# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:16:29 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 1H-benzimidazol-2-yl(4-{[3-(tetrahydro-2H-pyran-4-yl)pyridin-2-yl]oxy}phenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(c1[nH]c2ccccc2n1)c3ccc(Oc4ncccc4C5CCOCC5)cc3
#
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
 2W1  2W1  1H-benzimidazol-2-yl(4-{[3-(tetrahydro-2H-pyran-4-yl)pyridin-2-yl]oxy}phenyl)methanone  ligand  51  30  .  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_2W1
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
 2W1  O01  O  O     0  -0.389  -3.5322  -2.7787   0.9262
 2W1  C02  C  C     0   0.303  -3.1412  -1.6942   0.5345
 2W1  C03  C  CR5   0   0.358  -4.1608  -0.7444   0.0283
 2W1  N04  N  NR15  0  -0.685  -5.4780  -1.0405   0.1865
 2W1  C05  C  CR56  0   0.340  -6.1907  -0.0375  -0.3936
 2W1  C06  C  CR16  0  -0.301  -7.5584   0.1931  -0.5335
 2W1  C07  C  CR16  0  -0.269  -7.9221   1.3475  -1.1957
 2W1  C08  C  CR16  0  -0.268  -6.9643   2.2470  -1.7040
 2W1  C09  C  CR16  0  -0.325  -5.6128   2.0145  -1.5642
 2W1  C10  C  CR56  0   0.150  -5.2206   0.8500  -0.8960
 2W1  N11  N  N     0  -0.462  -3.9692   0.3768  -0.6169
 2W1  C12  C  CR6   0  -0.032  -1.7073  -1.3424   0.5432
 2W1  C13  C  CR16  0  -0.272  -1.2267  -0.0319   0.4818
 2W1  C14  C  CR16  0  -0.302   0.1291   0.2341   0.5451
 2W1  C15  C  CR6   0   0.393   1.0281  -0.8200   0.6650
 2W1  O16  O  O2    0  -0.501   2.3760  -0.6510   0.6515
 2W1  C17  C  CR6   0   0.446   2.9735   0.3977   1.2806
 2W1  N18  N  N     0  -0.427   2.4027   0.8659   2.3641
 2W1  C19  C  CR16  0  -0.068   3.0083   1.8485   3.0230
 2W1  C20  C  CR16  0  -0.328   4.2186   2.3764   2.6184
 2W1  C21  C  CR16  0  -0.203   4.8064   1.8586   1.4709
 2W1  C22  C  CR6   0   0.018   4.1870   0.8491   0.7478
 2W1  C23  C  CH1   0  -0.345   4.8059   0.2260  -0.4758
 2W1  C24  C  CH2   0  -0.435   5.8185  -0.8558  -0.0784
 2W1  C25  C  CH2   0  -0.180   6.4619  -1.4602  -1.3155
 2W1  O26  O  O2    0  -0.484   7.0665  -0.4803  -2.1309
 2W1  C27  C  CH2   0  -0.182   6.1454   0.4947  -2.5676
 2W1  C28  C  CH2   0  -0.440   5.4916   1.2282  -1.4056
 2W1  C29  C  CR16  0  -0.329   0.5702  -2.1314   0.7269
 2W1  C30  C  CR16  0  -0.252  -0.7854  -2.3855   0.6709
 2W1  H1   H  HNR5  0   0.424  -5.8466  -1.8625   0.6403
 2W1  H2   H  HCR6  0   0.273  -8.2973  -0.4953  -0.1459
 2W1  H3   H  HCR6  0   0.263  -8.9722   1.5716  -1.3291
 2W1  H4   H  HCR6  0   0.260  -7.3036   3.1394  -2.2127
 2W1  H5   H  HCR6  0   0.262  -4.8766   2.7060  -1.9528
 2W1  H7   H  HCR6  0   0.277  -1.9110   0.7965   0.3853
 2W1  H8   H  HCR6  0   0.285   0.4720   1.2581   0.4931
 2W1  H9   H  HCR6  0   0.269   2.5064   2.2161   3.9101
 2W1  H10  H  HCR6  0   0.271   4.6927   3.1666   3.1829
 2W1  H11  H  HCR6  0   0.269   5.7577   2.2567   1.1417
 2W1  H12  H  HCH1  0   0.250   4.0135  -0.2585  -1.0538
 2W1  H13  H  HCH2  0   0.230   6.5887  -0.4173   0.5642
 2W1  H14  H  HCH2  0   0.245   5.3313  -1.6462   0.4976
 2W1  H15  H  HCH2  0   0.237   7.2449  -2.1666  -1.0345
 2W1  H16  H  HCH2  0   0.198   5.7052  -2.0190  -1.8865
 2W1  H17  H  HCH2  0   0.238   6.6989   1.1946  -3.1955
 2W1  H18  H  HCH2  0   0.197   5.3681   0.0341  -3.1960
 2W1  H19  H  HCH2  0   0.246   4.7691   1.9467  -1.7995
 2W1  H20  H  HCH2  0   0.228   6.2585   1.7978  -0.8733
 2W1  H21  H  HCR6  0   0.278   1.2780  -2.9452   0.8150
 2W1  H22  H  HCR6  0   0.271  -1.1297  -3.4095   0.7227

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
 2W1  C09  C08  aromatic  1.378  0.020  1.378
 2W1  C09  C10  aromatic  1.399  0.020  1.399
 2W1  C08  C07  aromatic  1.409  0.020  1.409
 2W1  C10  N11  aromatic  1.367  0.020  1.367
 2W1  C10  C05  aromatic  1.408  0.020  1.408
 2W1  N11  C03  aromatic  1.308  0.020  1.308
 2W1  C07  C06  aromatic  1.380  0.020  1.380
 2W1  O01  C02  double    1.218  0.020  1.218
 2W1  C05  C06  aromatic  1.394  0.020  1.394
 2W1  C05  N04  aromatic  1.360  0.020  1.360
 2W1  C03  C02  single    1.483  0.020  1.483
 2W1  C03  N04  aromatic  1.359  0.020  1.359
 2W1  C02  C12  single    1.476  0.020  1.476
 2W1  C12  C30  aromatic  1.398  0.020  1.398
 2W1  C12  C13  aromatic  1.397  0.020  1.397
 2W1  C30  C29  aromatic  1.380  0.020  1.380
 2W1  C13  C14  aromatic  1.383  0.020  1.383
 2W1  C29  C15  aromatic  1.390  0.020  1.390
 2W1  C14  C15  aromatic  1.390  0.020  1.390
 2W1  C15  O16  single    1.359  0.020  1.359
 2W1  O16  C17  single    1.361  0.020  1.361
 2W1  C28  C27  single    1.522  0.020  1.522
 2W1  C28  C23  single    1.529  0.020  1.529
 2W1  C27  O26  single    1.411  0.020  1.411
 2W1  O26  C25  single    1.411  0.020  1.411
 2W1  C17  N18  aromatic  1.311  0.020  1.311
 2W1  C17  C22  aromatic  1.400  0.020  1.400
 2W1  N18  C19  aromatic  1.329  0.020  1.329
 2W1  C23  C22  single    1.506  0.020  1.506
 2W1  C23  C24  single    1.534  0.020  1.534
 2W1  C22  C21  aromatic  1.388  0.020  1.388
 2W1  C19  C20  aromatic  1.381  0.020  1.381
 2W1  C24  C25  single    1.520  0.020  1.520
 2W1  C21  C20  aromatic  1.389  0.020  1.389
 2W1  N04  H1   single    0.860  0.020  1.020
 2W1  C06  H2   single    0.930  0.020  1.080
 2W1  C07  H3   single    0.930  0.020  1.080
 2W1  C08  H4   single    0.930  0.020  1.080
 2W1  C09  H5   single    0.930  0.020  1.080
 2W1  C13  H7   single    0.930  0.020  1.080
 2W1  C14  H8   single    0.930  0.020  1.080
 2W1  C19  H9   single    0.930  0.020  1.080
 2W1  C20  H10  single    0.930  0.020  1.080
 2W1  C21  H11  single    0.930  0.020  1.080
 2W1  C23  H12  single    0.970  0.020  1.090
 2W1  C24  H13  single    0.970  0.020  1.090
 2W1  C24  H14  single    0.970  0.020  1.090
 2W1  C25  H15  single    0.970  0.020  1.090
 2W1  C25  H16  single    0.970  0.020  1.090
 2W1  C27  H17  single    0.970  0.020  1.090
 2W1  C27  H18  single    0.970  0.020  1.090
 2W1  C28  H19  single    0.970  0.020  1.090
 2W1  C28  H20  single    0.970  0.020  1.090
 2W1  C29  H21  single    0.930  0.020  1.080
 2W1  C30  H22  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
 2W1  C12  C02  C03  121.15  3.000
 2W1  C12  C02  O01  121.48  3.000
 2W1  C03  C02  O01  117.36  3.000
 2W1  N11  C03  N04  112.71  3.000
 2W1  N04  C03  C02  119.16  3.000
 2W1  N11  C03  C02  128.09  3.000
 2W1  H1   N04  C05  126.96  3.000
 2W1  H1   N04  C03  125.73  3.000
 2W1  C05  N04  C03  107.31  3.000
 2W1  C10  C05  C06  122.42  3.000
 2W1  C06  C05  N04  132.75  3.000
 2W1  C10  C05  N04  104.83  3.000
 2W1  H2   C06  C07  121.63  3.000
 2W1  H2   C06  C05  121.94  3.000
 2W1  C07  C06  C05  116.44  3.000
 2W1  H3   C07  C08  118.89  3.000
 2W1  H3   C07  C06  119.23  3.000
 2W1  C08  C07  C06  121.88  3.000
 2W1  H4   C08  C09  119.63  3.000
 2W1  H4   C08  C07  118.88  3.000
 2W1  C09  C08  C07  121.49  3.000
 2W1  H5   C09  C10  120.84  3.000
 2W1  H5   C09  C08  121.53  3.000
 2W1  C10  C09  C08  117.63  3.000
 2W1  N11  C10  C09  129.98  3.000
 2W1  N11  C10  C05  109.87  3.000
 2W1  C09  C10  C05  120.14  3.000
 2W1  C10  N11  C03  105.27  3.000
 2W1  C30  C12  C13  118.49  3.000
 2W1  C13  C12  C02  123.87  3.000
 2W1  C30  C12  C02  117.60  3.000
 2W1  H7   C13  C14  118.57  3.000
 2W1  H7   C13  C12  120.40  3.000
 2W1  C14  C13  C12  121.03  3.000
 2W1  H8   C14  C15  121.14  3.000
 2W1  H8   C14  C13  119.39  3.000
 2W1  C15  C14  C13  119.47  3.000
 2W1  C29  C15  O16  116.39  3.000
 2W1  O16  C15  C14  123.11  3.000
 2W1  C29  C15  C14  120.39  3.000
 2W1  C17  O16  C15  121.79  3.000
 2W1  C22  C17  N18  125.22  3.000
 2W1  C22  C17  O16  116.94  3.000
 2W1  N18  C17  O16  117.77  3.000
 2W1  C19  N18  C17  118.38  3.000
 2W1  H9   C19  C20  121.07  3.000
 2W1  H9   C19  N18  116.47  3.000
 2W1  C20  C19  N18  122.46  3.000
 2W1  H10  C20  C21  121.22  3.000
 2W1  H10  C20  C19  120.73  3.000
 2W1  C21  C20  C19  118.06  3.000
 2W1  H11  C21  C22  120.09  3.000
 2W1  H11  C21  C20  119.08  3.000
 2W1  C22  C21  C20  120.84  3.000
 2W1  C23  C22  C21  122.74  3.000
 2W1  C21  C22  C17  115.03  3.000
 2W1  C23  C22  C17  122.14  3.000
 2W1  H12  C23  C28  107.09  3.000
 2W1  H12  C23  C24  107.62  3.000
 2W1  C28  C23  C24  108.88  3.000
 2W1  H12  C23  C22  108.35  3.000
 2W1  C24  C23  C22  110.64  3.000
 2W1  C28  C23  C22  114.02  3.000
 2W1  H14  C24  H13  107.10  3.000
 2W1  H14  C24  C25  109.28  3.000
 2W1  H13  C24  C25  109.83  3.000
 2W1  H14  C24  C23  110.63  3.000
 2W1  H13  C24  C23  109.51  3.000
 2W1  C25  C24  C23  110.42  3.000
 2W1  H16  C25  H15  107.36  3.000
 2W1  H16  C25  O26  110.33  3.000
 2W1  H15  C25  O26  106.91  3.000
 2W1  H16  C25  C24  109.46  3.000
 2W1  H15  C25  C24  110.58  3.000
 2W1  O26  C25  C24  112.06  3.000
 2W1  C27  O26  C25  112.28  3.000
 2W1  H18  C27  H17  107.34  3.000
 2W1  H18  C27  C28  109.53  3.000
 2W1  H17  C27  C28  110.38  3.000
 2W1  H18  C27  O26  110.41  3.000
 2W1  H17  C27  O26  106.87  3.000
 2W1  C28  C27  O26  112.17  3.000
 2W1  H20  C28  H19  107.27  3.000
 2W1  H20  C28  C27  108.75  3.000
 2W1  H19  C28  C27  109.02  3.000
 2W1  H20  C28  C23  111.08  3.000
 2W1  H19  C28  C23  110.70  3.000
 2W1  C27  C28  C23  109.94  3.000
 2W1  H21  C29  C30  120.48  3.000
 2W1  H21  C29  C15  119.84  3.000
 2W1  C30  C29  C15  119.68  3.000
 2W1  H22  C30  C29  119.01  3.000
 2W1  H22  C30  C12  120.06  3.000
 2W1  C29  C30  C12  120.94  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
 2W1  CONST_01  C09  C10  N11  C03   180.00   0.0  0
 2W1  CONST_02  C05  C10  N11  C03     0.00   0.0  0
 2W1  CONST_03  C10  C05  N04  C03     0.00   0.0  0
 2W1  CONST_04  C06  C05  N04  C03   180.00   0.0  0
 2W1  CONST_05  C09  C10  C05  N04   180.00   0.0  0
 2W1  CONST_06  N11  C10  C05  N04     0.00   0.0  0
 2W1  CONST_07  C07  C06  C05  N04   180.00   0.0  0
 2W1  CONST_08  C10  N11  C03  N04     0.00   0.0  0
 2W1  CONST_09  C08  C09  C10  C05     0.00   0.0  0
 2W1  CONST_10  C08  C07  C06  C05     0.00   0.0  0
 2W1  CONST_11  N11  C03  N04  C05     0.00   0.0  0
 2W1  CONST_12  C09  C08  C07  C06     0.00   0.0  0
 2W1  CONST_13  C09  C10  C05  C06     0.00   0.0  0
 2W1  CONST_14  N11  C10  C05  C06   180.00   0.0  0
 2W1  CONST_15  C10  C09  C08  C07     0.00   0.0  0
 2W1  CONST_16  C10  C05  C06  C07     0.00   0.0  0
 2W1  CONST_17  N11  C10  C09  C08   180.00   0.0  0
 2W1  CONST_18  C15  C29  C30  C12     0.00   0.0  0
 2W1  CONST_19  C15  C14  C13  C12     0.00   0.0  0
 2W1  CONST_20  C29  C30  C12  C13     0.00   0.0  0
 2W1  CONST_21  C29  C15  C14  C13     0.00   0.0  0
 2W1  CONST_22  C30  C12  C13  C14     0.00   0.0  0
 2W1  CONST_23  C30  C29  C15  C14     0.00   0.0  0
 2W1  CONST_24  C20  C19  N18  C17     0.00   0.0  0
 2W1  CONST_25  C20  C21  C22  C17     0.00   0.0  0
 2W1  CONST_26  C21  C22  C17  N18     0.00   0.0  0
 2W1  CONST_27  C21  C20  C19  N18     0.00   0.0  0
 2W1  CONST_28  C22  C17  N18  C19     0.00   0.0  0
 2W1  CONST_29  C22  C21  C20  C19     0.00   0.0  0
 2W1  CONST_30  C23  C22  C17  N18   180.00   0.0  0
 2W1  CONST_31  C23  C22  C21  C20   180.00   0.0  0
 2W1  CONST_32  C10  N11  C03  C02   180.00   0.0  0
 2W1  CONST_33  C05  N04  C03  C02   180.00   0.0  0
 2W1  CONST_34  C29  C30  C12  C02   180.00   0.0  0
 2W1  CONST_35  C14  C13  C12  C02   180.00   0.0  0
 2W1  CONST_36  O16  C15  C14  C13   180.00   0.0  0
 2W1  CONST_37  C30  C29  C15  O16   180.00   0.0  0
 2W1  CONST_38  C19  N18  C17  O16   180.00   0.0  0
 2W1  CONST_39  C23  C22  C17  O16     0.00   0.0  0
 2W1  CONST_40  C21  C22  C17  O16   180.00   0.0  0
 2W1  CONST_41  H2   C06  C05  N04     0.00   0.0  0
 2W1  CONST_42  H5   C09  C10  C05   180.00   0.0  0
 2W1  CONST_43  H3   C07  C06  C05   180.00   0.0  0
 2W1  CONST_44  H4   C08  C07  C06   180.00   0.0  0
 2W1  CONST_45  H1   N04  C05  C06     0.00   0.0  0
 2W1  CONST_46  H21  C29  C30  C12   180.00   0.0  0
 2W1  CONST_47  H8   C14  C13  C12   180.00   0.0  0
 2W1  CONST_48  H22  C30  C12  C13   180.00   0.0  0
 2W1  CONST_49  H7   C13  C14  C15   180.00   0.0  0
 2W1  CONST_50  H9   C19  N18  C17   180.00   0.0  0
 2W1  CONST_51  H11  C21  C22  C17   180.00   0.0  0
 2W1  CONST_52  H10  C20  C19  N18   180.00   0.0  0
 2W1  Var_01    O26  C27  C28  C23   -56.78  30.0  1
 2W1  Var_02    O26  C25  C24  C23    55.84  30.0  1
 2W1  Var_03    C28  C27  O26  C25    59.60  30.0  1
 2W1  Var_04    C30  C12  C02  C03  -162.45  30.0  2
 2W1  Var_05    C12  C02  C03  N04  -172.11  30.0  2
 2W1  Var_06    N18  C17  O16  C15    31.50  30.0  2
 2W1  Var_07    C29  C15  O16  C17  -144.07  30.0  2

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
 2W1  chir_01  C23  C28  C22  C24  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
 2W1  plan-1  C02  0.020
 2W1  plan-1  C12  0.020
 2W1  plan-1  C13  0.020
 2W1  plan-1  C14  0.020
 2W1  plan-1  C15  0.020
 2W1  plan-1  O16  0.020
 2W1  plan-1  C29  0.020
 2W1  plan-1  C30  0.020
 2W1  plan-1  H7   0.020
 2W1  plan-1  H8   0.020
 2W1  plan-1  H21  0.020
 2W1  plan-1  H22  0.020
 2W1  plan-2  O16  0.020
 2W1  plan-2  C17  0.020
 2W1  plan-2  N18  0.020
 2W1  plan-2  C19  0.020
 2W1  plan-2  C20  0.020
 2W1  plan-2  C21  0.020
 2W1  plan-2  C22  0.020
 2W1  plan-2  C23  0.020
 2W1  plan-2  H9   0.020
 2W1  plan-2  H10  0.020
 2W1  plan-2  H11  0.020
 2W1  plan-3  C02  0.020
 2W1  plan-3  C03  0.020
 2W1  plan-3  N04  0.020
 2W1  plan-3  C05  0.020
 2W1  plan-3  C06  0.020
 2W1  plan-3  C07  0.020
 2W1  plan-3  C08  0.020
 2W1  plan-3  C09  0.020
 2W1  plan-3  C10  0.020
 2W1  plan-3  N11  0.020
 2W1  plan-3  H1   0.020
 2W1  plan-3  H2   0.020
 2W1  plan-3  H3   0.020
 2W1  plan-3  H4   0.020
 2W1  plan-3  H5   0.020
 2W1  plan-4  O01  0.020
 2W1  plan-4  C02  0.020
 2W1  plan-4  C03  0.020
 2W1  plan-4  C12  0.020

