# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:24:22 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: [4-(1H-benzimidazol-1-yl)phenyl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc(cc1)n2cnc3ccccc23
#
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
 JFS  JFS  '[4-(1H-benzimidazol-1-yl)phenyl]methanol'  ligand  29  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JFS
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
 JFS  C10   C  CR6   0   0.315   0.5757  -0.3531   0.0239
 JFS  C13   C  CR6   0   0.089   3.2759   0.3152   0.2272
 JFS  C15   C  CR16  0  -0.281   1.0870   0.6995  -0.7264
 JFS  C01   C  CR16  0  -0.271  -4.4190   1.1792   0.1284
 JFS  C02   C  CR16  0  -0.273  -3.2978   2.0083   0.2845
 JFS  C03   C  CR16  0  -0.295  -2.0096   1.5053   0.2322
 JFS  C04   C  CR56  0   0.317  -1.8821   0.1383   0.0128
 JFS  C05   C  CR56  0   0.125  -2.9929  -0.7075  -0.1342
 JFS  C06   C  CR16  0  -0.319  -4.2828  -0.1808  -0.0801
 JFS  N07   N  N     0  -0.459  -2.5784  -2.0088  -0.3080
 JFS  C08   C  CR15  0   0.101  -1.2827  -1.9562  -0.2639
 JFS  N09   N  NR5   0  -0.617  -0.7888  -0.6979  -0.0757
 JFS  C11   C  CR16  0  -0.278   1.4056  -1.0748   0.8721
 JFS  C12   C  CR16  0  -0.289   2.7500  -0.7459   0.9560
 JFS  C14   C  CR16  0  -0.282   2.4275   1.0301  -0.6140
 JFS  C16   C  CH2   0  -0.227   4.7381   0.6481   0.2971
 JFS  O17   O  OH1   0  -0.667   5.3845  -0.0024  -0.7786
 JFS  H151  H  HCR6  0   0.281   0.4477   1.2494  -1.4046
 JFS  H021  H  HCR6  0   0.259  -3.4431   3.0678   0.4491
 JFS  H031  H  HCR6  0   0.273  -1.1529   2.1533   0.3582
 JFS  H061  H  HCR6  0   0.258  -5.1468  -0.8225  -0.1949
 JFS  H081  H  HCR5  0   0.298  -0.6180  -2.8008  -0.3774
 JFS  H111  H  HCR6  0   0.279   1.0039  -1.8824   1.4708
 JFS  H121  H  HCR6  0   0.263   3.3920  -1.3127   1.6189
 JFS  H141  H  HCR6  0   0.262   2.8170   1.8568  -1.1956
 JFS  H162  H  HCH2  0   0.212   4.8666   1.7356   0.2428
 JFS  H161  H  HCH2  0   0.212   5.1413   0.3252   1.2642
 JFS  H171  H  HOH1  0   0.457   6.3196   0.2214  -0.7377
 JFS  H011  H  HCR6  0   0.255  -5.4079   1.6160   0.1763

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
 JFS  C08  N07   aromatic  1.298  0.020  1.298
 JFS  C08  N09   aromatic  1.365  0.020  1.365
 JFS  C15  C14   aromatic  1.385  0.020  1.385
 JFS  C15  C10   aromatic  1.390  0.020  1.390
 JFS  N07  C05   aromatic  1.377  0.020  1.377
 JFS  C14  C13   aromatic  1.392  0.020  1.392
 JFS  O17  C16   single    1.414  0.020  1.414
 JFS  N09  C10   single    1.411  0.020  1.411
 JFS  N09  C04   aromatic  1.379  0.020  1.379
 JFS  C10  C11   aromatic  1.389  0.020  1.389
 JFS  C05  C04   aromatic  1.404  0.020  1.404
 JFS  C05  C06   aromatic  1.394  0.020  1.394
 JFS  C13  C16   single    1.501  0.020  1.501
 JFS  C13  C12   aromatic  1.391  0.020  1.391
 JFS  C04  C03   aromatic  1.390  0.020  1.390
 JFS  C06  C01   aromatic  1.383  0.020  1.383
 JFS  C11  C12   aromatic  1.387  0.020  1.387
 JFS  C03  C02   aromatic  1.384  0.020  1.384
 JFS  C01  C02   aromatic  1.403  0.020  1.403
 JFS  C15  H151  single    0.930  0.020  1.080
 JFS  C01  H011  single    0.930  0.020  1.080
 JFS  C02  H021  single    0.930  0.020  1.080
 JFS  C03  H031  single    0.930  0.020  1.080
 JFS  C06  H061  single    0.930  0.020  1.080
 JFS  C08  H081  single    0.930  0.020  1.080
 JFS  C11  H111  single    0.930  0.020  1.080
 JFS  C12  H121  single    0.930  0.020  1.080
 JFS  C14  H141  single    0.930  0.020  1.080
 JFS  C16  H162  single    0.970  0.020  1.090
 JFS  C16  H161  single    0.970  0.020  1.090
 JFS  O17  H171  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
 JFS  C11   C10  N09   119.60  3.000
 JFS  C11   C10  C15   120.22  3.000
 JFS  N09   C10  C15   120.17  3.000
 JFS  C16   C13  C14   120.52  3.000
 JFS  C16   C13  C12   120.88  3.000
 JFS  C14   C13  C12   118.55  3.000
 JFS  H151  C15  C14   120.08  3.000
 JFS  H151  C15  C10   120.38  3.000
 JFS  C14   C15  C10   119.53  3.000
 JFS  H011  C01  C06   119.59  3.000
 JFS  H011  C01  C02   119.13  3.000
 JFS  C06   C01  C02   121.28  3.000
 JFS  H021  C02  C03   119.12  3.000
 JFS  H021  C02  C01   119.23  3.000
 JFS  C03   C02  C01   121.66  3.000
 JFS  H031  C03  C04   122.33  3.000
 JFS  H031  C03  C02   121.01  3.000
 JFS  C04   C03  C02   116.66  3.000
 JFS  N09   C04  C05   104.79  3.000
 JFS  C05   C04  C03   122.43  3.000
 JFS  N09   C04  C03   132.75  3.000
 JFS  N07   C05  C06   129.83  3.000
 JFS  C06   C05  C04   120.02  3.000
 JFS  N07   C05  C04   110.15  3.000
 JFS  H061  C06  C05   120.69  3.000
 JFS  H061  C06  C01   121.37  3.000
 JFS  C05   C06  C01   117.94  3.000
 JFS  C08   N07  C05   104.95  3.000
 JFS  H081  C08  N09   120.82  3.000
 JFS  H081  C08  N07   125.37  3.000
 JFS  N09   C08  N07   113.80  3.000
 JFS  C08   N09  C04   106.31  3.000
 JFS  C04   N09  C10   127.88  3.000
 JFS  C08   N09  C10   125.80  3.000
 JFS  H111  C11  C12   120.22  3.000
 JFS  H111  C11  C10   120.24  3.000
 JFS  C12   C11  C10   119.54  3.000
 JFS  H121  C12  C11   119.18  3.000
 JFS  H121  C12  C13   119.73  3.000
 JFS  C11   C12  C13   121.07  3.000
 JFS  H141  C14  C15   119.11  3.000
 JFS  H141  C14  C13   119.81  3.000
 JFS  C15   C14  C13   121.08  3.000
 JFS  H161  C16  H162  107.02  3.000
 JFS  H161  C16  O17   111.56  3.000
 JFS  H162  C16  O17   111.41  3.000
 JFS  H161  C16  C13   109.51  3.000
 JFS  H162  C16  C13   109.38  3.000
 JFS  O17   C16  C13   107.94  3.000
 JFS  H171  O17  C16   107.76  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
 JFS  CONST_01  C13   C14  C15  C10    0.00   0.0  0
 JFS  CONST_02  N07   C08  N09  C10  180.00   0.0  0
 JFS  CONST_03  C05   C04  N09  C10  180.00   0.0  0
 JFS  CONST_04  C03   C04  N09  C10    0.00   0.0  0
 JFS  CONST_05  C13   C12  C11  C10    0.00   0.0  0
 JFS  CONST_06  C12   C13  C14  C15    0.00   0.0  0
 JFS  CONST_09  C12   C11  C10  C15    0.00   0.0  0
 JFS  CONST_10  N07   C05  C06  C01  180.00   0.0  0
 JFS  CONST_11  C04   C05  C06  C01    0.00   0.0  0
 JFS  CONST_12  C04   C03  C02  C01    0.00   0.0  0
 JFS  CONST_13  N09   C04  C03  C02  180.00   0.0  0
 JFS  CONST_14  C05   C04  C03  C02    0.00   0.0  0
 JFS  CONST_15  C05   C06  C01  C02    0.00   0.0  0
 JFS  CONST_16  C08   N09  C04  C03  180.00   0.0  0
 JFS  CONST_17  N07   C05  C04  C03  180.00   0.0  0
 JFS  CONST_18  C06   C05  C04  C03    0.00   0.0  0
 JFS  CONST_19  C06   C01  C02  C03    0.00   0.0  0
 JFS  CONST_20  N07   C08  N09  C04    0.00   0.0  0
 JFS  CONST_22  C08   N07  C05  C04    0.00   0.0  0
 JFS  CONST_23  N09   C08  N07  C05    0.00   0.0  0
 JFS  CONST_24  C08   N09  C04  C05    0.00   0.0  0
 JFS  CONST_25  C08   N07  C05  C06  180.00   0.0  0
 JFS  CONST_26  N09   C04  C05  C06  180.00   0.0  0
 JFS  CONST_27  N09   C04  C05  N07    0.00   0.0  0
 JFS  CONST_29  C14   C15  C10  N09  180.00   0.0  0
 JFS  CONST_30  C12   C11  C10  N09  180.00   0.0  0
 JFS  CONST_31  C14   C15  C10  C11    0.00   0.0  0
 JFS  CONST_32  C14   C13  C12  C11    0.00   0.0  0
 JFS  CONST_33  C16   C13  C14  C15  180.00   0.0  0
 JFS  CONST_34  C16   C13  C12  C11  180.00   0.0  0
 JFS  CONST_35  H141  C14  C15  C10  180.00   0.0  0
 JFS  CONST_36  H081  C08  N09  C10    0.00   0.0  0
 JFS  CONST_37  H121  C12  C11  C10  180.00   0.0  0
 JFS  CONST_38  H151  C15  C14  C13  180.00   0.0  0
 JFS  CONST_39  H111  C11  C12  C13  180.00   0.0  0
 JFS  CONST_40  H031  C03  C02  C01  180.00   0.0  0
 JFS  CONST_41  H061  C06  C01  C02  180.00   0.0  0
 JFS  CONST_42  H011  C01  C02  C03  180.00   0.0  0
 JFS  CONST_43  H021  C02  C03  C04  180.00   0.0  0
 JFS  Var_01    O17   C16  C13  C12   94.40  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
 JFS  plan-1  C10   0.020
 JFS  plan-1  C13   0.020
 JFS  plan-1  C15   0.020
 JFS  plan-1  N09   0.020
 JFS  plan-1  C11   0.020
 JFS  plan-1  C12   0.020
 JFS  plan-1  C14   0.020
 JFS  plan-1  C16   0.020
 JFS  plan-1  H151  0.020
 JFS  plan-1  H111  0.020
 JFS  plan-1  H121  0.020
 JFS  plan-1  H141  0.020
 JFS  plan-2  C10   0.020
 JFS  plan-2  C01   0.020
 JFS  plan-2  C02   0.020
 JFS  plan-2  C03   0.020
 JFS  plan-2  C04   0.020
 JFS  plan-2  C05   0.020
 JFS  plan-2  C06   0.020
 JFS  plan-2  N07   0.020
 JFS  plan-2  C08   0.020
 JFS  plan-2  N09   0.020
 JFS  plan-2  H021  0.020
 JFS  plan-2  H031  0.020
 JFS  plan-2  H061  0.020
 JFS  plan-2  H081  0.020
 JFS  plan-2  H011  0.020

