# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 07:20:43 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)C(=O)Nc2cc(ccc12)C(=O)N[C@H](c3cccc(F)c3)c4nccn4C
#
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
 9LT  9LT  1-ethyl-~{N}-[(~{R})-(3-fluorophenyl)-(1-methylimidazol-2-yl)methyl]-2,3-bis(oxidanylidene)-4~{H}-quinoxaline-6-carboxamide  ligand  51  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9LT
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
 9LT  CAA  C  CH3   0  -0.662  -5.3855   3.2274   0.6140
 9LT  CAB  C  CH3   0  -0.538   4.9956  -2.6775   0.8689
 9LT  CAG  C  CR16  0  -0.227   4.9619   2.1484   1.7996
 9LT  CAH  C  CR15  0  -0.229   3.2571  -2.8351  -2.2649
 9LT  CAI  C  CR16  0  -0.415   5.3713   2.7394   0.6132
 9LT  CAJ  C  CR16  0  -0.324   4.1261   1.0400   1.7847
 9LT  CAK  C  CR16  0  -0.298  -1.2250   0.9916   0.2442
 9LT  CAL  C  CR16  0  -0.326  -2.4897   1.4805  -0.0244
 9LT  CAM  C  CR15  0  -0.116   4.2513  -3.2914  -1.4501
 9LT  CAN  C  CR16  0  -0.443   4.0986   1.0885  -0.6206
 9LT  CAO  C  CR16  0  -0.365  -2.0801  -1.2425   0.2443
 9LT  CAP  C  CH2   0  -0.352  -5.1050   2.4957  -0.6873
 9LT  CAU  C  CR6   0   0.552   4.9262   2.1925  -0.5752
 9LT  CAV  C  CR6   0  -0.052  -1.0037  -0.3773   0.3693
 9LT  CAW  C  CR6   0   0.130   3.6923   0.5071   0.5767
 9LT  CAX  C  CR5   0   0.498   3.1279  -1.6922  -0.4729
 9LT  CAY  C  CR6   0   0.441  -5.6836  -1.2616  -0.3920
 9LT  CAZ  C  CR6   0   0.437  -5.9292   0.2314  -0.5417
 9LT  CBA  C  CR66  0   0.393  -3.3468  -0.7572  -0.0349
 9LT  CBB  C  CR66  0   0.372  -3.5711   0.6156  -0.1860
 9LT  CBC  C  CH1   0  -0.237   2.7449  -0.6754   0.5638
 9LT  FAF  F  F     0  -0.313   5.3145   2.7520  -1.7316
 9LT  NAQ  N  N     0  -0.454   2.5635  -1.8353  -1.6446
 9LT  NAR  N  NH1   0  -0.648   1.3977  -0.1991   0.3555
 9LT  NAS  N  NR16  0  -0.726  -4.4094  -1.6311  -0.1662
 9LT  NBD  N  NR5   0  -0.440   4.1591  -2.5495  -0.3046
 9LT  NBE  N  NR6   0  -0.577  -4.8543   1.0661  -0.4866
 9LT  OAC  O  O     0  -0.475   0.4473  -2.0602   1.1968
 9LT  OAE  O  O     0  -0.439  -7.0639   0.6144  -0.7248
 9LT  H1   H  HCH3  0   0.247  -5.5499   4.2846   0.4081
 9LT  H2   H  HCH3  0   0.242  -6.2789   2.8367   1.1002
 9LT  H3   H  HCH3  0   0.236  -4.5543   3.1483   1.3139
 9LT  H4   H  HCH3  0   0.264   4.4145  -3.0099   1.7279
 9LT  H5   H  HCH3  0   0.276   5.7687  -3.4139   0.6726
 9LT  H6   H  HCH3  0   0.260   5.4761  -1.7301   1.1078
 9LT  H8   H  HCR5  0   0.250   3.0055  -3.1735  -3.2580
 9LT  H9   H  HCR6  0   0.284   6.0247   3.6017   0.6112
 9LT  H10  H  HCR6  0   0.265   3.8147   0.5860   2.7169
 9LT  H11  H  HCR6  0   0.267  -0.4244   1.7056   0.3823
 9LT  H12  H  HCR6  0   0.294  -2.6174   2.5501  -0.0942
 9LT  H13  H  HCR5  0   0.288   4.9962  -4.0598  -1.5743
 9LT  H14  H  HCR6  0   0.280   3.7802   0.6880  -1.5758
 9LT  H15  H  HCR6  0   0.284  -1.9375  -2.3101   0.3553
 9LT  H16  H  HCH2  0   0.284  -5.9481   2.5898  -1.3662
 9LT  H17  H  HCH2  0   0.272  -4.2480   2.9213  -1.2051
 9LT  H18  H  HCH1  0   0.291   2.7787  -1.1471   1.5505
 9LT  H19  H  HNH1  0   0.416   1.2755   0.5871  -0.2634
 9LT  H20  H  HNR6  0   0.429  -4.2269  -2.6222  -0.0657
 9LT  OAD  O  O     0  -0.434  -6.6095  -2.0374  -0.4836
 9LT  CAT  C  C     0   0.563   0.3334  -0.9621   0.6744
 9LT  H7   H  HCR6  0   0.274   5.2991   2.5566   2.7428

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
 9LT  OAE  CAZ  double    1.211  0.020  1.211
 9LT  OAD  CAY  double    1.211  0.020  1.211
 9LT  CAA  CAP  single    1.519  0.020  1.519
 9LT  CAZ  CAY  single    1.520  0.020  1.520
 9LT  CAZ  NBE  single    1.362  0.020  1.362
 9LT  CAY  NAS  single    1.346  0.020  1.346
 9LT  CAP  NBE  single    1.465  0.020  1.465
 9LT  NBE  CBB  single    1.393  0.020  1.393
 9LT  NAS  CBA  single    1.382  0.020  1.382
 9LT  CBB  CBA  aromatic  1.399  0.020  1.399
 9LT  CBB  CAL  aromatic  1.394  0.020  1.394
 9LT  CBA  CAO  aromatic  1.385  0.020  1.385
 9LT  CAL  CAK  aromatic  1.382  0.020  1.382
 9LT  CAO  CAV  aromatic  1.387  0.020  1.387
 9LT  CAK  CAV  aromatic  1.392  0.020  1.392
 9LT  CAV  CAT  single    1.491  0.020  1.491
 9LT  CAT  OAC  double    1.221  0.020  1.221
 9LT  CAT  NAR  single    1.348  0.020  1.348
 9LT  NAR  CBC  single    1.444  0.020  1.444
 9LT  CBC  CAW  single    1.515  0.020  1.515
 9LT  CBC  CAX  single    1.502  0.020  1.502
 9LT  CAJ  CAW  aromatic  1.390  0.020  1.390
 9LT  CAJ  CAG  aromatic  1.388  0.020  1.388
 9LT  CAW  CAN  aromatic  1.392  0.020  1.392
 9LT  CAG  CAI  aromatic  1.387  0.020  1.387
 9LT  CAN  CAU  aromatic  1.380  0.020  1.380
 9LT  CAI  CAU  aromatic  1.382  0.020  1.382
 9LT  CAU  FAF  single    1.342  0.020  1.342
 9LT  CAX  NAQ  aromatic  1.308  0.020  1.308
 9LT  CAX  NBD  aromatic  1.352  0.020  1.352
 9LT  NAQ  CAH  aromatic  1.366  0.020  1.366
 9LT  NBD  CAB  single    1.447  0.020  1.447
 9LT  NBD  CAM  aromatic  1.368  0.020  1.368
 9LT  CAH  CAM  aromatic  1.364  0.020  1.364
 9LT  CAA  H1   single    0.970  0.020  1.090
 9LT  CAA  H2   single    0.970  0.020  1.090
 9LT  CAA  H3   single    0.970  0.020  1.090
 9LT  CAB  H4   single    0.970  0.020  1.090
 9LT  CAB  H5   single    0.970  0.020  1.090
 9LT  CAB  H6   single    0.970  0.020  1.090
 9LT  CAG  H7   single    0.930  0.020  1.080
 9LT  CAH  H8   single    0.930  0.020  1.080
 9LT  CAI  H9   single    0.930  0.020  1.080
 9LT  CAJ  H10  single    0.930  0.020  1.080
 9LT  CAK  H11  single    0.930  0.020  1.080
 9LT  CAL  H12  single    0.930  0.020  1.080
 9LT  CAM  H13  single    0.930  0.020  1.080
 9LT  CAN  H14  single    0.930  0.020  1.080
 9LT  CAO  H15  single    0.930  0.020  1.080
 9LT  CAP  H16  single    0.970  0.020  1.090
 9LT  CAP  H17  single    0.970  0.020  1.090
 9LT  CBC  H18  single    0.970  0.020  1.090
 9LT  NAR  H19  single    0.860  0.020  1.020
 9LT  NAS  H20  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
 9LT  H3   CAA  H2   108.23  3.000
 9LT  H3   CAA  H1   107.88  3.000
 9LT  H2   CAA  H1   107.98  3.000
 9LT  H3   CAA  CAP  111.99  3.000
 9LT  H2   CAA  CAP  111.16  3.000
 9LT  H1   CAA  CAP  109.47  3.000
 9LT  H6   CAB  H5   108.40  3.000
 9LT  H6   CAB  H4   109.14  3.000
 9LT  H5   CAB  H4   108.39  3.000
 9LT  H6   CAB  NBD  110.86  3.000
 9LT  H5   CAB  NBD  108.97  3.000
 9LT  H4   CAB  NBD  110.99  3.000
 9LT  H7   CAG  CAJ  119.89  3.000
 9LT  H7   CAG  CAI  119.54  3.000
 9LT  CAJ  CAG  CAI  120.57  3.000
 9LT  H8   CAH  NAQ  121.95  3.000
 9LT  H8   CAH  CAM  127.95  3.000
 9LT  NAQ  CAH  CAM  110.10  3.000
 9LT  H9   CAI  CAU  120.56  3.000
 9LT  H9   CAI  CAG  121.29  3.000
 9LT  CAU  CAI  CAG  118.15  3.000
 9LT  H10  CAJ  CAW  119.86  3.000
 9LT  H10  CAJ  CAG  119.92  3.000
 9LT  CAW  CAJ  CAG  120.22  3.000
 9LT  H11  CAK  CAV  121.33  3.000
 9LT  H11  CAK  CAL  117.94  3.000
 9LT  CAV  CAK  CAL  120.71  3.000
 9LT  H12  CAL  CBB  121.03  3.000
 9LT  H12  CAL  CAK  118.12  3.000
 9LT  CBB  CAL  CAK  120.85  3.000
 9LT  H13  CAM  NBD  122.00  3.000
 9LT  H13  CAM  CAH  132.35  3.000
 9LT  NBD  CAM  CAH  105.65  3.000
 9LT  H14  CAN  CAW  121.21  3.000
 9LT  H14  CAN  CAU  120.04  3.000
 9LT  CAW  CAN  CAU  118.74  3.000
 9LT  H15  CAO  CBA  119.11  3.000
 9LT  H15  CAO  CAV  120.25  3.000
 9LT  CBA  CAO  CAV  120.64  3.000
 9LT  H17  CAP  H16  106.26  3.000
 9LT  H17  CAP  NBE  108.18  3.000
 9LT  H16  CAP  NBE  107.63  3.000
 9LT  H17  CAP  CAA  111.39  3.000
 9LT  H16  CAP  CAA  110.50  3.000
 9LT  NBE  CAP  CAA  112.60  3.000
 9LT  FAF  CAU  CAN  118.59  3.000
 9LT  FAF  CAU  CAI  118.87  3.000
 9LT  CAN  CAU  CAI  122.54  3.000
 9LT  CAT  CAV  CAO  118.02  3.000
 9LT  CAT  CAV  CAK  123.14  3.000
 9LT  CAO  CAV  CAK  118.81  3.000
 9LT  CBC  CAW  CAN  120.09  3.000
 9LT  CAN  CAW  CAJ  119.77  3.000
 9LT  CBC  CAW  CAJ  120.12  3.000
 9LT  NBD  CAX  NAQ  111.79  3.000
 9LT  NBD  CAX  CBC  122.55  3.000
 9LT  NAQ  CAX  CBC  125.61  3.000
 9LT  OAD  CAY  NAS  124.09  3.000
 9LT  NAS  CAY  CAZ  116.05  3.000
 9LT  OAD  CAY  CAZ  119.86  3.000
 9LT  OAE  CAZ  NBE  123.47  3.000
 9LT  NBE  CAZ  CAY  118.05  3.000
 9LT  OAE  CAZ  CAY  118.47  3.000
 9LT  NAS  CBA  CBB  119.13  3.000
 9LT  CBB  CBA  CAO  120.81  3.000
 9LT  NAS  CBA  CAO  120.06  3.000
 9LT  NBE  CBB  CBA  119.23  3.000
 9LT  CBA  CBB  CAL  118.15  3.000
 9LT  NBE  CBB  CAL  122.62  3.000
 9LT  H18  CBC  NAR  107.52  3.000
 9LT  H18  CBC  CAX  108.84  3.000
 9LT  NAR  CBC  CAX  111.20  3.000
 9LT  H18  CBC  CAW  108.03  3.000
 9LT  CAX  CBC  CAW  112.01  3.000
 9LT  NAR  CBC  CAW  109.10  3.000
 9LT  CAX  NAQ  CAH  105.53  3.000
 9LT  H19  NAR  CBC  117.32  3.000
 9LT  H19  NAR  CAT  119.41  3.000
 9LT  CBC  NAR  CAT  121.06  3.000
 9LT  H20  NAS  CBA  118.08  3.000
 9LT  H20  NAS  CAY  117.13  3.000
 9LT  CBA  NAS  CAY  124.77  3.000
 9LT  CAX  NBD  CAM  106.93  3.000
 9LT  CAM  NBD  CAB  126.32  3.000
 9LT  CAX  NBD  CAB  126.75  3.000
 9LT  CBB  NBE  CAZ  122.53  3.000
 9LT  CBB  NBE  CAP  120.18  3.000
 9LT  CAZ  NBE  CAP  117.21  3.000
 9LT  OAC  CAT  NAR  122.45  3.000
 9LT  NAR  CAT  CAV  115.96  3.000
 9LT  OAC  CAT  CAV  121.59  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
 9LT  CONST_01  CAN  CAW  CAJ  CAG     0.00   0.0  0
 9LT  CONST_02  CAN  CAU  CAI  CAG     0.00   0.0  0
 9LT  CONST_03  NBD  CAX  NAQ  CAH     0.00   0.0  0
 9LT  CONST_04  CAX  NBD  CAM  CAH     0.00   0.0  0
 9LT  CONST_05  CAW  CAJ  CAG  CAI     0.00   0.0  0
 9LT  CONST_06  CAW  CAN  CAU  CAI     0.00   0.0  0
 9LT  CONST_07  CAU  CAN  CAW  CAJ     0.00   0.0  0
 9LT  CONST_08  CAU  CAI  CAG  CAJ     0.00   0.0  0
 9LT  CONST_09  CBA  CBB  CAL  CAK     0.00   0.0  0
 9LT  CONST_10  CBA  CAO  CAV  CAK     0.00   0.0  0
 9LT  CONST_11  CAO  CBA  CBB  CAL     0.00   0.0  0
 9LT  CONST_12  CAO  CAV  CAK  CAL     0.00   0.0  0
 9LT  CONST_13  NAQ  CAX  NBD  CAM     0.00   0.0  0
 9LT  CONST_14  CAX  NAQ  CAH  CAM     0.00   0.0  0
 9LT  CONST_15  CBB  CBA  CAO  CAV     0.00   0.0  0
 9LT  CONST_16  CBB  CAL  CAK  CAV     0.00   0.0  0
 9LT  CONST_17  NBD  CAM  CAH  NAQ     0.00   0.0  0
 9LT  CONST_18  CBB  NBE  CAZ  CAY     0.00   0.0  0
 9LT  CONST_19  CBA  NAS  CAY  CAZ     0.00   0.0  0
 9LT  CONST_20  NAQ  CAX  NBD  CAB   180.00   0.0  0
 9LT  CONST_21  CAH  CAM  NBD  CAB   180.00   0.0  0
 9LT  CONST_22  CBC  CAW  CAJ  CAG   180.00   0.0  0
 9LT  CONST_23  FAF  CAU  CAI  CAG   180.00   0.0  0
 9LT  CONST_24  CBC  CAX  NAQ  CAH   180.00   0.0  0
 9LT  CONST_25  CAT  CAV  CAK  CAL   180.00   0.0  0
 9LT  CONST_26  CBC  CAX  NBD  CAM   180.00   0.0  0
 9LT  CONST_27  CBA  CAO  CAV  CAT   180.00   0.0  0
 9LT  CONST_28  CBC  CAW  CAN  CAU   180.00   0.0  0
 9LT  CONST_29  FAF  CAU  CAN  CAW   180.00   0.0  0
 9LT  CONST_30  CAY  CAZ  NBE  CAP   180.00   0.0  0
 9LT  CONST_31  OAD  CAY  NAS  CBA   180.00   0.0  0
 9LT  CONST_32  OAE  CAZ  NBE  CBB   180.00   0.0  0
 9LT  CONST_33  H10  CAJ  CAG  CAI   180.00   0.0  0
 9LT  CONST_34  H14  CAN  CAU  CAI   180.00   0.0  0
 9LT  CONST_35  H9   CAI  CAG  CAJ   180.00   0.0  0
 9LT  CONST_36  H15  CAO  CAV  CAK   180.00   0.0  0
 9LT  CONST_37  H11  CAK  CAV  CAO   180.00   0.0  0
 9LT  CONST_38  H7   CAG  CAI  CAU   180.00   0.0  0
 9LT  CONST_39  H12  CAL  CAK  CAV   180.00   0.0  0
 9LT  CONST_40  H8   CAH  NAQ  CAX   180.00   0.0  0
 9LT  CONST_41  H13  CAM  NBD  CAX   180.00   0.0  0
 9LT  CONST_42  H20  NAS  CAY  CAZ   180.00   0.0  0
 9LT  CONST_43  OAE  CAZ  NBE  CAP     0.00   0.0  0
 9LT  CONST_44  CBC  NAR  CAT  CAV   180.00   0.0  0
 9LT  CONST_46  OAC  CAT  NAR  CBC     0.00   0.0  0
 9LT  Var_01    CAZ  NBE  CAP  CAA    90.59  30.0  3
 9LT  Var_02    OAC  CAT  CAV  CAK   155.85  30.0  2
 9LT  Var_03    H4   CAB  NBD  CAM  -115.07  30.0  2
 9LT  Var_04    H1   CAA  CAP  NBE   179.19  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
 9LT  chir_01  CBC  NAR  CAW  CAX  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
 9LT  plan-1  CAB  0.020
 9LT  plan-1  CAH  0.020
 9LT  plan-1  CAM  0.020
 9LT  plan-1  CAX  0.020
 9LT  plan-1  CBC  0.020
 9LT  plan-1  NAQ  0.020
 9LT  plan-1  NBD  0.020
 9LT  plan-1  H8   0.020
 9LT  plan-1  H13  0.020
 9LT  plan-2  CAG  0.020
 9LT  plan-2  CAI  0.020
 9LT  plan-2  CAJ  0.020
 9LT  plan-2  CAN  0.020
 9LT  plan-2  CAU  0.020
 9LT  plan-2  CAW  0.020
 9LT  plan-2  CBC  0.020
 9LT  plan-2  FAF  0.020
 9LT  plan-2  H9   0.020
 9LT  plan-2  H10  0.020
 9LT  plan-2  H14  0.020
 9LT  plan-2  H7   0.020
 9LT  plan-3  CAK  0.020
 9LT  plan-3  CAL  0.020
 9LT  plan-3  CAO  0.020
 9LT  plan-3  CAP  0.020
 9LT  plan-3  CAV  0.020
 9LT  plan-3  CAY  0.020
 9LT  plan-3  CAZ  0.020
 9LT  plan-3  CBA  0.020
 9LT  plan-3  CBB  0.020
 9LT  plan-3  NAS  0.020
 9LT  plan-3  NBE  0.020
 9LT  plan-3  OAE  0.020
 9LT  plan-3  H11  0.020
 9LT  plan-3  H12  0.020
 9LT  plan-3  H15  0.020
 9LT  plan-3  H20  0.020
 9LT  plan-3  OAD  0.020
 9LT  plan-3  CAT  0.020
 9LT  plan-4  CAV  0.020
 9LT  plan-4  CBC  0.020
 9LT  plan-4  NAR  0.020
 9LT  plan-4  OAC  0.020
 9LT  plan-4  H19  0.020
 9LT  plan-4  CAT  0.020

