# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:44:04 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 6-(2-fluorophenyl)-N-(pyridin-3-ylmethyl)imidazo[1,2-a]pyrazin-8-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccccc1c2cn3ccnc3c(NCc4cccnc4)n2
#
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
 SC9  SC9  6-(2-fluorophenyl)-N-(pyridin-3-ylmethyl)imidazo[1,2-a]pyrazin-8-amine  ligand  38  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SC9
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
 SC9  C01   C  CR15  0  -0.106   1.4743  -3.9400  -0.3706
 SC9  N02   N  N     0  -0.474   1.4151  -2.5844  -0.2453
 SC9  C03   C  CR56  0   0.421   0.0987  -2.2600  -0.0863
 SC9  N04   N  N     0  -0.460  -0.6754  -3.3244  -0.1017
 SC9  C05   C  CR15  0  -0.206   0.1717  -4.3666  -0.2764
 SC9  C06   C  CR16  0  -0.057   2.3962  -1.6196  -0.2591
 SC9  C07   C  CR6   0   0.134   2.0005  -0.3333  -0.0898
 SC9  N08   N  N     0  -0.470   0.7017   0.0444   0.0793
 SC9  C09   C  CR6   0   0.447  -0.2283  -0.8735   0.0682
 SC9  N10   N  NH1   0  -0.667  -1.5237  -0.5424   0.1921
 SC9  C11   C  CH2   0  -0.323  -1.9508   0.8149   0.4555
 SC9  C12   C  CR6   0  -0.037  -3.4428   0.9106   0.3246
 SC9  C13   C  CR16  0  -0.174  -4.2831   0.8459   1.4279
 SC9  C14   C  CR16  0  -0.320  -5.6550   0.9148   1.2367
 SC9  C15   C  CR16  0  -0.067  -6.1357   1.0426  -0.0569
 SC9  N16   N  N     0  -0.402  -5.3455   1.1055  -1.1238
 SC9  C17   C  CR16  0  -0.076  -4.0362   1.0398  -0.9279
 SC9  C18   C  CR6   0  -0.163   3.0158   0.7388  -0.0604
 SC9  C19   C  CR6   0   0.527   2.9059   1.8692  -0.8615
 SC9  C20   C  CR16  0  -0.406   3.8396   2.8863  -0.8476
 SC9  C21   C  CR16  0  -0.244   4.9356   2.7792  -0.0022
 SC9  C22   C  CR16  0  -0.258   5.0828   1.6623   0.8082
 SC9  C23   C  CR16  0  -0.267   4.1277   0.6566   0.7766
 SC9  F24   F  F     0  -0.301   1.8701   1.9690  -1.7062
 SC9  H01   H  HCR5  0   0.304   2.4023  -4.4674  -0.5100
 SC9  H05   H  HCR5  0   0.262  -0.1811  -5.3851  -0.3279
 SC9  H06   H  HCR6  0   0.307   3.4142  -1.9401  -0.4147
 SC9  HN10  H  HNH1  0   0.405  -2.1861  -1.2905   0.3230
 SC9  H111  H  HCH2  0   0.254  -1.6381   1.1410   1.4528
 SC9  H112  H  HCH2  0   0.263  -1.4660   1.4823  -0.2596
 SC9  H13   H  HCR6  0   0.273  -3.8716   0.7461   2.4252
 SC9  H14   H  HCR6  0   0.274  -6.3404   0.8713   2.0716
 SC9  H15   H  HCR6  0   0.267  -7.2030   1.0983  -0.2399
 SC9  H17   H  HCR6  0   0.263  -3.4108   1.0975  -1.8144
 SC9  H20   H  HCR6  0   0.280   3.7136   3.7436  -1.4959
 SC9  H21   H  HCR6  0   0.270   5.6723   3.5708   0.0180
 SC9  H22   H  HCR6  0   0.264   5.9335   1.5770   1.4705
 SC9  H23   H  HCR6  0   0.266   4.2326  -0.2055   1.4231

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
 SC9  C01  C05   aromatic  1.374  0.020  1.374
 SC9  C01  N02   aromatic  1.363  0.020  1.363
 SC9  C05  N04   aromatic  1.354  0.020  1.354
 SC9  F24  C19   single    1.340  0.020  1.340
 SC9  N02  C06   aromatic  1.376  0.020  1.376
 SC9  N02  C03   aromatic  1.365  0.020  1.365
 SC9  C06  C07   aromatic  1.356  0.020  1.356
 SC9  N04  C03   aromatic  1.316  0.020  1.316
 SC9  C19  C20   aromatic  1.381  0.020  1.381
 SC9  C19  C18   aromatic  1.390  0.020  1.390
 SC9  C03  C09   aromatic  1.433  0.020  1.433
 SC9  C07  C18   single    1.477  0.020  1.477
 SC9  C07  N08   aromatic  1.363  0.020  1.363
 SC9  C20  C21   aromatic  1.388  0.020  1.388
 SC9  C18  C23   aromatic  1.394  0.020  1.394
 SC9  C09  N08   aromatic  1.307  0.020  1.307
 SC9  C09  N10   single    1.343  0.020  1.343
 SC9  C21  C22   aromatic  1.388  0.020  1.388
 SC9  C23  C22   aromatic  1.387  0.020  1.387
 SC9  N10  C11   single    1.447  0.020  1.447
 SC9  C15  C14   aromatic  1.386  0.020  1.386
 SC9  C15  N16   aromatic  1.329  0.020  1.329
 SC9  C14  C13   aromatic  1.387  0.020  1.387
 SC9  N16  C17   aromatic  1.325  0.020  1.325
 SC9  C13  C12   aromatic  1.388  0.020  1.388
 SC9  C17  C12   aromatic  1.392  0.020  1.392
 SC9  C12  C11   single    1.501  0.020  1.501
 SC9  C01  H01   single    0.930  0.020  1.080
 SC9  C05  H05   single    0.930  0.020  1.080
 SC9  C06  H06   single    0.930  0.020  1.080
 SC9  N10  HN10  single    0.860  0.020  1.020
 SC9  C11  H111  single    0.970  0.020  1.090
 SC9  C11  H112  single    0.970  0.020  1.090
 SC9  C13  H13   single    0.930  0.020  1.080
 SC9  C14  H14   single    0.930  0.020  1.080
 SC9  C15  H15   single    0.930  0.020  1.080
 SC9  C17  H17   single    0.930  0.020  1.080
 SC9  C20  H20   single    0.930  0.020  1.080
 SC9  C21  H21   single    0.930  0.020  1.080
 SC9  C22  H22   single    0.930  0.020  1.080
 SC9  C23  H23   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
 SC9  H01   C01  C05   132.38  3.000
 SC9  H01   C01  N02   122.46  3.000
 SC9  C05   C01  N02   105.16  3.000
 SC9  C06   N02  C03   121.47  3.000
 SC9  C03   N02  C01   106.80  3.000
 SC9  C06   N02  C01   131.73  3.000
 SC9  C09   C03  N04   130.51  3.000
 SC9  C09   C03  N02   117.56  3.000
 SC9  N04   C03  N02   111.93  3.000
 SC9  C05   N04  C03   104.83  3.000
 SC9  H05   C05  N04   121.87  3.000
 SC9  H05   C05  C01   126.86  3.000
 SC9  N04   C05  C01   111.28  3.000
 SC9  H06   C06  C07   125.11  3.000
 SC9  H06   C06  N02   117.78  3.000
 SC9  C07   C06  N02   117.11  3.000
 SC9  C18   C07  N08   116.83  3.000
 SC9  N08   C07  C06   123.79  3.000
 SC9  C18   C07  C06   119.37  3.000
 SC9  C09   N08  C07   118.85  3.000
 SC9  N10   C09  N08   120.84  3.000
 SC9  N10   C09  C03   117.95  3.000
 SC9  N08   C09  C03   121.21  3.000
 SC9  HN10  N10  C11   118.60  3.000
 SC9  HN10  N10  C09   117.58  3.000
 SC9  C11   N10  C09   122.19  3.000
 SC9  H112  C11  H111  106.73  3.000
 SC9  H112  C11  C12   110.21  3.000
 SC9  H111  C11  C12   110.14  3.000
 SC9  H112  C11  N10   108.85  3.000
 SC9  H111  C11  N10   111.15  3.000
 SC9  C12   C11  N10   109.71  3.000
 SC9  C17   C12  C13   117.47  3.000
 SC9  C17   C12  C11   120.54  3.000
 SC9  C13   C12  C11   121.97  3.000
 SC9  H13   C13  C14   120.48  3.000
 SC9  H13   C13  C12   120.39  3.000
 SC9  C14   C13  C12   119.13  3.000
 SC9  H14   C14  C15   120.30  3.000
 SC9  H14   C14  C13   121.24  3.000
 SC9  C15   C14  C13   118.45  3.000
 SC9  H15   C15  N16   116.57  3.000
 SC9  H15   C15  C14   120.24  3.000
 SC9  N16   C15  C14   123.18  3.000
 SC9  C17   N16  C15   117.79  3.000
 SC9  H17   C17  N16   116.45  3.000
 SC9  H17   C17  C12   119.59  3.000
 SC9  N16   C17  C12   123.96  3.000
 SC9  C23   C18  C19   117.20  3.000
 SC9  C23   C18  C07   121.16  3.000
 SC9  C19   C18  C07   121.65  3.000
 SC9  F24   C19  C20   118.30  3.000
 SC9  C20   C19  C18   122.68  3.000
 SC9  F24   C19  C18   119.01  3.000
 SC9  H20   C20  C21   121.18  3.000
 SC9  H20   C20  C19   119.92  3.000
 SC9  C21   C20  C19   118.89  3.000
 SC9  H21   C21  C22   120.39  3.000
 SC9  H21   C21  C20   119.52  3.000
 SC9  C22   C21  C20   120.09  3.000
 SC9  H22   C22  C23   119.89  3.000
 SC9  H22   C22  C21   120.30  3.000
 SC9  C23   C22  C21   119.81  3.000
 SC9  H23   C23  C22   119.80  3.000
 SC9  H23   C23  C18   118.86  3.000
 SC9  C22   C23  C18   121.33  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
 SC9  CONST_01  C03   N04  C05  C01    0.00   0.0  0
 SC9  CONST_02  C07   C06  N02  C01  180.00   0.0  0
 SC9  CONST_03  N04   C03  N02  C01    0.00   0.0  0
 SC9  CONST_04  C09   C03  N02  C01  180.00   0.0  0
 SC9  CONST_05  N04   C05  C01  N02    0.00   0.0  0
 SC9  CONST_06  C18   C07  C06  N02  180.00   0.0  0
 SC9  CONST_07  N08   C07  C06  N02    0.00   0.0  0
 SC9  CONST_08  C05   N04  C03  N02    0.00   0.0  0
 SC9  CONST_09  N08   C09  C03  N02    0.00   0.0  0
 SC9  CONST_10  C05   C01  N02  C03    0.00   0.0  0
 SC9  CONST_11  C07   C06  N02  C03    0.00   0.0  0
 SC9  CONST_12  C07   N08  C09  C03    0.00   0.0  0
 SC9  CONST_13  C06   N02  C03  N04  180.00   0.0  0
 SC9  CONST_14  N08   C09  C03  N04  180.00   0.0  0
 SC9  CONST_15  C06   N02  C01  C05  180.00   0.0  0
 SC9  CONST_16  C09   C03  N04  C05  180.00   0.0  0
 SC9  CONST_17  C09   C03  N02  C06    0.00   0.0  0
 SC9  CONST_20  C09   N08  C07  C06    0.00   0.0  0
 SC9  CONST_21  C20   C19  C18  C07  180.00   0.0  0
 SC9  CONST_22  C22   C23  C18  C07  180.00   0.0  0
 SC9  CONST_25  C18   C07  N08  C09  180.00   0.0  0
 SC9  CONST_26  C15   C14  C13  C12    0.00   0.0  0
 SC9  CONST_27  C15   N16  C17  C12    0.00   0.0  0
 SC9  CONST_28  N16   C15  C14  C13    0.00   0.0  0
 SC9  CONST_29  N16   C17  C12  C13    0.00   0.0  0
 SC9  CONST_30  C17   N16  C15  C14    0.00   0.0  0
 SC9  CONST_31  C17   C12  C13  C14    0.00   0.0  0
 SC9  CONST_32  C21   C20  C19  C18    0.00   0.0  0
 SC9  CONST_33  C21   C22  C23  C18    0.00   0.0  0
 SC9  CONST_34  C22   C21  C20  C19    0.00   0.0  0
 SC9  CONST_35  C22   C23  C18  C19    0.00   0.0  0
 SC9  CONST_36  C23   C18  C19  C20    0.00   0.0  0
 SC9  CONST_37  C23   C22  C21  C20    0.00   0.0  0
 SC9  CONST_38  N10   C09  C03  N02  180.00   0.0  0
 SC9  CONST_39  N10   C09  C03  N04    0.00   0.0  0
 SC9  CONST_40  F24   C19  C18  C07    0.00   0.0  0
 SC9  CONST_41  N10   C09  N08  C07  180.00   0.0  0
 SC9  CONST_42  C14   C13  C12  C11  180.00   0.0  0
 SC9  CONST_43  N16   C17  C12  C11  180.00   0.0  0
 SC9  CONST_44  F24   C19  C20  C21  180.00   0.0  0
 SC9  CONST_45  F24   C19  C18  C23  180.00   0.0  0
 SC9  CONST_46  H06   C06  N02  C01    0.00   0.0  0
 SC9  CONST_47  H05   C05  C01  N02  180.00   0.0  0
 SC9  CONST_48  H01   C01  N02  C03  180.00   0.0  0
 SC9  CONST_49  H23   C23  C18  C07    0.00   0.0  0
 SC9  CONST_50  H14   C14  C13  C12  180.00   0.0  0
 SC9  CONST_51  H15   C15  C14  C13  180.00   0.0  0
 SC9  CONST_52  H17   C17  C12  C13  180.00   0.0  0
 SC9  CONST_53  H13   C13  C14  C15  180.00   0.0  0
 SC9  CONST_54  H20   C20  C19  C18  180.00   0.0  0
 SC9  CONST_55  H22   C22  C23  C18  180.00   0.0  0
 SC9  CONST_56  H21   C21  C20  C19  180.00   0.0  0
 SC9  CONST_57  C11   N10  C09  C03  180.00   0.0  0
 SC9  CONST_58  C11   N10  C09  N08    0.00   0.0  0
 SC9  CONST_59  HN10  N10  C09  C03    0.00   0.0  0
 SC9  Var_01    C12   C11  N10  C09  171.09  30.0  3
 SC9  Var_02    C13   C12  C11  N10   97.26  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
 SC9  plan-1  C11   0.020
 SC9  plan-1  C12   0.020
 SC9  plan-1  C13   0.020
 SC9  plan-1  C14   0.020
 SC9  plan-1  C15   0.020
 SC9  plan-1  N16   0.020
 SC9  plan-1  C17   0.020
 SC9  plan-1  H13   0.020
 SC9  plan-1  H14   0.020
 SC9  plan-1  H15   0.020
 SC9  plan-1  H17   0.020
 SC9  plan-2  C07   0.020
 SC9  plan-2  C18   0.020
 SC9  plan-2  C19   0.020
 SC9  plan-2  C20   0.020
 SC9  plan-2  C21   0.020
 SC9  plan-2  C22   0.020
 SC9  plan-2  C23   0.020
 SC9  plan-2  F24   0.020
 SC9  plan-2  H20   0.020
 SC9  plan-2  H21   0.020
 SC9  plan-2  H22   0.020
 SC9  plan-2  H23   0.020
 SC9  plan-3  C01   0.020
 SC9  plan-3  N02   0.020
 SC9  plan-3  C03   0.020
 SC9  plan-3  N04   0.020
 SC9  plan-3  C05   0.020
 SC9  plan-3  C06   0.020
 SC9  plan-3  C07   0.020
 SC9  plan-3  N08   0.020
 SC9  plan-3  C09   0.020
 SC9  plan-3  N10   0.020
 SC9  plan-3  C18   0.020
 SC9  plan-3  H01   0.020
 SC9  plan-3  H05   0.020
 SC9  plan-3  H06   0.020
 SC9  plan-4  C09   0.020
 SC9  plan-4  N10   0.020
 SC9  plan-4  C11   0.020
 SC9  plan-4  HN10  0.020

