# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 17:24:11 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (3~{S})-3-methyl-3,4-dihydro-1~{H}-quinoxalin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1Nc2ccccc2NC1=O
#
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
 5QY  5QY  (3~{S})-3-methyl-3,4-dihydro-1~{H}-quinoxalin-2-one  ligand  22  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5QY
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
 5QY  O    O  O     0  -0.469  -2.9705   1.1971  -0.3166
 5QY  C    C  C     0   0.519  -1.8910   0.6375  -0.2455
 5QY  NAG  N  NH1   0  -0.717  -0.7230   1.3123  -0.1504
 5QY  CAJ  C  CR6   0   0.340   0.5335   0.7072  -0.0690
 5QY  CAE  C  CR16  0  -0.329   1.6593   1.4187   0.3132
 5QY  CAC  C  CR16  0  -0.281   2.9028   0.7985   0.3299
 5QY  CAD  C  CR16  0  -0.263   3.0085  -0.5371  -0.0318
 5QY  CAF  C  CR16  0  -0.355   1.8786  -1.2563  -0.3999
 5QY  CAK  C  CR6   0   0.295   0.6302  -0.6428  -0.4293
 5QY  N    N  NH1   0  -0.663  -0.5276  -1.2694  -0.8465
 5QY  CA   C  CH1   0  -0.254  -1.7582  -0.8739  -0.1874
 5QY  CB   C  CH3   0  -0.662  -1.8687  -1.3431   1.2654
 5QY  H1   H  HNH1  0   0.408  -0.7728   2.3206  -0.0990
 5QY  H2   H  HCR6  0   0.267   1.5638   2.4625   0.5886
 5QY  H3   H  HCR6  0   0.252   3.7800   1.3598   0.6218
 5QY  H4   H  HCR6  0   0.253   3.9719  -1.0296  -0.0223
 5QY  H5   H  HCR6  0   0.260   1.9639  -2.3007  -0.6756
 5QY  H6   H  HNH1  0   0.385  -0.4447  -2.2676  -0.9730
 5QY  H7   H  HCH1  0   0.284  -2.5884  -1.2885  -0.7599
 5QY  H8   H  HCH3  0   0.245  -2.8213  -1.0404   1.7004
 5QY  H9   H  HCH3  0   0.250  -1.8124  -2.4311   1.3085
 5QY  H10  H  HCH3  0   0.235  -1.0657  -0.9364   1.8822

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
 5QY  O    C    double    1.218  0.020  1.218
 5QY  C    NAG  single    1.352  0.020  1.352
 5QY  C    CA   single    1.518  0.020  1.518
 5QY  CB   CA   single    1.531  0.020  1.531
 5QY  NAG  CAJ  single    1.397  0.020  1.397
 5QY  CA   N    single    1.451  0.020  1.451
 5QY  CAJ  CAE  aromatic  1.386  0.020  1.386
 5QY  CAJ  CAK  aromatic  1.401  0.020  1.401
 5QY  N    CAK  single    1.381  0.020  1.381
 5QY  CAE  CAC  aromatic  1.390  0.020  1.390
 5QY  CAK  CAF  aromatic  1.391  0.020  1.391
 5QY  CAC  CAD  aromatic  1.388  0.020  1.388
 5QY  CAF  CAD  aromatic  1.389  0.020  1.389
 5QY  NAG  H1   single    0.860  0.020  1.020
 5QY  CAE  H2   single    0.930  0.020  1.080
 5QY  CAC  H3   single    0.930  0.020  1.080
 5QY  CAD  H4   single    0.930  0.020  1.080
 5QY  CAF  H5   single    0.930  0.020  1.080
 5QY  N    H6   single    0.890  0.020  1.040
 5QY  CA   H7   single    0.970  0.020  1.090
 5QY  CB   H8   single    0.970  0.020  1.090
 5QY  CB   H9   single    0.970  0.020  1.090
 5QY  CB   H10  single    0.970  0.020  1.090

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
 5QY  CA   C    NAG  114.74  3.000
 5QY  CA   C    O    122.49  3.000
 5QY  NAG  C    O    122.71  3.000
 5QY  H1   NAG  CAJ  118.26  3.000
 5QY  H1   NAG  C    117.31  3.000
 5QY  CAJ  NAG  C    124.39  3.000
 5QY  CAK  CAJ  CAE  120.65  3.000
 5QY  CAK  CAJ  NAG  117.68  3.000
 5QY  CAE  CAJ  NAG  121.63  3.000
 5QY  H2   CAE  CAC  120.38  3.000
 5QY  H2   CAE  CAJ  119.54  3.000
 5QY  CAC  CAE  CAJ  120.08  3.000
 5QY  H3   CAC  CAD  120.54  3.000
 5QY  H3   CAC  CAE  119.82  3.000
 5QY  CAD  CAC  CAE  119.64  3.000
 5QY  H4   CAD  CAF  119.40  3.000
 5QY  H4   CAD  CAC  120.24  3.000
 5QY  CAF  CAD  CAC  120.37  3.000
 5QY  H5   CAF  CAK  119.36  3.000
 5QY  H5   CAF  CAD  120.17  3.000
 5QY  CAK  CAF  CAD  120.47  3.000
 5QY  N    CAK  CAF  123.95  3.000
 5QY  CAF  CAK  CAJ  118.79  3.000
 5QY  N    CAK  CAJ  117.21  3.000
 5QY  H6   N    CA   113.33  3.000
 5QY  H6   N    CAK  114.68  3.000
 5QY  CA   N    CAK  116.75  3.000
 5QY  H7   CA   CB   109.08  3.000
 5QY  H7   CA   N    107.68  3.000
 5QY  CB   CA   N    114.13  3.000
 5QY  H7   CA   C    106.96  3.000
 5QY  N    CA   C    109.16  3.000
 5QY  CB   CA   C    109.58  3.000
 5QY  H10  CB   H9   108.16  3.000
 5QY  H10  CB   H8   108.31  3.000
 5QY  H9   CB   H8   107.84  3.000
 5QY  H10  CB   CA   111.66  3.000
 5QY  H9   CB   CA   109.85  3.000
 5QY  H8   CB   CA   110.90  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
 5QY  CONST_01  CAD  CAC  CAE  CAJ     0.00   0.0  0
 5QY  CONST_02  CAD  CAF  CAK  CAJ     0.00   0.0  0
 5QY  CONST_03  CAF  CAK  CAJ  CAE     0.00   0.0  0
 5QY  CONST_04  CAF  CAD  CAC  CAE     0.00   0.0  0
 5QY  CONST_05  CAK  CAJ  CAE  CAC     0.00   0.0  0
 5QY  CONST_06  CAK  CAF  CAD  CAC     0.00   0.0  0
 5QY  CONST_07  CA   C    NAG  CAJ     0.00   0.0  0
 5QY  CONST_08  CAJ  NAG  C    O     180.00   0.0  0
 5QY  CONST_09  H2   CAE  CAJ  NAG     0.00   0.0  0
 5QY  CONST_10  H3   CAC  CAE  CAJ   180.00   0.0  0
 5QY  CONST_11  H5   CAF  CAK  CAJ   180.00   0.0  0
 5QY  CONST_12  H4   CAD  CAC  CAE   180.00   0.0  0
 5QY  CONST_13  H1   NAG  C    CA    180.00   0.0  0
 5QY  Var_01    CAE  CAJ  NAG  C    -165.82  30.0  1
 5QY  Var_02    CA   N    CAK  CAJ   -35.82  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
 5QY  chir_01  CA  C  CB  N  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
 5QY  plan-1  O    0.020
 5QY  plan-1  C    0.020
 5QY  plan-1  NAG  0.020
 5QY  plan-1  CAJ  0.020
 5QY  plan-1  CA   0.020
 5QY  plan-1  H1   0.020
 5QY  plan-2  NAG  0.020
 5QY  plan-2  CAJ  0.020
 5QY  plan-2  CAE  0.020
 5QY  plan-2  CAC  0.020
 5QY  plan-2  CAD  0.020
 5QY  plan-2  CAF  0.020
 5QY  plan-2  CAK  0.020
 5QY  plan-2  N    0.020
 5QY  plan-2  H2   0.020
 5QY  plan-2  H3   0.020
 5QY  plan-2  H4   0.020
 5QY  plan-2  H5   0.020

