# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 19:05:58 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 6-chloro-3,4-dimethyl-1-(3-methylpyridin-4-yl)-8-(trifluoromethyl)imidazo[1,5-a]quinoxaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cnccc1c2nc(C)c3n2c4cc(cc(Cl)c4nc3C)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
 548  548  6-chloro-3,4-dimethyl-1-(3-methylpyridin-4-yl)-8-(trifluoromethyl)imidazo[1,5-a]quinoxaline  ligand  41  27  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_548
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
 548  C1    C   CH3   0  -0.750   1.4957   1.6845   2.2146
 548  F1    F   F     0  -0.310   2.2938  -3.4920   1.0440
 548  N1    N   N     0  -0.394   4.3181   2.1470  -0.2248
 548  CL1   CL  CL    0  -0.082  -3.0849  -3.1866   0.7155
 548  C2    C   CR6   0   0.003   2.2149   1.9340   0.9256
 548  F2    F   F     0  -0.298   3.0025  -2.0090  -0.3463
 548  N2    N   N     0  -0.426  -0.5659   3.4079  -0.4816
 548  C3    C   CR16  0  -0.089   3.6059   1.9242   0.8713
 548  F3    F   F     0  -0.309   1.9707  -3.7574  -1.0623
 548  N3    N   N     0  -0.632  -0.7978   1.2476  -0.1493
 548  C4    C   CR16  0  -0.060   3.6643   2.4081  -1.3484
 548  N4    N   N     0  -0.428  -3.0596  -0.3120   0.2624
 548  C5    C   CR16  0  -0.326   2.2809   2.4462  -1.4222
 548  C6    C   CR6   0   0.029   1.5436   2.1913  -0.2736
 548  C7    C   CR5   0   0.428   0.0747   2.2706  -0.3195
 548  C8    C   CR5   0   0.089  -1.8900   3.1546  -0.3991
 548  C9    C   CR56  0   0.296  -2.0738   1.8025  -0.1835
 548  C10   C   CR66  0   0.418  -0.6330  -0.1313  -0.0210
 548  C11   C   CR16  0  -0.336   0.5981  -0.7654  -0.1480
 548  C12   C   CR6   0  -0.209   0.6783  -2.1308   0.0289
 548  C13   C   CR16  0  -0.242  -0.4574  -2.8854   0.3142
 548  C14   C   CR6   0  -0.140  -1.6756  -2.2526   0.3969
 548  C15   C   CR66  0   0.258  -1.8082  -0.8644   0.2195
 548  C16   C   CR6   0   0.190  -3.1977   0.9550   0.0434
 548  C17   C   CH3   0  -0.758  -4.5733   1.5310   0.0384
 548  C18   C   CT    0   1.066   1.9921  -2.8413  -0.0866
 548  C19   C   CH3   0  -0.763  -2.8979   4.2437  -0.5181
 548  H1    H   HCH3  0   0.259   0.7291   2.4383   2.3973
 548  H1A   H   HCH3  0   0.254   1.0020   0.7101   2.2219
 548  H1B   H   HCH3  0   0.267   2.1886   1.7007   3.0542
 548  H3    H   HCR6  0   0.265   4.1676   1.7282   1.7794
 548  H4    H   HCR6  0   0.271   4.2625   2.5956  -2.2325
 548  H5    H   HCR6  0   0.279   1.7894   2.6629  -2.3609
 548  H11   H   HCR6  0   0.297   1.4824  -0.2007  -0.3947
 548  H13   H   HCR6  0   0.302  -0.3985  -3.9559   0.4576
 548  H17   H   HCH3  0   0.274  -5.2997   0.7528   0.2586
 548  H17A  H   HCH3  0   0.263  -4.6752   2.3248   0.7790
 548  H17B  H   HCH3  0   0.266  -4.8107   1.9621  -0.9352
 548  H19   H   HCH3  0   0.257  -3.5562   4.0975  -1.3748
 548  H19A  H   HCH3  0   0.255  -3.5279   4.3119   0.3691
 548  H19B  H   HCH3  0   0.266  -2.3915   5.1984  -0.6435

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
 548  C1   C2    single    1.497  0.020  1.497
 548  C1   H1    single    0.970  0.020  1.090
 548  C1   H1A   single    0.970  0.020  1.090
 548  C1   H1B   single    0.970  0.020  1.090
 548  F1   C18   single    1.339  0.020  1.339
 548  N1   C3    aromatic  1.326  0.020  1.326
 548  N1   C4    aromatic  1.326  0.020  1.326
 548  C14  CL1   single    1.720  0.020  1.720
 548  C2   C3    aromatic  1.392  0.020  1.392
 548  C2   C6    aromatic  1.398  0.020  1.398
 548  F2   C18   single    1.335  0.020  1.335
 548  C7   N2    aromatic  1.315  0.020  1.315
 548  N2   C8    aromatic  1.351  0.020  1.351
 548  C3   H3    single    0.930  0.020  1.080
 548  F3   C18   single    1.339  0.020  1.339
 548  C10  N3    aromatic  1.395  0.020  1.395
 548  N3   C7    aromatic  1.355  0.020  1.355
 548  N3   C9    aromatic  1.392  0.020  1.392
 548  C4   C5    aromatic  1.386  0.020  1.386
 548  C4   H4    single    0.930  0.020  1.080
 548  C15  N4    aromatic  1.369  0.020  1.369
 548  N4   C16   aromatic  1.293  0.020  1.293
 548  C5   C6    aromatic  1.389  0.020  1.389
 548  C5   H5    single    0.930  0.020  1.080
 548  C6   C7    single    1.472  0.020  1.472
 548  C9   C8    aromatic  1.381  0.020  1.381
 548  C8   C19   single    1.489  0.020  1.489
 548  C9   C16   aromatic  1.426  0.020  1.426
 548  C11  C10   aromatic  1.391  0.020  1.391
 548  C10  C15   aromatic  1.406  0.020  1.406
 548  C12  C11   aromatic  1.379  0.020  1.379
 548  C11  H11   single    0.930  0.020  1.080
 548  C18  C12   single    1.498  0.020  1.498
 548  C12  C13   aromatic  1.393  0.020  1.393
 548  C13  C14   aromatic  1.375  0.020  1.375
 548  C13  H13   single    0.930  0.020  1.080
 548  C14  C15   aromatic  1.406  0.020  1.406
 548  C16  C17   single    1.491  0.020  1.491
 548  C17  H17   single    0.970  0.020  1.090
 548  C17  H17A  single    0.970  0.020  1.090
 548  C17  H17B  single    0.970  0.020  1.090
 548  C19  H19   single    0.970  0.020  1.090
 548  C19  H19A  single    0.970  0.020  1.090
 548  C19  H19B  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
 548  H1B   C1   H1A   107.21  3.000
 548  H1B   C1   H1    107.94  3.000
 548  H1A   C1   H1    107.32  3.000
 548  H1B   C1   C2    110.84  3.000
 548  H1A   C1   C2    111.81  3.000
 548  H1    C1   C2    111.51  3.000
 548  C4    N1   C3    117.95  3.000
 548  C6    C2   C3    116.59  3.000
 548  C6    C2   C1    122.58  3.000
 548  C3    C2   C1    120.82  3.000
 548  C8    N2   C7    107.92  3.000
 548  H3    C3   C2    119.05  3.000
 548  H3    C3   N1    116.36  3.000
 548  C2    C3   N1    124.59  3.000
 548  C10   N3   C9    120.31  3.000
 548  C9    N3   C7    106.63  3.000
 548  C10   N3   C7    132.99  3.000
 548  H4    C4   C5    120.18  3.000
 548  H4    C4   N1    116.95  3.000
 548  C5    C4   N1    122.87  3.000
 548  C16   N4   C15   119.20  3.000
 548  H5    C5   C6    120.89  3.000
 548  H5    C5   C4    120.36  3.000
 548  C6    C5   C4    118.75  3.000
 548  C7    C6   C5    119.62  3.000
 548  C7    C6   C2    121.06  3.000
 548  C5    C6   C2    119.23  3.000
 548  C6    C7   N3    126.72  3.000
 548  C6    C7   N2    122.44  3.000
 548  N3    C7   N2    110.77  3.000
 548  C19   C8   C9    129.68  3.000
 548  C19   C8   N2    121.44  3.000
 548  C9    C8   N2    108.88  3.000
 548  C16   C9   C8    135.35  3.000
 548  C16   C9   N3    118.80  3.000
 548  C8    C9   N3    105.79  3.000
 548  C15   C10  C11   121.19  3.000
 548  C15   C10  N3    115.63  3.000
 548  C11   C10  N3    123.16  3.000
 548  H11   C11  C12   120.03  3.000
 548  H11   C11  C10   120.55  3.000
 548  C12   C11  C10   119.42  3.000
 548  C18   C12  C13   118.28  3.000
 548  C13   C12  C11   121.01  3.000
 548  C18   C12  C11   120.71  3.000
 548  H13   C13  C14   119.71  3.000
 548  H13   C13  C12   121.26  3.000
 548  C14   C13  C12   119.03  3.000
 548  C15   C14  C13   122.03  3.000
 548  C15   C14  CL1   118.83  3.000
 548  C13   C14  CL1   119.14  3.000
 548  C14   C15  C10   117.24  3.000
 548  C14   C15  N4    118.74  3.000
 548  C10   C15  N4    124.00  3.000
 548  C17   C16  C9    119.80  3.000
 548  C17   C16  N4    118.52  3.000
 548  C9    C16  N4    121.68  3.000
 548  H17B  C17  H17A  107.35  3.000
 548  H17B  C17  H17   108.55  3.000
 548  H17A  C17  H17   108.73  3.000
 548  H17B  C17  C16   110.88  3.000
 548  H17A  C17  C16   111.41  3.000
 548  H17   C17  C16   109.83  3.000
 548  C12   C18  F3    111.52  3.000
 548  C12   C18  F2    112.53  3.000
 548  F3    C18  F2    107.28  3.000
 548  C12   C18  F1    111.29  3.000
 548  F3    C18  F1    106.65  3.000
 548  F2    C18  F1    107.27  3.000
 548  H19B  C19  H19A  107.93  3.000
 548  H19B  C19  H19   107.95  3.000
 548  H19A  C19  H19   107.39  3.000
 548  H19B  C19  C8    109.64  3.000
 548  H19A  C19  C8    111.83  3.000
 548  H19   C19  C8    111.93  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
 548  CONST_01  C6   C2   C3   N1     0.00   0.0  0
 548  CONST_02  C6   C5   C4   N1     0.00   0.0  0
 548  CONST_03  C4   N1   C3   C2     0.00   0.0  0
 548  CONST_04  C4   C5   C6   C2     0.00   0.0  0
 548  CONST_07  C10  N3   C7   N2   180.00   0.0  0
 548  CONST_08  C9   N3   C7   N2     0.00   0.0  0
 548  CONST_10  N3   C9   C8   N2     0.00   0.0  0
 548  CONST_11  C16  C9   C8   N2   180.00   0.0  0
 548  CONST_12  C5   C4   N1   C3     0.00   0.0  0
 548  CONST_13  C5   C6   C2   C3     0.00   0.0  0
 548  CONST_14  C7   C6   C2   C3   180.00   0.0  0
 548  CONST_15  C12  C11  C10  N3   180.00   0.0  0
 548  CONST_16  N4   C15  C10  N3     0.00   0.0  0
 548  CONST_17  C14  C15  C10  N3   180.00   0.0  0
 548  CONST_18  C8   N2   C7   N3     0.00   0.0  0
 548  CONST_20  N4   C16  C9   N3     0.00   0.0  0
 548  CONST_21  C7   C6   C5   C4   180.00   0.0  0
 548  CONST_22  C11  C10  C15  N4   180.00   0.0  0
 548  CONST_23  C13  C14  C15  N4   180.00   0.0  0
 548  CONST_24  C8   C9   C16  N4   180.00   0.0  0
 548  CONST_25  C8   N2   C7   C6   180.00   0.0  0
 548  CONST_26  C10  N3   C7   C6     0.00   0.0  0
 548  CONST_27  C9   N3   C7   C6   180.00   0.0  0
 548  CONST_28  C9   C8   N2   C7     0.00   0.0  0
 548  CONST_29  C11  C10  N3   C7     0.00   0.0  0
 548  CONST_30  C15  C10  N3   C7   180.00   0.0  0
 548  CONST_31  C8   C9   N3   C7     0.00   0.0  0
 548  CONST_32  C16  C9   N3   C7   180.00   0.0  0
 548  CONST_33  C10  N3   C9   C8   180.00   0.0  0
 548  CONST_34  C11  C10  N3   C9   180.00   0.0  0
 548  CONST_35  C15  C10  N3   C9     0.00   0.0  0
 548  CONST_36  C15  N4   C16  C9     0.00   0.0  0
 548  CONST_37  C16  C9   N3   C10    0.00   0.0  0
 548  CONST_38  C13  C12  C11  C10    0.00   0.0  0
 548  CONST_39  C16  N4   C15  C10    0.00   0.0  0
 548  CONST_40  C13  C14  C15  C10    0.00   0.0  0
 548  CONST_41  C14  C15  C10  C11    0.00   0.0  0
 548  CONST_42  C14  C13  C12  C11    0.00   0.0  0
 548  CONST_43  C15  C10  C11  C12    0.00   0.0  0
 548  CONST_44  C15  C14  C13  C12    0.00   0.0  0
 548  CONST_45  C16  N4   C15  C14  180.00   0.0  0
 548  CONST_46  N1   C3   C2   C1   180.00   0.0  0
 548  CONST_47  C5   C6   C2   C1   180.00   0.0  0
 548  CONST_48  C7   C6   C2   C1     0.00   0.0  0
 548  CONST_49  C12  C13  C14  CL1  180.00   0.0  0
 548  CONST_50  N4   C15  C14  CL1    0.00   0.0  0
 548  CONST_51  C10  C15  C14  CL1  180.00   0.0  0
 548  CONST_52  C19  C8   C9   N3   180.00   0.0  0
 548  CONST_53  C17  C16  C9   N3   180.00   0.0  0
 548  CONST_54  C19  C8   N2   C7   180.00   0.0  0
 548  CONST_55  C17  C16  C9   C8     0.00   0.0  0
 548  CONST_56  C18  C12  C11  C10  180.00   0.0  0
 548  CONST_57  C18  C12  C13  C14  180.00   0.0  0
 548  CONST_58  C17  C16  N4   C15  180.00   0.0  0
 548  CONST_59  C19  C8   C9   C16    0.00   0.0  0
 548  CONST_60  H5   C5   C4   N1   180.00   0.0  0
 548  CONST_61  H4   C4   N1   C3   180.00   0.0  0
 548  CONST_62  H11  C11  C10  N3     0.00   0.0  0
 548  CONST_63  H3   C3   N1   C4   180.00   0.0  0
 548  CONST_64  H13  C13  C12  C11  180.00   0.0  0
 548  Var_01    C11  C12  C18  F1   121.39  30.0  2
 548  Var_02    H19  C19  C8   N2   118.23  30.0  2
 548  Var_03    H1   C1   C2   C3   131.16  30.0  2
 548  Var_04    H17  C17  C16  N4     1.50  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
 548  plan-1  C1   0.020
 548  plan-1  N1   0.020
 548  plan-1  C2   0.020
 548  plan-1  C3   0.020
 548  plan-1  C4   0.020
 548  plan-1  C5   0.020
 548  plan-1  C6   0.020
 548  plan-1  C7   0.020
 548  plan-1  H3   0.020
 548  plan-1  H4   0.020
 548  plan-1  H5   0.020
 548  plan-2  CL1  0.020
 548  plan-2  N2   0.020
 548  plan-2  N3   0.020
 548  plan-2  N4   0.020
 548  plan-2  C6   0.020
 548  plan-2  C7   0.020
 548  plan-2  C8   0.020
 548  plan-2  C9   0.020
 548  plan-2  C10  0.020
 548  plan-2  C11  0.020
 548  plan-2  C12  0.020
 548  plan-2  C13  0.020
 548  plan-2  C14  0.020
 548  plan-2  C15  0.020
 548  plan-2  C16  0.020
 548  plan-2  C17  0.020
 548  plan-2  C18  0.020
 548  plan-2  C19  0.020
 548  plan-2  H11  0.020
 548  plan-2  H13  0.020

