# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 04:32:20 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 3-(4-methyl-3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C(=Nc2ccccc12)CCC(O)=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
 EYM  EYM  '3-(4-methyl-3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid'  ligand  28  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EYM
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
 EYM  C8   C  CR16   0  -0.265  -3.2508   2.5249  -0.0695
 EYM  C5   C  C      0   0.418   4.2829   0.4570   0.0576
 EYM  C6   C  CR66   0   0.180  -1.3889   0.9907  -0.0564
 EYM  N1   N  N      0  -0.392  -0.0274   0.8114  -0.0628
 EYM  C2   C  CR6    0   0.094   0.4572  -0.3735  -0.0523
 EYM  C4   C  CH2    0  -0.586   2.7594   0.6723   0.0229
 EYM  C1   C  CR6    0   0.533  -0.3923  -1.5915  -0.0347
 EYM  C3   C  CH2    0  -0.483   1.9361  -0.5982  -0.0564
 EYM  O1   O  OC    -1  -0.631   4.9717   1.4975   0.1077
 EYM  O    O  O      0  -0.607   4.7135  -0.7128   0.0372
 EYM  C11  C  CR66   0   0.394  -2.2746  -0.0971  -0.0267
 EYM  N    N  NR6    0  -0.570  -1.7434  -1.3736  -0.0100
 EYM  C    C  CH3    0  -0.563  -2.6439  -2.5148   0.0297
 EYM  C10  C  CR16   0  -0.338  -3.6524   0.1415  -0.0157
 EYM  C9   C  CR16   0  -0.251  -4.1263   1.4397  -0.0370
 EYM  C7   C  CR16   0  -0.315  -1.8917   2.2941  -0.0781
 EYM  H1   H  HCR6   0   0.262  -3.6345   3.5359  -0.0872
 EYM  H2   H  HCH2   0   0.227   2.4755   1.2445   0.9115
 EYM  H3   H  HCH2   0   0.227   2.5250   1.3298  -0.8193
 EYM  H4   H  HCH2   0   0.248   2.1862  -1.2674   0.7713
 EYM  H5   H  HCH2   0   0.250   2.1945  -1.1655  -0.9562
 EYM  H7   H  HCH3   0   0.264  -3.2797  -2.5295  -0.8543
 EYM  H8   H  HCH3   0   0.285  -2.0631  -3.4284   0.0563
 EYM  H9   H  HCH3   0   0.264  -3.2701  -2.4719   0.9195
 EYM  H10  H  HCR6   0   0.289  -4.3605  -0.6737   0.0072
 EYM  H11  H  HCR6   0   0.267  -5.1951   1.6070  -0.0284
 EYM  H12  H  HCR6   0   0.267  -1.1830   3.1118  -0.1018
 EYM  O2   O  O      0  -0.466   0.0954  -2.7112  -0.0375

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
 EYM  C8   C9   aromatic  1.395  0.020  1.395
 EYM  C8   C7   aromatic  1.379  0.020  1.379
 EYM  C9   C10  aromatic  1.382  0.020  1.382
 EYM  C7   C6   aromatic  1.397  0.020  1.397
 EYM  C10  C11  aromatic  1.398  0.020  1.398
 EYM  C6   C11  aromatic  1.403  0.020  1.403
 EYM  C6   N1   single    1.373  0.020  1.373
 EYM  C11  N    single    1.383  0.020  1.383
 EYM  N1   C2   double    1.280  0.020  1.280
 EYM  O    C5   deloc     1.247  0.020  1.247
 EYM  N    C    single    1.454  0.020  1.454
 EYM  N    C1   single    1.369  0.020  1.369
 EYM  C2   C1   single    1.485  0.020  1.485
 EYM  C2   C3   single    1.496  0.020  1.496
 EYM  C4   C5   single    1.539  0.020  1.539
 EYM  C4   C3   single    1.516  0.020  1.516
 EYM  C1   O2   double    1.221  0.020  1.221
 EYM  C5   O1   deloc     1.249  0.020  1.249
 EYM  C8   H1   single    0.930  0.020  1.080
 EYM  C4   H2   single    0.970  0.020  1.090
 EYM  C4   H3   single    0.970  0.020  1.090
 EYM  C3   H4   single    0.970  0.020  1.090
 EYM  C3   H5   single    0.970  0.020  1.090
 EYM  C    H7   single    0.970  0.020  1.090
 EYM  C    H8   single    0.970  0.020  1.090
 EYM  C    H9   single    0.970  0.020  1.090
 EYM  C10  H10  single    0.930  0.020  1.080
 EYM  C9   H11  single    0.930  0.020  1.080
 EYM  C7   H12  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
 EYM  H1   C8   C7   120.41  3.000
 EYM  H1   C8   C9   120.34  3.000
 EYM  C7   C8   C9   119.26  3.000
 EYM  O    C5   O1   126.30  3.000
 EYM  O1   C5   C4   115.49  3.000
 EYM  O    C5   C4   118.21  3.000
 EYM  C7   C6   C11  119.76  3.000
 EYM  C11  C6   N1   121.65  3.000
 EYM  C7   C6   N1   118.58  3.000
 EYM  C2   N1   C6   119.74  3.000
 EYM  C3   C2   C1   116.26  3.000
 EYM  C3   C2   N1   120.88  3.000
 EYM  C1   C2   N1   122.87  3.000
 EYM  H3   C4   H2   104.79  3.000
 EYM  H3   C4   C3   110.31  3.000
 EYM  H2   C4   C3   109.86  3.000
 EYM  H3   C4   C5   108.27  3.000
 EYM  H2   C4   C5   108.16  3.000
 EYM  C3   C4   C5   114.93  3.000
 EYM  N    C1   O2   122.70  3.000
 EYM  O2   C1   C2   121.56  3.000
 EYM  N    C1   C2   115.74  3.000
 EYM  H5   C3   H4   104.54  3.000
 EYM  H5   C3   C4   110.43  3.000
 EYM  H4   C3   C4   110.43  3.000
 EYM  H5   C3   C2   108.27  3.000
 EYM  H4   C3   C2   108.42  3.000
 EYM  C4   C3   C2   114.26  3.000
 EYM  C10  C11  N    122.41  3.000
 EYM  N    C11  C6   118.26  3.000
 EYM  C10  C11  C6   119.33  3.000
 EYM  C    N    C11  119.14  3.000
 EYM  C    N    C1   119.13  3.000
 EYM  C11  N    C1   121.73  3.000
 EYM  H9   C    H8   108.76  3.000
 EYM  H9   C    H7   109.16  3.000
 EYM  H8   C    H7   108.76  3.000
 EYM  H9   C    N    110.33  3.000
 EYM  H8   C    N    109.30  3.000
 EYM  H7   C    N    110.48  3.000
 EYM  H10  C10  C9   118.98  3.000
 EYM  H10  C10  C11  121.15  3.000
 EYM  C9   C10  C11  119.86  3.000
 EYM  H11  C9   C10  118.94  3.000
 EYM  H11  C9   C8   120.00  3.000
 EYM  C10  C9   C8   121.07  3.000
 EYM  H12  C7   C6   118.00  3.000
 EYM  H12  C7   C8   121.28  3.000
 EYM  C6   C7   C8   120.72  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
 EYM  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 EYM  CONST_02  C11  C6   C7   C8      0.00   0.0  0
 EYM  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 EYM  CONST_04  C9   C10  C11  C6      0.00   0.0  0
 EYM  CONST_05  C7   C8   C9   C10     0.00   0.0  0
 EYM  CONST_06  C7   C6   C11  C10     0.00   0.0  0
 EYM  CONST_07  C11  N    C1   C2      0.00   0.0  0
 EYM  CONST_08  C    N    C1   C2    180.00   0.0  0
 EYM  CONST_09  C11  N    C1   O2    180.00   0.0  0
 EYM  CONST_10  H10  C10  C9   C8    180.00   0.0  0
 EYM  CONST_11  H1   C8   C7   C6    180.00   0.0  0
 EYM  CONST_12  H12  C7   C6   N1      0.00   0.0  0
 EYM  CONST_13  H11  C9   C10  C11   180.00   0.0  0
 EYM  CONST_14  C    N    C1   O2      0.00   0.0  0
 EYM  Var_01    C4   C3   C2   N1      4.00  30.0  3
 EYM  Var_02    H7   C    N    C1   -118.39  30.0  3
 EYM  Var_03    C2   C3   C4   C5    178.45  30.0  3
 EYM  Var_04    O    C5   C4   C3     -0.96  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
 EYM  plan-1  C8   0.020
 EYM  plan-1  C6   0.020
 EYM  plan-1  N1   0.020
 EYM  plan-1  C2   0.020
 EYM  plan-1  C1   0.020
 EYM  plan-1  C3   0.020
 EYM  plan-1  C11  0.020
 EYM  plan-1  N    0.020
 EYM  plan-1  C    0.020
 EYM  plan-1  C10  0.020
 EYM  plan-1  C9   0.020
 EYM  plan-1  C7   0.020
 EYM  plan-1  H1   0.020
 EYM  plan-1  H10  0.020
 EYM  plan-1  H11  0.020
 EYM  plan-1  H12  0.020
 EYM  plan-1  O2   0.020
 EYM  plan-2  C5   0.020
 EYM  plan-2  C4   0.020
 EYM  plan-2  O1   0.020
 EYM  plan-2  O    0.020

