# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 10:17:47 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-{8-[(3,4-dimethoxyphenyl)amino]imidazo[1,2-a]pyrazin-6-yl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Nc2nc(cn3ccnc23)c4cccc(c4)C(N)=O)cc1OC
#
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
 50H  50H  3-{8-[(3,4-dimethoxyphenyl)amino]imidazo[1,2-a]pyrazin-6-yl}benzamide  ligand  48  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_50H
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
 50H  N2   N  N     0  -0.496  -1.1744   0.5419  -0.0177
 50H  C6   C  CR16  0  -0.061  -3.4148   1.3518   0.2053
 50H  C9   C  C     0   0.489  -1.5373  -4.4881   0.3572
 50H  C13  C  CR16  0  -0.321  -2.1223  -2.0973   0.1355
 50H  C20  C  CR16  0  -0.373   2.8444  -0.9068  -0.4483
 50H  C18  C  CR6   0   0.296   4.0866  -0.3133  -0.3442
 50H  C16  C  CR6   0   0.334   4.1525   1.0705  -0.0765
 50H  C26  C  CR16  0  -0.295  -3.7882  -3.7016  -0.5172
 50H  C27  C  CR16  0  -0.225  -4.6407  -2.6616  -0.8573
 50H  C25  C  CR16  0  -0.319  -4.2425  -1.3451  -0.6919
 50H  C22  C  CR16  0  -0.337   1.6638  -0.1768  -0.2963
 50H  C15  C  CR16  0  -0.517   2.9874   1.7955   0.0778
 50H  C12  C  CR15  0  -0.203  -2.4984   4.7309   0.6762
 50H  C14  C  CR15  0  -0.103  -3.5203   3.8181   0.5833
 50H  C10  C  CR6   0   0.083  -2.9771  -1.0467  -0.1847
 50H  C11  C  CR6   0  -0.015  -2.5216  -3.4207  -0.0108
 50H  C17  C  CR6   0   0.383   1.7288   1.1817  -0.0299
 50H  C3   C  CR56  0   0.395  -1.5659   2.8601   0.3491
 50H  C5   C  CR6   0   0.171  -2.5247   0.3462   0.0030
 50H  C1   C  CR6   0   0.476  -0.6949   1.7412   0.1476
 50H  C29  C  CH3   0  -0.436   5.2516  -2.3319  -0.7344
 50H  C28  C  CH3   0  -0.440   5.5238   2.9701   0.2724
 50H  N7   N  N     0  -0.463  -1.2913   4.1332   0.5309
 50H  N4   N  N     0  -0.480  -2.9087   2.6180   0.3717
 50H  N21  N  NH2   0  -0.815  -2.0486  -5.6972   0.6337
 50H  N8   N  NH1   0  -0.788   0.6277   2.0214   0.1387
 50H  O19  O  O     0  -0.475  -0.3379  -4.2504   0.3934
 50H  O23  O  O2    0  -0.464   5.3904   1.5878   0.0107
 50H  H1   H  HCR6  0   0.309  -4.4856   1.2378   0.2639
 50H  H2   H  HCR6  0   0.261  -1.1375  -1.8791   0.5237
 50H  H3   H  HCR6  0   0.279   2.7577  -1.9655  -0.6532
 50H  H4   H  HCR6  0   0.263  -4.1146  -4.7206  -0.6805
 50H  H5   H  HCR6  0   0.268  -5.6162  -2.8804  -1.2703
 50H  H6   H  HCR6  0   0.260  -4.9168  -0.5503  -0.9845
 50H  H7   H  HCR6  0   0.291   0.7173  -0.6798  -0.3958
 50H  H8   H  HCR6  0   0.294   3.0337   2.8575   0.2849
 50H  H9   H  HCR5  0   0.265  -2.5911   5.7932   0.8406
 50H  H10  H  HCR5  0   0.306  -4.5903   3.9180   0.6450
 50H  H11  H  HCH3  0   0.226   4.7694  -2.8900   0.0734
 50H  H12  H  HCH3  0   0.226   4.7461  -2.5709  -1.6745
 50H  H13  H  HCH3  0   0.258   6.2894  -2.6484  -0.8063
 50H  H14  H  HCH3  0   0.229   5.0796   3.5803  -0.5188
 50H  H15  H  HCH3  0   0.229   5.0727   3.2498   1.2280
 50H  H16  H  HCH3  0   0.262   6.5906   3.1743   0.3147
 50H  H17  H  HNH2  0   0.406  -1.4330  -6.4440   0.9125
 50H  H18  H  HNH2  0   0.413  -3.0342  -5.8563   0.7471
 50H  H19  H  HNH1  0   0.419   0.8463   2.9954   0.2931
 50H  O24  O  O2    0  -0.465   5.2710  -0.9436  -0.4801

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
 50H  C29  O24  single    1.412  0.020  1.412
 50H  N7   C12  aromatic  1.355  0.020  1.355
 50H  N7   C3   aromatic  1.315  0.020  1.315
 50H  C12  C14  aromatic  1.373  0.020  1.373
 50H  C22  C20  aromatic  1.396  0.020  1.396
 50H  C22  C17  aromatic  1.386  0.020  1.386
 50H  C20  C18  aromatic  1.381  0.020  1.381
 50H  N8   C17  single    1.395  0.020  1.395
 50H  N8   C1   single    1.352  0.020  1.352
 50H  C17  C15  aromatic  1.404  0.020  1.404
 50H  C18  O24  single    1.348  0.020  1.348
 50H  C18  C16  aromatic  1.411  0.020  1.411
 50H  C3   C1   aromatic  1.432  0.020  1.432
 50H  C3   N4   aromatic  1.365  0.020  1.365
 50H  C14  N4   aromatic  1.363  0.020  1.363
 50H  C1   N2   aromatic  1.302  0.020  1.302
 50H  C15  C16  aromatic  1.381  0.020  1.381
 50H  N4   C6   aromatic  1.374  0.020  1.374
 50H  C16  O23  single    1.344  0.020  1.344
 50H  N2   C5   aromatic  1.365  0.020  1.365
 50H  O23  C28  single    1.413  0.020  1.413
 50H  C6   C5   aromatic  1.358  0.020  1.358
 50H  C5   C10  single    1.476  0.020  1.476
 50H  C10  C13  aromatic  1.392  0.020  1.392
 50H  C10  C25  aromatic  1.396  0.020  1.396
 50H  C13  C11  aromatic  1.390  0.020  1.390
 50H  C25  C27  aromatic  1.385  0.020  1.385
 50H  C11  C26  aromatic  1.393  0.020  1.393
 50H  C11  C9   single    1.498  0.020  1.498
 50H  C27  C26  aromatic  1.387  0.020  1.387
 50H  N21  C9   single    1.342  0.020  1.342
 50H  C9   O19  double    1.223  0.020  1.223
 50H  C6   H1   single    0.930  0.020  1.080
 50H  C13  H2   single    0.930  0.020  1.080
 50H  C20  H3   single    0.930  0.020  1.080
 50H  C26  H4   single    0.930  0.020  1.080
 50H  C27  H5   single    0.930  0.020  1.080
 50H  C25  H6   single    0.930  0.020  1.080
 50H  C22  H7   single    0.930  0.020  1.080
 50H  C15  H8   single    0.930  0.020  1.080
 50H  C12  H9   single    0.930  0.020  1.080
 50H  C14  H10  single    0.930  0.020  1.080
 50H  C29  H11  single    0.970  0.020  1.090
 50H  C29  H12  single    0.970  0.020  1.090
 50H  C29  H13  single    0.970  0.020  1.090
 50H  C28  H14  single    0.970  0.020  1.090
 50H  C28  H15  single    0.970  0.020  1.090
 50H  C28  H16  single    0.970  0.020  1.090
 50H  N21  H17  single    0.860  0.020  1.020
 50H  N21  H18  single    0.860  0.020  1.020
 50H  N8   H19  single    0.860  0.020  1.020

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
 50H  C1   N2   C5   119.64  3.000
 50H  H1   C6   N4   117.17  3.000
 50H  H1   C6   C5   125.50  3.000
 50H  N4   C6   C5   117.33  3.000
 50H  O19  C9   N21  122.87  3.000
 50H  O19  C9   C11  120.87  3.000
 50H  N21  C9   C11  116.26  3.000
 50H  H2   C13  C11  119.46  3.000
 50H  H2   C13  C10  119.33  3.000
 50H  C11  C13  C10  121.20  3.000
 50H  H3   C20  C22  117.68  3.000
 50H  H3   C20  C18  120.47  3.000
 50H  C22  C20  C18  121.86  3.000
 50H  O24  C18  C16  115.88  3.000
 50H  C16  C18  C20  118.55  3.000
 50H  O24  C18  C20  125.57  3.000
 50H  O23  C16  C15  124.58  3.000
 50H  O23  C16  C18  115.64  3.000
 50H  C15  C16  C18  119.78  3.000
 50H  H4   C26  C11  121.26  3.000
 50H  H4   C26  C27  118.92  3.000
 50H  C11  C26  C27  119.80  3.000
 50H  H5   C27  C25  119.80  3.000
 50H  H5   C27  C26  119.75  3.000
 50H  C25  C27  C26  120.44  3.000
 50H  H6   C25  C10  120.40  3.000
 50H  H6   C25  C27  119.11  3.000
 50H  C10  C25  C27  120.48  3.000
 50H  H7   C22  C17  121.14  3.000
 50H  H7   C22  C20  119.28  3.000
 50H  C17  C22  C20  119.59  3.000
 50H  H8   C15  C17  118.79  3.000
 50H  H8   C15  C16  120.01  3.000
 50H  C17  C15  C16  121.20  3.000
 50H  H9   C12  N7   121.82  3.000
 50H  H9   C12  C14  126.92  3.000
 50H  N7   C12  C14  111.25  3.000
 50H  H10  C14  N4   122.44  3.000
 50H  H10  C14  C12  132.39  3.000
 50H  N4   C14  C12  105.17  3.000
 50H  C5   C10  C25  121.72  3.000
 50H  C25  C10  C13  118.63  3.000
 50H  C5   C10  C13  119.65  3.000
 50H  C26  C11  C13  119.44  3.000
 50H  C26  C11  C9   122.91  3.000
 50H  C13  C11  C9   117.63  3.000
 50H  N8   C17  C15  115.78  3.000
 50H  C15  C17  C22  119.03  3.000
 50H  N8   C17  C22  125.19  3.000
 50H  N4   C3   N7   112.02  3.000
 50H  N4   C3   C1   117.53  3.000
 50H  N7   C3   C1   130.45  3.000
 50H  C10  C5   C6   121.11  3.000
 50H  C10  C5   N2   115.88  3.000
 50H  C6   C5   N2   123.00  3.000
 50H  N8   C1   C3   115.71  3.000
 50H  C3   C1   N2   120.89  3.000
 50H  N8   C1   N2   123.39  3.000
 50H  H13  C29  H12  108.71  3.000
 50H  H13  C29  H11  108.73  3.000
 50H  H12  C29  H11  108.63  3.000
 50H  H13  C29  O24  106.56  3.000
 50H  H12  C29  O24  112.09  3.000
 50H  H11  C29  O24  112.01  3.000
 50H  H16  C28  H15  108.84  3.000
 50H  H16  C28  H14  108.78  3.000
 50H  H15  C28  H14  108.79  3.000
 50H  H16  C28  O23  106.47  3.000
 50H  H15  C28  O23  111.91  3.000
 50H  H14  C28  O23  111.93  3.000
 50H  C3   N7   C12  104.83  3.000
 50H  C3   N4   C14  106.73  3.000
 50H  C14  N4   C6   131.67  3.000
 50H  C3   N4   C6   121.60  3.000
 50H  H18  N21  H17  116.80  3.000
 50H  H18  N21  C9   122.67  3.000
 50H  H17  N21  C9   119.50  3.000
 50H  H19  N8   C1   114.24  3.000
 50H  H19  N8   C17  115.35  3.000
 50H  C1   N8   C17  130.40  3.000
 50H  C28  O23  C16  118.38  3.000
 50H  C29  O24  C18  117.76  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
 50H  CONST_01  N7   C3   C1   N2   180.00   0.0  0
 50H  CONST_02  N4   C3   C1   N2     0.00   0.0  0
 50H  CONST_03  N4   C6   C5   N2     0.00   0.0  0
 50H  CONST_06  N7   C3   N4   C6   180.00   0.0  0
 50H  CONST_07  C1   C3   N4   C6     0.00   0.0  0
 50H  CONST_08  C12  C14  N4   C6   180.00   0.0  0
 50H  CONST_09  C1   N2   C5   C6     0.00   0.0  0
 50H  CONST_12  C27  C25  C10  C13    0.00   0.0  0
 50H  CONST_13  C27  C26  C11  C13    0.00   0.0  0
 50H  CONST_14  C15  C17  C22  C20    0.00   0.0  0
 50H  CONST_15  C15  C16  C18  C20    0.00   0.0  0
 50H  CONST_16  C17  C22  C20  C18    0.00   0.0  0
 50H  CONST_17  C17  C15  C16  C18    0.00   0.0  0
 50H  CONST_18  C22  C20  C18  C16    0.00   0.0  0
 50H  CONST_19  C22  C17  C15  C16    0.00   0.0  0
 50H  CONST_20  C10  C13  C11  C26    0.00   0.0  0
 50H  CONST_21  C10  C25  C27  C26    0.00   0.0  0
 50H  CONST_22  C5   C10  C25  C27  180.00   0.0  0
 50H  CONST_23  C11  C13  C10  C25    0.00   0.0  0
 50H  CONST_24  C11  C26  C27  C25    0.00   0.0  0
 50H  CONST_25  C1   C3   N7   C12  180.00   0.0  0
 50H  CONST_26  N4   C3   N7   C12    0.00   0.0  0
 50H  CONST_27  C3   N4   C14  C12    0.00   0.0  0
 50H  CONST_28  C3   N7   C12  C14    0.00   0.0  0
 50H  CONST_29  N7   C3   N4   C14    0.00   0.0  0
 50H  CONST_30  C1   C3   N4   C14  180.00   0.0  0
 50H  CONST_31  C5   C6   N4   C14  180.00   0.0  0
 50H  CONST_32  C1   N2   C5   C10  180.00   0.0  0
 50H  CONST_33  N4   C6   C5   C10  180.00   0.0  0
 50H  CONST_34  C5   C10  C13  C11  180.00   0.0  0
 50H  CONST_35  C5   N2   C1   C3     0.00   0.0  0
 50H  CONST_36  C5   C6   N4   C3     0.00   0.0  0
 50H  CONST_37  N4   C14  C12  N7     0.00   0.0  0
 50H  CONST_38  C10  C13  C11  C9   180.00   0.0  0
 50H  CONST_39  C27  C26  C11  C9   180.00   0.0  0
 50H  CONST_40  N8   C17  C22  C20  180.00   0.0  0
 50H  CONST_41  O23  C16  C18  C20  180.00   0.0  0
 50H  CONST_42  N8   C17  C15  C16  180.00   0.0  0
 50H  CONST_43  O24  C18  C20  C22  180.00   0.0  0
 50H  CONST_44  O24  C18  C16  C15  180.00   0.0  0
 50H  CONST_45  O23  C16  C15  C17  180.00   0.0  0
 50H  CONST_46  N8   C1   N2   C5   180.00   0.0  0
 50H  CONST_47  N8   C1   C3   N7     0.00   0.0  0
 50H  CONST_48  N8   C1   C3   N4   180.00   0.0  0
 50H  CONST_49  H1   C6   C5   N2   180.00   0.0  0
 50H  CONST_50  H10  C14  N4   C6     0.00   0.0  0
 50H  CONST_51  H6   C25  C10  C13  180.00   0.0  0
 50H  CONST_52  H4   C26  C11  C13  180.00   0.0  0
 50H  CONST_53  H7   C22  C20  C18  180.00   0.0  0
 50H  CONST_54  H8   C15  C16  C18  180.00   0.0  0
 50H  CONST_55  H3   C20  C18  C16  180.00   0.0  0
 50H  CONST_56  H2   C13  C11  C26  180.00   0.0  0
 50H  CONST_57  H5   C27  C25  C10  180.00   0.0  0
 50H  CONST_58  H9   C12  N7   C3   180.00   0.0  0
 50H  CONST_59  H17  N21  C9   C11  180.00   0.0  0
 50H  CONST_60  H18  N21  C9   C11    0.00   0.0  0
 50H  Var_01    C17  N8   C1   N2    -0.18  30.0  3
 50H  Var_02    C1   N8   C17  C22    3.23  30.0  2
 50H  Var_03    N21  C9   C11  C13  158.78  30.0  2
 50H  Var_04    H11  C29  O24  C18  -61.00  30.0  3
 50H  Var_05    H14  C28  O23  C16  -61.95  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
 50H  plan-1  C20  0.020
 50H  plan-1  C18  0.020
 50H  plan-1  C16  0.020
 50H  plan-1  C22  0.020
 50H  plan-1  C15  0.020
 50H  plan-1  C17  0.020
 50H  plan-1  N8   0.020
 50H  plan-1  O23  0.020
 50H  plan-1  H3   0.020
 50H  plan-1  H7   0.020
 50H  plan-1  H8   0.020
 50H  plan-1  O24  0.020
 50H  plan-2  C9   0.020
 50H  plan-2  C13  0.020
 50H  plan-2  C26  0.020
 50H  plan-2  C27  0.020
 50H  plan-2  C25  0.020
 50H  plan-2  C10  0.020
 50H  plan-2  C11  0.020
 50H  plan-2  C5   0.020
 50H  plan-2  H2   0.020
 50H  plan-2  H4   0.020
 50H  plan-2  H5   0.020
 50H  plan-2  H6   0.020
 50H  plan-3  N2   0.020
 50H  plan-3  C6   0.020
 50H  plan-3  C12  0.020
 50H  plan-3  C14  0.020
 50H  plan-3  C10  0.020
 50H  plan-3  C3   0.020
 50H  plan-3  C5   0.020
 50H  plan-3  C1   0.020
 50H  plan-3  N7   0.020
 50H  plan-3  N4   0.020
 50H  plan-3  N8   0.020
 50H  plan-3  H1   0.020
 50H  plan-3  H9   0.020
 50H  plan-3  H10  0.020
 50H  plan-4  C9   0.020
 50H  plan-4  C11  0.020
 50H  plan-4  N21  0.020
 50H  plan-4  O19  0.020
 50H  plan-4  H17  0.020
 50H  plan-4  H18  0.020

