# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:53:00 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 8-fluoro-6-methoxy-3,4-dimethyl-1-(3-methylpyridin-4-yl)imidazo[1,5-a]quinoxaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(F)cc2n3c(nc(C)c3c(C)nc12)c4ccncc4C
#
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
 540  540  8-fluoro-6-methoxy-3,4-dimethyl-1-(3-methylpyridin-4-yl)imidazo[1,5-a]quinoxaline  ligand  42  25  .  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_540
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
 540  C1    C  CH3   0  -0.749  -2.0853  -0.3350   2.2250
 540  F1    F  F     0  -0.310   0.5133  -3.8180  -0.2954
 540  N1    N  N     0  -0.395  -4.6283  -1.7547  -0.1520
 540  O1    O  O2    0  -0.443   4.1527  -0.8807   0.3944
 540  C2    C  CR6   0   0.005  -2.8430  -0.5822   0.9578
 540  N2    N  N     0  -0.428  -1.7607   2.3802  -0.4267
 540  C3    C  CR16  0  -0.093  -3.8996  -1.4875   0.9236
 540  N3    N  N     0  -0.625  -0.1509   0.9076  -0.1578
 540  C4    C  CR16  0  -0.062  -4.3385  -1.1089  -1.2733
 540  N4    N  N     0  -0.420   2.5834   1.2213   0.1825
 540  C5    C  CR16  0  -0.330  -3.3112  -0.1832  -1.3648
 540  C6    C  CR6   0   0.041  -2.5416   0.0762  -0.2386
 540  C7    C  CR5   0   0.419  -1.4868   1.1010  -0.2968
 540  C8    C  CR5   0   0.078  -0.5968   3.0641  -0.3516
 540  C9    C  CR56  0   0.286   0.4380   2.1682  -0.1728
 540  C10   C  CR66  0   0.421   0.6377  -0.2412  -0.0984
 540  C11   C  CR16  0  -0.503   0.1155  -1.5255  -0.2500
 540  C12   C  CR6   0   0.579   0.9928  -2.5761  -0.1576
 540  C13   C  CR16  0  -0.571   2.3520  -2.4305   0.0682
 540  C14   C  CR6   0   0.349   2.8637  -1.1495   0.1925
 540  C15   C  CR66  0   0.056   2.0079  -0.0229   0.0991
 540  C16   C  CR6   0   0.172   1.8488   2.2703   0.0307
 540  C17   C  CH3   0  -0.755   2.4911   3.6170   0.0901
 540  C18   C  CH3   0  -0.444   5.0697  -1.9589   0.4577
 540  C19   C  CH3   0  -0.761  -0.5665   4.5506  -0.4445
 540  H1    H  HCH3  0   0.257  -2.0001   0.7311   2.4384
 540  H1A   H  HCH3  0   0.264  -2.5804  -0.8077   3.0715
 540  H1B   H  HCH3  0   0.255  -1.0724  -0.7391   2.1745
 540  H3    H  HCR6  0   0.263  -4.1677  -2.0203   1.8307
 540  H4    H  HCR6  0   0.269  -4.9469  -1.3346  -2.1415
 540  H5    H  HCR6  0   0.275  -3.1104   0.3197  -2.3011
 540  H11   H  HCR6  0   0.298  -0.9271  -1.7140  -0.4492
 540  H13   H  HCR6  0   0.310   2.9745  -3.3118   0.1312
 540  H17   H  HCH3  0   0.268   3.5559   3.5100   0.2825
 540  H17A  H  HCH3  0   0.258   2.3616   4.1603  -0.8469
 540  H17B  H  HCH3  0   0.257   2.0536   4.2289   0.8799
 540  H18   H  HCH3  0   0.268   6.0501  -1.5162   0.6102
 540  H18A  H  HCH3  0   0.236   4.8507  -2.6305   1.2913
 540  H18B  H  HCH3  0   0.237   5.0811  -2.5342  -0.4709
 540  H19   H  HCH3  0   0.253  -0.2495   5.0121   0.4917
 540  H19A  H  HCH3  0   0.252   0.1092   4.8995  -1.2251
 540  H19B  H  HCH3  0   0.263  -1.5634   4.9204  -0.6763

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
 540  C1   C2    single    1.497  0.020  1.497
 540  C1   H1    single    0.970  0.020  1.090
 540  C1   H1A   single    0.970  0.020  1.090
 540  C1   H1B   single    0.970  0.020  1.090
 540  F1   C12   single    1.338  0.020  1.338
 540  C3   N1    aromatic  1.326  0.020  1.326
 540  N1   C4    aromatic  1.326  0.020  1.326
 540  C18  O1    single    1.417  0.020  1.417
 540  O1   C14   single    1.332  0.020  1.332
 540  C3   C2    aromatic  1.392  0.020  1.392
 540  C2   C6    aromatic  1.398  0.020  1.398
 540  C7   N2    aromatic  1.315  0.020  1.315
 540  N2   C8    aromatic  1.352  0.020  1.352
 540  C3   H3    single    0.930  0.020  1.080
 540  C10  N3    aromatic  1.395  0.020  1.395
 540  N3   C7    aromatic  1.357  0.020  1.357
 540  N3   C9    aromatic  1.391  0.020  1.391
 540  C4   C5    aromatic  1.386  0.020  1.386
 540  C4   H4    single    0.930  0.020  1.080
 540  C15  N4    aromatic  1.373  0.020  1.373
 540  N4   C16   aromatic  1.290  0.020  1.290
 540  C6   C5    aromatic  1.389  0.020  1.389
 540  C5   H5    single    0.930  0.020  1.080
 540  C6   C7    single    1.472  0.020  1.472
 540  C9   C8    aromatic  1.380  0.020  1.380
 540  C8   C19   single    1.490  0.020  1.490
 540  C16  C9    aromatic  1.429  0.020  1.429
 540  C11  C10   aromatic  1.395  0.020  1.395
 540  C15  C10   aromatic  1.402  0.020  1.402
 540  C12  C11   aromatic  1.372  0.020  1.372
 540  C11  H11   single    0.930  0.020  1.080
 540  C13  C12   aromatic  1.385  0.020  1.385
 540  C13  C14   aromatic  1.385  0.020  1.385
 540  C13  H13   single    0.930  0.020  1.080
 540  C14  C15   aromatic  1.418  0.020  1.418
 540  C16  C17   single    1.493  0.020  1.493
 540  C17  H17   single    0.970  0.020  1.090
 540  C17  H17A  single    0.970  0.020  1.090
 540  C17  H17B  single    0.970  0.020  1.090
 540  C18  H18   single    0.970  0.020  1.090
 540  C18  H18A  single    0.970  0.020  1.090
 540  C18  H18B  single    0.970  0.020  1.090
 540  C19  H19   single    0.970  0.020  1.090
 540  C19  H19A  single    0.970  0.020  1.090
 540  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
 540  H1B   C1   H1A   107.29  3.000
 540  H1B   C1   H1    107.37  3.000
 540  H1A   C1   H1    107.93  3.000
 540  H1B   C1   C2    111.67  3.000
 540  H1A   C1   C2    110.87  3.000
 540  H1    C1   C2    111.50  3.000
 540  C4    N1   C3    117.88  3.000
 540  C18   O1   C14   118.65  3.000
 540  C6    C2   C3    116.67  3.000
 540  C6    C2   C1    122.50  3.000
 540  C3    C2   C1    120.83  3.000
 540  C8    N2   C7    107.90  3.000
 540  H3    C3   C2    119.09  3.000
 540  H3    C3   N1    116.30  3.000
 540  C2    C3   N1    124.61  3.000
 540  C10   N3   C9    120.49  3.000
 540  C9    N3   C7    106.65  3.000
 540  C10   N3   C7    132.72  3.000
 540  H4    C4   C5    120.15  3.000
 540  H4    C4   N1    116.95  3.000
 540  C5    C4   N1    122.90  3.000
 540  C16   N4   C15   119.41  3.000
 540  H5    C5   C6    120.82  3.000
 540  H5    C5   C4    120.35  3.000
 540  C6    C5   C4    118.82  3.000
 540  C7    C6   C5    119.68  3.000
 540  C7    C6   C2    121.07  3.000
 540  C5    C6   C2    119.11  3.000
 540  C6    C7   N3    127.03  3.000
 540  C6    C7   N2    122.15  3.000
 540  N3    C7   N2    110.73  3.000
 540  C19   C8   C9    129.82  3.000
 540  C19   C8   N2    121.25  3.000
 540  C9    C8   N2    108.92  3.000
 540  C16   C9   C8    135.42  3.000
 540  C16   C9   N3    118.75  3.000
 540  C8    C9   N3    105.79  3.000
 540  C15   C10  C11   121.66  3.000
 540  C15   C10  N3    115.50  3.000
 540  C11   C10  N3    122.83  3.000
 540  H11   C11  C12   119.80  3.000
 540  H11   C11  C10   122.90  3.000
 540  C12   C11  C10   117.29  3.000
 540  C13   C12  C11   123.91  3.000
 540  C13   C12  F1    117.76  3.000
 540  C11   C12  F1    118.34  3.000
 540  H13   C13  C14   122.42  3.000
 540  H13   C13  C12   119.26  3.000
 540  C14   C13  C12   118.31  3.000
 540  C15   C14  C13   120.40  3.000
 540  C15   C14  O1    115.70  3.000
 540  C13   C14  O1    123.90  3.000
 540  C14   C15  C10   118.40  3.000
 540  C14   C15  N4    117.58  3.000
 540  C10   C15  N4    124.01  3.000
 540  C17   C16  C9    119.65  3.000
 540  C17   C16  N4    118.94  3.000
 540  C9    C16  N4    121.40  3.000
 540  H17B  C17  H17A  107.16  3.000
 540  H17B  C17  H17   108.66  3.000
 540  H17A  C17  H17   108.50  3.000
 540  H17B  C17  C16   111.24  3.000
 540  H17A  C17  C16   111.34  3.000
 540  H17   C17  C16   109.84  3.000
 540  H18B  C18  H18A  109.08  3.000
 540  H18B  C18  H18   108.93  3.000
 540  H18A  C18  H18   108.92  3.000
 540  H18B  C18  O1    111.69  3.000
 540  H18A  C18  O1    111.85  3.000
 540  H18   C18  O1    106.27  3.000
 540  H19B  C19  H19A  107.85  3.000
 540  H19B  C19  H19   107.77  3.000
 540  H19A  C19  H19   107.41  3.000
 540  H19B  C19  C8    109.50  3.000
 540  H19A  C19  C8    112.13  3.000
 540  H19   C19  C8    112.00  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
 540  CONST_01  C6   C2   C3   N1      0.00   0.0  0
 540  CONST_02  C6   C5   C4   N1      0.00   0.0  0
 540  CONST_03  C4   N1   C3   C2      0.00   0.0  0
 540  CONST_04  C4   C5   C6   C2      0.00   0.0  0
 540  CONST_07  C10  N3   C7   N2    180.00   0.0  0
 540  CONST_08  C9   N3   C7   N2      0.00   0.0  0
 540  CONST_10  N3   C9   C8   N2      0.00   0.0  0
 540  CONST_11  C16  C9   C8   N2    180.00   0.0  0
 540  CONST_12  C5   C4   N1   C3      0.00   0.0  0
 540  CONST_13  C5   C6   C2   C3      0.00   0.0  0
 540  CONST_14  C7   C6   C2   C3    180.00   0.0  0
 540  CONST_15  C12  C11  C10  N3    180.00   0.0  0
 540  CONST_16  N4   C15  C10  N3      0.00   0.0  0
 540  CONST_17  C14  C15  C10  N3    180.00   0.0  0
 540  CONST_18  C8   N2   C7   N3      0.00   0.0  0
 540  CONST_20  N4   C16  C9   N3      0.00   0.0  0
 540  CONST_21  C7   C6   C5   C4    180.00   0.0  0
 540  CONST_22  C11  C10  C15  N4    180.00   0.0  0
 540  CONST_23  C13  C14  C15  N4    180.00   0.0  0
 540  CONST_24  C8   C9   C16  N4    180.00   0.0  0
 540  CONST_25  C8   N2   C7   C6    180.00   0.0  0
 540  CONST_26  C10  N3   C7   C6      0.00   0.0  0
 540  CONST_27  C9   N3   C7   C6    180.00   0.0  0
 540  CONST_28  C9   C8   N2   C7      0.00   0.0  0
 540  CONST_29  C11  C10  N3   C7      0.00   0.0  0
 540  CONST_30  C15  C10  N3   C7    180.00   0.0  0
 540  CONST_31  C8   C9   N3   C7      0.00   0.0  0
 540  CONST_32  C16  C9   N3   C7    180.00   0.0  0
 540  CONST_33  C10  N3   C9   C8    180.00   0.0  0
 540  CONST_34  C11  C10  N3   C9    180.00   0.0  0
 540  CONST_35  C15  C10  N3   C9      0.00   0.0  0
 540  CONST_36  C15  N4   C16  C9      0.00   0.0  0
 540  CONST_37  C16  C9   N3   C10     0.00   0.0  0
 540  CONST_38  C13  C12  C11  C10     0.00   0.0  0
 540  CONST_39  C16  N4   C15  C10     0.00   0.0  0
 540  CONST_40  C13  C14  C15  C10     0.00   0.0  0
 540  CONST_41  C14  C15  C10  C11     0.00   0.0  0
 540  CONST_42  C14  C13  C12  C11     0.00   0.0  0
 540  CONST_43  C15  C10  C11  C12     0.00   0.0  0
 540  CONST_44  C15  C14  C13  C12     0.00   0.0  0
 540  CONST_45  C16  N4   C15  C14   180.00   0.0  0
 540  CONST_46  N1   C3   C2   C1    180.00   0.0  0
 540  CONST_47  C5   C6   C2   C1    180.00   0.0  0
 540  CONST_48  C7   C6   C2   C1      0.00   0.0  0
 540  CONST_49  C10  C11  C12  F1    180.00   0.0  0
 540  CONST_50  C14  C13  C12  F1    180.00   0.0  0
 540  CONST_51  C12  C13  C14  O1    180.00   0.0  0
 540  CONST_52  N4   C15  C14  O1      0.00   0.0  0
 540  CONST_53  C10  C15  C14  O1    180.00   0.0  0
 540  CONST_54  C19  C8   C9   N3    180.00   0.0  0
 540  CONST_55  C17  C16  C9   N3    180.00   0.0  0
 540  CONST_56  C19  C8   N2   C7    180.00   0.0  0
 540  CONST_57  C17  C16  C9   C8      0.00   0.0  0
 540  CONST_58  C17  C16  N4   C15   180.00   0.0  0
 540  CONST_59  C19  C8   C9   C16     0.00   0.0  0
 540  CONST_60  H5   C5   C4   N1    180.00   0.0  0
 540  CONST_61  H4   C4   N1   C3    180.00   0.0  0
 540  CONST_62  H11  C11  C10  N3      0.00   0.0  0
 540  CONST_63  H3   C3   N1   C4    180.00   0.0  0
 540  CONST_64  H13  C13  C12  C11   180.00   0.0  0
 540  Var_01    H19  C19  C8   N2    113.61  30.0  2
 540  Var_02    H1   C1   C2   C3   -129.87  30.0  2
 540  Var_03    H17  C17  C16  N4     -1.00  30.0  2
 540  Var_04    H18  C18  O1   C14   179.12  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
 540  plan-1  C1   0.020
 540  plan-1  N1   0.020
 540  plan-1  C2   0.020
 540  plan-1  C3   0.020
 540  plan-1  C4   0.020
 540  plan-1  C5   0.020
 540  plan-1  C6   0.020
 540  plan-1  C7   0.020
 540  plan-1  H3   0.020
 540  plan-1  H4   0.020
 540  plan-1  H5   0.020
 540  plan-2  F1   0.020
 540  plan-2  O1   0.020
 540  plan-2  N2   0.020
 540  plan-2  N3   0.020
 540  plan-2  N4   0.020
 540  plan-2  C6   0.020
 540  plan-2  C7   0.020
 540  plan-2  C8   0.020
 540  plan-2  C9   0.020
 540  plan-2  C10  0.020
 540  plan-2  C11  0.020
 540  plan-2  C12  0.020
 540  plan-2  C13  0.020
 540  plan-2  C14  0.020
 540  plan-2  C15  0.020
 540  plan-2  C16  0.020
 540  plan-2  C17  0.020
 540  plan-2  C19  0.020
 540  plan-2  H11  0.020
 540  plan-2  H13  0.020

