# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:10:05 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: N-{(1S)-1-[3-fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@@H](NC(=O)N1CC(=O)Nc2cc(OC)cnc12)c3ccc(OC(F)(F)F)c(F)c3
#
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
 9GJ  9GJ  N-{(1S)-1-[3-fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide  ligand  50  32  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9GJ
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
 9GJ  N1   N  N     0  -0.391  -3.8961  -0.6042  -1.3176
 9GJ  N3   N  NT    0  -0.601  -2.5032   0.3196   0.3289
 9GJ  C4   C  CR16  0  -0.321  -6.1331   0.4288  -0.0694
 9GJ  C5   C  CR16  0  -0.214  -5.1035  -0.8267  -1.8259
 9GJ  C6   C  CR6   0   0.171   2.0439  -0.9622   0.5352
 9GJ  C7   C  CR6   0   0.294  -4.8748   0.6272   0.4602
 9GJ  C8   C  CR6   0   0.149   4.5581  -0.5396  -0.5885
 9GJ  C10  C  CR6   0   0.535   4.0242  -1.8147  -0.5138
 9GJ  C13  C  C     0   0.714  -1.6163  -0.7420   0.4858
 9GJ  C15  C  CH3   0  -0.440  -7.6716  -1.2423  -2.9025
 9GJ  C17  C  CH2   0  -0.122   0.7057  -1.1083   2.6736
 9GJ  C1   C  CR16  0  -0.318   2.5887   0.3187   0.4746
 9GJ  C2   C  CR16  0  -0.279   3.8372   0.5303  -0.0886
 9GJ  C3   C  CR16  0  -0.489   2.7793  -2.0328   0.0398
 9GJ  C9   C  CR6   0   0.326  -6.2609  -0.3241  -1.2357
 9GJ  C11  C  CR6   0   0.442  -3.7733   0.0810  -0.2073
 9GJ  C12  C  C     0   0.515  -3.4720   1.8580   1.9959
 9GJ  C14  C  CH2   0  -0.453  -2.3388   1.5840   1.0232
 9GJ  C16  C  CH3   0  -0.391   0.8275   0.4544   4.4078
 9GJ  C18  C  CH1   0  -0.211   0.6912  -1.2336   1.1512
 9GJ  C19  C  CT    0   1.078   5.9293  -0.0262  -2.4007
 9GJ  N2   N  NH1   0  -0.728  -4.6698   1.3338   1.6372
 9GJ  N4   N  NH1   0  -0.669  -0.3181  -0.3713   0.5716
 9GJ  O1   O  O     0  -0.447  -3.3158   2.5240   2.9981
 9GJ  O2   O  O     0  -0.491  -1.9904  -1.8997   0.5259
 9GJ  O3   O  O2    0  -0.468  -7.5036  -0.4975  -1.7094
 9GJ  O4   O  O2    0  -0.514   5.8282  -0.3714  -1.1067
 9GJ  F1   F  F     0  -0.296   4.7299  -2.8454  -0.9823
 9GJ  F2   F  F     0  -0.296   5.4409   1.1909  -2.6439
 9GJ  F3   F  F     0  -0.273   7.2125  -0.0307  -2.7162
 9GJ  F4   F  F     0  -0.296   5.2872  -0.8684  -3.2088
 9GJ  H1   H  HCR6  0   0.296  -7.0106   0.8376   0.4168
 9GJ  H2   H  HCR6  0   0.279  -5.1353  -1.4161  -2.7337
 9GJ  H3   H  HCH3  0   0.263  -8.7374  -1.2457  -3.1151
 9GJ  H4   H  HCH3  0   0.233  -7.1448  -0.7863  -3.7442
 9GJ  H5   H  HCH3  0   0.233  -7.3305  -2.2742  -2.7882
 9GJ  H6   H  HCH2  0   0.217  -0.2534  -1.4801   3.0628
 9GJ  H7   H  HCH2  0   0.221   1.4922  -1.7566   3.0854
 9GJ  H8   H  HCR6  0   0.267   2.0561   1.1710   0.8727
 9GJ  H9   H  HCR6  0   0.294   4.2579   1.5264  -0.1180
 9GJ  H10  H  HCR6  0   0.291   2.3882  -3.0421   0.0786
 9GJ  H11  H  HCH2  0   0.284  -1.4192   1.5776   1.6036
 9GJ  H12  H  HCH2  0   0.302  -2.2798   2.4219   0.3198
 9GJ  H13  H  HCH3  0   0.236   0.9948   1.5155   4.5860
 9GJ  H14  H  HCH3  0   0.207  -0.1552   0.1841   4.8115
 9GJ  H15  H  HCH3  0   0.208   1.5872  -0.1138   4.9567
 9GJ  H16  H  HCH1  0   0.295   0.4193  -2.2652   0.9244
 9GJ  H17  H  HNH1  0   0.420  -5.4710   1.5599   2.2119
 9GJ  H18  H  HNH1  0   0.416  -0.0674   0.5874   0.3940
 9GJ  O5   O  O2    0  -0.477   0.9028   0.2319   3.0220

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
 9GJ  F4   C19  single    1.332  0.020  1.332
 9GJ  O4   C19  single    1.343  0.020  1.343
 9GJ  O4   C8   single    1.382  0.020  1.382
 9GJ  F3   C19  single    1.321  0.020  1.321
 9GJ  C19  F2   single    1.334  0.020  1.334
 9GJ  C2   C8   aromatic  1.384  0.020  1.384
 9GJ  C2   C1   aromatic  1.386  0.020  1.386
 9GJ  C8   C10  aromatic  1.384  0.020  1.384
 9GJ  C1   C6   aromatic  1.393  0.020  1.393
 9GJ  C16  O5   single    1.406  0.020  1.406
 9GJ  C10  F1   single    1.334  0.020  1.334
 9GJ  C10  C3   aromatic  1.380  0.020  1.380
 9GJ  O5   C17  single    1.399  0.020  1.399
 9GJ  C6   C3   aromatic  1.390  0.020  1.390
 9GJ  C6   C18  single    1.511  0.020  1.511
 9GJ  C17  C18  single    1.528  0.020  1.528
 9GJ  C18  N4   single    1.449  0.020  1.449
 9GJ  N4   C13  single    1.353  0.020  1.353
 9GJ  O2   C13  double    1.217  0.020  1.217
 9GJ  C13  N3   single    1.392  0.020  1.392
 9GJ  N1   C5   aromatic  1.329  0.020  1.329
 9GJ  N1   C11  aromatic  1.310  0.020  1.310
 9GJ  C5   C9   aromatic  1.393  0.020  1.393
 9GJ  N3   C11  single    1.399  0.020  1.399
 9GJ  N3   C14  single    1.452  0.020  1.452
 9GJ  C11  C7   aromatic  1.399  0.020  1.399
 9GJ  O3   C9   single    1.341  0.020  1.341
 9GJ  O3   C15  single    1.416  0.020  1.416
 9GJ  C9   C4   aromatic  1.394  0.020  1.394
 9GJ  C14  C12  single    1.518  0.020  1.518
 9GJ  C7   C4   aromatic  1.380  0.020  1.380
 9GJ  C7   N2   single    1.388  0.020  1.388
 9GJ  N2   C12  single    1.356  0.020  1.356
 9GJ  C12  O1   double    1.213  0.020  1.213
 9GJ  C4   H1   single    0.930  0.020  1.080
 9GJ  C5   H2   single    0.930  0.020  1.080
 9GJ  C15  H3   single    0.970  0.020  1.090
 9GJ  C15  H4   single    0.970  0.020  1.090
 9GJ  C15  H5   single    0.970  0.020  1.090
 9GJ  C17  H6   single    0.970  0.020  1.090
 9GJ  C17  H7   single    0.970  0.020  1.090
 9GJ  C1   H8   single    0.930  0.020  1.080
 9GJ  C2   H9   single    0.930  0.020  1.080
 9GJ  C3   H10  single    0.930  0.020  1.080
 9GJ  C14  H11  single    0.970  0.020  1.090
 9GJ  C14  H12  single    0.970  0.020  1.090
 9GJ  C16  H13  single    0.970  0.020  1.090
 9GJ  C16  H14  single    0.970  0.020  1.090
 9GJ  C16  H15  single    0.970  0.020  1.090
 9GJ  C18  H16  single    0.970  0.020  1.090
 9GJ  N2   H17  single    0.860  0.020  1.020
 9GJ  N4   H18  single    0.860  0.020  1.020

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
 9GJ  C11  N1   C5   119.79  3.000
 9GJ  C14  N3   C11  115.76  3.000
 9GJ  C14  N3   C13  122.55  3.000
 9GJ  C11  N3   C13  119.44  3.000
 9GJ  H1   C4   C9   120.33  3.000
 9GJ  H1   C4   C7   120.82  3.000
 9GJ  C9   C4   C7   118.84  3.000
 9GJ  H2   C5   C9   121.82  3.000
 9GJ  H2   C5   N1   116.01  3.000
 9GJ  C9   C5   N1   122.17  3.000
 9GJ  C18  C6   C3   118.72  3.000
 9GJ  C18  C6   C1   122.20  3.000
 9GJ  C3   C6   C1   119.06  3.000
 9GJ  N2   C7   C11  119.14  3.000
 9GJ  N2   C7   C4   122.24  3.000
 9GJ  C11  C7   C4   118.61  3.000
 9GJ  O4   C8   C2   121.34  3.000
 9GJ  C2   C8   C10  119.46  3.000
 9GJ  O4   C8   C10  119.13  3.000
 9GJ  F1   C10  C3   119.73  3.000
 9GJ  C3   C10  C8   121.01  3.000
 9GJ  F1   C10  C8   119.26  3.000
 9GJ  O2   C13  N4   123.60  3.000
 9GJ  O2   C13  N3   122.22  3.000
 9GJ  N4   C13  N3   114.17  3.000
 9GJ  H5   C15  H4   108.91  3.000
 9GJ  H5   C15  H3   108.88  3.000
 9GJ  H4   C15  H3   108.87  3.000
 9GJ  H5   C15  O3   111.80  3.000
 9GJ  H4   C15  O3   111.85  3.000
 9GJ  H3   C15  O3   106.42  3.000
 9GJ  H7   C17  H6   106.97  3.000
 9GJ  H7   C17  O5   111.77  3.000
 9GJ  H6   C17  O5   111.02  3.000
 9GJ  H7   C17  C18  109.38  3.000
 9GJ  H6   C17  C18  108.46  3.000
 9GJ  O5   C17  C18  109.16  3.000
 9GJ  H8   C1   C2   118.24  3.000
 9GJ  H8   C1   C6   121.08  3.000
 9GJ  C2   C1   C6   120.68  3.000
 9GJ  H9   C2   C1   120.13  3.000
 9GJ  H9   C2   C8   119.98  3.000
 9GJ  C1   C2   C8   119.88  3.000
 9GJ  H10  C3   C10  119.18  3.000
 9GJ  H10  C3   C6   120.92  3.000
 9GJ  C10  C3   C6   119.90  3.000
 9GJ  O3   C9   C5   125.00  3.000
 9GJ  O3   C9   C4   116.76  3.000
 9GJ  C5   C9   C4   118.24  3.000
 9GJ  C7   C11  N3   117.73  3.000
 9GJ  C7   C11  N1   122.31  3.000
 9GJ  N3   C11  N1   119.93  3.000
 9GJ  O1   C12  N2   122.99  3.000
 9GJ  O1   C12  C14  122.15  3.000
 9GJ  N2   C12  C14  114.84  3.000
 9GJ  H12  C14  H11  107.55  3.000
 9GJ  H12  C14  C12  108.27  3.000
 9GJ  H11  C14  C12  106.87  3.000
 9GJ  H12  C14  N3   111.42  3.000
 9GJ  H11  C14  N3   110.23  3.000
 9GJ  C12  C14  N3   112.27  3.000
 9GJ  H15  C16  H14  108.00  3.000
 9GJ  H15  C16  H13  108.47  3.000
 9GJ  H14  C16  H13  108.52  3.000
 9GJ  H15  C16  O5   112.00  3.000
 9GJ  H14  C16  O5   111.85  3.000
 9GJ  H13  C16  O5   107.90  3.000
 9GJ  H16  C18  N4   107.83  3.000
 9GJ  H16  C18  C17  106.69  3.000
 9GJ  N4   C18  C17  110.89  3.000
 9GJ  H16  C18  C6   107.96  3.000
 9GJ  N4   C18  C6   110.72  3.000
 9GJ  C17  C18  C6   112.52  3.000
 9GJ  F4   C19  F3   108.73  3.000
 9GJ  F3   C19  F2   108.37  3.000
 9GJ  F4   C19  F2   106.84  3.000
 9GJ  F2   C19  O4   112.50  3.000
 9GJ  F3   C19  O4   107.59  3.000
 9GJ  F4   C19  O4   112.68  3.000
 9GJ  H17  N2   C12  117.58  3.000
 9GJ  H17  N2   C7   118.59  3.000
 9GJ  C12  N2   C7   123.48  3.000
 9GJ  H18  N4   C18  117.64  3.000
 9GJ  H18  N4   C13  119.26  3.000
 9GJ  C18  N4   C13  122.06  3.000
 9GJ  C9   O3   C15  118.38  3.000
 9GJ  C19  O4   C8   117.50  3.000
 9GJ  C16  O5   C17  112.94  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
 9GJ  CONST_01  C4   C9   C5   N1      0.00   0.0  0
 9GJ  CONST_02  C4   C7   C11  N1      0.00   0.0  0
 9GJ  CONST_03  C7   C11  N1   C5      0.00   0.0  0
 9GJ  CONST_04  C7   C4   C9   C5      0.00   0.0  0
 9GJ  CONST_05  C8   C2   C1   C6      0.00   0.0  0
 9GJ  CONST_06  C8   C10  C3   C6      0.00   0.0  0
 9GJ  CONST_07  C1   C2   C8   C10     0.00   0.0  0
 9GJ  CONST_08  C1   C6   C3   C10     0.00   0.0  0
 9GJ  CONST_09  C3   C10  C8   C2      0.00   0.0  0
 9GJ  CONST_10  C3   C6   C1   C2      0.00   0.0  0
 9GJ  CONST_11  C11  N1   C5   C9      0.00   0.0  0
 9GJ  CONST_12  C11  C7   C4   C9      0.00   0.0  0
 9GJ  CONST_13  C14  C12  N2   C7      0.00   0.0  0
 9GJ  CONST_14  O3   C9   C5   N1    180.00   0.0  0
 9GJ  CONST_15  F1   C10  C3   C6    180.00   0.0  0
 9GJ  CONST_16  O3   C9   C4   C7    180.00   0.0  0
 9GJ  CONST_17  C18  C6   C3   C10   180.00   0.0  0
 9GJ  CONST_18  O4   C8   C2   C1    180.00   0.0  0
 9GJ  CONST_19  F1   C10  C8   C2    180.00   0.0  0
 9GJ  CONST_20  C18  C6   C1   C2    180.00   0.0  0
 9GJ  CONST_21  O4   C8   C10  C3    180.00   0.0  0
 9GJ  CONST_22  O1   C12  N2   C7    180.00   0.0  0
 9GJ  CONST_23  H2   C5   C9   C4    180.00   0.0  0
 9GJ  CONST_24  H1   C4   C9   C5    180.00   0.0  0
 9GJ  CONST_25  H9   C2   C1   C6    180.00   0.0  0
 9GJ  CONST_26  H8   C1   C2   C8    180.00   0.0  0
 9GJ  CONST_27  H10  C3   C10  C8    180.00   0.0  0
 9GJ  CONST_28  H17  N2   C12  C14   180.00   0.0  0
 9GJ  CONST_34  H18  N4   C13  N3      0.00   0.0  0
 9GJ  Var_01    C14  N3   C11  N1    146.96  30.0  1
 9GJ  Var_02    N2   C12  C14  N3    -30.64  30.0  1
 9GJ  Var_03    C12  N2   C7   C4   -161.42  30.0  1
 9GJ  Var_04    C12  C14  N3   C11    47.24  30.0  1
 9GJ  Var_05    F4   C19  O4   C8    -54.90  30.0  3
 9GJ  Var_06    H3   C15  O3   C9   -179.01  30.0  3
 9GJ  Var_07    C18  C17  O5   C16   175.42  30.0  3
 9GJ  Var_08    H13  C16  O5   C17   179.82  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
 9GJ  chir_01  C18  C6  C17  N4  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
 9GJ  plan-1  C6   0.020
 9GJ  plan-1  C8   0.020
 9GJ  plan-1  C10  0.020
 9GJ  plan-1  C1   0.020
 9GJ  plan-1  C2   0.020
 9GJ  plan-1  C3   0.020
 9GJ  plan-1  C18  0.020
 9GJ  plan-1  O4   0.020
 9GJ  plan-1  F1   0.020
 9GJ  plan-1  H8   0.020
 9GJ  plan-1  H9   0.020
 9GJ  plan-1  H10  0.020
 9GJ  plan-2  N1   0.020
 9GJ  plan-2  N3   0.020
 9GJ  plan-2  C4   0.020
 9GJ  plan-2  C5   0.020
 9GJ  plan-2  C7   0.020
 9GJ  plan-2  C9   0.020
 9GJ  plan-2  C11  0.020
 9GJ  plan-2  N2   0.020
 9GJ  plan-2  O3   0.020
 9GJ  plan-2  H1   0.020
 9GJ  plan-2  H2   0.020
 9GJ  plan-3  N3   0.020
 9GJ  plan-3  C13  0.020
 9GJ  plan-3  C11  0.020
 9GJ  plan-3  C14  0.020
 9GJ  plan-3  C18  0.020
 9GJ  plan-3  N4   0.020
 9GJ  plan-3  O2   0.020
 9GJ  plan-3  H18  0.020
 9GJ  plan-4  C7   0.020
 9GJ  plan-4  C12  0.020
 9GJ  plan-4  C14  0.020
 9GJ  plan-4  N2   0.020
 9GJ  plan-4  O1   0.020
 9GJ  plan-4  H17  0.020

