# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 21:45:00 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 7-[[(4~{S})-5,7-bis(fluoranyl)-3,4-dihydro-2~{H}-chromen-4-yl]oxy]-~{N},~{N},2-trimethyl-3~{H}-benzimidazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)c1cc2[nH]c(C)nc2c(O[C@H]3CCOc4cc(F)cc(F)c34)c1
#
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
 8BN  8BN  "Tegoprazan"
  ligand  47  28  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8BN
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
 8BN  C10  C  CR5   0   0.421  39.7658  -41.3540  -66.5141
 8BN  C13  C  CR6   0   0.562  46.0319  -40.2224  -68.5857
 8BN  C15  C  CH2   0  -0.521  43.8392  -37.1925  -68.2277
 8BN  C02  C  CR16  0  -0.357  39.1999  -39.7923  -69.6856
 8BN  C04  C  CR16  0  -0.400  41.5031  -39.0074  -69.8886
 8BN  C05  C  CR6   0   0.332  41.8601  -39.5487  -68.6647
 8BN  C06  C  CR56  0   0.034  40.8735  -40.2369  -67.9457
 8BN  C07  C  CH3   0  -0.749  39.3551  -42.1352  -65.3211
 8BN  C09  C  CH1   0  -0.057  44.0797  -38.6369  -68.6370
 8BN  C11  C  CR6   0  -0.232  45.3853  -39.1074  -68.0726
 8BN  C12  C  CR6   0   0.438  46.0062  -38.4363  -67.0157
 8BN  C14  C  CH2   0  -0.190  44.1234  -37.0232  -66.7529
 8BN  C16  C  CR16  0  -0.528  47.2407  -38.8644  -66.5226
 8BN  O03  O  O2    0  -0.467  45.4753  -37.3529  -66.4381
 8BN  C01  C  CR56  0   0.369  39.5799  -40.3469  -68.4675
 8BN  C03  C  CR6   0  -0.070  40.1941  -39.1401  -70.3908
 8BN  C08  C  C     0   0.494  39.8455  -38.4788  -71.6884
 8BN  C17  C  CR16  0  -0.590  47.2457  -40.6865  -68.1296
 8BN  C18  C  CR6   0   0.555  47.8230  -39.9727  -67.0927
 8BN  C35  C  CH3   0  -0.525  41.4265  -39.9749  -72.8714
 8BN  C36  C  CH3   0  -0.523  40.4043  -38.0669  -74.0019
 8BN  F02  F  F     0  -0.306  49.0038  -40.3897  -66.6235
 8BN  N01  N  NR15  0  -0.694  38.9001  -41.0676  -67.5244
 8BN  N02  N  N     0  -0.462  40.9595  -40.8705  -66.7322
 8BN  N03  N  NT    0  -0.435  40.5986  -38.7906  -72.7629
 8BN  O02  O  O     0  -0.484  38.9323  -37.6641  -71.7345
 8BN  O04  O  O2    0  -0.474  43.0790  -39.4989  -68.0966
 8BN  H1   H  HCH2  0   0.269  44.4883  -36.5418  -68.8186
 8BN  H2   H  HCH2  0   0.277  42.8120  -36.8889  -68.4371
 8BN  H3   H  HCR6  0   0.265  38.1922  -39.8805  -70.0690
 8BN  H4   H  HCR6  0   0.282  42.2226  -38.4644  -70.4870
 8BN  H5   H  HCH3  0   0.263  40.1959  -42.2411  -64.6409
 8BN  H6   H  HCH3  0   0.263  38.5384  -41.6449  -64.7898
 8BN  H7   H  HCH3  0   0.263  39.0100  -43.1304  -65.6039
 8BN  H8   H  HCH1  0   0.279  44.1064  -38.7182  -69.7273
 8BN  H9   H  HCH2  0   0.261  43.9897  -35.9903  -66.4368
 8BN  H10  H  HCH2  0   0.238  43.4532  -37.6496  -66.1560
 8BN  H11  H  HCR6  0   0.291  47.7215  -38.3362  -65.7096
 8BN  H12  H  HCR6  0   0.299  47.7202  -41.5591  -68.5576
 8BN  H13  H  HCH3  0   0.264  41.3303  -40.6106  -71.9970
 8BN  H14  H  HCH3  0   0.250  41.1155  -40.5563  -73.7415
 8BN  H15  H  HCH3  0   0.241  42.4788  -39.7133  -72.9964
 8BN  H16  H  HCH3  0   0.252  40.1063  -37.0402  -73.8097
 8BN  H17  H  HCH3  0   0.245  41.3435  -38.0541  -74.5536
 8BN  H18  H  HCH3  0   0.237  39.6461  -38.5386  -74.6323
 8BN  H19  H  HNR5  0   0.419  37.9304  -41.3415  -67.5661
 8BN  F01  F  F     0  -0.300  45.4420  -40.8763  -69.5932

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
 8BN  C36  N03  single    1.448  0.020  1.448
 8BN  C35  N03  single    1.449  0.020  1.449
 8BN  N03  C08  single    1.349  0.020  1.349
 8BN  C08  O02  double    1.225  0.020  1.225
 8BN  C08  C03  single    1.497  0.020  1.497
 8BN  C03  C04  aromatic  1.408  0.020  1.408
 8BN  C03  C02  aromatic  1.382  0.020  1.382
 8BN  C04  C05  aromatic  1.385  0.020  1.385
 8BN  C02  C01  aromatic  1.391  0.020  1.391
 8BN  F01  C13  single    1.338  0.020  1.338
 8BN  C09  C15  single    1.520  0.020  1.520
 8BN  C09  O04  single    1.427  0.020  1.427
 8BN  C09  C11  single    1.498  0.020  1.498
 8BN  C15  C14  single    1.512  0.020  1.512
 8BN  C05  O04  single    1.346  0.020  1.346
 8BN  C05  C06  aromatic  1.401  0.020  1.401
 8BN  C01  C06  aromatic  1.399  0.020  1.399
 8BN  C01  N01  aromatic  1.368  0.020  1.368
 8BN  C13  C11  aromatic  1.387  0.020  1.387
 8BN  C13  C17  aromatic  1.377  0.020  1.377
 8BN  C11  C12  aromatic  1.397  0.020  1.397
 8BN  C06  N02  aromatic  1.372  0.020  1.372
 8BN  N01  C10  aromatic  1.361  0.020  1.361
 8BN  C17  C18  aromatic  1.385  0.020  1.385
 8BN  C14  O03  single    1.427  0.020  1.427
 8BN  N02  C10  aromatic  1.306  0.020  1.306
 8BN  C12  O03  single    1.338  0.020  1.338
 8BN  C12  C16  aromatic  1.397  0.020  1.397
 8BN  C10  C07  single    1.484  0.020  1.484
 8BN  C18  C16  aromatic  1.376  0.020  1.376
 8BN  C18  F02  single    1.337  0.020  1.337
 8BN  C15  H1   single    0.970  0.020  1.090
 8BN  C15  H2   single    0.970  0.020  1.090
 8BN  C02  H3   single    0.930  0.020  1.080
 8BN  C04  H4   single    0.930  0.020  1.080
 8BN  C07  H5   single    0.970  0.020  1.090
 8BN  C07  H6   single    0.970  0.020  1.090
 8BN  C07  H7   single    0.970  0.020  1.090
 8BN  C09  H8   single    0.970  0.020  1.090
 8BN  C14  H9   single    0.970  0.020  1.090
 8BN  C14  H10  single    0.970  0.020  1.090
 8BN  C16  H11  single    0.930  0.020  1.080
 8BN  C17  H12  single    0.930  0.020  1.080
 8BN  C35  H13  single    0.970  0.020  1.090
 8BN  C35  H14  single    0.970  0.020  1.090
 8BN  C35  H15  single    0.970  0.020  1.090
 8BN  C36  H16  single    0.970  0.020  1.090
 8BN  C36  H17  single    0.970  0.020  1.090
 8BN  C36  H18  single    0.970  0.020  1.090
 8BN  N01  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
 8BN  N02  C10  N01  112.30  3.000
 8BN  N02  C10  C07  125.59  3.000
 8BN  N01  C10  C07  122.11  3.000
 8BN  F01  C13  C17  118.25  3.000
 8BN  C17  C13  C11  124.00  3.000
 8BN  F01  C13  C11  117.75  3.000
 8BN  H2   C15  H1   106.84  3.000
 8BN  H2   C15  C14  109.45  3.000
 8BN  H1   C15  C14  110.44  3.000
 8BN  H2   C15  C09  111.20  3.000
 8BN  H1   C15  C09  109.04  3.000
 8BN  C14  C15  C09  109.84  3.000
 8BN  H3   C02  C03  121.84  3.000
 8BN  H3   C02  C01  122.15  3.000
 8BN  C03  C02  C01  116.00  3.000
 8BN  H4   C04  C03  117.92  3.000
 8BN  H4   C04  C05  120.89  3.000
 8BN  C03  C04  C05  121.19  3.000
 8BN  O04  C05  C06  116.05  3.000
 8BN  C06  C05  C04  117.63  3.000
 8BN  O04  C05  C04  126.30  3.000
 8BN  N02  C06  C01  110.58  3.000
 8BN  N02  C06  C05  129.54  3.000
 8BN  C01  C06  C05  119.88  3.000
 8BN  H7   C07  H6   107.43  3.000
 8BN  H7   C07  H5   108.56  3.000
 8BN  H6   C07  H5   108.56  3.000
 8BN  H7   C07  C10  111.06  3.000
 8BN  H6   C07  C10  111.23  3.000
 8BN  H5   C07  C10  109.90  3.000
 8BN  H8   C09  O04  110.47  3.000
 8BN  H8   C09  C11  109.33  3.000
 8BN  O04  C09  C11  106.19  3.000
 8BN  H8   C09  C15  110.05  3.000
 8BN  C11  C09  C15  109.56  3.000
 8BN  O04  C09  C15  111.16  3.000
 8BN  C12  C11  C09  121.42  3.000
 8BN  C12  C11  C13  117.29  3.000
 8BN  C09  C11  C13  121.28  3.000
 8BN  O03  C12  C16  116.53  3.000
 8BN  C16  C12  C11  120.84  3.000
 8BN  O03  C12  C11  122.62  3.000
 8BN  H10  C14  H9   108.04  3.000
 8BN  H10  C14  O03  109.13  3.000
 8BN  H9   C14  O03  105.76  3.000
 8BN  H10  C14  C15  110.67  3.000
 8BN  H9   C14  C15  111.50  3.000
 8BN  O03  C14  C15  111.56  3.000
 8BN  H11  C16  C18  121.10  3.000
 8BN  H11  C16  C12  120.55  3.000
 8BN  C18  C16  C12  118.35  3.000
 8BN  C14  O03  C12  117.91  3.000
 8BN  N01  C01  C06  104.11  3.000
 8BN  N01  C01  C02  132.68  3.000
 8BN  C06  C01  C02  123.20  3.000
 8BN  C08  C03  C04  118.93  3.000
 8BN  C04  C03  C02  122.07  3.000
 8BN  C08  C03  C02  118.88  3.000
 8BN  O02  C08  N03  122.70  3.000
 8BN  O02  C08  C03  120.00  3.000
 8BN  N03  C08  C03  117.28  3.000
 8BN  H12  C17  C18  121.95  3.000
 8BN  H12  C17  C13  121.84  3.000
 8BN  C18  C17  C13  116.21  3.000
 8BN  F02  C18  C17  118.04  3.000
 8BN  F02  C18  C16  118.66  3.000
 8BN  C17  C18  C16  123.31  3.000
 8BN  H15  C35  H14  108.12  3.000
 8BN  H15  C35  H13  108.55  3.000
 8BN  H14  C35  H13  107.76  3.000
 8BN  H15  C35  N03  111.31  3.000
 8BN  H14  C35  N03  109.40  3.000
 8BN  H13  C35  N03  111.58  3.000
 8BN  H18  C36  H17  108.12  3.000
 8BN  H18  C36  H16  108.64  3.000
 8BN  H17  C36  H16  108.36  3.000
 8BN  H18  C36  N03  111.77  3.000
 8BN  H17  C36  N03  108.88  3.000
 8BN  H16  C36  N03  110.97  3.000
 8BN  H19  N01  C01  126.33  3.000
 8BN  H19  N01  C10  125.82  3.000
 8BN  C01  N01  C10  107.85  3.000
 8BN  C06  N02  C10  105.15  3.000
 8BN  C36  N03  C35  114.91  3.000
 8BN  C35  N03  C08  124.58  3.000
 8BN  C36  N03  C08  119.42  3.000
 8BN  C09  O04  C05  119.84  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
 8BN  CONST_01  C02  C01  N01  C10   180.00   0.0  0
 8BN  CONST_02  C06  C01  N01  C10     0.00   0.0  0
 8BN  CONST_03  C05  C06  N02  C10   180.00   0.0  0
 8BN  CONST_04  C01  C06  N02  C10     0.00   0.0  0
 8BN  CONST_05  C16  C12  C11  C13     0.00   0.0  0
 8BN  CONST_06  C16  C18  C17  C13     0.00   0.0  0
 8BN  CONST_07  C05  C04  C03  C02     0.00   0.0  0
 8BN  CONST_08  C05  C06  C01  C02     0.00   0.0  0
 8BN  CONST_09  N02  C06  C01  C02   180.00   0.0  0
 8BN  CONST_10  C01  C02  C03  C04     0.00   0.0  0
 8BN  CONST_11  C01  C06  C05  C04     0.00   0.0  0
 8BN  CONST_12  N02  C06  C05  C04   180.00   0.0  0
 8BN  CONST_13  N01  C01  C06  C05   180.00   0.0  0
 8BN  CONST_14  C03  C04  C05  C06     0.00   0.0  0
 8BN  CONST_15  C03  C02  C01  C06     0.00   0.0  0
 8BN  CONST_16  N01  C10  N02  C06     0.00   0.0  0
 8BN  CONST_17  C18  C17  C13  C11     0.00   0.0  0
 8BN  CONST_18  C18  C16  C12  C11     0.00   0.0  0
 8BN  CONST_19  C17  C13  C11  C12     0.00   0.0  0
 8BN  CONST_20  C17  C18  C16  C12     0.00   0.0  0
 8BN  CONST_21  N02  C10  N01  C01     0.00   0.0  0
 8BN  CONST_22  N01  C01  C02  C03   180.00   0.0  0
 8BN  CONST_23  N02  C06  C01  N01     0.00   0.0  0
 8BN  CONST_24  F02  C18  C17  C13   180.00   0.0  0
 8BN  CONST_25  C08  C03  C04  C05   180.00   0.0  0
 8BN  CONST_26  C07  C10  N02  C06   180.00   0.0  0
 8BN  CONST_27  C01  N01  C10  C07   180.00   0.0  0
 8BN  CONST_28  F01  C13  C11  C09     0.00   0.0  0
 8BN  CONST_29  F01  C13  C11  C12   180.00   0.0  0
 8BN  CONST_30  F02  C18  C16  C12   180.00   0.0  0
 8BN  CONST_31  C08  C03  C02  C01   180.00   0.0  0
 8BN  CONST_32  O04  C05  C06  C01   180.00   0.0  0
 8BN  CONST_33  O04  C05  C04  C03   180.00   0.0  0
 8BN  CONST_34  F01  C13  C17  C18   180.00   0.0  0
 8BN  CONST_35  O04  C05  C06  N02     0.00   0.0  0
 8BN  CONST_36  H4   C04  C03  C02   180.00   0.0  0
 8BN  CONST_37  H19  N01  C01  C02     0.00   0.0  0
 8BN  CONST_38  H3   C02  C03  C04   180.00   0.0  0
 8BN  CONST_39  H4   C04  C05  C06   180.00   0.0  0
 8BN  CONST_40  H3   C02  C01  C06   180.00   0.0  0
 8BN  CONST_41  H19  N01  C01  C06   180.00   0.0  0
 8BN  CONST_42  H12  C17  C13  C11   180.00   0.0  0
 8BN  CONST_43  H11  C16  C12  C11   180.00   0.0  0
 8BN  CONST_44  H12  C17  C18  C16   180.00   0.0  0
 8BN  CONST_45  H11  C16  C12  O03     0.00   0.0  0
 8BN  CONST_46  H11  C16  C18  C17   180.00   0.0  0
 8BN  CONST_47  H3   C02  C01  N01     0.00   0.0  0
 8BN  CONST_48  H19  N01  C10  N02   180.00   0.0  0
 8BN  CONST_49  C36  N03  C08  C03   180.00   0.0  0
 8BN  CONST_52  O02  C08  N03  C36     0.00   0.0  0
 8BN  Var_01    C12  O03  C14  C15   -42.14  30.0  1
 8BN  Var_02    O03  C14  C15  C09    60.20  30.0  1
 8BN  Var_03    C14  O03  C12  C11    11.53  30.0  1
 8BN  Var_04    C16  C12  O03  C14  -169.45  30.0  1
 8BN  Var_05    C09  O04  C05  C04    11.67  30.0  2
 8BN  Var_06    C09  O04  C05  C06  -169.43  30.0  2
 8BN  Var_07    H9   C14  C15  C09   178.21  30.0  1
 8BN  Var_08    H10  C14  C15  C09   -61.51  30.0  1
 8BN  Var_09    H9   C14  O03  C12  -163.54  30.0  1
 8BN  Var_10    H10  C14  O03  C12    80.46  30.0  1
 8BN  Var_11    H1   C15  C14  O03   -60.10  30.0  1
 8BN  Var_12    H2   C15  C14  O03  -177.45  30.0  1
 8BN  Var_13    N03  C08  C03  C02  -127.86  30.0  2
 8BN  Var_14    O02  C08  C03  C02    54.10  30.0  2
 8BN  Var_15    N03  C08  C03  C04    56.01  30.0  2
 8BN  Var_16    O02  C08  C03  C04  -122.03  30.0  2
 8BN  Var_17    H5   C07  C10  N01  -179.66  30.0  2
 8BN  Var_18    H6   C07  C10  N01   -59.41  30.0  2
 8BN  Var_19    H7   C07  C10  N01    60.19  30.0  2
 8BN  Var_20    H5   C07  C10  N02     0.58  30.0  2
 8BN  Var_21    H6   C07  C10  N02   120.83  30.0  2
 8BN  Var_22    H7   C07  C10  N02  -119.57  30.0  2
 8BN  Var_23    H16  C36  N03  C08    32.17  30.0  3
 8BN  Var_24    H17  C36  N03  C08   151.35  30.0  3
 8BN  Var_25    H18  C36  N03  C08   -89.28  30.0  3
 8BN  Var_26    H13  C35  N03  C08     2.77  30.0  3
 8BN  Var_27    H14  C35  N03  C08   121.91  30.0  3
 8BN  Var_28    H15  C35  N03  C08  -118.66  30.0  3
 8BN  Var_29    H16  C36  N03  C35  -159.21  30.0  3
 8BN  Var_30    H17  C36  N03  C35   -40.03  30.0  3
 8BN  Var_31    H18  C36  N03  C35    79.34  30.0  3
 8BN  Var_32    H13  C35  N03  C36  -165.17  30.0  3
 8BN  Var_33    H14  C35  N03  C36   -46.03  30.0  3
 8BN  Var_34    H15  C35  N03  C36    73.39  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 8BN  chir_01  C09  C15  O04  C11  positiv

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
 8BN  plan-1  C10  0.020
 8BN  plan-1  C02  0.020
 8BN  plan-1  C04  0.020
 8BN  plan-1  C05  0.020
 8BN  plan-1  C06  0.020
 8BN  plan-1  C07  0.020
 8BN  plan-1  C01  0.020
 8BN  plan-1  C03  0.020
 8BN  plan-1  C08  0.020
 8BN  plan-1  N01  0.020
 8BN  plan-1  N02  0.020
 8BN  plan-1  O04  0.020
 8BN  plan-1  H3   0.020
 8BN  plan-1  H4   0.020
 8BN  plan-1  H19  0.020
 8BN  plan-2  C13  0.020
 8BN  plan-2  C09  0.020
 8BN  plan-2  C11  0.020
 8BN  plan-2  C12  0.020
 8BN  plan-2  C16  0.020
 8BN  plan-2  O03  0.020
 8BN  plan-2  C17  0.020
 8BN  plan-2  C18  0.020
 8BN  plan-2  F02  0.020
 8BN  plan-2  H11  0.020
 8BN  plan-2  H12  0.020
 8BN  plan-2  F01  0.020
 8BN  plan-3  C03  0.020
 8BN  plan-3  C08  0.020
 8BN  plan-3  C35  0.020
 8BN  plan-3  C36  0.020
 8BN  plan-3  N03  0.020
 8BN  plan-3  O02  0.020

