.000
 VT5  H6   C11  C6   110.60  3.000
 VT5  C10  C11  C6   110.64  3.000
 VT5  H9   C10  H8   106.49  3.000
 VT5  H9   C10  C9   110.39  3.000
 VT5  H8   C10  C9   109.30  3.000
 VT5  H9   C10  C11  109.78  3.000
 VT5  H8   C10  C11  109.20  3.000
 VT5  C9   C10  C11  111.54  3.000
 VT5  H11  C9   H10  106.58  3.000
 VT5  H11  C9   C8   109.15  3.000
 VT5  H10  C9   C8   110.31  3.000
 VT5  H11  C9   C10  109.29  3.000
 VT5  H10  C9   C10  110.20  3.000
 VT5  C8   C9   C10  111.17  3.000
 VT5  H13  C8   H12  106.67  3.000
 VT5  H13  C8   C7   109.98  3.000
 VT5  H12  C8   C7   109.20  3.000
 VT5  H13  C8   C9   110.39  3.000
 VT5  H12  C8   C9   109.46  3.000
 VT5  C7   C8   C9   111.04  3.000
 VT5  H15  C7   H14  106.66  3.000
 VT5  H15  C7   C8   110.37  3.000
 VT5  H14  C7   C8   108.62  3.000
 VT5  H15  C7   C6   110.17  3.000
 VT5  H14  C7   C6   110.56  3.000
 VT5  C8   C7   C6   110.38  3.000
 VT5  C17  C12  C13  118.02  3.000
 VT5  C13  C12  N    121.09  3.000
 VT5  C17  C12  N    120.90  3.000
 VT5  H16  C13  C14  119.31  3.000
 VT5  H16  C13  C12  119.49  3.000
 VT5  C14  C13  C12  121.20  3.000
 VT5  H17  C14  C15  120.84  3.000
 VT5  H17  C14  C13  120.19  3.000
 VT5  C15  C14  C13  118.97  3.000
 VT5  CL   C15  C16  118.99  3.000
 VT5  C16  C15  C14  121.37  3.000
 VT5  CL   C15  C14  119.64  3.000
 VT5  H18  C16  C17  120.15  3.000
 VT5  H18  C16  C15  121.66  3.000
 VT5  C17  C16  C15  118.19  3.000
 VT5  F    C17  C16  118.53  3.000
 VT5  F    C17  C12  119.22  3.000
 VT5  C16  C17  C12  122.24  3.000
 VT5  H19  O2   C3   109.50  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
 VT5  CONST_01  C15  C16  C17  C12    0.00   0.0  0
 VT5  CONST_02  C15  C14  C13  C12    0.00   0.0  0
 VT5  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 VT5  CONST_04  C16  C17  C12  C13    0.00   0.0  0
 VT5  CONST_05  C17  C16  C15  C14    0.00   0.0  0
 VT5  CONST_06  C17  C12  C13  C14    0.00   0.0  0
 VT5  CONST_07  C16  C17  C12  N    180.00   0.0  0
 VT5  CONST_08  C14  C13  C12  N    180.00   0.0  0
 VT5  CONST_09  C12  N    C4   C3   180.00   0.0  0
 VT5  CONST_10  C5   N    C4   C3     0.00   0.0  0
 VT5  CONST_11  F    C17  C12  N      0.00   0.0  0
 VT5  CONST_12  CL   C15  C14  C13  180.00   0.0  0
 VT5  CONST_13  F    C17  C12  C13  180.00   0.0  0
 VT5  CONST_14  F    C17  C16  C15  180.00   0.0  0
 VT5  CONST_15  CL   C15  C16  C17  180.00   0.0  0
 VT5  CONST_16  C12  N    C4   O1     0.00   0.0  0
 VT5  CONST_17  C5   N    C4   O1   180.00   0.0  0
 VT5  CONST_18  H16  C13  C12  N      0.00   0.0  0
 VT5  CONST_19  H18  C16  C17  C12  180.00   0.0  0
 VT5  CONST_20  H17  C14  C13  C12  180.00   0.0  0
 VT5  Var_01    N    C4   C3   C2     2.40  30.0  1
 VT5  Var_02    C17  C12  N    C4   -63.19  30.0  2
 VT5  Var_03    C5   C2   C3   C4    -3.39  30.0  1
 VT5  Var_04    C9   C8   C7   C6    57.04  30.0  1
 VT5  Var_05    C9   C10  C11  C6   -55.59  30.0  1
 VT5  Var_06    C8   C9   C10  C11   54.86  30.0  1
 VT5  Var_07    C7   C8   C9   C10  -55.54  30.0  1
 VT5  Var_08    H1   C    C1   C2   148.89  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
 VT5  chir_01  C5  C6  N    C2  negativ
 VT5  chir_02  C6  C7  C11  C5  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
 VT5  plan-1  C    0.020
 VT5  plan-1  C1   0.020
 VT5  plan-1  O    0.020
 VT5  plan-1  C2   0.020
 VT5  plan-2  N    0.020
 VT5  plan-2  C12  0.020
 VT5  plan-2  C13  0.020
 VT5  plan-2  C14  0.020
 VT5  plan-2  C15  0.020
 VT5  plan-2  C16  0.020
 VT5  plan-2  C17  0.020
 VT5  plan-2  F    0.020
 VT5  plan-2  CL   0.020
 VT5  plan-2  H16  0.020
 VT5  plan-2  H17  0.020
 VT5  plan-2  H18  0.020
 VT5  plan-3  C3   0.020
 VT5  plan-3  C4   0.020
 VT5  plan-3  O1   0.020
 VT5  plan-3  N    0.020
 VT5  plan-3  C5   0.020
 VT5  plan-3  C12  0.020

