# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:44:01 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 7-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-b]pyridazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2n(c(CCc3ncc4cccnn34)nc2c1)c5ccccc5
#
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
 X4D  X4D  7-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-b]pyridazine  ligand  46  27  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X4D
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
 X4D  C25  C  CR16  0  -0.245  -1.4374   4.5209   0.3237
 X4D  C24  C  CR16  0  -0.253  -0.9493   3.8386  -0.7827
 X4D  C26  C  CR16  0  -0.255  -2.0320   3.8194   1.3648
 X4D  C17  C  CR16  0  -0.312  -5.1912  -0.9622  -0.2965
 X4D  C15  C  CR16  0  -0.287  -4.2519   0.0447  -0.1641
 X4D  C23  C  CR16  0  -0.266  -1.0583   2.4570  -0.8537
 X4D  C27  C  CR16  0  -0.265  -2.1317   2.4369   1.3070
 X4D  C12  C  CR16  0  -0.388  -3.5175  -2.6970  -0.1250
 X4D  C9   C  CR15  0  -0.268   4.6893   1.1821  -1.0087
 X4D  C16  C  CR6   0   0.081  -4.8450  -2.3277  -0.2798
 X4D  C8   C  CR56  0   0.150  -2.5512  -1.6999   0.0088
 X4D  C10  C  CR56  0   0.306  -2.9306  -0.3528  -0.0110
 X4D  C18  C  CR6   0   0.262  -1.6408   1.7611   0.1971
 X4D  C7   C  CR56  0   0.385   5.0073   0.0549  -0.2841
 X4D  C2   C  CR5   0   0.443   2.8557   0.0600  -0.8421
 X4D  C1   C  CR5   0   0.450  -0.7516  -0.5751   0.2455
 X4D  C19  C  CR16  0  -0.286   6.1392  -0.5215   0.3286
 X4D  C22  C  CR16  0  -0.292   5.9819  -1.7128   0.9608
 X4D  C21  C  CR16  0  -0.065   4.6910  -2.3217   0.9733
 X4D  C20  C  CH3   0  -0.721  -5.9190  -3.3654  -0.4515
 X4D  C13  C  CH2   0  -0.531   1.4404  -0.3754  -0.9344
 X4D  C11  C  CH2   0  -0.556   0.6808  -0.2000   0.3923
 X4D  N3   N  N     0  -0.426   3.3769   1.1643  -1.3358
 X4D  N4   N  N     0  -0.472  -1.1904  -1.8010   0.1717
 X4D  N14  N  N     0  -0.232   3.6324  -1.8230   0.4229
 X4D  N5   N  NR5   0  -0.636  -1.7554   0.3505   0.1368
 X4D  N6   N  N     0  -0.395   3.8093  -0.6464  -0.1920
 X4D  H1   H  HCR6  0   0.266  -1.3555   5.5985   0.3745
 X4D  H2   H  HCR6  0   0.268  -0.4893   4.3801  -1.5984
 X4D  H3   H  HCR6  0   0.268  -2.4141   4.3469   2.2286
 X4D  H4   H  HCR6  0   0.247  -6.2334  -0.6914  -0.4168
 X4D  H5   H  HCR6  0   0.265  -4.5420   1.0876  -0.1784
 X4D  H6   H  HCR6  0   0.274  -0.6976   1.9240  -1.7238
 X4D  H7   H  HCR6  0   0.276  -2.5809   1.8841   2.1220
 X4D  H8   H  HCR6  0   0.245  -3.2299  -3.7419  -0.1064
 X4D  H10  H  HCR6  0   0.288   7.0932  -0.0145   0.2824
 X4D  H11  H  HCR6  0   0.284   6.8045  -2.2105   1.4521
 X4D  H12  H  HCR6  0   0.294   4.5449  -3.2720   1.4697
 X4D  H13  H  HCH3  0   0.244  -6.2274  -3.4464  -1.4959
 X4D  H14  H  HCH3  0   0.242  -5.5795  -4.3502  -0.1333
 X4D  H15  H  HCH3  0   0.241  -6.8100  -3.1145   0.1250
 X4D  H16  H  HCH2  0   0.275   0.9665   0.2159  -1.7181
 X4D  H17  H  HCH2  0   0.274   1.3829  -1.4211  -1.2433
 X4D  H18  H  HCH2  0   0.276   0.7758   0.8297   0.7389
 X4D  H19  H  HCH2  0   0.283   1.1269  -0.8389   1.1552
 X4D  H9   H  HCR5  0   0.265   5.3487   1.9844  -1.3017

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
 X4D  C17  C15  aromatic  1.383  0.020  1.383
 X4D  C17  C16  aromatic  1.409  0.020  1.409
 X4D  C15  C10  aromatic  1.388  0.020  1.388
 X4D  C26  C25  aromatic  1.389  0.020  1.389
 X4D  C26  C27  aromatic  1.387  0.020  1.387
 X4D  C25  C24  aromatic  1.388  0.020  1.388
 X4D  C20  C16  single    1.503  0.020  1.503
 X4D  C27  C18  aromatic  1.389  0.020  1.389
 X4D  C16  C12  aromatic  1.387  0.020  1.387
 X4D  C24  C23  aromatic  1.388  0.020  1.388
 X4D  C10  N5   aromatic  1.378  0.020  1.378
 X4D  C10  C8   aromatic  1.400  0.020  1.400
 X4D  C18  C23  aromatic  1.388  0.020  1.388
 X4D  C18  N5   single    1.416  0.020  1.416
 X4D  N5   C1   aromatic  1.370  0.020  1.370
 X4D  C12  C8   aromatic  1.395  0.020  1.395
 X4D  C8   N4   aromatic  1.374  0.020  1.374
 X4D  C1   N4   aromatic  1.304  0.020  1.304
 X4D  C1   C11  single    1.488  0.020  1.488
 X4D  C11  C13  single    1.539  0.020  1.539
 X4D  C13  C2   single    1.484  0.020  1.484
 X4D  N3   C2   aromatic  1.317  0.020  1.317
 X4D  N3   C9   aromatic  1.353  0.020  1.353
 X4D  C2   N6   aromatic  1.353  0.020  1.353
 X4D  C9   C7   aromatic  1.377  0.020  1.377
 X4D  N6   C7   aromatic  1.391  0.020  1.391
 X4D  N6   N14  aromatic  1.339  0.020  1.339
 X4D  C7   C19  aromatic  1.410  0.020  1.410
 X4D  N14  C21  aromatic  1.293  0.020  1.293
 X4D  C19  C22  aromatic  1.358  0.020  1.358
 X4D  C21  C22  aromatic  1.427  0.020  1.427
 X4D  C25  H1   single    0.930  0.020  1.080
 X4D  C24  H2   single    0.930  0.020  1.080
 X4D  C26  H3   single    0.930  0.020  1.080
 X4D  C17  H4   single    0.930  0.020  1.080
 X4D  C15  H5   single    0.930  0.020  1.080
 X4D  C23  H6   single    0.930  0.020  1.080
 X4D  C27  H7   single    0.930  0.020  1.080
 X4D  C12  H8   single    0.930  0.020  1.080
 X4D  C9   H9   single    0.930  0.020  1.080
 X4D  C19  H10  single    0.930  0.020  1.080
 X4D  C22  H11  single    0.930  0.020  1.080
 X4D  C21  H12  single    0.930  0.020  1.080
 X4D  C20  H13  single    0.970  0.020  1.090
 X4D  C20  H14  single    0.970  0.020  1.090
 X4D  C20  H15  single    0.970  0.020  1.090
 X4D  C13  H16  single    0.970  0.020  1.090
 X4D  C13  H17  single    0.970  0.020  1.090
 X4D  C11  H18  single    0.970  0.020  1.090
 X4D  C11  H19  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
 X4D  H1   C25  C26  120.01  3.000
 X4D  H1   C25  C24  120.02  3.000
 X4D  C26  C25  C24  119.97  3.000
 X4D  H2   C24  C23  119.55  3.000
 X4D  H2   C24  C25  120.29  3.000
 X4D  C23  C24  C25  120.16  3.000
 X4D  H3   C26  C27  119.60  3.000
 X4D  H3   C26  C25  120.22  3.000
 X4D  C27  C26  C25  120.18  3.000
 X4D  H4   C17  C16  118.68  3.000
 X4D  H4   C17  C15  118.80  3.000
 X4D  C16  C17  C15  122.52  3.000
 X4D  H5   C15  C10  122.16  3.000
 X4D  H5   C15  C17  121.20  3.000
 X4D  C10  C15  C17  116.64  3.000
 X4D  H6   C23  C18  120.09  3.000
 X4D  H6   C23  C24  120.35  3.000
 X4D  C18  C23  C24  119.56  3.000
 X4D  H7   C27  C18  119.98  3.000
 X4D  H7   C27  C26  120.49  3.000
 X4D  C18  C27  C26  119.53  3.000
 X4D  H8   C12  C8   120.24  3.000
 X4D  H8   C12  C16  120.84  3.000
 X4D  C8   C12  C16  118.91  3.000
 X4D  H9   C9   N3   122.48  3.000
 X4D  H9   C9   C7   127.61  3.000
 X4D  N3   C9   C7   109.91  3.000
 X4D  C20  C16  C12  120.85  3.000
 X4D  C12  C16  C17  119.65  3.000
 X4D  C20  C16  C17  119.49  3.000
 X4D  N4   C8   C10  109.93  3.000
 X4D  N4   C8   C12  130.15  3.000
 X4D  C10  C8   C12  119.92  3.000
 X4D  N5   C10  C8   104.99  3.000
 X4D  C8   C10  C15  122.36  3.000
 X4D  N5   C10  C15  132.65  3.000
 X4D  N5   C18  C27  119.33  3.000
 X4D  N5   C18  C23  120.06  3.000
 X4D  C27  C18  C23  120.60  3.000
 X4D  N6   C7   C19  117.15  3.000
 X4D  C19  C7   C9   138.46  3.000
 X4D  N6   C7   C9   104.39  3.000
 X4D  N6   C2   N3   109.82  3.000
 X4D  N6   C2   C13  123.29  3.000
 X4D  N3   C2   C13  126.88  3.000
 X4D  N5   C1   N4   112.59  3.000
 X4D  N4   C1   C11  124.50  3.000
 X4D  N5   C1   C11  122.89  3.000
 X4D  H10  C19  C22  122.24  3.000
 X4D  H10  C19  C7   119.86  3.000
 X4D  C22  C19  C7   117.90  3.000
 X4D  H11  C22  C21  119.24  3.000
 X4D  H11  C22  C19  121.87  3.000
 X4D  C21  C22  C19  118.89  3.000
 X4D  H12  C21  N14  115.05  3.000
 X4D  H12  C21  C22  120.05  3.000
 X4D  N14  C21  C22  124.90  3.000
 X4D  H15  C20  H14  107.95  3.000
 X4D  H15  C20  H13  106.97  3.000
 X4D  H14  C20  H13  107.49  3.000
 X4D  H15  C20  C16  111.38  3.000
 X4D  H14  C20  C16  111.60  3.000
 X4D  H13  C20  C16  111.24  3.000
 X4D  H17  C13  H16  107.05  3.000
 X4D  H17  C13  C11  109.09  3.000
 X4D  H16  C13  C11  110.08  3.000
 X4D  H17  C13  C2   110.42  3.000
 X4D  H16  C13  C2   107.47  3.000
 X4D  C11  C13  C2   112.57  3.000
 X4D  H19  C11  H18  107.17  3.000
 X4D  H19  C11  C13  109.54  3.000
 X4D  H18  C11  C13  109.79  3.000
 X4D  H19  C11  C1   108.37  3.000
 X4D  H18  C11  C1   110.68  3.000
 X4D  C13  C11  C1   111.18  3.000
 X4D  C2   N3   C9   107.71  3.000
 X4D  C1   N4   C8   105.71  3.000
 X4D  N6   N14  C21  115.22  3.000
 X4D  C1   N5   C18  127.61  3.000
 X4D  C1   N5   C10  106.78  3.000
 X4D  C18  N5   C10  125.59  3.000
 X4D  N14  N6   C2   125.89  3.000
 X4D  N14  N6   C7   125.94  3.000
 X4D  C2   N6   C7   108.17  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
 X4D  CONST_01  C18  C27  C26  C25     0.00   0.0  0
 X4D  CONST_02  C18  C23  C24  C25     0.00   0.0  0
 X4D  CONST_03  C27  C26  C25  C24     0.00   0.0  0
 X4D  CONST_04  C27  C18  C23  C24     0.00   0.0  0
 X4D  CONST_05  N5   C18  C23  C24   180.00   0.0  0
 X4D  CONST_06  C23  C24  C25  C26     0.00   0.0  0
 X4D  CONST_07  C23  C18  C27  C26     0.00   0.0  0
 X4D  CONST_08  N5   C18  C27  C26   180.00   0.0  0
 X4D  CONST_09  N5   C10  C15  C17   180.00   0.0  0
 X4D  CONST_10  C8   C10  C15  C17     0.00   0.0  0
 X4D  CONST_11  C8   C12  C16  C17     0.00   0.0  0
 X4D  CONST_12  C12  C16  C17  C15     0.00   0.0  0
 X4D  CONST_13  C18  N5   C10  C15     0.00   0.0  0
 X4D  CONST_14  C1   N5   C10  C15   180.00   0.0  0
 X4D  CONST_15  C12  C8   C10  C15     0.00   0.0  0
 X4D  CONST_16  N4   C8   C10  C15   180.00   0.0  0
 X4D  CONST_21  N5   C10  C8   C12   180.00   0.0  0
 X4D  CONST_22  C1   N4   C8   C12   180.00   0.0  0
 X4D  CONST_23  N6   C2   N3   C9      0.00   0.0  0
 X4D  CONST_24  C2   N6   C7   C9      0.00   0.0  0
 X4D  CONST_25  N14  N6   C7   C9    180.00   0.0  0
 X4D  CONST_26  C22  C19  C7   C9    180.00   0.0  0
 X4D  CONST_27  C10  C15  C17  C16     0.00   0.0  0
 X4D  CONST_28  C10  C8   C12  C16     0.00   0.0  0
 X4D  CONST_29  N4   C8   C12  C16   180.00   0.0  0
 X4D  CONST_30  C18  N5   C10  C8    180.00   0.0  0
 X4D  CONST_31  C1   N5   C10  C8      0.00   0.0  0
 X4D  CONST_32  N5   C1   N4   C8      0.00   0.0  0
 X4D  CONST_33  N4   C1   N5   C10     0.00   0.0  0
 X4D  CONST_34  C1   N4   C8   C10     0.00   0.0  0
 X4D  CONST_35  N4   C1   N5   C18   180.00   0.0  0
 X4D  CONST_36  C2   N3   C9   C7      0.00   0.0  0
 X4D  CONST_37  N3   C2   N6   C7      0.00   0.0  0
 X4D  CONST_38  C21  N14  N6   C7      0.00   0.0  0
 X4D  CONST_39  C21  C22  C19  C7      0.00   0.0  0
 X4D  CONST_40  C19  C7   N6   C2    180.00   0.0  0
 X4D  CONST_41  C21  N14  N6   C2    180.00   0.0  0
 X4D  CONST_42  N3   C9   C7   C19   180.00   0.0  0
 X4D  CONST_43  N14  N6   C7   C19     0.00   0.0  0
 X4D  CONST_44  N14  C21  C22  C19     0.00   0.0  0
 X4D  CONST_45  N6   C7   C19  C22     0.00   0.0  0
 X4D  CONST_46  N6   N14  C21  C22     0.00   0.0  0
 X4D  CONST_47  N14  N6   C2   N3    180.00   0.0  0
 X4D  CONST_48  N6   C7   C9   N3      0.00   0.0  0
 X4D  CONST_49  N5   C10  C8   N4      0.00   0.0  0
 X4D  CONST_50  C20  C16  C17  C15   180.00   0.0  0
 X4D  CONST_51  C13  C2   N3   C9    180.00   0.0  0
 X4D  CONST_52  C20  C16  C12  C8    180.00   0.0  0
 X4D  CONST_53  C11  C1   N4   C8    180.00   0.0  0
 X4D  CONST_54  C11  C1   N5   C10   180.00   0.0  0
 X4D  CONST_55  C11  C1   N5   C18     0.00   0.0  0
 X4D  CONST_56  C13  C2   N6   C7    180.00   0.0  0
 X4D  CONST_57  N14  N6   C2   C13     0.00   0.0  0
 X4D  CONST_58  H7   C27  C26  C25   180.00   0.0  0
 X4D  CONST_59  H6   C23  C24  C25   180.00   0.0  0
 X4D  CONST_60  H3   C26  C25  C24   180.00   0.0  0
 X4D  CONST_61  H2   C24  C25  C26   180.00   0.0  0
 X4D  CONST_62  H8   C12  C16  C17   180.00   0.0  0
 X4D  CONST_63  H1   C25  C24  C23   180.00   0.0  0
 X4D  CONST_64  H4   C17  C16  C12   180.00   0.0  0
 X4D  CONST_65  H10  C19  C7   C9      0.00   0.0  0
 X4D  CONST_66  H5   C15  C17  C16   180.00   0.0  0
 X4D  CONST_67  H11  C22  C19  C7    180.00   0.0  0
 X4D  CONST_68  H9   C9   N3   C2    180.00   0.0  0
 X4D  CONST_69  H12  C21  C22  C19   180.00   0.0  0
 X4D  Var_01    C1   C11  C13  C2    176.89  30.0  1
 X4D  Var_02    N5   C1   C11  C13  -102.85  30.0  2
 X4D  Var_03    N3   C2   C13  C11  -105.11  30.0  2
 X4D  Var_04    H13  C20  C16  C17    76.66  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
 X4D  plan-1  C25  0.020
 X4D  plan-1  C24  0.020
 X4D  plan-1  C26  0.020
 X4D  plan-1  C23  0.020
 X4D  plan-1  C27  0.020
 X4D  plan-1  C18  0.020
 X4D  plan-1  N5   0.020
 X4D  plan-1  H1   0.020
 X4D  plan-1  H2   0.020
 X4D  plan-1  H3   0.020
 X4D  plan-1  H6   0.020
 X4D  plan-1  H7   0.020
 X4D  plan-2  C17  0.020
 X4D  plan-2  C15  0.020
 X4D  plan-2  C12  0.020
 X4D  plan-2  C16  0.020
 X4D  plan-2  C8   0.020
 X4D  plan-2  C10  0.020
 X4D  plan-2  C18  0.020
 X4D  plan-2  C1   0.020
 X4D  plan-2  C20  0.020
 X4D  plan-2  C11  0.020
 X4D  plan-2  N4   0.020
 X4D  plan-2  N5   0.020
 X4D  plan-2  H4   0.020
 X4D  plan-2  H5   0.020
 X4D  plan-2  H8   0.020
 X4D  plan-3  C9   0.020
 X4D  plan-3  C7   0.020
 X4D  plan-3  C2   0.020
 X4D  plan-3  C19  0.020
 X4D  plan-3  C22  0.020
 X4D  plan-3  C21  0.020
 X4D  plan-3  C13  0.020
 X4D  plan-3  N3   0.020
 X4D  plan-3  N14  0.020
 X4D  plan-3  N6   0.020
 X4D  plan-3  H10  0.020
 X4D  plan-3  H11  0.020
 X4D  plan-3  H12  0.020
 X4D  plan-3  H9   0.020

