# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 20:13:49 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: 7-(trifluoromethyl)-3,4-dihydroquinoxalin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc2NCC(=O)Nc2c1
#
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
 5GT  5GT  7-(trifluoromethyl)-3,4-dihydroquinoxalin-2(1H)-one  ligand  22  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5GT
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
 5GT  FAB  F  F     0  -0.304  -3.7046  -0.6627  -0.0502
 5GT  CAO  C  CT    0   1.049  -2.7901   0.3122  -0.0516
 5GT  FAC  F  F     0  -0.319  -2.9978   1.0386  -1.1634
 5GT  FAD  F  F     0  -0.319  -3.0851   1.1239   0.9782
 5GT  CAL  C  CR6   0  -0.218  -1.3947  -0.2043   0.0258
 5GT  CAG  C  CR16  0  -0.356  -0.3471   0.7164   0.0425
 5GT  CAN  C  CR6   0   0.370   0.9582   0.2782   0.1172
 5GT  NAJ  N  NH1   0  -0.724   2.0224   1.1761   0.1981
 5GT  C    C  C     0   0.503   3.3212   0.8453   0.0089
 5GT  O    O  O     0  -0.462   4.2198   1.6636   0.0498
 5GT  CA   C  CH2   0  -0.416   3.5652  -0.6105  -0.3201
 5GT  N    N  NH1   0  -0.676   2.5652  -1.4607   0.2847
 5GT  CAM  C  CR6   0   0.320   1.2510  -1.0954   0.1655
 5GT  CAF  C  CR16  0  -0.342   0.1962  -2.0017   0.1404
 5GT  CAE  C  CR16  0  -0.296  -1.1176  -1.5620   0.0792
 5GT  H1   H  HCR6  0   0.284  -0.5384   1.7826   0.0071
 5GT  H2   H  HNH1  0   0.414   1.8117   2.1547   0.3412
 5GT  H3   H  HCH2  0   0.268   3.5964  -0.6993  -1.4159
 5GT  H4   H  HCH2  0   0.286   4.5481  -0.8871   0.0561
 5GT  H5   H  HNH1  0   0.398   2.7530  -2.4477   0.1986
 5GT  H6   H  HCR6  0   0.272   0.4046  -3.0634   0.1789
 5GT  H7   H  HCR6  0   0.268  -1.9094  -2.2973   0.0650

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
 5GT  O    C    double    1.216  0.020  1.216
 5GT  C    CA   single    1.512  0.020  1.512
 5GT  C    NAJ  single    1.354  0.020  1.354
 5GT  CA   N    single    1.445  0.020  1.445
 5GT  NAJ  CAN  single    1.395  0.020  1.395
 5GT  N    CAM  single    1.369  0.020  1.369
 5GT  CAN  CAM  aromatic  1.405  0.020  1.405
 5GT  CAN  CAG  aromatic  1.379  0.020  1.379
 5GT  CAM  CAF  aromatic  1.391  0.020  1.391
 5GT  CAG  CAL  aromatic  1.395  0.020  1.395
 5GT  CAF  CAE  aromatic  1.387  0.020  1.387
 5GT  CAL  CAE  aromatic  1.387  0.020  1.387
 5GT  CAL  CAO  single    1.490  0.020  1.490
 5GT  FAC  CAO  single    1.344  0.020  1.344
 5GT  FAD  CAO  single    1.344  0.020  1.344
 5GT  CAO  FAB  single    1.337  0.020  1.337
 5GT  CAG  H1   single    0.930  0.020  1.080
 5GT  NAJ  H2   single    0.860  0.020  1.020
 5GT  CA   H3   single    0.970  0.020  1.090
 5GT  CA   H4   single    0.970  0.020  1.090
 5GT  N    H5   single    0.890  0.020  1.040
 5GT  CAF  H6   single    0.930  0.020  1.080
 5GT  CAE  H7   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
 5GT  CAL  CAO  FAD  112.03  3.000
 5GT  FAD  CAO  FAC  105.87  3.000
 5GT  CAL  CAO  FAC  112.02  3.000
 5GT  FAD  CAO  FAB  106.83  3.000
 5GT  FAC  CAO  FAB  106.81  3.000
 5GT  CAL  CAO  FAB  112.82  3.000
 5GT  CAE  CAL  CAG  119.71  3.000
 5GT  CAE  CAL  CAO  121.91  3.000
 5GT  CAG  CAL  CAO  118.38  3.000
 5GT  H1   CAG  CAN  118.79  3.000
 5GT  H1   CAG  CAL  121.09  3.000
 5GT  CAN  CAG  CAL  120.12  3.000
 5GT  CAM  CAN  NAJ  117.93  3.000
 5GT  CAM  CAN  CAG  120.64  3.000
 5GT  NAJ  CAN  CAG  121.38  3.000
 5GT  H2   NAJ  C    117.14  3.000
 5GT  H2   NAJ  CAN  118.19  3.000
 5GT  C    NAJ  CAN  124.52  3.000
 5GT  CA   C    O    122.40  3.000
 5GT  CA   C    NAJ  114.87  3.000
 5GT  O    C    NAJ  122.68  3.000
 5GT  H4   CA   H3   107.36  3.000
 5GT  H4   CA   N    109.32  3.000
 5GT  H3   CA   N    112.90  3.000
 5GT  H4   CA   C    108.38  3.000
 5GT  H3   CA   C    107.40  3.000
 5GT  N    CA   C    111.32  3.000
 5GT  H5   N    CAM  115.62  3.000
 5GT  H5   N    CA   114.28  3.000
 5GT  CAM  N    CA   118.09  3.000
 5GT  CAF  CAM  N    123.76  3.000
 5GT  CAF  CAM  CAN  118.57  3.000
 5GT  N    CAM  CAN  117.63  3.000
 5GT  H6   CAF  CAE  119.66  3.000
 5GT  H6   CAF  CAM  119.50  3.000
 5GT  CAE  CAF  CAM  120.84  3.000
 5GT  H7   CAE  CAF  118.62  3.000
 5GT  H7   CAE  CAL  121.28  3.000
 5GT  CAF  CAE  CAL  120.10  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
 5GT  CONST_01  CAM  CAN  CAG  CAL     0.00   0.0  0
 5GT  CONST_02  CAM  CAF  CAE  CAL     0.00   0.0  0
 5GT  CONST_03  CAF  CAM  CAN  CAG     0.00   0.0  0
 5GT  CONST_04  CAF  CAE  CAL  CAG     0.00   0.0  0
 5GT  CONST_05  CAE  CAF  CAM  CAN     0.00   0.0  0
 5GT  CONST_06  CAE  CAL  CAG  CAN     0.00   0.0  0
 5GT  CONST_07  CA   C    NAJ  CAN     0.00   0.0  0
 5GT  CONST_08  CAN  CAG  CAL  CAO   180.00   0.0  0
 5GT  CONST_09  CAF  CAE  CAL  CAO   180.00   0.0  0
 5GT  CONST_10  O    C    NAJ  CAN   180.00   0.0  0
 5GT  CONST_11  H6   CAF  CAE  CAL   180.00   0.0  0
 5GT  CONST_12  H7   CAE  CAL  CAG   180.00   0.0  0
 5GT  CONST_13  H1   CAG  CAN  NAJ     0.00   0.0  0
 5GT  CONST_14  H2   NAJ  C    CA    180.00   0.0  0
 5GT  Var_01    C    NAJ  CAN  CAG  -166.28  30.0  1
 5GT  Var_02    CA   N    CAM  CAN   -31.91  30.0  1
 5GT  Var_03    N    CA   C    NAJ   -30.05  30.0  1
 5GT  Var_04    CAM  N    CA   C      46.68  30.0  1
 5GT  Var_05    CAG  CAL  CAO  FAB  -179.51  30.0  3

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
 5GT  plan-1  CAN  0.020
 5GT  plan-1  NAJ  0.020
 5GT  plan-1  C    0.020
 5GT  plan-1  O    0.020
 5GT  plan-1  CA   0.020
 5GT  plan-1  H2   0.020
 5GT  plan-2  CAO  0.020
 5GT  plan-2  CAL  0.020
 5GT  plan-2  CAG  0.020
 5GT  plan-2  CAN  0.020
 5GT  plan-2  NAJ  0.020
 5GT  plan-2  N    0.020
 5GT  plan-2  CAM  0.020
 5GT  plan-2  CAF  0.020
 5GT  plan-2  CAE  0.020
 5GT  plan-2  H1   0.020
 5GT  plan-2  H6   0.020
 5GT  plan-2  H7   0.020

