# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 19:44:15 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3-[(4-chlorobenzyl)amino]-6-(trifluoromethyl)quinoxaline-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1nc2ccc(cc2nc1NCc3ccc(Cl)cc3)C(F)(F)F
#
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
 RG2  RG2  '3-[(4-chlorobenzyl)amino]-6-(trifluoromethyl)quinoxaline-2-carboxylic acid'  ligand  37  26  .  2021-08-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RG2
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
 RG2  CLAW  CL  CL    0  -0.127  -7.7427  -1.0666  -0.0769
 RG2  CAV   C   CR6   0  -0.049  -6.0094  -1.0497  -0.0599
 RG2  CAY   C   CR16  0  -0.197  -5.3404  -1.0790   1.1536
 RG2  CAZ   C   CR16  0  -0.289  -3.9534  -1.0672   1.1566
 RG2  CAU   C   CR16  0  -0.197  -5.3177  -1.0110  -1.2609
 RG2  CAT   C   CR16  0  -0.289  -3.9312  -0.9994  -1.2373
 RG2  CAS   C   CR6   0   0.055  -3.2346  -1.0303  -0.0334
 RG2  CAR   C   CH2   0  -0.319  -1.7332  -0.9794  -0.0178
 RG2  NAQ   N   NH1   0  -0.679  -1.3020   0.4045  -0.0038
 RG2  CAP   C   CR6   0   0.522  -0.0121   0.7505   0.0027
 RG2  CAC   C   CR6   0  -0.007   0.4134   2.1416   0.0339
 RG2  CAB   C   C     0   0.561  -0.5693   3.2652   0.0657
 RG2  OAA   O   OH1   0  -0.570   0.0079   4.4461   0.0851
 RG2  OBA   O   O     0  -0.438  -1.7690   3.1023   0.0737
 RG2  NAD   N   N     0  -0.372   1.6679   2.4618   0.0375
 RG2  CAE   C   CR66  0   0.199   2.5981   1.4838   0.0108
 RG2  CAF   C   CR16  0  -0.286   3.9652   1.8148   0.0139
 RG2  CAG   C   CR16  0  -0.296   4.9113   0.8259  -0.0129
 RG2  NAO   N   N     0  -0.485   0.8902  -0.2076  -0.0211
 RG2  CAN   C   CR66  0   0.296   2.1900   0.1319  -0.0195
 RG2  CAM   C   CR16  0  -0.344   3.1781  -0.8723  -0.0474
 RG2  CAH   C   CR6   0  -0.185   4.5059  -0.5246  -0.0444
 RG2  CAI   C   CT    0   1.055   5.5226  -1.6284  -0.0708
 RG2  FAL   F   F     0  -0.299   6.7770  -1.1733  -0.0895
 RG2  FAJ   F   F     0  -0.311   5.4094  -2.4251   1.0005
 RG2  FAK   F   F     0  -0.311   5.3715  -2.4105  -1.1479
 RG2  H1    H   HCR6  0   0.282  -5.8895  -1.1128   2.0847
 RG2  H2    H   HCR6  0   0.267  -3.4275  -1.0933   2.1033
 RG2  H3    H   HCR6  0   0.282  -5.8489  -0.9928  -2.2027
 RG2  H4    H   HCR6  0   0.267  -3.3872  -0.9714  -2.1737
 RG2  H5    H   HCH2  0   0.259  -1.3441  -1.5025   0.8599
 RG2  H6    H   HCH2  0   0.259  -1.3255  -1.4882  -0.8950
 RG2  H7    H   HNH1  0   0.415  -1.9911   1.1389   0.0279
 RG2  H8    H   HOH1  0   0.495  -0.6676   5.1412   0.1083
 RG2  H9    H   HCR6  0   0.279   4.2511   2.8583   0.0379
 RG2  H10   H   HCR6  0   0.276   5.9587   1.0904  -0.0096
 RG2  H11   H   HCR6  0   0.282   2.8540  -1.9056  -0.0710

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
 RG2  OBA   CAB  double    1.211  0.020  1.211
 RG2  OAA   CAB  single    1.315  0.020  1.315
 RG2  CAB   CAC  single    1.493  0.020  1.493
 RG2  CAC   NAD  aromatic  1.295  0.020  1.295
 RG2  CAC   CAP  aromatic  1.455  0.020  1.455
 RG2  CAU   CAT  aromatic  1.387  0.020  1.387
 RG2  CAU   CAV  aromatic  1.386  0.020  1.386
 RG2  NAD   CAE  aromatic  1.350  0.020  1.350
 RG2  CAT   CAS  aromatic  1.391  0.020  1.391
 RG2  NAQ   CAP  single    1.336  0.020  1.336
 RG2  NAQ   CAR  single    1.450  0.020  1.450
 RG2  CLAW  CAV  single    1.734  0.020  1.734
 RG2  CAP   NAO  aromatic  1.316  0.020  1.316
 RG2  CAV   CAY  aromatic  1.386  0.020  1.386
 RG2  CAE   CAF  aromatic  1.407  0.020  1.407
 RG2  CAE   CAN  aromatic  1.412  0.020  1.412
 RG2  CAF   CAG  aromatic  1.369  0.020  1.369
 RG2  CAS   CAR  single    1.502  0.020  1.502
 RG2  CAS   CAZ  aromatic  1.391  0.020  1.391
 RG2  NAO   CAN  aromatic  1.343  0.020  1.343
 RG2  CAN   CAM  aromatic  1.409  0.020  1.409
 RG2  CAY   CAZ  aromatic  1.387  0.020  1.387
 RG2  CAG   CAH  aromatic  1.410  0.020  1.410
 RG2  CAM   CAH  aromatic  1.373  0.020  1.373
 RG2  CAH   CAI  single    1.501  0.020  1.501
 RG2  FAJ   CAI  single    1.340  0.020  1.340
 RG2  CAI   FAL  single    1.335  0.020  1.335
 RG2  CAI   FAK  single    1.340  0.020  1.340
 RG2  CAY   H1   single    0.930  0.020  1.080
 RG2  CAZ   H2   single    0.930  0.020  1.080
 RG2  CAU   H3   single    0.930  0.020  1.080
 RG2  CAT   H4   single    0.930  0.020  1.080
 RG2  CAR   H5   single    0.970  0.020  1.090
 RG2  CAR   H6   single    0.970  0.020  1.090
 RG2  NAQ   H7   single    0.860  0.020  1.020
 RG2  OAA   H8   single    0.850  0.020  0.980
 RG2  CAF   H9   single    0.930  0.020  1.080
 RG2  CAG   H10  single    0.930  0.020  1.080
 RG2  CAM   H11  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
 RG2  CAU  CAV  CAY   121.21  3.000
 RG2  CAY  CAV  CLAW  119.40  3.000
 RG2  CAU  CAV  CLAW  119.38  3.000
 RG2  H1   CAY  CAZ   120.40  3.000
 RG2  H1   CAY  CAV   120.63  3.000
 RG2  CAZ  CAY  CAV   118.97  3.000
 RG2  H2   CAZ  CAS   119.84  3.000
 RG2  H2   CAZ  CAY   119.15  3.000
 RG2  CAS  CAZ  CAY   121.01  3.000
 RG2  H3   CAU  CAT   120.38  3.000
 RG2  H3   CAU  CAV   120.65  3.000
 RG2  CAT  CAU  CAV   118.97  3.000
 RG2  H4   CAT  CAS   119.81  3.000
 RG2  H4   CAT  CAU   119.18  3.000
 RG2  CAS  CAT  CAU   121.01  3.000
 RG2  CAR  CAS  CAT   120.57  3.000
 RG2  CAR  CAS  CAZ   120.57  3.000
 RG2  CAT  CAS  CAZ   118.83  3.000
 RG2  H6   CAR  H5    106.78  3.000
 RG2  H6   CAR  NAQ   109.96  3.000
 RG2  H5   CAR  NAQ   110.07  3.000
 RG2  H6   CAR  CAS   110.40  3.000
 RG2  H5   CAR  CAS   110.35  3.000
 RG2  NAQ  CAR  CAS   109.25  3.000
 RG2  H7   NAQ  CAP   118.13  3.000
 RG2  H7   NAQ  CAR   119.52  3.000
 RG2  CAP  NAQ  CAR   122.32  3.000
 RG2  NAO  CAP  CAC   119.73  3.000
 RG2  NAO  CAP  NAQ   118.25  3.000
 RG2  CAC  CAP  NAQ   122.02  3.000
 RG2  NAD  CAC  CAB   116.84  3.000
 RG2  NAD  CAC  CAP   121.32  3.000
 RG2  CAB  CAC  CAP   121.84  3.000
 RG2  OBA  CAB  OAA   123.77  3.000
 RG2  OAA  CAB  CAC   112.79  3.000
 RG2  OBA  CAB  CAC   123.44  3.000
 RG2  H8   OAA  CAB   109.78  3.000
 RG2  CAE  NAD  CAC   119.24  3.000
 RG2  CAN  CAE  CAF   120.40  3.000
 RG2  CAN  CAE  NAD   119.65  3.000
 RG2  CAF  CAE  NAD   119.94  3.000
 RG2  H9   CAF  CAG   120.96  3.000
 RG2  H9   CAF  CAE   118.93  3.000
 RG2  CAG  CAF  CAE   120.11  3.000
 RG2  H10  CAG  CAH   120.87  3.000
 RG2  H10  CAG  CAF   119.56  3.000
 RG2  CAH  CAG  CAF   119.57  3.000
 RG2  CAN  NAO  CAP   118.63  3.000
 RG2  CAM  CAN  NAO   119.89  3.000
 RG2  CAM  CAN  CAE   118.68  3.000
 RG2  NAO  CAN  CAE   121.43  3.000
 RG2  H11  CAM  CAH   122.08  3.000
 RG2  H11  CAM  CAN   118.07  3.000
 RG2  CAH  CAM  CAN   119.85  3.000
 RG2  CAI  CAH  CAM   117.96  3.000
 RG2  CAI  CAH  CAG   120.65  3.000
 RG2  CAM  CAH  CAG   121.38  3.000
 RG2  FAK  CAI  FAJ   106.63  3.000
 RG2  FAK  CAI  FAL   107.09  3.000
 RG2  FAJ  CAI  FAL   107.06  3.000
 RG2  FAK  CAI  CAH   111.54  3.000
 RG2  FAL  CAI  CAH   112.71  3.000
 RG2  FAJ  CAI  CAH   111.47  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
 RG2  CONST_01  CAS  CAT  CAU  CAV      0.00   0.0  0
 RG2  CONST_02  CAS  CAZ  CAY  CAV      0.00   0.0  0
 RG2  CONST_03  CAT  CAU  CAV  CAY      0.00   0.0  0
 RG2  CONST_04  CAT  CAS  CAZ  CAY      0.00   0.0  0
 RG2  CONST_05  CAU  CAT  CAS  CAZ      0.00   0.0  0
 RG2  CONST_06  CAU  CAV  CAY  CAZ      0.00   0.0  0
 RG2  CONST_07  CAE  NAD  CAC  CAP      0.00   0.0  0
 RG2  CONST_08  CAE  CAN  NAO  CAP      0.00   0.0  0
 RG2  CONST_09  CAM  CAN  NAO  CAP    180.00   0.0  0
 RG2  CONST_10  CAF  CAE  NAD  CAC    180.00   0.0  0
 RG2  CONST_11  CAN  CAE  NAD  CAC      0.00   0.0  0
 RG2  CONST_12  CAN  NAO  CAP  CAC      0.00   0.0  0
 RG2  CONST_13  NAO  CAP  CAC  NAD      0.00   0.0  0
 RG2  CONST_14  CAG  CAF  CAE  NAD    180.00   0.0  0
 RG2  CONST_15  NAO  CAN  CAE  NAD      0.00   0.0  0
 RG2  CONST_16  CAM  CAN  CAE  NAD    180.00   0.0  0
 RG2  CONST_17  CAH  CAG  CAF  CAE      0.00   0.0  0
 RG2  CONST_18  CAH  CAM  CAN  CAE      0.00   0.0  0
 RG2  CONST_19  NAO  CAN  CAE  CAF    180.00   0.0  0
 RG2  CONST_20  CAM  CAN  CAE  CAF      0.00   0.0  0
 RG2  CONST_21  CAM  CAH  CAG  CAF      0.00   0.0  0
 RG2  CONST_22  CAN  CAE  CAF  CAG      0.00   0.0  0
 RG2  CONST_23  CAN  CAM  CAH  CAG      0.00   0.0  0
 RG2  CONST_24  CAH  CAM  CAN  NAO    180.00   0.0  0
 RG2  CONST_25  CAT  CAU  CAV  CLAW   180.00   0.0  0
 RG2  CONST_26  CAZ  CAY  CAV  CLAW   180.00   0.0  0
 RG2  CONST_27  CAR  CAS  CAZ  CAY    180.00   0.0  0
 RG2  CONST_28  CAR  CAS  CAT  CAU    180.00   0.0  0
 RG2  CONST_29  NAD  CAC  CAP  NAQ    180.00   0.0  0
 RG2  CONST_30  CAN  NAO  CAP  NAQ    180.00   0.0  0
 RG2  CONST_31  CAE  NAD  CAC  CAB    180.00   0.0  0
 RG2  CONST_32  NAO  CAP  CAC  CAB    180.00   0.0  0
 RG2  CONST_33  CAI  CAH  CAG  CAF    180.00   0.0  0
 RG2  CONST_34  CAI  CAH  CAM  CAN    180.00   0.0  0
 RG2  CONST_35  H4   CAT  CAU  CAV    180.00   0.0  0
 RG2  CONST_36  H2   CAZ  CAY  CAV    180.00   0.0  0
 RG2  CONST_37  H3   CAU  CAV  CAY    180.00   0.0  0
 RG2  CONST_38  H1   CAY  CAV  CAU    180.00   0.0  0
 RG2  CONST_39  H9   CAF  CAE  NAD      0.00   0.0  0
 RG2  CONST_40  H10  CAG  CAF  CAE    180.00   0.0  0
 RG2  CONST_41  H11  CAM  CAN  CAE    180.00   0.0  0
 RG2  CONST_42  CAC  CAP  NAQ  CAR    180.00   0.0  0
 RG2  CONST_43  NAO  CAP  NAQ  CAR      0.00   0.0  0
 RG2  CONST_44  H7   NAQ  CAP  CAC      0.00   0.0  0
 RG2  CONST_45  H8   OAA  CAB  CAC    180.00   0.0  0
 RG2  Var_01    NAQ  CAR  CAS  CAZ    -90.22  30.0  2
 RG2  Var_02    CAP  NAQ  CAR  CAS   -179.54  30.0  1
 RG2  Var_03    OBA  CAB  CAC  CAP      0.33  30.0  2
 RG2  Var_04    FAJ  CAI  CAH  CAG    119.09  30.0  2

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
 RG2  plan-1  CLAW  0.020
 RG2  plan-1  CAV   0.020
 RG2  plan-1  CAY   0.020
 RG2  plan-1  CAZ   0.020
 RG2  plan-1  CAU   0.020
 RG2  plan-1  CAT   0.020
 RG2  plan-1  CAS   0.020
 RG2  plan-1  CAR   0.020
 RG2  plan-1  H1    0.020
 RG2  plan-1  H2    0.020
 RG2  plan-1  H3    0.020
 RG2  plan-1  H4    0.020
 RG2  plan-2  NAQ   0.020
 RG2  plan-2  CAP   0.020
 RG2  plan-2  CAC   0.020
 RG2  plan-2  CAB   0.020
 RG2  plan-2  NAD   0.020
 RG2  plan-2  CAE   0.020
 RG2  plan-2  CAF   0.020
 RG2  plan-2  CAG   0.020
 RG2  plan-2  NAO   0.020
 RG2  plan-2  CAN   0.020
 RG2  plan-2  CAM   0.020
 RG2  plan-2  CAH   0.020
 RG2  plan-2  CAI   0.020
 RG2  plan-2  H9    0.020
 RG2  plan-2  H10   0.020
 RG2  plan-2  H11   0.020
 RG2  plan-3  CAR   0.020
 RG2  plan-3  NAQ   0.020
 RG2  plan-3  CAP   0.020
 RG2  plan-3  H7    0.020
 RG2  plan-4  CAC   0.020
 RG2  plan-4  CAB   0.020
 RG2  plan-4  OAA   0.020
 RG2  plan-4  OBA   0.020
 RG2  plan-4  H8    0.020

