# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 04:25:39 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: N-(2,6-dimethylphenyl)-5-phenylimidazo[1,5-a]pyrazin-8-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(C)c1Nc2ncc(n3cncc23)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
 KSL  KSL  N-(2,6-dimethylphenyl)-5-phenylimidazo[1,5-a]pyrazin-8-amine  ligand  42  24  .  2022-07-25  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_KSL
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
 KSL  C8   C  CH3   0  -0.732  -3.6412   1.0815  -2.1191
 KSL  C7   C  CR6   0   0.096  -3.9804   0.0940  -1.0411
 KSL  C5   C  CR16  0  -0.342  -5.0873  -0.7400  -1.1626
 KSL  C4   C  CR16  0  -0.225  -5.3925  -1.6587  -0.1702
 KSL  C3   C  CR16  0  -0.341  -4.5992  -1.7438   0.9631
 KSL  C6   C  CR6   0   0.209  -3.1910  -0.0085   0.1085
 KSL  C2   C  CR6   0   0.114  -3.4908  -0.9171   1.1275
 KSL  C1   C  CH3   0  -0.737  -2.6609  -1.0003   2.3721
 KSL  N9   N  NH1   0  -0.770  -2.0897   0.8692   0.2484
 KSL  C10  C  CR6   0   0.462  -0.7974   0.4864   0.1370
 KSL  C18  C  CR56  0   0.252   0.2096   1.5015   0.2213
 KSL  C17  C  CR15  0  -0.249   0.2404   2.8738   0.3419
 KSL  N16  N  N     0  -0.427   1.5175   3.3065   0.2896
 KSL  C15  C  CR15  0   0.083   2.2734   2.2403   0.1429
 KSL  N14  N  N     0  -0.540   1.5301   1.1127   0.1019
 KSL  C13  C  CR6   0   0.260   1.8717  -0.2265  -0.0613
 KSL  C12  C  CR16  0  -0.179   0.8335  -1.0944  -0.1240
 KSL  N11  N  N     0  -0.446  -0.4852  -0.7658  -0.0428
 KSL  C19  C  CR6   0   0.051   3.2842  -0.6222  -0.1362
 KSL  C24  C  CR16  0  -0.289   3.7171  -1.4489  -1.1730
 KSL  C23  C  CR16  0  -0.240   5.0373  -1.8725  -1.2337
 KSL  C22  C  CR16  0  -0.259   5.9456  -1.4657  -0.2665
 KSL  C21  C  CR16  0  -0.241   5.5242  -0.6392   0.7679
 KSL  C20  C  CR16  0  -0.297   4.2038  -0.2226   0.8365
 KSL  H8   H  HCH3  0   0.246  -3.7030   2.1123  -1.7633
 KSL  H8A  H  HCH3  0   0.249  -2.6280   0.9338  -2.4965
 KSL  H8B  H  HCH3  0   0.252  -4.3269   0.9869  -2.9594
 KSL  H5   H  HCR6  0   0.249  -5.7102  -0.6724  -2.0462
 KSL  H4   H  HCR6  0   0.253  -6.2547  -2.3046  -0.2756
 KSL  H3   H  HCR6  0   0.248  -4.8486  -2.4521   1.7438
 KSL  H1   H  HCH3  0   0.251  -1.7029  -1.4824   2.1713
 KSL  H1A  H  HCH3  0   0.242  -2.4431  -0.0114   2.7775
 KSL  H1B  H  HCH3  0   0.247  -3.1719  -1.5780   3.1410
 KSL  HN9  H  HNH1  0   0.405  -2.2835   1.8580   0.2130
 KSL  H17  H  HCR5  0   0.270  -0.5901   3.5533   0.4581
 KSL  H15  H  HCR5  0   0.298   3.3474   2.2381   0.0563
 KSL  H12  H  HCR6  0   0.265   1.0485  -2.1497  -0.2356
 KSL  H24  H  HCR6  0   0.259   3.0184  -1.7538  -1.9417
 KSL  H23  H  HCR6  0   0.262   5.3572  -2.5117  -2.0463
 KSL  H22  H  HCR6  0   0.262   6.9766  -1.7905  -0.3168
 KSL  H21  H  HCR6  0   0.262   6.2242  -0.3243   1.5307
 KSL  H20  H  HCR6  0   0.269   3.8877   0.3968   1.6671

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
 KSL  C8   C7   single    1.501  0.020  1.501
 KSL  C7   C5   aromatic  1.391  0.020  1.391
 KSL  C7   C6   aromatic  1.398  0.020  1.398
 KSL  C5   C4   aromatic  1.386  0.020  1.386
 KSL  C4   C3   aromatic  1.386  0.020  1.386
 KSL  C3   C2   aromatic  1.392  0.020  1.392
 KSL  C6   C2   aromatic  1.398  0.020  1.398
 KSL  C6   N9   single    1.415  0.020  1.415
 KSL  C2   C1   single    1.498  0.020  1.498
 KSL  N9   C10  single    1.352  0.020  1.352
 KSL  C10  C18  aromatic  1.432  0.020  1.432
 KSL  C10  N11  aromatic  1.303  0.020  1.303
 KSL  C18  C17  aromatic  1.378  0.020  1.378
 KSL  C18  N14  aromatic  1.382  0.020  1.382
 KSL  C17  N16  aromatic  1.349  0.020  1.349
 KSL  N16  C15  aromatic  1.315  0.020  1.315
 KSL  C15  N14  aromatic  1.351  0.020  1.351
 KSL  N14  C13  aromatic  1.392  0.020  1.392
 KSL  C13  C12  aromatic  1.355  0.020  1.355
 KSL  C13  C19  single    1.469  0.020  1.469
 KSL  C12  N11  aromatic  1.361  0.020  1.361
 KSL  C19  C24  aromatic  1.395  0.020  1.395
 KSL  C19  C20  aromatic  1.397  0.020  1.397
 KSL  C24  C23  aromatic  1.388  0.020  1.388
 KSL  C23  C22  aromatic  1.388  0.020  1.388
 KSL  C22  C21  aromatic  1.389  0.020  1.389
 KSL  C21  C20  aromatic  1.386  0.020  1.386
 KSL  C8   H8   single    0.970  0.020  1.090
 KSL  C8   H8A  single    0.970  0.020  1.090
 KSL  C8   H8B  single    0.970  0.020  1.090
 KSL  C5   H5   single    0.930  0.020  1.080
 KSL  C4   H4   single    0.930  0.020  1.080
 KSL  C3   H3   single    0.930  0.020  1.080
 KSL  C1   H1   single    0.970  0.020  1.090
 KSL  C1   H1A  single    0.970  0.020  1.090
 KSL  C1   H1B  single    0.970  0.020  1.090
 KSL  N9   HN9  single    0.860  0.020  1.020
 KSL  C17  H17  single    0.930  0.020  1.080
 KSL  C15  H15  single    0.930  0.020  1.080
 KSL  C12  H12  single    0.930  0.020  1.080
 KSL  C24  H24  single    0.930  0.020  1.080
 KSL  C23  H23  single    0.930  0.020  1.080
 KSL  C22  H22  single    0.930  0.020  1.080
 KSL  C21  H21  single    0.930  0.020  1.080
 KSL  C20  H20  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
 KSL  H8B  C8   H8A  107.82  3.000
 KSL  H8B  C8   H8   107.32  3.000
 KSL  H8A  C8   H8   107.03  3.000
 KSL  H8B  C8   C7   110.79  3.000
 KSL  H8A  C8   C7   111.67  3.000
 KSL  H8   C8   C7   111.98  3.000
 KSL  C6   C7   C5   118.49  3.000
 KSL  C6   C7   C8   120.74  3.000
 KSL  C5   C7   C8   120.77  3.000
 KSL  H5   C5   C4   119.92  3.000
 KSL  H5   C5   C7   119.42  3.000
 KSL  C4   C5   C7   120.66  3.000
 KSL  H4   C4   C3   119.93  3.000
 KSL  H4   C4   C5   120.07  3.000
 KSL  C3   C4   C5   120.00  3.000
 KSL  H3   C3   C2   119.10  3.000
 KSL  H3   C3   C4   119.84  3.000
 KSL  C2   C3   C4   121.05  3.000
 KSL  N9   C6   C2   119.87  3.000
 KSL  N9   C6   C7   118.37  3.000
 KSL  C2   C6   C7   121.73  3.000
 KSL  C1   C2   C6   121.52  3.000
 KSL  C1   C2   C3   120.40  3.000
 KSL  C6   C2   C3   118.07  3.000
 KSL  H1B  C1   H1A  108.20  3.000
 KSL  H1B  C1   H1   107.91  3.000
 KSL  H1A  C1   H1   107.08  3.000
 KSL  H1B  C1   C2   110.85  3.000
 KSL  H1A  C1   C2   111.65  3.000
 KSL  H1   C1   C2   110.97  3.000
 KSL  HN9  N9   C10  117.28  3.000
 KSL  HN9  N9   C6   117.08  3.000
 KSL  C10  N9   C6   124.05  3.000
 KSL  N11  C10  C18  121.38  3.000
 KSL  N11  C10  N9   120.82  3.000
 KSL  C18  C10  N9   117.80  3.000
 KSL  N14  C18  C17  105.45  3.000
 KSL  N14  C18  C10  117.87  3.000
 KSL  C17  C18  C10  136.60  3.000
 KSL  H17  C17  N16  122.04  3.000
 KSL  H17  C17  C18  128.26  3.000
 KSL  N16  C17  C18  109.70  3.000
 KSL  C15  N16  C17  106.76  3.000
 KSL  H15  C15  N14  122.97  3.000
 KSL  H15  C15  N16  125.70  3.000
 KSL  N14  C15  N16  111.33  3.000
 KSL  C13  N14  C15  132.19  3.000
 KSL  C13  N14  C18  121.03  3.000
 KSL  C15  N14  C18  106.76  3.000
 KSL  C19  C13  C12  124.20  3.000
 KSL  C19  C13  N14  120.08  3.000
 KSL  C12  C13  N14  115.71  3.000
 KSL  H12  C12  N11  115.70  3.000
 KSL  H12  C12  C13  118.49  3.000
 KSL  N11  C12  C13  125.80  3.000
 KSL  C12  N11  C10  118.18  3.000
 KSL  C20  C19  C24  118.87  3.000
 KSL  C20  C19  C13  121.37  3.000
 KSL  C24  C19  C13  119.74  3.000
 KSL  H24  C24  C23  119.80  3.000
 KSL  H24  C24  C19  119.63  3.000
 KSL  C23  C24  C19  120.57  3.000
 KSL  H23  C23  C22  120.20  3.000
 KSL  H23  C23  C24  119.62  3.000
 KSL  C22  C23  C24  120.18  3.000
 KSL  H22  C22  C21  120.14  3.000
 KSL  H22  C22  C23  120.21  3.000
 KSL  C21  C22  C23  119.65  3.000
 KSL  H21  C21  C20  119.59  3.000
 KSL  H21  C21  C22  120.11  3.000
 KSL  C20  C21  C22  120.29  3.000
 KSL  H20  C20  C21  119.19  3.000
 KSL  H20  C20  C19  120.35  3.000
 KSL  C21  C20  C19  120.44  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
 KSL  CONST_01  C3   C4   C5   C7      0.00   0.0  0
 KSL  CONST_02  C3   C2   C6   C7      0.00   0.0  0
 KSL  CONST_03  C2   C6   C7   C5      0.00   0.0  0
 KSL  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 KSL  CONST_05  C6   C7   C5   C4      0.00   0.0  0
 KSL  CONST_06  C6   C2   C3   C4      0.00   0.0  0
 KSL  CONST_07  N16  C17  C18  C10   180.00   0.0  0
 KSL  CONST_08  C15  N14  C18  C10   180.00   0.0  0
 KSL  CONST_09  C13  N14  C18  C10     0.00   0.0  0
 KSL  CONST_10  C13  C12  N11  C10     0.00   0.0  0
 KSL  CONST_11  C12  N11  C10  C18     0.00   0.0  0
 KSL  CONST_12  C15  N16  C17  C18     0.00   0.0  0
 KSL  CONST_13  N16  C15  N14  C18     0.00   0.0  0
 KSL  CONST_14  C12  C13  N14  C18     0.00   0.0  0
 KSL  CONST_15  C19  C13  N14  C18   180.00   0.0  0
 KSL  CONST_16  N11  C10  C18  C17   180.00   0.0  0
 KSL  CONST_17  C15  N14  C18  C17     0.00   0.0  0
 KSL  CONST_18  C13  N14  C18  C17   180.00   0.0  0
 KSL  CONST_19  N14  C15  N16  C17     0.00   0.0  0
 KSL  CONST_20  N14  C18  C17  N16     0.00   0.0  0
 KSL  CONST_21  C13  N14  C15  N16   180.00   0.0  0
 KSL  CONST_22  C12  C13  N14  C15   180.00   0.0  0
 KSL  CONST_23  C19  C13  N14  C15     0.00   0.0  0
 KSL  CONST_24  N11  C10  C18  N14     0.00   0.0  0
 KSL  CONST_25  N11  C12  C13  N14     0.00   0.0  0
 KSL  CONST_28  C23  C24  C19  C13   180.00   0.0  0
 KSL  CONST_29  C21  C20  C19  C13   180.00   0.0  0
 KSL  CONST_32  C19  C13  C12  N11   180.00   0.0  0
 KSL  CONST_33  C22  C23  C24  C19     0.00   0.0  0
 KSL  CONST_34  C22  C21  C20  C19     0.00   0.0  0
 KSL  CONST_35  C21  C20  C19  C24     0.00   0.0  0
 KSL  CONST_36  C21  C22  C23  C24     0.00   0.0  0
 KSL  CONST_37  C20  C19  C24  C23     0.00   0.0  0
 KSL  CONST_38  C20  C21  C22  C23     0.00   0.0  0
 KSL  CONST_39  C4   C5   C7   C8    180.00   0.0  0
 KSL  CONST_40  C2   C6   C7   C8    180.00   0.0  0
 KSL  CONST_41  C1   C2   C6   C7    180.00   0.0  0
 KSL  CONST_42  N9   C6   C7   C5    180.00   0.0  0
 KSL  CONST_43  C1   C2   C3   C4    180.00   0.0  0
 KSL  CONST_44  N9   C6   C2   C3    180.00   0.0  0
 KSL  CONST_45  C17  C18  C10  N9      0.00   0.0  0
 KSL  CONST_46  N14  C18  C10  N9    180.00   0.0  0
 KSL  CONST_47  C12  N11  C10  N9    180.00   0.0  0
 KSL  CONST_48  H4   C4   C5   C7    180.00   0.0  0
 KSL  CONST_49  H3   C3   C4   C5    180.00   0.0  0
 KSL  CONST_50  H5   C5   C4   C3    180.00   0.0  0
 KSL  CONST_51  H17  C17  C18  C10     0.00   0.0  0
 KSL  CONST_52  H12  C12  N11  C10   180.00   0.0  0
 KSL  CONST_53  H15  C15  N14  C18   180.00   0.0  0
 KSL  CONST_54  H24  C24  C19  C13     0.00   0.0  0
 KSL  CONST_55  H20  C20  C19  C13     0.00   0.0  0
 KSL  CONST_56  H23  C23  C24  C19   180.00   0.0  0
 KSL  CONST_57  H21  C21  C20  C19   180.00   0.0  0
 KSL  CONST_58  H22  C22  C23  C24   180.00   0.0  0
 KSL  Var_01    C10  N9   C6   C7   -108.10  30.0  2
 KSL  Var_02    C18  C10  N9   C6    176.22  30.0  2
 KSL  Var_03    H8   C8   C7   C5    116.68  30.0  2
 KSL  Var_04    H1   C1   C2   C3    106.87  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
 KSL  plan-1  C8   0.020
 KSL  plan-1  C7   0.020
 KSL  plan-1  C5   0.020
 KSL  plan-1  C4   0.020
 KSL  plan-1  C3   0.020
 KSL  plan-1  C6   0.020
 KSL  plan-1  C2   0.020
 KSL  plan-1  C1   0.020
 KSL  plan-1  N9   0.020
 KSL  plan-1  H5   0.020
 KSL  plan-1  H4   0.020
 KSL  plan-1  H3   0.020
 KSL  plan-2  C13  0.020
 KSL  plan-2  C19  0.020
 KSL  plan-2  C24  0.020
 KSL  plan-2  C23  0.020
 KSL  plan-2  C22  0.020
 KSL  plan-2  C21  0.020
 KSL  plan-2  C20  0.020
 KSL  plan-2  H24  0.020
 KSL  plan-2  H23  0.020
 KSL  plan-2  H22  0.020
 KSL  plan-2  H21  0.020
 KSL  plan-2  H20  0.020
 KSL  plan-3  N9   0.020
 KSL  plan-3  C10  0.020
 KSL  plan-3  C18  0.020
 KSL  plan-3  C17  0.020
 KSL  plan-3  N16  0.020
 KSL  plan-3  C15  0.020
 KSL  plan-3  N14  0.020
 KSL  plan-3  C13  0.020
 KSL  plan-3  C12  0.020
 KSL  plan-3  N11  0.020
 KSL  plan-3  C19  0.020
 KSL  plan-3  H17  0.020
 KSL  plan-3  H15  0.020
 KSL  plan-3  H12  0.020

