# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:47:44 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccccc1CNc2[nH]c3ccccc3n2
#
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
 T1J  T1J  2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol  ligand  31  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T1J
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
 T1J  C10   C  CR5   0   0.685   0.9203  -0.0654  -0.3175
 T1J  C13   C  CR16  0  -0.346   4.2650  -0.6618  -1.1428
 T1J  C15   C  CR16  0  -0.286   5.2176   0.0891   0.9640
 T1J  C17   C  CR56  0   0.340   2.8771   0.1573   0.6579
 T1J  C02   C  CR6   0   0.323  -3.2011  -0.7388   0.2996
 T1J  C03   C  CR16  0  -0.334  -4.5622  -1.0149   0.2003
 T1J  C04   C  CR16  0  -0.254  -5.4548  -0.0085  -0.1351
 T1J  C05   C  CR16  0  -0.270  -5.0005   1.2785  -0.3905
 T1J  C06   C  CR16  0  -0.302  -3.6426   1.5478  -0.2950
 T1J  C07   C  CR6   0  -0.035  -2.7314   0.5598   0.0591
 T1J  C08   C  CH2   0  -0.365  -1.2760   0.8911   0.2381
 T1J  C12   C  CR56  0   0.161   3.0014  -0.3633  -0.6413
 T1J  C14   C  CR16  0  -0.271   5.3632  -0.4290  -0.3271
 T1J  C16   C  CR16  0  -0.311   3.9653   0.3934   1.4815
 T1J  N09   N  NH1   0  -0.739  -0.4409  -0.0749  -0.4735
 T1J  N11   N  N     0  -0.519   1.7609  -0.4856  -1.2250
 T1J  N18   N  NR15  0  -0.730   1.5236   0.3396   0.8311
 T1J  H131  H  HCR6  0   0.250   4.3860  -1.0638  -2.1407
 T1J  H151  H  HCR6  0   0.251   6.0971   0.2564   1.5719
 T1J  H031  H  HCR6  0   0.261  -4.9131  -2.0221   0.3895
 T1J  H041  H  HCR6  0   0.257  -6.5105  -0.2367  -0.2056
 T1J  H051  H  HCR6  0   0.253  -5.6936   2.0637  -0.6612
 T1J  H061  H  HCR6  0   0.257  -3.2783   2.5491  -0.4923
 T1J  H081  H  HCH2  0   0.276  -1.0795   1.9157  -0.0892
 T1J  H082  H  HCH2  0   0.269  -1.0327   0.8440   1.3030
 T1J  H141  H  HCR6  0   0.249   6.3555  -0.6517  -0.6971
 T1J  H161  H  HCR6  0   0.264   3.8499   0.7950   2.4799
 T1J  H091  H  HNH1  0   0.405  -0.6923  -0.1784  -1.4485
 T1J  H181  H  HNR5  0   0.423   1.0770   0.6789   1.6675
 T1J  H011  H  HOH1  0   0.479  -1.4634  -1.5055   0.3829
 T1J  O01   O  OH1   0  -0.641  -2.3713  -1.7436   0.6456

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
 T1J  C02  O01   single    1.348  0.020  1.348
 T1J  C03  C02   aromatic  1.392  0.020  1.392
 T1J  C04  C03   aromatic  1.386  0.020  1.386
 T1J  C05  C04   aromatic  1.388  0.020  1.388
 T1J  C06  C05   aromatic  1.388  0.020  1.388
 T1J  C07  C06   aromatic  1.390  0.020  1.390
 T1J  C08  C07   single    1.503  0.020  1.503
 T1J  N09  C08   single    1.462  0.020  1.462
 T1J  C10  N09   single    1.370  0.020  1.370
 T1J  N11  C10   aromatic  1.306  0.020  1.306
 T1J  C12  N11   aromatic  1.376  0.020  1.376
 T1J  C13  C12   aromatic  1.392  0.020  1.392
 T1J  C14  C13   aromatic  1.388  0.020  1.388
 T1J  C15  C14   aromatic  1.399  0.020  1.399
 T1J  C16  C15   aromatic  1.389  0.020  1.389
 T1J  C17  C16   aromatic  1.385  0.020  1.385
 T1J  N18  C17   aromatic  1.377  0.020  1.377
 T1J  C02  C07   aromatic  1.402  0.020  1.402
 T1J  C10  N18   aromatic  1.359  0.020  1.359
 T1J  C12  C17   aromatic  1.405  0.020  1.405
 T1J  C13  H131  single    0.930  0.020  1.080
 T1J  C15  H151  single    0.930  0.020  1.080
 T1J  C03  H031  single    0.930  0.020  1.080
 T1J  C04  H041  single    0.930  0.020  1.080
 T1J  C05  H051  single    0.930  0.020  1.080
 T1J  C06  H061  single    0.930  0.020  1.080
 T1J  C08  H081  single    0.970  0.020  1.090
 T1J  C08  H082  single    0.970  0.020  1.090
 T1J  C14  H141  single    0.930  0.020  1.080
 T1J  C16  H161  single    0.930  0.020  1.080
 T1J  N09  H091  single    0.890  0.020  1.040
 T1J  N18  H181  single    0.860  0.020  1.020
 T1J  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
 T1J  N18   C10  N11   113.41  3.000
 T1J  N18   C10  N09   122.63  3.000
 T1J  N11   C10  N09   123.91  3.000
 T1J  H131  C13  C14   121.04  3.000
 T1J  H131  C13  C12   120.88  3.000
 T1J  C14   C13  C12   118.08  3.000
 T1J  H151  C15  C16   119.32  3.000
 T1J  H151  C15  C14   119.42  3.000
 T1J  C16   C15  C14   121.26  3.000
 T1J  N18   C17  C16   132.47  3.000
 T1J  N18   C17  C12   104.61  3.000
 T1J  C16   C17  C12   122.92  3.000
 T1J  O01   C02  C07   121.89  3.000
 T1J  C07   C02  C03   119.94  3.000
 T1J  O01   C02  C03   118.17  3.000
 T1J  H031  C03  C04   120.57  3.000
 T1J  H031  C03  C02   119.25  3.000
 T1J  C04   C03  C02   120.18  3.000
 T1J  H041  C04  C05   120.17  3.000
 T1J  H041  C04  C03   119.39  3.000
 T1J  C05   C04  C03   120.44  3.000
 T1J  H051  C05  C06   120.22  3.000
 T1J  H051  C05  C04   120.61  3.000
 T1J  C06   C05  C04   119.17  3.000
 T1J  H061  C06  C07   118.87  3.000
 T1J  H061  C06  C05   119.72  3.000
 T1J  C07   C06  C05   121.41  3.000
 T1J  C08   C07  C06   120.55  3.000
 T1J  C08   C07  C02   120.54  3.000
 T1J  C06   C07  C02   118.85  3.000
 T1J  H082  C08  H081  106.97  3.000
 T1J  H082  C08  N09   108.58  3.000
 T1J  H081  C08  N09   111.77  3.000
 T1J  H082  C08  C07   108.78  3.000
 T1J  H081  C08  C07   110.17  3.000
 T1J  N09   C08  C07   110.46  3.000
 T1J  N11   C12  C17   110.20  3.000
 T1J  C17   C12  C13   119.53  3.000
 T1J  N11   C12  C13   130.27  3.000
 T1J  H141  C14  C15   119.16  3.000
 T1J  H141  C14  C13   119.35  3.000
 T1J  C15   C14  C13   121.49  3.000
 T1J  H161  C16  C17   121.87  3.000
 T1J  H161  C16  C15   121.41  3.000
 T1J  C17   C16  C15   116.72  3.000
 T1J  H091  N09  C08   113.24  3.000
 T1J  H091  N09  C10   110.92  3.000
 T1J  C08   N09  C10   120.50  3.000
 T1J  C12   N11  C10   104.88  3.000
 T1J  H181  N18  C17   125.81  3.000
 T1J  H181  N18  C10   127.26  3.000
 T1J  C17   N18  C10   106.90  3.000
 T1J  H011  O01  C02   108.78  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
 T1J  CONST_01  C13   C12  N11  C10   180.00   0.0  0
 T1J  CONST_02  C17   C12  N11  C10     0.00   0.0  0
 T1J  CONST_03  C16   C17  N18  C10   180.00   0.0  0
 T1J  CONST_04  C12   C17  N18  C10     0.00   0.0  0
 T1J  CONST_05  C16   C17  C12  C13     0.00   0.0  0
 T1J  CONST_06  N18   C17  C12  C13   180.00   0.0  0
 T1J  CONST_07  C16   C15  C14  C13     0.00   0.0  0
 T1J  CONST_08  C12   C13  C14  C15     0.00   0.0  0
 T1J  CONST_09  N18   C17  C16  C15   180.00   0.0  0
 T1J  CONST_10  C12   C17  C16  C15     0.00   0.0  0
 T1J  CONST_11  C14   C15  C16  C17     0.00   0.0  0
 T1J  CONST_12  N11   C10  N18  C17     0.00   0.0  0
 T1J  CONST_13  C14   C13  C12  C17     0.00   0.0  0
 T1J  CONST_14  C05   C04  C03  C02     0.00   0.0  0
 T1J  CONST_15  C05   C06  C07  C02     0.00   0.0  0
 T1J  CONST_16  C06   C07  C02  C03     0.00   0.0  0
 T1J  CONST_17  C06   C05  C04  C03     0.00   0.0  0
 T1J  CONST_18  C07   C02  C03  C04     0.00   0.0  0
 T1J  CONST_19  C07   C06  C05  C04     0.00   0.0  0
 T1J  CONST_20  N18   C10  N11  C12     0.00   0.0  0
 T1J  CONST_21  N11   C12  C13  C14   180.00   0.0  0
 T1J  CONST_22  N11   C12  C17  C16   180.00   0.0  0
 T1J  CONST_23  N18   C17  C12  N11     0.00   0.0  0
 T1J  CONST_24  N09   C10  N18  C17   180.00   0.0  0
 T1J  CONST_25  C08   C07  C02  C03   180.00   0.0  0
 T1J  CONST_26  O01   C02  C03  C04   180.00   0.0  0
 T1J  CONST_27  C08   C07  C06  C05   180.00   0.0  0
 T1J  CONST_28  O01   C02  C07  C06   180.00   0.0  0
 T1J  CONST_29  N09   C10  N11  C12   180.00   0.0  0
 T1J  CONST_30  H151  C15  C14  C13   180.00   0.0  0
 T1J  CONST_31  H131  C13  C14  C15   180.00   0.0  0
 T1J  CONST_32  H041  C04  C03  C02   180.00   0.0  0
 T1J  CONST_33  H061  C06  C07  C02   180.00   0.0  0
 T1J  CONST_34  H051  C05  C04  C03   180.00   0.0  0
 T1J  CONST_35  H031  C03  C04  C05   180.00   0.0  0
 T1J  CONST_36  H141  C14  C13  C12   180.00   0.0  0
 T1J  CONST_37  H161  C16  C17  C12   180.00   0.0  0
 T1J  CONST_38  H181  N18  C17  C12   180.00   0.0  0
 T1J  Var_01    C07   C08  N09  C10  -172.04  30.0  3
 T1J  Var_02    N09   C08  C07  C02    50.35  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
 T1J  plan-1  C02   0.020
 T1J  plan-1  C03   0.020
 T1J  plan-1  C04   0.020
 T1J  plan-1  C05   0.020
 T1J  plan-1  C06   0.020
 T1J  plan-1  C07   0.020
 T1J  plan-1  C08   0.020
 T1J  plan-1  H031  0.020
 T1J  plan-1  H041  0.020
 T1J  plan-1  H051  0.020
 T1J  plan-1  H061  0.020
 T1J  plan-1  O01   0.020
 T1J  plan-2  C10   0.020
 T1J  plan-2  C13   0.020
 T1J  plan-2  C15   0.020
 T1J  plan-2  C17   0.020
 T1J  plan-2  C12   0.020
 T1J  plan-2  C14   0.020
 T1J  plan-2  C16   0.020
 T1J  plan-2  N09   0.020
 T1J  plan-2  N11   0.020
 T1J  plan-2  N18   0.020
 T1J  plan-2  H131  0.020
 T1J  plan-2  H151  0.020
 T1J  plan-2  H141  0.020
 T1J  plan-2  H161  0.020
 T1J  plan-2  H181  0.020
 T1J  plan-3  C10   0.020
 T1J  plan-3  C08   0.020
 T1J  plan-3  N09   0.020
 T1J  plan-3  H091  0.020

