# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 04:31:54 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 1-ethyl-~{N}-methyl-2,3-bis(oxidanylidene)-~{N}-[(1-phenylpyrazol-4-yl)methyl]-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)Cc3cnn(c3)c4ccccc4
#
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
 9LN  9LN  1-ethyl-~{N}-methyl-2,3-bis(oxidanylidene)-~{N}-[(1-phenylpyrazol-4-yl)methyl]-4~{H}-quinoxaline-6-carboxamide  ligand  51  30  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9LN
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
 9LN  CAA  C  CH3   0  -0.662  -6.7968  -0.7942   0.8587
 9LN  CAB  C  CH3   0  -0.534   0.0287  -2.3769  -1.9938
 9LN  CAF  C  CR16  0  -0.262   6.5198   2.8654   1.3033
 9LN  CAG  C  CR16  0  -0.246   6.2249   2.9036  -0.0531
 9LN  CAH  C  CR16  0  -0.248   6.0955   1.7838   2.0623
 9LN  CAI  C  CR16  0  -0.301   5.5043   1.8796  -0.6493
 9LN  CAJ  C  CR16  0  -0.318   5.3852   0.7464   1.4763
 9LN  CAK  C  CR16  0  -0.278  -2.2293  -2.0089   1.2476
 9LN  CAL  C  CR16  0  -0.331  -3.4270  -1.3268   1.3540
 9LN  CAM  C  CR15  0  -0.058   3.6209  -1.4543  -2.0459
 9LN  CAN  C  CR16  0  -0.335  -1.3522  -0.2716  -0.1442
 9LN  CAO  C  CR15  0   0.028   3.5254  -1.1299   0.1192
 9LN  CAP  C  CH2   0  -0.351  -5.8960   0.1392   1.6491
 9LN  CAQ  C  CH2   0  -0.437   2.0336  -3.0533  -0.7285
 9LN  CAU  C  CR5   0  -0.127   3.0257  -1.9453  -0.8669
 9LN  CAV  C  CR6   0  -0.067  -1.1856  -1.4924   0.4879
 9LN  CAW  C  CR6   0   0.379   5.0843   0.7991   0.1196
 9LN  CAX  C  CR6   0   0.439  -3.8237   2.3859  -0.6270
 9LN  CAY  C  CR6   0   0.435  -4.9791   1.8189   0.1818
 9LN  CAZ  C  CR66  0   0.379  -2.5459   0.4254  -0.0221
 9LN  CBA  C  CR66  0   0.364  -3.6016  -0.0891   0.7359
 9LN  NAR  N  N     0  -0.279   4.4140  -0.4336  -1.8031
 9LN  NAS  N  NR16  0  -0.725  -2.7000   1.6461  -0.6514
 9LN  NBB  N  NT    0  -0.431   0.6616  -2.5590  -0.7042
 9LN  NBC  N  NR5   0  -0.403   4.3502  -0.2424  -0.4834
 9LN  NBD  N  NR6   0  -0.576  -4.7799   0.6497   0.8491
 9LN  OAC  O  O     0  -0.488   0.6999  -2.3994   1.5476
 9LN  OAE  O  O     0  -0.443  -6.0209   2.4382   0.2126
 9LN  H1   H  HCH3  0   0.246  -7.6151  -1.1364   1.4916
 9LN  H2   H  HCH3  0   0.241  -7.2297  -0.2850  -0.0009
 9LN  H3   H  HCH3  0   0.236  -6.2613  -1.6733   0.5009
 9LN  H4   H  HCH3  0   0.244   0.4494  -1.5270  -2.5365
 9LN  H5   H  HCH3  0   0.258   0.1804  -3.2718  -2.5970
 9LN  H6   H  HCH3  0   0.270  -1.0410  -2.2254  -1.8906
 9LN  H8   H  HCR6  0   0.264   6.5509   3.7407  -0.6564
 9LN  H9   H  HCR6  0   0.266   6.3249   1.7355   3.1185
 9LN  H10  H  HCR6  0   0.276   5.2676   1.9222  -1.7029
 9LN  H11  H  HCR6  0   0.279   5.0832  -0.0985   2.0807
 9LN  H12  H  HCR6  0   0.270  -2.1192  -2.9581   1.7543
 9LN  H13  H  HCR6  0   0.290  -4.2204  -1.7793   1.9292
 9LN  H14  H  HCR5  0   0.269   3.4993  -1.8238  -3.0539
 9LN  H15  H  HCR6  0   0.289  -0.5537   0.1654  -0.7324
 9LN  H16  H  HCR5  0   0.298   3.3301  -1.1129   1.1784
 9LN  H17  H  HCH2  0   0.283  -6.4598   0.9954   2.0087
 9LN  H18  H  HCH2  0   0.271  -5.4904  -0.3516   2.5314
 9LN  H19  H  HCH2  0   0.274   2.1250  -3.7389  -1.5716
 9LN  H20  H  HCH2  0   0.279   2.2213  -3.6331   0.1727
 9LN  H21  H  HNR6  0   0.428  -1.9240   2.0057  -1.1933
 9LN  OAD  O  O     0  -0.435  -3.9505   3.4458  -1.2004
 9LN  CAT  C  C     0   0.518   0.1363  -2.1928   0.4797
 9LN  H7   H  HCR6  0   0.262   7.0766   3.6703   1.7640

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
 9LN  OAE  CAY  double    1.212  0.020  1.212
 9LN  OAD  CAX  double    1.212  0.020  1.212
 9LN  CAY  CAX  single    1.520  0.020  1.520
 9LN  CAY  NBD  single    1.361  0.020  1.361
 9LN  CAX  NAS  single    1.346  0.020  1.346
 9LN  CAA  CAP  single    1.519  0.020  1.519
 9LN  CAP  NBD  single    1.465  0.020  1.465
 9LN  NBD  CBA  single    1.395  0.020  1.395
 9LN  NAS  CAZ  single    1.382  0.020  1.382
 9LN  CBA  CAZ  aromatic  1.398  0.020  1.398
 9LN  CBA  CAL  aromatic  1.394  0.020  1.394
 9LN  CAZ  CAN  aromatic  1.388  0.020  1.388
 9LN  CAL  CAK  aromatic  1.382  0.020  1.382
 9LN  CAN  CAV  aromatic  1.385  0.020  1.385
 9LN  CAK  CAV  aromatic  1.390  0.020  1.390
 9LN  CAV  CAT  single    1.496  0.020  1.496
 9LN  CAT  OAC  double    1.225  0.020  1.225
 9LN  CAT  NBB  single    1.346  0.020  1.346
 9LN  CAB  NBB  single    1.448  0.020  1.448
 9LN  NBB  CAQ  single    1.459  0.020  1.459
 9LN  CAQ  CAU  single    1.494  0.020  1.494
 9LN  CAU  CAO  aromatic  1.374  0.020  1.374
 9LN  CAU  CAM  aromatic  1.409  0.020  1.409
 9LN  CAO  NBC  aromatic  1.353  0.020  1.353
 9LN  CAM  NAR  aromatic  1.315  0.020  1.315
 9LN  NBC  NAR  aromatic  1.335  0.020  1.335
 9LN  NBC  CAW  single    1.410  0.020  1.410
 9LN  CAI  CAW  aromatic  1.391  0.020  1.391
 9LN  CAI  CAG  aromatic  1.387  0.020  1.387
 9LN  CAW  CAJ  aromatic  1.391  0.020  1.391
 9LN  CAG  CAF  aromatic  1.389  0.020  1.389
 9LN  CAJ  CAH  aromatic  1.387  0.020  1.387
 9LN  CAF  CAH  aromatic  1.388  0.020  1.388
 9LN  CAA  H1   single    0.970  0.020  1.090
 9LN  CAA  H2   single    0.970  0.020  1.090
 9LN  CAA  H3   single    0.970  0.020  1.090
 9LN  CAB  H4   single    0.970  0.020  1.090
 9LN  CAB  H5   single    0.970  0.020  1.090
 9LN  CAB  H6   single    0.970  0.020  1.090
 9LN  CAF  H7   single    0.930  0.020  1.080
 9LN  CAG  H8   single    0.930  0.020  1.080
 9LN  CAH  H9   single    0.930  0.020  1.080
 9LN  CAI  H10  single    0.930  0.020  1.080
 9LN  CAJ  H11  single    0.930  0.020  1.080
 9LN  CAK  H12  single    0.930  0.020  1.080
 9LN  CAL  H13  single    0.930  0.020  1.080
 9LN  CAM  H14  single    0.930  0.020  1.080
 9LN  CAN  H15  single    0.930  0.020  1.080
 9LN  CAO  H16  single    0.930  0.020  1.080
 9LN  CAP  H17  single    0.970  0.020  1.090
 9LN  CAP  H18  single    0.970  0.020  1.090
 9LN  CAQ  H19  single    0.970  0.020  1.090
 9LN  CAQ  H20  single    0.970  0.020  1.090
 9LN  NAS  H21  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
 9LN  H3   CAA  H2   108.26  3.000
 9LN  H3   CAA  H1   107.84  3.000
 9LN  H2   CAA  H1   107.87  3.000
 9LN  H3   CAA  CAP  112.03  3.000
 9LN  H2   CAA  CAP  111.05  3.000
 9LN  H1   CAA  CAP  109.64  3.000
 9LN  H6   CAB  H5   107.73  3.000
 9LN  H6   CAB  H4   108.55  3.000
 9LN  H5   CAB  H4   108.07  3.000
 9LN  H6   CAB  NBB  111.32  3.000
 9LN  H5   CAB  NBB  109.19  3.000
 9LN  H4   CAB  NBB  111.83  3.000
 9LN  H7   CAF  CAH  120.29  3.000
 9LN  H7   CAF  CAG  120.32  3.000
 9LN  CAH  CAF  CAG  119.39  3.000
 9LN  H8   CAG  CAI  119.21  3.000
 9LN  H8   CAG  CAF  120.13  3.000
 9LN  CAI  CAG  CAF  120.66  3.000
 9LN  H9   CAH  CAJ  119.18  3.000
 9LN  H9   CAH  CAF  120.26  3.000
 9LN  CAJ  CAH  CAF  120.55  3.000
 9LN  H10  CAI  CAW  120.22  3.000
 9LN  H10  CAI  CAG  120.25  3.000
 9LN  CAW  CAI  CAG  119.52  3.000
 9LN  H11  CAJ  CAW  120.94  3.000
 9LN  H11  CAJ  CAH  119.41  3.000
 9LN  CAW  CAJ  CAH  119.64  3.000
 9LN  H12  CAK  CAV  120.37  3.000
 9LN  H12  CAK  CAL  119.02  3.000
 9LN  CAV  CAK  CAL  120.60  3.000
 9LN  H13  CAL  CBA  121.08  3.000
 9LN  H13  CAL  CAK  118.10  3.000
 9LN  CBA  CAL  CAK  120.82  3.000
 9LN  H14  CAM  NAR  120.36  3.000
 9LN  H14  CAM  CAU  127.87  3.000
 9LN  NAR  CAM  CAU  111.76  3.000
 9LN  H15  CAN  CAZ  118.62  3.000
 9LN  H15  CAN  CAV  120.97  3.000
 9LN  CAZ  CAN  CAV  120.40  3.000
 9LN  H16  CAO  NBC  122.55  3.000
 9LN  H16  CAO  CAU  130.49  3.000
 9LN  NBC  CAO  CAU  106.94  3.000
 9LN  H18  CAP  H17  106.29  3.000
 9LN  H18  CAP  NBD  108.42  3.000
 9LN  H17  CAP  NBD  107.54  3.000
 9LN  H18  CAP  CAA  111.46  3.000
 9LN  H17  CAP  CAA  110.41  3.000
 9LN  NBD  CAP  CAA  112.45  3.000
 9LN  H20  CAQ  H19  106.91  3.000
 9LN  H20  CAQ  NBB  109.21  3.000
 9LN  H19  CAQ  NBB  107.74  3.000
 9LN  H20  CAQ  CAU  110.95  3.000
 9LN  H19  CAQ  CAU  109.82  3.000
 9LN  NBB  CAQ  CAU  112.02  3.000
 9LN  CAQ  CAU  CAO  127.98  3.000
 9LN  CAO  CAU  CAM  103.90  3.000
 9LN  CAQ  CAU  CAM  128.07  3.000
 9LN  CAT  CAV  CAN  121.10  3.000
 9LN  CAT  CAV  CAK  119.49  3.000
 9LN  CAN  CAV  CAK  119.12  3.000
 9LN  NBC  CAW  CAJ  120.13  3.000
 9LN  CAJ  CAW  CAI  120.22  3.000
 9LN  NBC  CAW  CAI  119.65  3.000
 9LN  OAD  CAX  NAS  124.03  3.000
 9LN  NAS  CAX  CAY  116.07  3.000
 9LN  OAD  CAX  CAY  119.90  3.000
 9LN  OAE  CAY  NBD  123.51  3.000
 9LN  NBD  CAY  CAX  118.04  3.000
 9LN  OAE  CAY  CAX  118.44  3.000
 9LN  NAS  CAZ  CBA  119.20  3.000
 9LN  CBA  CAZ  CAN  120.83  3.000
 9LN  NAS  CAZ  CAN  119.97  3.000
 9LN  NBD  CBA  CAZ  119.14  3.000
 9LN  CAZ  CBA  CAL  118.20  3.000
 9LN  NBD  CBA  CAL  122.67  3.000
 9LN  NBC  NAR  CAM  105.35  3.000
 9LN  H21  NAS  CAZ  118.16  3.000
 9LN  H21  NAS  CAX  117.04  3.000
 9LN  CAZ  NAS  CAX  124.78  3.000
 9LN  CAT  NBB  CAQ  118.30  3.000
 9LN  CAQ  NBB  CAB  116.03  3.000
 9LN  CAT  NBB  CAB  125.35  3.000
 9LN  NAR  NBC  CAW  120.25  3.000
 9LN  CAW  NBC  CAO  127.69  3.000
 9LN  NAR  NBC  CAO  112.06  3.000
 9LN  CBA  NBD  CAY  122.60  3.000
 9LN  CBA  NBD  CAP  120.20  3.000
 9LN  CAY  NBD  CAP  117.11  3.000
 9LN  OAC  CAT  NBB  122.77  3.000
 9LN  NBB  CAT  CAV  118.50  3.000
 9LN  OAC  CAT  CAV  118.73  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
 9LN  CONST_01  CAW  CAI  CAG  CAF     0.00   0.0  0
 9LN  CONST_02  CAW  CAJ  CAH  CAF     0.00   0.0  0
 9LN  CONST_03  NBC  CAW  CAI  CAG   180.00   0.0  0
 9LN  CONST_04  CAJ  CAW  CAI  CAG     0.00   0.0  0
 9LN  CONST_05  CAJ  CAH  CAF  CAG     0.00   0.0  0
 9LN  CONST_06  NBC  CAW  CAJ  CAH   180.00   0.0  0
 9LN  CONST_07  CAI  CAW  CAJ  CAH     0.00   0.0  0
 9LN  CONST_08  CAI  CAG  CAF  CAH     0.00   0.0  0
 9LN  CONST_13  CAZ  CBA  CAL  CAK     0.00   0.0  0
 9LN  CONST_14  CAZ  CAN  CAV  CAK     0.00   0.0  0
 9LN  CONST_15  CAN  CAZ  CBA  CAL     0.00   0.0  0
 9LN  CONST_16  CAN  CAV  CAK  CAL     0.00   0.0  0
 9LN  CONST_17  NBC  CAO  CAU  CAM     0.00   0.0  0
 9LN  CONST_18  CAO  NBC  NAR  CAM     0.00   0.0  0
 9LN  CONST_19  CAW  NBC  NAR  CAM   180.00   0.0  0
 9LN  CONST_20  NAR  CAM  CAU  CAO     0.00   0.0  0
 9LN  CONST_21  NAR  NBC  CAO  CAU     0.00   0.0  0
 9LN  CONST_22  CAW  NBC  CAO  CAU   180.00   0.0  0
 9LN  CONST_23  NBC  NAR  CAM  CAU     0.00   0.0  0
 9LN  CONST_24  CBA  CAZ  CAN  CAV     0.00   0.0  0
 9LN  CONST_25  CBA  CAL  CAK  CAV     0.00   0.0  0
 9LN  CONST_26  CBA  NBD  CAY  CAX     0.00   0.0  0
 9LN  CONST_27  CAZ  NAS  CAX  CAY     0.00   0.0  0
 9LN  CONST_28  CAT  CAV  CAK  CAL   180.00   0.0  0
 9LN  CONST_29  NBC  CAO  CAU  CAQ   180.00   0.0  0
 9LN  CONST_30  NAR  CAM  CAU  CAQ   180.00   0.0  0
 9LN  CONST_31  CAZ  CAN  CAV  CAT   180.00   0.0  0
 9LN  CONST_32  CAX  CAY  NBD  CAP   180.00   0.0  0
 9LN  CONST_33  OAD  CAX  NAS  CAZ   180.00   0.0  0
 9LN  CONST_34  OAE  CAY  NBD  CBA   180.00   0.0  0
 9LN  CONST_35  H10  CAI  CAG  CAF   180.00   0.0  0
 9LN  CONST_36  H11  CAJ  CAH  CAF   180.00   0.0  0
 9LN  CONST_37  H9   CAH  CAF  CAG   180.00   0.0  0
 9LN  CONST_38  H8   CAG  CAF  CAH   180.00   0.0  0
 9LN  CONST_39  H7   CAF  CAG  CAI   180.00   0.0  0
 9LN  CONST_40  H15  CAN  CAV  CAK   180.00   0.0  0
 9LN  CONST_41  H16  CAO  CAU  CAM   180.00   0.0  0
 9LN  CONST_42  H12  CAK  CAV  CAN   180.00   0.0  0
 9LN  CONST_43  H14  CAM  CAU  CAO   180.00   0.0  0
 9LN  CONST_44  H13  CAL  CAK  CAV   180.00   0.0  0
 9LN  CONST_45  H21  NAS  CAX  CAY   180.00   0.0  0
 9LN  CONST_46  OAE  CAY  NBD  CAP     0.00   0.0  0
 9LN  CONST_47  CAV  CAT  NBB  CAB     0.00   0.0  0
 9LN  CONST_48  CAV  CAT  NBB  CAQ   180.00   0.0  0
 9LN  CONST_49  OAC  CAT  NBB  CAB   180.00   0.0  0
 9LN  CONST_50  OAC  CAT  NBB  CAQ     0.00   0.0  0
 9LN  Var_01    CAY  NBD  CAP  CAA    90.83  30.0  3
 9LN  Var_02    OAC  CAT  CAV  CAK   -55.68  30.0  2
 9LN  Var_03    NBB  CAQ  CAU  CAM   -94.87  30.0  1
 9LN  Var_04    CAU  CAQ  NBB  CAB    86.55  30.0  3
 9LN  Var_05    H1   CAA  CAP  NBD  -179.33  30.0  3
 9LN  Var_06    H4   CAB  NBB  CAQ   -71.10  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
 9LN  plan-1  CAM  0.020
 9LN  plan-1  CAO  0.020
 9LN  plan-1  CAQ  0.020
 9LN  plan-1  CAU  0.020
 9LN  plan-1  CAW  0.020
 9LN  plan-1  NAR  0.020
 9LN  plan-1  NBC  0.020
 9LN  plan-1  H14  0.020
 9LN  plan-1  H16  0.020
 9LN  plan-2  CAF  0.020
 9LN  plan-2  CAG  0.020
 9LN  plan-2  CAH  0.020
 9LN  plan-2  CAI  0.020
 9LN  plan-2  CAJ  0.020
 9LN  plan-2  CAW  0.020
 9LN  plan-2  NBC  0.020
 9LN  plan-2  H8   0.020
 9LN  plan-2  H9   0.020
 9LN  plan-2  H10  0.020
 9LN  plan-2  H11  0.020
 9LN  plan-2  H7   0.020
 9LN  plan-3  CAK  0.020
 9LN  plan-3  CAL  0.020
 9LN  plan-3  CAN  0.020
 9LN  plan-3  CAP  0.020
 9LN  plan-3  CAV  0.020
 9LN  plan-3  CAX  0.020
 9LN  plan-3  CAY  0.020
 9LN  plan-3  CAZ  0.020
 9LN  plan-3  CBA  0.020
 9LN  plan-3  NAS  0.020
 9LN  plan-3  NBD  0.020
 9LN  plan-3  OAE  0.020
 9LN  plan-3  H12  0.020
 9LN  plan-3  H13  0.020
 9LN  plan-3  H15  0.020
 9LN  plan-3  H21  0.020
 9LN  plan-3  OAD  0.020
 9LN  plan-3  CAT  0.020
 9LN  plan-4  CAB  0.020
 9LN  plan-4  CAQ  0.020
 9LN  plan-4  CAV  0.020
 9LN  plan-4  NBB  0.020
 9LN  plan-4  OAC  0.020
 9LN  plan-4  CAT  0.020

