# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 08:37:28 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-[(4-methoxybenzyl)amino]-6-(trifluoromethyl)quinoxaline-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CNc2nc3cc(ccc3nc2C(O)=O)C(F)(F)F)cc1
#
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
 38C  38C  '3-[(4-methoxybenzyl)amino]-6-(trifluoromethyl)quinoxaline-2-carboxylic acid'  ligand  40  27  .  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_38C
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
 38C  FAJ  F  F      0  -0.314  -5.4269   2.4209   0.9196
 38C  CAI  C  CT     0   1.051  -5.5205   1.5973  -0.1349
 38C  FAK  F  F      0  -0.302  -6.7659   1.1146  -0.1416
 38C  FAL  F  F      0  -0.314  -5.3937   2.3655  -1.2272
 38C  CAH  C  CR6    0  -0.193  -4.4797   0.5206  -0.0918
 38C  CAG  C  CR16   0  -0.305  -4.8454  -0.8370  -0.0952
 38C  CAF  C  CR16   0  -0.295  -3.8660  -1.7988  -0.0578
 38C  CAM  C  CR16   0  -0.355  -3.1575   0.9000  -0.0526
 38C  CAN  C  CR66   0   0.282  -2.1438  -0.0744  -0.0149
 38C  CAE  C  CR66   0   0.189  -2.5116  -1.4356  -0.0173
 38C  NAD  N  N      0  -0.383  -1.5548  -2.4021   0.0242
 38C  NAO  N  N      0  -0.497  -0.8491   0.3010   0.0247
 38C  CAP  C  CR6    0   0.484   0.0644  -0.6457   0.0540
 38C  CAC  C  CR6    0  -0.066  -0.3089  -2.0623   0.0598
 38C  CAB  C  C      0   0.439   0.7234  -3.2016   0.1129
 38C  OBA  O  OC    -1  -0.558   0.2728  -4.3493   0.1285
 38C  OAA  O  O      0  -0.588   1.9306  -2.8645   0.1356
 38C  NAQ  N  NH1    0  -0.676   1.3524  -0.3008   0.0818
 38C  CAR  C  CH2    0  -0.320   1.8045   1.0718   0.0922
 38C  CAS  C  CR6    0   0.038   3.3021   1.1088  -0.0163
 38C  CAZ  C  CR16   0  -0.268   3.9301   0.8972  -1.2445
 38C  CAY  C  CR16   0  -0.329   5.3071   0.8869  -1.3531
 38C  CAV  C  CR6    0   0.371   6.1023   1.0869  -0.2212
 38C  OAW  O  O2     0  -0.471   7.4346   1.0573  -0.4150
 38C  CAX  C  CH3    0  -0.437   8.2816   1.2358   0.7027
 38C  CAU  C  CR16   0  -0.372   5.4911   1.3018   1.0107
 38C  CAT  C  CR16   0  -0.282   4.1026   1.3076   1.0983
 38C  H1   H  HCR6   0   0.268  -5.8837  -1.1347  -0.1265
 38C  H2   H  HCR6   0   0.268  -4.1237  -2.8502  -0.0587
 38C  H3   H  HCR6   0   0.271  -2.8616   1.9425  -0.0499
 38C  H5   H  HCH2   0   0.244   1.3478   1.6171  -0.7391
 38C  H6   H  HCR6   0   0.254   3.3308   0.7392  -2.1338
 38C  H7   H  HCR6   0   0.262   5.7790   0.7238  -2.3142
 38C  H8   H  HCH3   0   0.229   8.1203   0.4678   1.4635
 38C  H9   H  HCH3   0   0.259   9.3012   1.1552   0.3341
 38C  H10  H  HCH3   0   0.228   8.1516   2.2191   1.1624
 38C  H11  H  HCR6   0   0.278   6.0714   1.4643   1.9088
 38C  H12  H  HCR6   0   0.255   3.6435   1.4760   2.0654
 38C  H13  H  HNH1   0   0.410   2.0020  -1.0850   0.1197
 38C  H14  H  HCH2   0   0.244   1.4780   1.5759   1.0076

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
 38C  CAX  OAW  single    1.414  0.020  1.414
 38C  OAA  CAB  deloc     1.254  0.020  1.254
 38C  OBA  CAB  deloc     1.233  0.020  1.233
 38C  CAB  CAC  single    1.538  0.020  1.538
 38C  OAW  CAV  single    1.347  0.020  1.347
 38C  CAU  CAV  aromatic  1.392  0.020  1.392
 38C  CAU  CAT  aromatic  1.391  0.020  1.391
 38C  CAV  CAY  aromatic  1.398  0.020  1.398
 38C  CAT  CAS  aromatic  1.387  0.020  1.387
 38C  CAC  NAD  aromatic  1.292  0.020  1.292
 38C  CAC  CAP  aromatic  1.465  0.020  1.465
 38C  NAD  CAE  aromatic  1.361  0.020  1.361
 38C  CAY  CAZ  aromatic  1.381  0.020  1.381
 38C  CAS  CAZ  aromatic  1.396  0.020  1.396
 38C  CAS  CAR  single    1.502  0.020  1.502
 38C  NAQ  CAP  single    1.334  0.020  1.334
 38C  NAQ  CAR  single    1.445  0.020  1.445
 38C  CAP  NAO  aromatic  1.316  0.020  1.316
 38C  CAE  CAF  aromatic  1.403  0.020  1.403
 38C  CAE  CAN  aromatic  1.410  0.020  1.410
 38C  CAF  CAG  aromatic  1.373  0.020  1.373
 38C  NAO  CAN  aromatic  1.349  0.020  1.349
 38C  CAN  CAM  aromatic  1.407  0.020  1.407
 38C  CAG  CAH  aromatic  1.406  0.020  1.406
 38C  CAM  CAH  aromatic  1.376  0.020  1.376
 38C  CAH  CAI  single    1.498  0.020  1.498
 38C  FAL  CAI  single    1.341  0.020  1.341
 38C  CAI  FAK  single    1.336  0.020  1.336
 38C  CAI  FAJ  single    1.341  0.020  1.341
 38C  CAG  H1   single    0.930  0.020  1.080
 38C  CAF  H2   single    0.930  0.020  1.080
 38C  CAM  H3   single    0.930  0.020  1.080
 38C  CAR  H5   single    0.970  0.020  1.090
 38C  CAZ  H6   single    0.930  0.020  1.080
 38C  CAY  H7   single    0.930  0.020  1.080
 38C  CAX  H8   single    0.970  0.020  1.090
 38C  CAX  H9   single    0.970  0.020  1.090
 38C  CAX  H10  single    0.970  0.020  1.090
 38C  CAU  H11  single    0.930  0.020  1.080
 38C  CAT  H12  single    0.930  0.020  1.080
 38C  NAQ  H13  single    0.860  0.020  1.020
 38C  CAR  H14  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
 38C  CAH  CAI  FAL  111.68  3.000
 38C  FAL  CAI  FAK  106.91  3.000
 38C  CAH  CAI  FAK  112.84  3.000
 38C  FAK  CAI  FAJ  106.91  3.000
 38C  FAL  CAI  FAJ  106.37  3.000
 38C  CAH  CAI  FAJ  111.73  3.000
 38C  CAM  CAH  CAG  121.08  3.000
 38C  CAM  CAH  CAI  118.04  3.000
 38C  CAG  CAH  CAI  120.88  3.000
 38C  H1   CAG  CAF  119.55  3.000
 38C  H1   CAG  CAH  121.07  3.000
 38C  CAF  CAG  CAH  119.39  3.000
 38C  H2   CAF  CAE  118.77  3.000
 38C  H2   CAF  CAG  120.69  3.000
 38C  CAE  CAF  CAG  120.53  3.000
 38C  H3   CAM  CAN  118.01  3.000
 38C  H3   CAM  CAH  121.84  3.000
 38C  CAN  CAM  CAH  120.14  3.000
 38C  NAO  CAN  CAE  121.28  3.000
 38C  NAO  CAN  CAM  119.98  3.000
 38C  CAE  CAN  CAM  118.73  3.000
 38C  NAD  CAE  CAN  120.15  3.000
 38C  CAN  CAE  CAF  120.12  3.000
 38C  NAD  CAE  CAF  119.73  3.000
 38C  CAC  NAD  CAE  119.48  3.000
 38C  CAP  NAO  CAN  117.83  3.000
 38C  NAQ  CAP  CAC  119.74  3.000
 38C  NAQ  CAP  NAO  119.00  3.000
 38C  CAC  CAP  NAO  121.26  3.000
 38C  CAB  CAC  CAP  123.05  3.000
 38C  CAP  CAC  NAD  120.00  3.000
 38C  CAB  CAC  NAD  116.95  3.000
 38C  OAA  CAB  OBA  127.01  3.000
 38C  OBA  CAB  CAC  116.40  3.000
 38C  OAA  CAB  CAC  116.60  3.000
 38C  H13  NAQ  CAR  122.09  3.000
 38C  H13  NAQ  CAP  114.67  3.000
 38C  CAR  NAQ  CAP  123.22  3.000
 38C  H14  CAR  H5   106.34  3.000
 38C  H14  CAR  CAS  110.27  3.000
 38C  H5   CAR  CAS  110.43  3.000
 38C  H14  CAR  NAQ  110.49  3.000
 38C  H5   CAR  NAQ  109.71  3.000
 38C  CAS  CAR  NAQ  109.56  3.000
 38C  CAT  CAS  CAZ  118.00  3.000
 38C  CAZ  CAS  CAR  120.56  3.000
 38C  CAT  CAS  CAR  121.41  3.000
 38C  H6   CAZ  CAY  119.05  3.000
 38C  H6   CAZ  CAS  119.69  3.000
 38C  CAY  CAZ  CAS  121.26  3.000
 38C  H7   CAY  CAV  119.49  3.000
 38C  H7   CAY  CAZ  120.35  3.000
 38C  CAV  CAY  CAZ  120.16  3.000
 38C  CAU  CAV  OAW  124.42  3.000
 38C  CAU  CAV  CAY  119.28  3.000
 38C  OAW  CAV  CAY  116.30  3.000
 38C  CAX  OAW  CAV  118.44  3.000
 38C  H10  CAX  H9   108.72  3.000
 38C  H10  CAX  H8   108.76  3.000
 38C  H9   CAX  H8   108.81  3.000
 38C  H10  CAX  OAW  112.01  3.000
 38C  H9   CAX  OAW  106.53  3.000
 38C  H8   CAX  OAW  111.91  3.000
 38C  H11  CAU  CAT  118.86  3.000
 38C  H11  CAU  CAV  121.50  3.000
 38C  CAT  CAU  CAV  119.64  3.000
 38C  H12  CAT  CAU  118.66  3.000
 38C  H12  CAT  CAS  119.68  3.000
 38C  CAU  CAT  CAS  121.67  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
 38C  CONST_01  CAE  CAF  CAG  CAH     0.00   0.0  0
 38C  CONST_02  CAE  CAN  CAM  CAH     0.00   0.0  0
 38C  CONST_03  NAO  CAN  CAM  CAH   180.00   0.0  0
 38C  CONST_04  NAD  CAE  CAF  CAG   180.00   0.0  0
 38C  CONST_05  CAN  CAE  CAF  CAG     0.00   0.0  0
 38C  CONST_06  CAN  CAM  CAH  CAG     0.00   0.0  0
 38C  CONST_07  CAC  NAD  CAE  CAF   180.00   0.0  0
 38C  CONST_08  NAO  CAN  CAE  CAF   180.00   0.0  0
 38C  CONST_09  CAM  CAN  CAE  CAF     0.00   0.0  0
 38C  CONST_10  CAM  CAH  CAG  CAF     0.00   0.0  0
 38C  CONST_11  NAD  CAE  CAN  CAM   180.00   0.0  0
 38C  CONST_12  CAP  NAO  CAN  CAM   180.00   0.0  0
 38C  CONST_13  CAC  NAD  CAE  CAN     0.00   0.0  0
 38C  CONST_14  CAC  CAP  NAO  CAN     0.00   0.0  0
 38C  CONST_15  CAP  CAC  NAD  CAE     0.00   0.0  0
 38C  CONST_16  CAP  NAO  CAN  CAE     0.00   0.0  0
 38C  CONST_17  NAO  CAP  CAC  NAD     0.00   0.0  0
 38C  CONST_18  NAO  CAN  CAE  NAD     0.00   0.0  0
 38C  CONST_19  CAV  CAU  CAT  CAS     0.00   0.0  0
 38C  CONST_20  CAV  CAY  CAZ  CAS     0.00   0.0  0
 38C  CONST_21  CAU  CAV  CAY  CAZ     0.00   0.0  0
 38C  CONST_22  CAU  CAT  CAS  CAZ     0.00   0.0  0
 38C  CONST_23  CAT  CAU  CAV  CAY     0.00   0.0  0
 38C  CONST_24  CAT  CAS  CAZ  CAY     0.00   0.0  0
 38C  CONST_25  CAF  CAG  CAH  CAI   180.00   0.0  0
 38C  CONST_26  CAN  CAM  CAH  CAI   180.00   0.0  0
 38C  CONST_27  NAQ  CAP  NAO  CAN   180.00   0.0  0
 38C  CONST_28  CAB  CAC  NAD  CAE   180.00   0.0  0
 38C  CONST_29  NAQ  CAP  CAC  NAD   180.00   0.0  0
 38C  CONST_30  CAB  CAC  CAP  NAO   180.00   0.0  0
 38C  CONST_31  CAU  CAT  CAS  CAR   180.00   0.0  0
 38C  CONST_32  CAY  CAZ  CAS  CAR   180.00   0.0  0
 38C  CONST_33  OAW  CAV  CAY  CAZ   180.00   0.0  0
 38C  CONST_34  CAT  CAU  CAV  OAW   180.00   0.0  0
 38C  CONST_35  H2   CAF  CAG  CAH   180.00   0.0  0
 38C  CONST_36  H3   CAM  CAH  CAG   180.00   0.0  0
 38C  CONST_37  H1   CAG  CAH  CAM   180.00   0.0  0
 38C  CONST_38  H11  CAU  CAT  CAS   180.00   0.0  0
 38C  CONST_39  H7   CAY  CAZ  CAS   180.00   0.0  0
 38C  CONST_40  H12  CAT  CAS  CAZ   180.00   0.0  0
 38C  CONST_41  H6   CAZ  CAY  CAV   180.00   0.0  0
 38C  CONST_42  CAR  NAQ  CAP  NAO     0.00   0.0  0
 38C  CONST_43  CAR  NAQ  CAP  CAC   180.00   0.0  0
 38C  CONST_44  H13  NAQ  CAP  NAO   180.00   0.0  0
 38C  Var_01    CAG  CAH  CAI  FAJ   122.04  30.0  3
 38C  Var_02    OAA  CAB  CAC  NAD   179.40  30.0  3
 38C  Var_03    CAS  CAR  NAQ  CAP  -174.30  30.0  3
 38C  Var_04    CAT  CAS  CAR  NAQ  -100.61  30.0  2
 38C  Var_05    CAU  CAV  OAW  CAX     0.97  30.0  2
 38C  Var_06    H8   CAX  OAW  CAV    59.95  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
 38C  plan-1  CAR  0.020
 38C  plan-1  CAS  0.020
 38C  plan-1  CAZ  0.020
 38C  plan-1  CAY  0.020
 38C  plan-1  CAV  0.020
 38C  plan-1  OAW  0.020
 38C  plan-1  CAU  0.020
 38C  plan-1  CAT  0.020
 38C  plan-1  H6   0.020
 38C  plan-1  H7   0.020
 38C  plan-1  H11  0.020
 38C  plan-1  H12  0.020
 38C  plan-2  CAI  0.020
 38C  plan-2  CAH  0.020
 38C  plan-2  CAG  0.020
 38C  plan-2  CAF  0.020
 38C  plan-2  CAM  0.020
 38C  plan-2  CAN  0.020
 38C  plan-2  CAE  0.020
 38C  plan-2  NAD  0.020
 38C  plan-2  NAO  0.020
 38C  plan-2  CAP  0.020
 38C  plan-2  CAC  0.020
 38C  plan-2  CAB  0.020
 38C  plan-2  NAQ  0.020
 38C  plan-2  H1   0.020
 38C  plan-2  H2   0.020
 38C  plan-2  H3   0.020
 38C  plan-3  CAP  0.020
 38C  plan-3  NAQ  0.020
 38C  plan-3  CAR  0.020
 38C  plan-3  H13  0.020
 38C  plan-4  CAC  0.020
 38C  plan-4  CAB  0.020
 38C  plan-4  OBA  0.020
 38C  plan-4  OAA  0.020

