# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:32:12 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (2~{S})-1-(benzimidazol-1-yl)-3-(2,3-dihydro-1~{H}-inden-5-yloxy)propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](COc1ccc2CCCc2c1)Cn3cnc4ccccc34
#
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
 JVZ  JVZ  (2~{S})-1-(benzimidazol-1-yl)-3-(2,3-dihydro-1~{H}-inden-5-yloxy)propan-2-ol  ligand  43  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JVZ
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
 JVZ  C02   C  CH1   0  -0.014  -0.8544  -0.4441   0.1771
 JVZ  C03   C  CH2   0  -0.197   0.4951  -0.5789  -0.5072
 JVZ  C05   C  CR6   0   0.386   2.7758  -0.1295  -0.0093
 JVZ  C06   C  CR16  0  -0.424   3.7000   0.3609   0.9183
 JVZ  C07   C  CR6   0   0.106   5.0404   0.3791   0.5873
 JVZ  C08   C  CH2   0  -0.490   6.2023   0.8697   1.4067
 JVZ  C09   C  CH2   0  -0.464   7.4145   0.2443   0.6961
 JVZ  C10   C  CH2   0  -0.487   6.9763   0.0649  -0.7681
 JVZ  C11   C  CR6   0   0.065   5.4827  -0.0765  -0.6550
 JVZ  C12   C  CR16  0  -0.312   4.5657  -0.5554  -1.5710
 JVZ  C13   C  CR16  0  -0.388   3.2085  -0.5862  -1.2531
 JVZ  C14   C  CH2   0  -0.348  -1.9337  -1.0636  -0.7133
 JVZ  C16   C  CR56  0   0.354  -4.1515   0.0446  -0.2388
 JVZ  C17   C  CR16  0  -0.312  -4.1496   1.2194  -0.9837
 JVZ  C18   C  CR16  0  -0.277  -5.2717   2.0217  -0.8821
 JVZ  C19   C  CR16  0  -0.274  -6.3569   1.6695  -0.0638
 JVZ  C20   C  CR16  0  -0.324  -6.3513   0.4999   0.6734
 JVZ  C21   C  CR56  0   0.124  -5.2302  -0.3255   0.5819
 JVZ  C23   C  CR15  0   0.105  -3.7894  -1.8709   0.7498
 JVZ  N15   N  NR5   0  -0.505  -3.2441  -0.9772  -0.1145
 JVZ  N22   N  N     0  -0.469  -4.9671  -1.5321   1.1880
 JVZ  O01   O  OH1   0  -0.645  -1.1567   0.8780   0.5346
 JVZ  O04   O  O2    0  -0.477   1.4840  -0.1288   0.3915
 JVZ  H021  H  HCH1  0   0.253  -0.8269  -1.0090   1.1142
 JVZ  H031  H  HCH2  0   0.235   0.6627  -1.6265  -0.7831
 JVZ  H032  H  HCH2  0   0.230   0.5102   0.0130  -1.4324
 JVZ  H061  H  HCR6  0   0.250   3.3545   0.7131   1.8836
 JVZ  H081  H  HCH2  0   0.246   6.2481   1.9630   1.3702
 JVZ  H082  H  HCH2  0   0.248   6.1343   0.5928   2.4597
 JVZ  H091  H  HCH2  0   0.236   8.3167   0.8475   0.7949
 JVZ  H092  H  HCH2  0   0.236   7.6250  -0.7341   1.1328
 JVZ  H101  H  HCH2  0   0.240   7.2335   0.9469  -1.3636
 JVZ  H102  H  HCH2  0   0.244   7.4552  -0.7905  -1.2473
 JVZ  H121  H  HCR6  0   0.248   4.8869  -0.9184  -2.5400
 JVZ  H131  H  HCR6  0   0.273   2.5114  -0.9751  -1.9832
 JVZ  H141  H  HCH2  0   0.275  -1.9675  -0.5726  -1.6881
 JVZ  H142  H  HCH2  0   0.287  -1.7073  -2.1144  -0.8973
 JVZ  H171  H  HCR6  0   0.263  -3.3204   1.5006  -1.6203
 JVZ  H181  H  HCR6  0   0.256  -5.3131   2.9451  -1.4448
 JVZ  H191  H  HCR6  0   0.253  -7.2128   2.3298  -0.0135
 JVZ  H201  H  HCR6  0   0.254  -7.1895   0.2279   1.3023
 JVZ  H231  H  HCR5  0   0.289  -3.2638  -2.7766   1.0185
 JVZ  H011  H  HOH1  0   0.448  -1.0932   1.4418  -0.2445

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
 JVZ  C19  C18   aromatic  1.404  0.020  1.404
 JVZ  C19  C20   aromatic  1.383  0.020  1.383
 JVZ  C18  C17   aromatic  1.383  0.020  1.383
 JVZ  C20  C21   aromatic  1.395  0.020  1.395
 JVZ  C17  C16   aromatic  1.391  0.020  1.391
 JVZ  C21  C16   aromatic  1.405  0.020  1.405
 JVZ  C21  N22   aromatic  1.376  0.020  1.376
 JVZ  C16  N15   aromatic  1.372  0.020  1.372
 JVZ  N22  C23   aromatic  1.301  0.020  1.301
 JVZ  O04  C03   single    1.410  0.020  1.410
 JVZ  O04  C05   single    1.353  0.020  1.353
 JVZ  C03  C02   single    1.519  0.020  1.519
 JVZ  N15  C23   aromatic  1.358  0.020  1.358
 JVZ  N15  C14   single    1.443  0.020  1.443
 JVZ  C05  C13   aromatic  1.394  0.020  1.394
 JVZ  C05  C06   aromatic  1.398  0.020  1.398
 JVZ  C13  C12   aromatic  1.394  0.020  1.394
 JVZ  C02  C14   single    1.530  0.020  1.530
 JVZ  C02  O01   single    1.403  0.020  1.403
 JVZ  C06  C07   aromatic  1.381  0.020  1.381
 JVZ  C12  C11   aromatic  1.382  0.020  1.382
 JVZ  C07  C11   aromatic  1.395  0.020  1.395
 JVZ  C07  C08   single    1.504  0.020  1.504
 JVZ  C11  C10   single    1.505  0.020  1.505
 JVZ  C08  C09   single    1.538  0.020  1.538
 JVZ  C10  C09   single    1.539  0.020  1.539
 JVZ  C02  H021  single    0.970  0.020  1.090
 JVZ  C03  H031  single    0.970  0.020  1.090
 JVZ  C03  H032  single    0.970  0.020  1.090
 JVZ  C06  H061  single    0.930  0.020  1.080
 JVZ  C08  H081  single    0.970  0.020  1.090
 JVZ  C08  H082  single    0.970  0.020  1.090
 JVZ  C09  H091  single    0.970  0.020  1.090
 JVZ  C09  H092  single    0.970  0.020  1.090
 JVZ  C10  H101  single    0.970  0.020  1.090
 JVZ  C10  H102  single    0.970  0.020  1.090
 JVZ  C12  H121  single    0.930  0.020  1.080
 JVZ  C13  H131  single    0.930  0.020  1.080
 JVZ  C14  H141  single    0.970  0.020  1.090
 JVZ  C14  H142  single    0.970  0.020  1.090
 JVZ  C17  H171  single    0.930  0.020  1.080
 JVZ  C18  H181  single    0.930  0.020  1.080
 JVZ  C19  H191  single    0.930  0.020  1.080
 JVZ  C20  H201  single    0.930  0.020  1.080
 JVZ  C23  H231  single    0.930  0.020  1.080
 JVZ  O01  H011  single    0.850  0.020  0.980

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
 JVZ  H021  C02  O01   105.88  3.000
 JVZ  H021  C02  C14   107.88  3.000
 JVZ  O01   C02  C14   112.20  3.000
 JVZ  H021  C02  C03   108.51  3.000
 JVZ  O01   C02  C03   112.96  3.000
 JVZ  C14   C02  C03   109.18  3.000
 JVZ  H032  C03  H031  107.51  3.000
 JVZ  H032  C03  O04   110.81  3.000
 JVZ  H031  C03  O04   110.99  3.000
 JVZ  H032  C03  C02   110.11  3.000
 JVZ  H031  C03  C02   109.51  3.000
 JVZ  O04   C03  C02   107.91  3.000
 JVZ  O04   C05  C13   124.13  3.000
 JVZ  C13   C05  C06   120.12  3.000
 JVZ  O04   C05  C06   115.76  3.000
 JVZ  H061  C06  C07   121.23  3.000
 JVZ  H061  C06  C05   119.61  3.000
 JVZ  C07   C06  C05   119.16  3.000
 JVZ  C11   C07  C08   110.28  3.000
 JVZ  C08   C07  C06   128.59  3.000
 JVZ  C11   C07  C06   121.12  3.000
 JVZ  H082  C08  H081  106.75  3.000
 JVZ  H082  C08  C09   113.07  3.000
 JVZ  H081  C08  C09   110.96  3.000
 JVZ  H082  C08  C07   113.26  3.000
 JVZ  H081  C08  C07   109.87  3.000
 JVZ  C09   C08  C07   102.98  3.000
 JVZ  H092  C09  H091  107.46  3.000
 JVZ  H092  C09  C10   109.32  3.000
 JVZ  H091  C09  C10   112.74  3.000
 JVZ  H092  C09  C08   109.36  3.000
 JVZ  H091  C09  C08   112.68  3.000
 JVZ  C10   C09  C08   105.23  3.000
 JVZ  H102  C10  H101  106.83  3.000
 JVZ  H102  C10  C11   113.27  3.000
 JVZ  H101  C10  C11   110.47  3.000
 JVZ  H102  C10  C09   112.61  3.000
 JVZ  H101  C10  C09   110.90  3.000
 JVZ  C11   C10  C09   102.83  3.000
 JVZ  C12   C11  C10   129.91  3.000
 JVZ  C10   C11  C07   110.55  3.000
 JVZ  C12   C11  C07   119.54  3.000
 JVZ  H121  C12  C13   119.02  3.000
 JVZ  H121  C12  C11   120.82  3.000
 JVZ  C13   C12  C11   120.16  3.000
 JVZ  H131  C13  C12   118.77  3.000
 JVZ  H131  C13  C05   121.33  3.000
 JVZ  C12   C13  C05   119.90  3.000
 JVZ  H142  C14  H141  106.81  3.000
 JVZ  H142  C14  N15   108.43  3.000
 JVZ  H141  C14  N15   108.38  3.000
 JVZ  H142  C14  C02   109.98  3.000
 JVZ  H141  C14  C02   111.05  3.000
 JVZ  N15   C14  C02   112.01  3.000
 JVZ  N15   C16  C21   104.99  3.000
 JVZ  N15   C16  C17   132.57  3.000
 JVZ  C21   C16  C17   122.43  3.000
 JVZ  H171  C17  C18   120.92  3.000
 JVZ  H171  C17  C16   122.37  3.000
 JVZ  C18   C17  C16   116.71  3.000
 JVZ  H181  C18  C19   119.18  3.000
 JVZ  H181  C18  C17   119.20  3.000
 JVZ  C19   C18  C17   121.63  3.000
 JVZ  H191  C19  C20   119.65  3.000
 JVZ  H191  C19  C18   119.04  3.000
 JVZ  C20   C19  C18   121.32  3.000
 JVZ  H201  C20  C21   120.77  3.000
 JVZ  H201  C20  C19   121.27  3.000
 JVZ  C21   C20  C19   117.96  3.000
 JVZ  N22   C21  C20   130.07  3.000
 JVZ  N22   C21  C16   109.97  3.000
 JVZ  C20   C21  C16   119.96  3.000
 JVZ  H231  C23  N22   125.05  3.000
 JVZ  H231  C23  N15   120.96  3.000
 JVZ  N22   C23  N15   113.99  3.000
 JVZ  C23   N15  C16   106.39  3.000
 JVZ  C23   N15  C14   126.12  3.000
 JVZ  C16   N15  C14   127.40  3.000
 JVZ  C23   N22  C21   104.65  3.000
 JVZ  H011  O01  C02   109.34  3.000
 JVZ  C05   O04  C03   118.74  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
 JVZ  CONST_01  C11   C12  C13  C05    0.00   0.0  0
 JVZ  CONST_02  C11   C07  C06  C05    0.00   0.0  0
 JVZ  CONST_03  C12   C13  C05  C06    0.00   0.0  0
 JVZ  CONST_04  C12   C11  C07  C06    0.00   0.0  0
 JVZ  CONST_05  C13   C05  C06  C07    0.00   0.0  0
 JVZ  CONST_06  C13   C12  C11  C07    0.00   0.0  0
 JVZ  CONST_07  C19   C18  C17  C16    0.00   0.0  0
 JVZ  CONST_08  C19   C20  C21  C16    0.00   0.0  0
 JVZ  CONST_09  C23   N22  C21  C16    0.00   0.0  0
 JVZ  CONST_10  N22   C23  N15  C16    0.00   0.0  0
 JVZ  CONST_11  C20   C19  C18  C17    0.00   0.0  0
 JVZ  CONST_12  C20   C21  C16  C17    0.00   0.0  0
 JVZ  CONST_13  N22   C21  C16  C17  180.00   0.0  0
 JVZ  CONST_14  C23   N15  C16  C17  180.00   0.0  0
 JVZ  CONST_15  C21   C20  C19  C18    0.00   0.0  0
 JVZ  CONST_16  C21   C16  C17  C18    0.00   0.0  0
 JVZ  CONST_17  N15   C16  C17  C18  180.00   0.0  0
 JVZ  CONST_18  N22   C21  C20  C19  180.00   0.0  0
 JVZ  CONST_19  N15   C16  C21  C20  180.00   0.0  0
 JVZ  CONST_20  C23   N22  C21  C20  180.00   0.0  0
 JVZ  CONST_21  C23   N15  C16  C21    0.00   0.0  0
 JVZ  CONST_22  N15   C23  N22  C21    0.00   0.0  0
 JVZ  CONST_23  N22   C21  C16  N15    0.00   0.0  0
 JVZ  CONST_24  O04   C05  C06  C07  180.00   0.0  0
 JVZ  CONST_25  O04   C05  C13  C12  180.00   0.0  0
 JVZ  CONST_26  C17   C16  N15  C14    0.00   0.0  0
 JVZ  CONST_27  C21   C16  N15  C14  180.00   0.0  0
 JVZ  CONST_28  N22   C23  N15  C14  180.00   0.0  0
 JVZ  CONST_29  H121  C12  C13  C05  180.00   0.0  0
 JVZ  CONST_30  H131  C13  C05  C06  180.00   0.0  0
 JVZ  CONST_31  H061  C06  C07  C08    0.00   0.0  0
 JVZ  CONST_32  H181  C18  C17  C16  180.00   0.0  0
 JVZ  CONST_33  H201  C20  C21  C16  180.00   0.0  0
 JVZ  CONST_34  H231  C23  N15  C16  180.00   0.0  0
 JVZ  CONST_35  H191  C19  C18  C17  180.00   0.0  0
 JVZ  CONST_36  H171  C17  C18  C19  180.00   0.0  0
 JVZ  Var_01    C09   C08  C07  C06  163.52  30.0  1
 JVZ  Var_02    C09   C10  C11  C07   17.03  30.0  1
 JVZ  Var_03    C10   C09  C08  C07   27.33  30.0  1
 JVZ  Var_04    C11   C10  C09  C08  -27.13  30.0  1
 JVZ  Var_05    C16   N15  C14  C02   89.23  30.0  2
 JVZ  Var_06    C13   C05  O04  C03   -1.93  30.0  2
 JVZ  Var_07    H031  C03  O04  C05   61.29  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
 JVZ  chir_01  C02  C03  C14  O01  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
 JVZ  plan-1  C14   0.020
 JVZ  plan-1  C16   0.020
 JVZ  plan-1  C17   0.020
 JVZ  plan-1  C18   0.020
 JVZ  plan-1  C19   0.020
 JVZ  plan-1  C20   0.020
 JVZ  plan-1  C21   0.020
 JVZ  plan-1  C23   0.020
 JVZ  plan-1  N15   0.020
 JVZ  plan-1  N22   0.020
 JVZ  plan-1  H171  0.020
 JVZ  plan-1  H181  0.020
 JVZ  plan-1  H191  0.020
 JVZ  plan-1  H201  0.020
 JVZ  plan-1  H231  0.020
 JVZ  plan-2  C05   0.020
 JVZ  plan-2  C06   0.020
 JVZ  plan-2  C07   0.020
 JVZ  plan-2  C08   0.020
 JVZ  plan-2  C10   0.020
 JVZ  plan-2  C11   0.020
 JVZ  plan-2  C12   0.020
 JVZ  plan-2  C13   0.020
 JVZ  plan-2  O04   0.020
 JVZ  plan-2  H061  0.020
 JVZ  plan-2  H121  0.020
 JVZ  plan-2  H131  0.020

