# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:39:20 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2n(c(CCc3nc(C)c4ncccn34)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
 X4C  X4C  8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine  ligand  49  28  .  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_X4C
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
 X4C  C25  C  CR16  0  -0.246   0.1333   3.8328  -0.2967
 X4C  C24  C  CR16  0  -0.257  -0.2940   3.1212  -1.4107
 X4C  C26  C  CR16  0  -0.259  -0.0935   3.3291   0.9779
 X4C  C17  C  CR16  0  -0.312  -5.4651   0.1805  -0.5287
 X4C  C15  C  CR16  0  -0.289  -4.2132   0.7625  -0.4379
 X4C  C23  C  CR16  0  -0.266  -0.9399   1.9023  -1.2547
 X4C  C27  C  CR16  0  -0.260  -0.7512   2.1179   1.1422
 X4C  C12  C  CR16  0  -0.387  -4.6375  -1.9748   0.1858
 X4C  C16  C  CR6   0   0.081  -5.6939  -1.1758  -0.2257
 X4C  C8   C  CR56  0   0.153  -3.3650  -1.4122   0.2823
 X4C  C10  C  CR56  0   0.312  -3.1731  -0.0616  -0.0316
 X4C  C18  C  CR6   0   0.246  -1.1640   1.4050   0.0234
 X4C  C9   C  CR5   0   0.090   4.4860  -1.9471   0.0941
 X4C  C7   C  CR56  0   0.383   4.4578  -0.5714   0.1593
 X4C  C1   C  CR5   0   0.438  -1.2905  -1.0210   0.6020
 X4C  C2   C  CR5   0   0.444   2.4215  -1.3711  -0.2291
 X4C  C21  C  CR16  0  -0.404   3.6950   2.0275   0.1523
 X4C  C14  C  CR16  0   0.086   2.7429   1.0949  -0.0585
 X4C  C22  C  CR16  0  -0.061   5.0439   1.6029   0.3678
 X4C  C20  C  CH3   0  -0.721  -7.0773  -1.7452  -0.3713
 X4C  C11  C  CH2   0  -0.563   0.1658  -1.1735   0.8613
 X4C  C13  C  CH2   0  -0.561   0.9527  -1.4042  -0.4448
 X4C  N4   N  N     0  -0.471  -2.1725  -1.9778   0.6702
 X4C  N3   N  N     0  -0.451   3.2288  -2.4032  -0.1420
 X4C  N19  N  N     0  -0.406   5.4092   0.3582   0.3680
 X4C  N5   N  NR5   0  -0.634  -1.8326   0.1664   0.1840
 X4C  N6   N  N     0  -0.531   3.1177  -0.2191  -0.0519
 X4C  H1   H  HCR6  0   0.270   0.6429   4.7789  -0.4222
 X4C  H2   H  HCR6  0   0.272  -0.1173   3.5092  -2.4048
 X4C  H3   H  HCR6  0   0.272   0.2354   3.8806   1.8484
 X4C  H4   H  HCR6  0   0.247  -6.3033   0.7926  -0.8398
 X4C  H5   H  HCR6  0   0.266  -4.0621   1.8092  -0.6690
 X4C  H6   H  HCR6  0   0.281  -1.2652   1.3386  -2.1199
 X4C  H7   H  HCR6  0   0.282  -0.9446   1.7275   2.1331
 X4C  H8   H  HCR6  0   0.247  -4.7941  -3.0186   0.4317
 X4C  H9   H  HCR6  0   0.286   3.4427   3.0769   0.1556
 X4C  H10  H  HCR6  0   0.299   1.7014   1.3206  -0.2368
 X4C  H11  H  HCR6  0   0.272   5.8120   2.3479   0.5398
 X4C  H12  H  HCH3  0   0.244  -7.2987  -1.9834  -1.4138
 X4C  H13  H  HCH3  0   0.242  -7.1959  -2.6622   0.2047
 X4C  H14  H  HCH3  0   0.241  -7.8371  -1.0384  -0.0367
 X4C  H15  H  HCH3  0   0.244   5.5534  -3.5072   1.1048
 X4C  H16  H  HCH3  0   0.244   5.8023  -3.4710  -0.6350
 X4C  H17  H  HCH3  0   0.244   6.5732  -2.2618   0.3888
 X4C  H18  H  HCH2  0   0.275   0.5482  -0.2964   1.3873
 X4C  H19  H  HCH2  0   0.291   0.3100  -2.0253   1.5250
 X4C  H20  H  HCH2  0   0.273   0.6680  -0.6627  -1.1968
 X4C  H21  H  HCH2  0   0.292   0.6887  -2.3779  -0.8563
 X4C  C28  C  CH3   0  -0.737   5.6632  -2.8425   0.2463

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
 X4C  C17  C15  aromatic  1.384  0.020  1.384
 X4C  C17  C16  aromatic  1.408  0.020  1.408
 X4C  C15  C10  aromatic  1.388  0.020  1.388
 X4C  C20  C16  single    1.503  0.020  1.503
 X4C  C26  C25  aromatic  1.389  0.020  1.389
 X4C  C26  C27  aromatic  1.388  0.020  1.388
 X4C  C25  C24  aromatic  1.389  0.020  1.389
 X4C  C16  C12  aromatic  1.387  0.020  1.387
 X4C  C27  C18  aromatic  1.389  0.020  1.389
 X4C  C24  C23  aromatic  1.388  0.020  1.388
 X4C  C10  N5   aromatic  1.377  0.020  1.377
 X4C  C10  C8   aromatic  1.400  0.020  1.400
 X4C  C18  C23  aromatic  1.390  0.020  1.390
 X4C  C18  N5   single    1.417  0.020  1.417
 X4C  C12  C8   aromatic  1.395  0.020  1.395
 X4C  N5   C1   aromatic  1.371  0.020  1.371
 X4C  C8   N4   aromatic  1.376  0.020  1.376
 X4C  C1   N4   aromatic  1.303  0.020  1.303
 X4C  C1   C11  single    1.487  0.020  1.487
 X4C  C11  C13  single    1.542  0.020  1.542
 X4C  C21  C14  aromatic  1.349  0.020  1.349
 X4C  C21  C22  aromatic  1.430  0.020  1.430
 X4C  C14  N6   aromatic  1.366  0.020  1.366
 X4C  C13  C2   single    1.485  0.020  1.485
 X4C  N6   C2   aromatic  1.358  0.020  1.358
 X4C  N6   C7   aromatic  1.402  0.020  1.402
 X4C  C22  N19  aromatic  1.297  0.020  1.297
 X4C  C2   N3   aromatic  1.313  0.020  1.313
 X4C  C7   N19  aromatic  1.346  0.020  1.346
 X4C  C7   C9   aromatic  1.378  0.020  1.378
 X4C  N3   C9   aromatic  1.358  0.020  1.358
 X4C  C9   C28  single    1.487  0.020  1.487
 X4C  C25  H1   single    0.930  0.020  1.080
 X4C  C24  H2   single    0.930  0.020  1.080
 X4C  C26  H3   single    0.930  0.020  1.080
 X4C  C17  H4   single    0.930  0.020  1.080
 X4C  C15  H5   single    0.930  0.020  1.080
 X4C  C23  H6   single    0.930  0.020  1.080
 X4C  C27  H7   single    0.930  0.020  1.080
 X4C  C12  H8   single    0.930  0.020  1.080
 X4C  C21  H9   single    0.930  0.020  1.080
 X4C  C14  H10  single    0.930  0.020  1.080
 X4C  C22  H11  single    0.930  0.020  1.080
 X4C  C20  H12  single    0.970  0.020  1.090
 X4C  C20  H13  single    0.970  0.020  1.090
 X4C  C20  H14  single    0.970  0.020  1.090
 X4C  C28  H15  single    0.970  0.020  1.090
 X4C  C28  H16  single    0.970  0.020  1.090
 X4C  C28  H17  single    0.970  0.020  1.090
 X4C  C11  H18  single    0.970  0.020  1.090
 X4C  C11  H19  single    0.970  0.020  1.090
 X4C  C13  H20  single    0.970  0.020  1.090
 X4C  C13  H21  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
 X4C  H1   C25  C26  120.03  3.000
 X4C  H1   C25  C24  119.98  3.000
 X4C  C26  C25  C24  119.99  3.000
 X4C  H2   C24  C23  119.62  3.000
 X4C  H2   C24  C25  120.20  3.000
 X4C  C23  C24  C25  120.18  3.000
 X4C  H3   C26  C27  119.59  3.000
 X4C  H3   C26  C25  120.26  3.000
 X4C  C27  C26  C25  120.16  3.000
 X4C  H4   C17  C16  118.69  3.000
 X4C  H4   C17  C15  118.76  3.000
 X4C  C16  C17  C15  122.55  3.000
 X4C  H5   C15  C10  122.14  3.000
 X4C  H5   C15  C17  121.27  3.000
 X4C  C10  C15  C17  116.59  3.000
 X4C  H6   C23  C18  120.01  3.000
 X4C  H6   C23  C24  120.47  3.000
 X4C  C18  C23  C24  119.51  3.000
 X4C  H7   C27  C18  119.94  3.000
 X4C  H7   C27  C26  120.51  3.000
 X4C  C18  C27  C26  119.55  3.000
 X4C  H8   C12  C8   120.31  3.000
 X4C  H8   C12  C16  120.80  3.000
 X4C  C8   C12  C16  118.89  3.000
 X4C  C20  C16  C12  120.77  3.000
 X4C  C12  C16  C17  119.66  3.000
 X4C  C20  C16  C17  119.57  3.000
 X4C  N4   C8   C10  109.94  3.000
 X4C  N4   C8   C12  130.14  3.000
 X4C  C10  C8   C12  119.92  3.000
 X4C  N5   C10  C8   104.97  3.000
 X4C  C8   C10  C15  122.40  3.000
 X4C  N5   C10  C15  132.62  3.000
 X4C  N5   C18  C27  119.83  3.000
 X4C  N5   C18  C23  119.56  3.000
 X4C  C27  C18  C23  120.60  3.000
 X4C  N3   C9   C28  123.27  3.000
 X4C  C28  C9   C7   127.79  3.000
 X4C  N3   C9   C7   108.95  3.000
 X4C  N6   C7   N19  121.69  3.000
 X4C  N19  C7   C9   133.03  3.000
 X4C  N6   C7   C9   105.27  3.000
 X4C  N5   C1   N4   112.60  3.000
 X4C  N4   C1   C11  125.34  3.000
 X4C  N5   C1   C11  121.97  3.000
 X4C  N6   C2   N3   110.06  3.000
 X4C  N3   C2   C13  126.88  3.000
 X4C  N6   C2   C13  123.04  3.000
 X4C  H9   C21  C22  120.57  3.000
 X4C  H9   C21  C14  120.50  3.000
 X4C  C22  C21  C14  118.93  3.000
 X4C  H10  C14  N6   117.78  3.000
 X4C  H10  C14  C21  124.16  3.000
 X4C  N6   C14  C21  118.06  3.000
 X4C  H11  C22  N19  117.39  3.000
 X4C  H11  C22  C21  119.22  3.000
 X4C  N19  C22  C21  123.39  3.000
 X4C  H14  C20  H13  107.91  3.000
 X4C  H14  C20  H12  107.04  3.000
 X4C  H13  C20  H12  107.41  3.000
 X4C  H14  C20  C16  111.47  3.000
 X4C  H13  C20  C16  111.58  3.000
 X4C  H12  C20  C16  111.21  3.000
 X4C  H19  C11  H18  106.75  3.000
 X4C  H19  C11  C13  109.36  3.000
 X4C  H18  C11  C13  110.46  3.000
 X4C  H19  C11  C1   108.42  3.000
 X4C  H18  C11  C1   110.16  3.000
 X4C  C13  C11  C1   111.55  3.000
 X4C  H21  C13  H20  106.45  3.000
 X4C  H21  C13  C11  109.27  3.000
 X4C  H20  C13  C11  110.37  3.000
 X4C  H21  C13  C2   108.33  3.000
 X4C  H20  C13  C2   110.01  3.000
 X4C  C11  C13  C2   112.23  3.000
 X4C  C1   N4   C8   105.67  3.000
 X4C  C2   N3   C9   108.46  3.000
 X4C  C22  N19  C7   117.61  3.000
 X4C  C1   N5   C18  127.25  3.000
 X4C  C1   N5   C10  106.82  3.000
 X4C  C18  N5   C10  125.92  3.000
 X4C  C14  N6   C2   132.43  3.000
 X4C  C2   N6   C7   107.26  3.000
 X4C  C14  N6   C7   120.31  3.000
 X4C  H17  C28  H16  107.83  3.000
 X4C  H17  C28  H15  107.82  3.000
 X4C  H16  C28  H15  107.29  3.000
 X4C  H17  C28  C9   110.73  3.000
 X4C  H16  C28  C9   111.41  3.000
 X4C  H15  C28  C9   111.58  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
 X4C  CONST_01  C18  C27  C26  C25    0.00   0.0  0
 X4C  CONST_02  C18  C23  C24  C25    0.00   0.0  0
 X4C  CONST_03  C27  C26  C25  C24    0.00   0.0  0
 X4C  CONST_04  C27  C18  C23  C24    0.00   0.0  0
 X4C  CONST_05  N5   C18  C23  C24  180.00   0.0  0
 X4C  CONST_06  C23  C24  C25  C26    0.00   0.0  0
 X4C  CONST_07  C23  C18  C27  C26    0.00   0.0  0
 X4C  CONST_08  N5   C18  C27  C26  180.00   0.0  0
 X4C  CONST_09  N5   C10  C15  C17  180.00   0.0  0
 X4C  CONST_10  C8   C10  C15  C17    0.00   0.0  0
 X4C  CONST_11  C8   C12  C16  C17    0.00   0.0  0
 X4C  CONST_12  C12  C16  C17  C15    0.00   0.0  0
 X4C  CONST_13  C18  N5   C10  C15    0.00   0.0  0
 X4C  CONST_14  C1   N5   C10  C15  180.00   0.0  0
 X4C  CONST_15  C12  C8   C10  C15    0.00   0.0  0
 X4C  CONST_16  N4   C8   C10  C15  180.00   0.0  0
 X4C  CONST_21  N5   C10  C8   C12  180.00   0.0  0
 X4C  CONST_22  C1   N4   C8   C12  180.00   0.0  0
 X4C  CONST_23  C10  C15  C17  C16    0.00   0.0  0
 X4C  CONST_24  C10  C8   C12  C16    0.00   0.0  0
 X4C  CONST_25  N4   C8   C12  C16  180.00   0.0  0
 X4C  CONST_26  C18  N5   C10  C8   180.00   0.0  0
 X4C  CONST_27  C1   N5   C10  C8     0.00   0.0  0
 X4C  CONST_28  N5   C1   N4   C8     0.00   0.0  0
 X4C  CONST_29  N4   C1   N5   C10    0.00   0.0  0
 X4C  CONST_30  C1   N4   C8   C10    0.00   0.0  0
 X4C  CONST_31  N4   C1   N5   C18  180.00   0.0  0
 X4C  CONST_32  C14  N6   C7   C9   180.00   0.0  0
 X4C  CONST_33  C2   N6   C7   C9     0.00   0.0  0
 X4C  CONST_34  C22  N19  C7   C9   180.00   0.0  0
 X4C  CONST_35  N6   C2   N3   C9     0.00   0.0  0
 X4C  CONST_36  C21  C14  N6   C7     0.00   0.0  0
 X4C  CONST_37  N3   C2   N6   C7     0.00   0.0  0
 X4C  CONST_38  C21  C22  N19  C7     0.00   0.0  0
 X4C  CONST_39  C2   N3   C9   C7     0.00   0.0  0
 X4C  CONST_40  C21  C14  N6   C2   180.00   0.0  0
 X4C  CONST_41  N19  C7   N6   C2   180.00   0.0  0
 X4C  CONST_42  N19  C22  C21  C14    0.00   0.0  0
 X4C  CONST_43  N3   C2   N6   C14  180.00   0.0  0
 X4C  CONST_44  N19  C7   N6   C14    0.00   0.0  0
 X4C  CONST_45  N6   C14  C21  C22    0.00   0.0  0
 X4C  CONST_46  N6   C7   N19  C22    0.00   0.0  0
 X4C  CONST_47  N5   C10  C8   N4     0.00   0.0  0
 X4C  CONST_48  N6   C7   C9   N3     0.00   0.0  0
 X4C  CONST_49  N19  C7   C9   N3   180.00   0.0  0
 X4C  CONST_50  C20  C16  C17  C15  180.00   0.0  0
 X4C  CONST_51  C20  C16  C12  C8   180.00   0.0  0
 X4C  CONST_52  C11  C1   N4   C8   180.00   0.0  0
 X4C  CONST_53  C11  C1   N5   C10  180.00   0.0  0
 X4C  CONST_54  C11  C1   N5   C18    0.00   0.0  0
 X4C  CONST_55  C13  C2   N3   C9   180.00   0.0  0
 X4C  CONST_56  C13  C2   N6   C7   180.00   0.0  0
 X4C  CONST_57  C28  C9   N3   C2   180.00   0.0  0
 X4C  CONST_58  C13  C2   N6   C14    0.00   0.0  0
 X4C  CONST_59  N6   C7   C9   C28  180.00   0.0  0
 X4C  CONST_60  N19  C7   C9   C28    0.00   0.0  0
 X4C  CONST_61  H7   C27  C26  C25  180.00   0.0  0
 X4C  CONST_62  H6   C23  C24  C25  180.00   0.0  0
 X4C  CONST_63  H3   C26  C25  C24  180.00   0.0  0
 X4C  CONST_64  H2   C24  C25  C26  180.00   0.0  0
 X4C  CONST_65  H8   C12  C16  C17  180.00   0.0  0
 X4C  CONST_66  H1   C25  C24  C23  180.00   0.0  0
 X4C  CONST_67  H4   C17  C16  C12  180.00   0.0  0
 X4C  CONST_68  H5   C15  C17  C16  180.00   0.0  0
 X4C  CONST_69  H10  C14  N6   C7   180.00   0.0  0
 X4C  CONST_70  H11  C22  N19  C7   180.00   0.0  0
 X4C  CONST_71  H9   C21  C22  N19  180.00   0.0  0
 X4C  Var_01    C2   C13  C11  C1   172.09  30.0  3
 X4C  Var_02    N6   C2   C13  C11  -76.43  30.0  2
 X4C  Var_03    N5   C1   C11  C13  -81.16  30.0  2
 X4C  Var_04    H12  C20  C16  C17   79.99  30.0  2
 X4C  Var_05    H15  C28  C9   C7   117.88  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
 X4C  plan-1  C25  0.020
 X4C  plan-1  C24  0.020
 X4C  plan-1  C26  0.020
 X4C  plan-1  C23  0.020
 X4C  plan-1  C27  0.020
 X4C  plan-1  C18  0.020
 X4C  plan-1  N5   0.020
 X4C  plan-1  H1   0.020
 X4C  plan-1  H2   0.020
 X4C  plan-1  H3   0.020
 X4C  plan-1  H6   0.020
 X4C  plan-1  H7   0.020
 X4C  plan-2  C17  0.020
 X4C  plan-2  C15  0.020
 X4C  plan-2  C12  0.020
 X4C  plan-2  C16  0.020
 X4C  plan-2  C8   0.020
 X4C  plan-2  C10  0.020
 X4C  plan-2  C18  0.020
 X4C  plan-2  C1   0.020
 X4C  plan-2  C20  0.020
 X4C  plan-2  C11  0.020
 X4C  plan-2  N4   0.020
 X4C  plan-2  N5   0.020
 X4C  plan-2  H4   0.020
 X4C  plan-2  H5   0.020
 X4C  plan-2  H8   0.020
 X4C  plan-3  C9   0.020
 X4C  plan-3  C7   0.020
 X4C  plan-3  C2   0.020
 X4C  plan-3  C21  0.020
 X4C  plan-3  C14  0.020
 X4C  plan-3  C22  0.020
 X4C  plan-3  C13  0.020
 X4C  plan-3  N3   0.020
 X4C  plan-3  N19  0.020
 X4C  plan-3  N6   0.020
 X4C  plan-3  H9   0.020
 X4C  plan-3  H10  0.020
 X4C  plan-3  H11  0.020
 X4C  plan-3  C28  0.020

