# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 10:08:11 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: ~{N}-[7-imidazol-1-yl-2,3-bis(oxidanylidene)-6-(trifluoromethyl)-4~{H}-quinoxalin-1-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cc2NC(=O)C(=O)N(NC(=O)c3ccccc3)c2cc1n4ccnc4
#
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
 L5H  L5H  ~{N}-[7-imidazol-1-yl-2,3-bis(oxidanylidene)-6-(trifluoromethyl)-4~{H}-quinoxalin-1-yl]benzamide  ligand  42  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L5H
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
 L5H  N1   N  NR16  0  -0.733   0.6624   3.3688  -0.0100
 L5H  N3   N  NH1   0  -0.530  -2.1819   0.4646  -0.5248
 L5H  C4   C  CR16  0  -0.321   0.4863  -0.2734  -0.3144
 L5H  C5   C  CR6   0   0.323   1.8195  -0.6115  -0.1841
 L5H  C6   C  CR6   0  -0.215   2.7853   0.3771   0.0071
 L5H  C7   C  CR6   0   0.442  -0.6105   3.8057  -0.1191
 L5H  C8   C  CR6   0   0.455  -1.6761   2.7352  -0.3054
 L5H  C10  C  CR6   0  -0.032  -3.9712  -0.9047   0.3356
 L5H  C13  C  CR16  0  -0.243  -6.0432  -2.7230  -0.0290
 L5H  C15  C  CR16  0  -0.262  -5.0195  -0.9653   1.2519
 L5H  C17  C  CR15  0   0.088   2.1962  -2.8556   0.7858
 L5H  C1   C  CR16  0  -0.412   2.3918   1.7015   0.0647
 L5H  C11  C  CR16  0  -0.283  -3.9585  -1.7711  -0.7565
 L5H  C12  C  CR16  0  -0.239  -4.9917  -2.6790  -0.9343
 L5H  C14  C  CR16  0  -0.241  -6.0553  -1.8655   1.0643
 L5H  C16  C  CT    0   1.087   4.2349   0.0171   0.1563
 L5H  C18  C  CR15  0  -0.208   2.6852  -3.9691  -0.9625
 L5H  C19  C  CR15  0  -0.111   2.4794  -2.6915  -1.3863
 L5H  C2   C  CR66  0   0.396   1.0542   2.0468  -0.0656
 L5H  C3   C  CR66  0   0.406   0.0947   1.0551  -0.2534
 L5H  C9   C  C     0   0.539  -2.8867   0.0774   0.5880
 L5H  F1   F  F     0  -0.305   4.4378  -0.7970   1.1987
 L5H  F2   F  F     0  -0.304   4.7072  -0.6085  -0.9274
 L5H  F3   F  F     0  -0.295   4.9990   1.0935   0.3484
 L5H  N2   N  NR6   0  -0.465  -1.2384   1.4370  -0.3822
 L5H  N4   N  NR5   0  -0.536   2.1691  -1.9810  -0.2528
 L5H  N5   N  N     0  -0.442   2.5060  -4.0576   0.3917
 L5H  O1   O  O     0  -0.428  -2.6130   0.5037   1.6881
 L5H  O2   O  O     0  -0.416  -0.9375   4.9675  -0.0727
 L5H  O3   O  O     0  -0.397  -2.8362   3.0405  -0.3908
 L5H  H3   H  HNR6  0   0.438   1.3773   4.0744   0.1207
 L5H  H4   H  HNH1  0   0.439  -2.5569   0.3528  -1.4567
 L5H  H2   H  HCR6  0   0.306  -0.2424  -1.0571  -0.4631
 L5H  H7   H  HCR6  0   0.270  -6.8513  -3.4280  -0.1731
 L5H  H9   H  HCR6  0   0.269  -5.0314  -0.3007   2.1054
 L5H  H10  H  HCR5  0   0.291   1.9780  -2.5468   1.7969
 L5H  H1   H  HCR6  0   0.307   3.1150   2.4919   0.2100
 L5H  H5   H  HCR6  0   0.268  -3.1376  -1.7682  -1.4621
 L5H  H6   H  HCR6  0   0.270  -4.9713  -3.3544  -1.7788
 L5H  H8   H  HCR6  0   0.269  -6.8724  -1.8997   1.7722
 L5H  H11  H  HCR5  0   0.259   2.9518  -4.8265  -1.5607
 L5H  H12  H  HCR5  0   0.300   2.5203  -2.2313  -2.3590

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
 L5H  C12  C11  aromatic  1.387  0.020  1.387
 L5H  C12  C13  aromatic  1.388  0.020  1.388
 L5H  C11  C10  aromatic  1.394  0.020  1.394
 L5H  O1   C9   double    1.211  0.020  1.211
 L5H  C18  C19  aromatic  1.362  0.020  1.362
 L5H  C18  N5   aromatic  1.369  0.020  1.369
 L5H  C19  N4   aromatic  1.373  0.020  1.373
 L5H  C13  C14  aromatic  1.389  0.020  1.389
 L5H  C10  C9   single    1.485  0.020  1.485
 L5H  C10  C15  aromatic  1.394  0.020  1.394
 L5H  C9   N3   single    1.373  0.020  1.373
 L5H  N5   C17  aromatic  1.302  0.020  1.302
 L5H  F1   C16  single    1.338  0.020  1.338
 L5H  N4   C5   single    1.415  0.020  1.415
 L5H  N4   C17  aromatic  1.358  0.020  1.358
 L5H  C14  C15  aromatic  1.385  0.020  1.385
 L5H  C4   C5   aromatic  1.382  0.020  1.382
 L5H  C4   C3   aromatic  1.386  0.020  1.386
 L5H  N3   N2   single    1.362  0.020  1.362
 L5H  C5   C6   aromatic  1.395  0.020  1.395
 L5H  C3   N2   single    1.393  0.020  1.393
 L5H  C3   C2   aromatic  1.393  0.020  1.393
 L5H  N2   C8   single    1.372  0.020  1.372
 L5H  C6   C16  single    1.501  0.020  1.501
 L5H  C6   C1   aromatic  1.383  0.020  1.383
 L5H  C16  F3   single    1.334  0.020  1.334
 L5H  C16  F2   single    1.337  0.020  1.337
 L5H  C8   O3   double    1.203  0.020  1.203
 L5H  C8   C7   single    1.522  0.020  1.522
 L5H  C2   C1   aromatic  1.388  0.020  1.388
 L5H  C2   N1   single    1.380  0.020  1.380
 L5H  N1   C7   single    1.350  0.020  1.350
 L5H  C7   O2   double    1.208  0.020  1.208
 L5H  N1   H3   single    0.860  0.020  1.020
 L5H  N3   H4   single    0.890  0.020  1.040
 L5H  C4   H2   single    0.930  0.020  1.080
 L5H  C13  H7   single    0.930  0.020  1.080
 L5H  C15  H9   single    0.930  0.020  1.080
 L5H  C17  H10  single    0.930  0.020  1.080
 L5H  C1   H1   single    0.930  0.020  1.080
 L5H  C11  H5   single    0.930  0.020  1.080
 L5H  C12  H6   single    0.930  0.020  1.080
 L5H  C14  H8   single    0.930  0.020  1.080
 L5H  C18  H11  single    0.930  0.020  1.080
 L5H  C19  H12  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
 L5H  H3   N1   C2   118.17  3.000
 L5H  H3   N1   C7   116.77  3.000
 L5H  C2   N1   C7   125.06  3.000
 L5H  H4   N3   N2   115.62  3.000
 L5H  H4   N3   C9   121.71  3.000
 L5H  N2   N3   C9   118.16  3.000
 L5H  H2   C4   C3   120.70  3.000
 L5H  H2   C4   C5   119.10  3.000
 L5H  C3   C4   C5   120.20  3.000
 L5H  N4   C5   C6   121.42  3.000
 L5H  C6   C5   C4   120.50  3.000
 L5H  N4   C5   C4   118.08  3.000
 L5H  C16  C6   C1   120.03  3.000
 L5H  C1   C6   C5   119.17  3.000
 L5H  C16  C6   C5   120.80  3.000
 L5H  O2   C7   C8   119.45  3.000
 L5H  O2   C7   N1   124.29  3.000
 L5H  C8   C7   N1   116.26  3.000
 L5H  O3   C8   N2   122.95  3.000
 L5H  O3   C8   C7   120.37  3.000
 L5H  N2   C8   C7   116.68  3.000
 L5H  C9   C10  C11  122.52  3.000
 L5H  C9   C10  C15  117.81  3.000
 L5H  C11  C10  C15  119.66  3.000
 L5H  H7   C13  C14  120.03  3.000
 L5H  H7   C13  C12  119.96  3.000
 L5H  C14  C13  C12  120.01  3.000
 L5H  H9   C15  C14  119.86  3.000
 L5H  H9   C15  C10  120.02  3.000
 L5H  C14  C15  C10  120.12  3.000
 L5H  H10  C17  N5   126.55  3.000
 L5H  H10  C17  N4   121.87  3.000
 L5H  N5   C17  N4   111.57  3.000
 L5H  H1   C1   C2   118.39  3.000
 L5H  H1   C1   C6   121.03  3.000
 L5H  C2   C1   C6   120.58  3.000
 L5H  H5   C11  C12  118.89  3.000
 L5H  H5   C11  C10  121.05  3.000
 L5H  C12  C11  C10  120.03  3.000
 L5H  H6   C12  C11  119.66  3.000
 L5H  H6   C12  C13  120.25  3.000
 L5H  C11  C12  C13  120.09  3.000
 L5H  H8   C14  C15  119.79  3.000
 L5H  H8   C14  C13  120.14  3.000
 L5H  C15  C14  C13  120.08  3.000
 L5H  F3   C16  F2   106.97  3.000
 L5H  F2   C16  F1   107.04  3.000
 L5H  F3   C16  F1   106.97  3.000
 L5H  F2   C16  C6   111.88  3.000
 L5H  F3   C16  C6   111.96  3.000
 L5H  F1   C16  C6   111.70  3.000
 L5H  H11  C18  N5   121.97  3.000
 L5H  H11  C18  C19  127.62  3.000
 L5H  N5   C18  C19  110.41  3.000
 L5H  H12  C19  N4   122.21  3.000
 L5H  H12  C19  C18  132.56  3.000
 L5H  N4   C19  C18  105.23  3.000
 L5H  C3   C2   C1   119.97  3.000
 L5H  C1   C2   N1   120.55  3.000
 L5H  C3   C2   N1   119.47  3.000
 L5H  N2   C3   C2   118.47  3.000
 L5H  C2   C3   C4   119.59  3.000
 L5H  N2   C3   C4   121.94  3.000
 L5H  O1   C9   C10  123.53  3.000
 L5H  C10  C9   N3   115.07  3.000
 L5H  O1   C9   N3   121.39  3.000
 L5H  C3   N2   C8   124.03  3.000
 L5H  C8   N2   N3   117.40  3.000
 L5H  C3   N2   N3   118.48  3.000
 L5H  C19  N4   C17  107.07  3.000
 L5H  C17  N4   C5   126.23  3.000
 L5H  C19  N4   C5   126.63  3.000
 L5H  C18  N5   C17  105.71  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
 L5H  CONST_03  C1   C6   C5   C4     0.00   0.0  0
 L5H  CONST_04  C1   C2   C3   C4     0.00   0.0  0
 L5H  CONST_05  C18  C19  N4   C5   180.00   0.0  0
 L5H  CONST_06  N5   C17  N4   C5   180.00   0.0  0
 L5H  CONST_07  C2   C3   C4   C5     0.00   0.0  0
 L5H  CONST_08  C2   C1   C6   C5     0.00   0.0  0
 L5H  CONST_11  C3   C4   C5   C6     0.00   0.0  0
 L5H  CONST_12  C3   C2   C1   C6     0.00   0.0  0
 L5H  CONST_13  C13  C12  C11  C10    0.00   0.0  0
 L5H  CONST_14  C13  C14  C15  C10    0.00   0.0  0
 L5H  CONST_15  C12  C11  C10  C15    0.00   0.0  0
 L5H  CONST_16  C12  C13  C14  C15    0.00   0.0  0
 L5H  CONST_17  C19  C18  N5   C17    0.00   0.0  0
 L5H  CONST_18  C18  C19  N4   C17    0.00   0.0  0
 L5H  CONST_19  N4   C5   C6   C1   180.00   0.0  0
 L5H  CONST_20  C14  C13  C12  C11    0.00   0.0  0
 L5H  CONST_21  C14  C15  C10  C11    0.00   0.0  0
 L5H  CONST_22  N4   C17  N5   C18    0.00   0.0  0
 L5H  CONST_23  N5   C17  N4   C19    0.00   0.0  0
 L5H  CONST_24  N4   C5   C4   C3   180.00   0.0  0
 L5H  CONST_25  N5   C18  C19  N4     0.00   0.0  0
 L5H  CONST_26  C3   N2   C8   C7     0.00   0.0  0
 L5H  CONST_27  C2   N1   C7   C8     0.00   0.0  0
 L5H  CONST_28  C16  C6   C5   C4   180.00   0.0  0
 L5H  CONST_29  C9   C10  C11  C12  180.00   0.0  0
 L5H  CONST_30  C9   C10  C15  C14  180.00   0.0  0
 L5H  CONST_31  N4   C5   C6   C16    0.00   0.0  0
 L5H  CONST_32  C2   C1   C6   C16  180.00   0.0  0
 L5H  CONST_33  C7   C8   N2   N3   180.00   0.0  0
 L5H  CONST_34  O2   C7   N1   C2   180.00   0.0  0
 L5H  CONST_35  O3   C8   N2   C3   180.00   0.0  0
 L5H  CONST_36  H1   C1   C2   N1     0.00   0.0  0
 L5H  CONST_37  H12  C19  N4   C5     0.00   0.0  0
 L5H  CONST_38  H10  C17  N4   C5     0.00   0.0  0
 L5H  CONST_39  H2   C4   C5   C6   180.00   0.0  0
 L5H  CONST_40  H6   C12  C11  C10  180.00   0.0  0
 L5H  CONST_41  H8   C14  C15  C10  180.00   0.0  0
 L5H  CONST_42  H5   C11  C12  C13  180.00   0.0  0
 L5H  CONST_43  H9   C15  C14  C13  180.00   0.0  0
 L5H  CONST_44  H7   C13  C14  C15  180.00   0.0  0
 L5H  CONST_45  H11  C18  N5   C17  180.00   0.0  0
 L5H  CONST_46  H3   N1   C7   C8   180.00   0.0  0
 L5H  CONST_47  N2   N3   C9   C10  180.00   0.0  0
 L5H  CONST_48  O3   C8   N2   N3     0.00   0.0  0
 L5H  CONST_49  O1   C9   N3   N2     0.00   0.0  0
 L5H  Var_01    C11  C10  C9   N3    25.00  30.0  2
 L5H  Var_02    F1   C16  C6   C5   -59.20  30.0  2
 L5H  Var_03    C9   N3   N2   C8   -78.24  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
 L5H  plan-1  C5   0.020
 L5H  plan-1  C17  0.020
 L5H  plan-1  C18  0.020
 L5H  plan-1  C19  0.020
 L5H  plan-1  N4   0.020
 L5H  plan-1  N5   0.020
 L5H  plan-1  H10  0.020
 L5H  plan-1  H11  0.020
 L5H  plan-1  H12  0.020
 L5H  plan-2  C10  0.020
 L5H  plan-2  C13  0.020
 L5H  plan-2  C15  0.020
 L5H  plan-2  C11  0.020
 L5H  plan-2  C12  0.020
 L5H  plan-2  C14  0.020
 L5H  plan-2  C9   0.020
 L5H  plan-2  H7   0.020
 L5H  plan-2  H9   0.020
 L5H  plan-2  H5   0.020
 L5H  plan-2  H6   0.020
 L5H  plan-2  H8   0.020
 L5H  plan-3  N1   0.020
 L5H  plan-3  N3   0.020
 L5H  plan-3  C4   0.020
 L5H  plan-3  C5   0.020
 L5H  plan-3  C6   0.020
 L5H  plan-3  C7   0.020
 L5H  plan-3  C8   0.020
 L5H  plan-3  C1   0.020
 L5H  plan-3  C16  0.020
 L5H  plan-3  C2   0.020
 L5H  plan-3  C3   0.020
 L5H  plan-3  N2   0.020
 L5H  plan-3  N4   0.020
 L5H  plan-3  O2   0.020
 L5H  plan-3  O3   0.020
 L5H  plan-3  H3   0.020
 L5H  plan-3  H2   0.020
 L5H  plan-3  H1   0.020
 L5H  plan-4  N3   0.020
 L5H  plan-4  C10  0.020
 L5H  plan-4  C9   0.020
 L5H  plan-4  N2   0.020
 L5H  plan-4  O1   0.020
 L5H  plan-4  H4   0.020

