# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 18:15:01 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: ~{N}2-(1~{H}-benzimidazol-2-yl)benzene-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccccc1Nc2[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
 AWG  AWG  ~{N}2-(1~{H}-benzimidazol-2-yl)benzene-1,2-diamine  ligand  29  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AWG
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
 AWG  N1   N  NH2   0  -0.867   3.2622   2.0017   0.3588
 AWG  N3   N  NR15  0  -0.745  -1.3775   1.4311  -0.3265
 AWG  C4   C  CR6   0   0.311   2.0095  -0.0033  -0.1434
 AWG  C5   C  CR6   0   0.201   3.2392   0.6231   0.1448
 AWG  C6   C  CR16  0  -0.319   4.3997  -0.1437   0.1434
 AWG  C7   C  CR5   0   0.700  -0.4144   0.4857  -0.1276
 AWG  C8   C  CR56  0   0.330  -2.5924   0.8107  -0.1562
 AWG  C10  C  CR16  0  -0.288  -4.9018   0.3365   0.0066
 AWG  C13  C  CR56  0   0.176  -2.2686  -0.5246   0.1420
 AWG  C1   C  CR16  0  -0.270   4.3583  -1.5078  -0.1129
 AWG  C2   C  CR16  0  -0.275   3.1417  -2.1231  -0.3598
 AWG  C3   C  CR16  0  -0.311   1.9720  -1.3734  -0.3812
 AWG  C9   C  CR16  0  -0.312  -3.8973   1.2676  -0.2302
 AWG  C11  C  CR16  0  -0.272  -4.6007  -0.9956   0.3046
 AWG  C12  C  CR16  0  -0.348  -3.2875  -1.4422   0.3750
 AWG  N4   N  N     0  -0.528  -0.9027  -0.6957   0.1509
 AWG  H1   H  HNH2  0   0.377   2.6125   2.3151   1.0679
 AWG  H2   H  HNH2  0   0.381   4.1827   2.3499   0.5827
 AWG  H4   H  HCR6  0   0.257   5.3455   0.3382   0.3624
 AWG  H5   H  HCR6  0   0.250  -5.9365   0.6498  -0.0424
 AWG  H6   H  HCR6  0   0.250   5.2736  -2.0850  -0.1025
 AWG  H7   H  HCR6  0   0.249   3.0929  -3.1879  -0.5457
 AWG  H8   H  HCR6  0   0.272   1.0271  -1.8540  -0.5847
 AWG  H10  H  HCR6  0   0.262  -4.1288   2.2989  -0.4626
 AWG  H11  H  HCR6  0   0.247  -5.4091  -1.6927   0.4832
 AWG  H12  H  HCR6  0   0.248  -3.0605  -2.4754   0.6055
 AWG  N2   N  NH1   0  -0.801   0.8920   0.8316  -0.2099
 AWG  H3   H  HNR5  0   0.418  -1.2259   2.4029  -0.5450
 AWG  H9   H  HNH1  0   0.408   1.0885   1.7989  -0.4233

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
 AWG  C2   C3   aromatic  1.390  0.020  1.390
 AWG  C2   C1   aromatic  1.385  0.020  1.385
 AWG  C3   C4   aromatic  1.391  0.020  1.391
 AWG  C1   C6   aromatic  1.389  0.020  1.389
 AWG  C4   N2   single    1.396  0.020  1.396
 AWG  C4   C5   aromatic  1.410  0.020  1.410
 AWG  C6   C5   aromatic  1.391  0.020  1.391
 AWG  N2   C7   single    1.354  0.020  1.354
 AWG  C5   N1   single    1.395  0.020  1.395
 AWG  C7   N3   aromatic  1.364  0.020  1.364
 AWG  C7   N4   aromatic  1.308  0.020  1.308
 AWG  N3   C8   aromatic  1.375  0.020  1.375
 AWG  N4   C13  aromatic  1.377  0.020  1.377
 AWG  C8   C13  aromatic  1.406  0.020  1.406
 AWG  C8   C9   aromatic  1.385  0.020  1.385
 AWG  C13  C12  aromatic  1.391  0.020  1.391
 AWG  C9   C10  aromatic  1.390  0.020  1.390
 AWG  C12  C11  aromatic  1.389  0.020  1.389
 AWG  C10  C11  aromatic  1.398  0.020  1.398
 AWG  N1   H1   single    0.890  0.020  1.040
 AWG  N1   H2   single    0.890  0.020  1.040
 AWG  N3   H3   single    0.860  0.020  1.020
 AWG  C6   H4   single    0.930  0.020  1.080
 AWG  C10  H5   single    0.930  0.020  1.080
 AWG  C1   H6   single    0.930  0.020  1.080
 AWG  C2   H7   single    0.930  0.020  1.080
 AWG  C3   H8   single    0.930  0.020  1.080
 AWG  N2   H9   single    0.860  0.020  1.020
 AWG  C9   H10  single    0.930  0.020  1.080
 AWG  C11  H11  single    0.930  0.020  1.080
 AWG  C12  H12  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
 AWG  H2   N1   H1   108.87  3.000
 AWG  H2   N1   C5   112.95  3.000
 AWG  H1   N1   C5   113.77  3.000
 AWG  H3   N3   C8   126.52  3.000
 AWG  H3   N3   C7   126.42  3.000
 AWG  C8   N3   C7   107.05  3.000
 AWG  N2   C4   C3   124.00  3.000
 AWG  N2   C4   C5   116.23  3.000
 AWG  C3   C4   C5   119.74  3.000
 AWG  C6   C5   C4   118.85  3.000
 AWG  C6   C5   N1   122.08  3.000
 AWG  C4   C5   N1   119.00  3.000
 AWG  H4   C6   C1   120.01  3.000
 AWG  H4   C6   C5   118.86  3.000
 AWG  C1   C6   C5   121.12  3.000
 AWG  N4   C7   N2   127.14  3.000
 AWG  N4   C7   N3   113.16  3.000
 AWG  N2   C7   N3   119.69  3.000
 AWG  C9   C8   C13  122.81  3.000
 AWG  C9   C8   N3   132.63  3.000
 AWG  C13  C8   N3   104.56  3.000
 AWG  H5   C10  C11  119.44  3.000
 AWG  H5   C10  C9   119.29  3.000
 AWG  C11  C10  C9   121.26  3.000
 AWG  N4   C13  C12  130.07  3.000
 AWG  C12  C13  C8   119.57  3.000
 AWG  N4   C13  C8   110.36  3.000
 AWG  H6   C1   C2   120.50  3.000
 AWG  H6   C1   C6   119.80  3.000
 AWG  C2   C1   C6   119.70  3.000
 AWG  H7   C2   C3   119.36  3.000
 AWG  H7   C2   C1   120.49  3.000
 AWG  C3   C2   C1   120.15  3.000
 AWG  H8   C3   C2   119.97  3.000
 AWG  H8   C3   C4   119.62  3.000
 AWG  C2   C3   C4   120.41  3.000
 AWG  H10  C9   C10  121.36  3.000
 AWG  H10  C9   C8   121.84  3.000
 AWG  C10  C9   C8   116.80  3.000
 AWG  H11  C11  C12  119.39  3.000
 AWG  H11  C11  C10  119.21  3.000
 AWG  C12  C11  C10  121.40  3.000
 AWG  H12  C12  C11  121.06  3.000
 AWG  H12  C12  C13  120.78  3.000
 AWG  C11  C12  C13  118.16  3.000
 AWG  C13  N4   C7   104.88  3.000
 AWG  H9   N2   C7   116.44  3.000
 AWG  H9   N2   C4   115.28  3.000
 AWG  C7   N2   C4   128.06  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
 AWG  CONST_01  C13  N4   C7   N3      0.00   0.0  0
 AWG  CONST_02  N4   C13  C8   N3      0.00   0.0  0
 AWG  CONST_03  C12  C13  C8   N3    180.00   0.0  0
 AWG  CONST_04  C10  C9   C8   N3    180.00   0.0  0
 AWG  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 AWG  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 AWG  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 AWG  CONST_08  C2   C1   C6   C5      0.00   0.0  0
 AWG  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 AWG  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 AWG  CONST_11  C13  C8   N3   C7      0.00   0.0  0
 AWG  CONST_12  C9   C8   N3   C7    180.00   0.0  0
 AWG  CONST_13  C8   C13  N4   C7      0.00   0.0  0
 AWG  CONST_14  C12  C13  N4   C7    180.00   0.0  0
 AWG  CONST_15  N4   C7   N3   C8      0.00   0.0  0
 AWG  CONST_16  C11  C12  C13  C8      0.00   0.0  0
 AWG  CONST_17  C11  C10  C9   C8      0.00   0.0  0
 AWG  CONST_18  C13  C8   C9   C10     0.00   0.0  0
 AWG  CONST_19  C13  C12  C11  C10     0.00   0.0  0
 AWG  CONST_20  N4   C13  C8   C9    180.00   0.0  0
 AWG  CONST_21  C12  C13  C8   C9      0.00   0.0  0
 AWG  CONST_22  C12  C11  C10  C9      0.00   0.0  0
 AWG  CONST_23  N4   C13  C12  C11   180.00   0.0  0
 AWG  CONST_24  C3   C4   C5   N1    180.00   0.0  0
 AWG  CONST_25  C1   C6   C5   N1    180.00   0.0  0
 AWG  CONST_26  N2   C4   C5   C6    180.00   0.0  0
 AWG  CONST_27  N2   C7   N3   C8    180.00   0.0  0
 AWG  CONST_28  N2   C7   N4   C13   180.00   0.0  0
 AWG  CONST_29  N2   C4   C3   C2    180.00   0.0  0
 AWG  CONST_30  H10  C9   C8   N3      0.00   0.0  0
 AWG  CONST_31  H7   C2   C3   C4    180.00   0.0  0
 AWG  CONST_32  H4   C6   C5   C4    180.00   0.0  0
 AWG  CONST_33  H8   C3   C4   C5    180.00   0.0  0
 AWG  CONST_34  H6   C1   C6   C5    180.00   0.0  0
 AWG  CONST_35  H12  C12  C13  C8    180.00   0.0  0
 AWG  CONST_36  H5   C10  C9   C8    180.00   0.0  0
 AWG  CONST_37  H3   N3   C8   C13   180.00   0.0  0
 AWG  CONST_38  H11  C11  C12  C13   180.00   0.0  0
 AWG  CONST_40  H2   N1   C5   C4    180.00   0.0  0
 AWG  Var_01    C4   N2   C7   N3   -174.51  30.0  1
 AWG  Var_02    C7   N2   C4   C5   -161.61  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
 AWG  plan-1  N1   0.020
 AWG  plan-1  C4   0.020
 AWG  plan-1  C5   0.020
 AWG  plan-1  C6   0.020
 AWG  plan-1  C1   0.020
 AWG  plan-1  C2   0.020
 AWG  plan-1  C3   0.020
 AWG  plan-1  H4   0.020
 AWG  plan-1  H6   0.020
 AWG  plan-1  H7   0.020
 AWG  plan-1  H8   0.020
 AWG  plan-1  N2   0.020
 AWG  plan-2  N3   0.020
 AWG  plan-2  C7   0.020
 AWG  plan-2  C8   0.020
 AWG  plan-2  C10  0.020
 AWG  plan-2  C13  0.020
 AWG  plan-2  C9   0.020
 AWG  plan-2  C11  0.020
 AWG  plan-2  C12  0.020
 AWG  plan-2  N4   0.020
 AWG  plan-2  H5   0.020
 AWG  plan-2  H10  0.020
 AWG  plan-2  H11  0.020
 AWG  plan-2  H12  0.020
 AWG  plan-2  N2   0.020
 AWG  plan-2  H3   0.020
 AWG  plan-3  N1   0.020
 AWG  plan-3  C5   0.020
 AWG  plan-3  H1   0.020
 AWG  plan-3  H2   0.020

