# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 23:22:50 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 1-(1H-benzimidazol-1-yl)propan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Cn1cnc2ccccc12
#
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
 2NZ  2NZ  1-(1H-benzimidazol-1-yl)propan-2-one  ligand  23  13  .  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_2NZ
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
 2NZ  CAA  C  CH3   0  -0.772   3.9204  -0.9283   0.0453
 2NZ  C    C  C     0   0.382   2.5893  -0.3214  -0.2775
 2NZ  O    O  O     0  -0.377   2.1217  -0.2734  -1.3879
 2NZ  CA   C  CH2   0  -0.443   1.8357   0.2383   0.9177
 2NZ  N    N  NR5   0  -0.497   0.5253   0.7038   0.5764
 2NZ  CAL  C  CR56  0   0.349  -0.5834  -0.0701   0.3443
 2NZ  CAF  C  CR16  0  -0.306  -0.8140  -1.4360   0.4609
 2NZ  CAD  C  CR16  0  -0.275  -2.0885  -1.8781   0.1517
 2NZ  CAC  C  CR16  0  -0.273  -3.0944  -0.9898  -0.2591
 2NZ  CAE  C  CR16  0  -0.322  -2.8552   0.3677  -0.3724
 2NZ  CAK  C  CR56  0   0.124  -1.5769   0.8334  -0.0664
 2NZ  NAI  N  N     0  -0.467  -1.0666   2.1114  -0.0948
 2NZ  CAG  C  CR15  0   0.110   0.1714   1.9817   0.2813
 2NZ  H1   H  HCH3  0   0.278   3.7643  -1.8764   0.5654
 2NZ  H2   H  HCH3  0   0.271   4.4984  -1.1162  -0.8564
 2NZ  H3   H  HCH3  0   0.267   4.4904  -0.2891   0.7205
 2NZ  H4   H  HCH2  0   0.305   1.7771  -0.5183   1.7047
 2NZ  H5   H  HCH2  0   0.321   2.4144   1.0630   1.3398
 2NZ  H6   H  HCR6  0   0.267  -0.0435  -2.1298   0.7736
 2NZ  H7   H  HCR6  0   0.257  -2.3139  -2.9339   0.2253
 2NZ  H8   H  HCR6  0   0.254  -4.0764  -1.3792  -0.4939
 2NZ  H9   H  HCR6  0   0.256  -3.6332   1.0504  -0.6898
 2NZ  H10  H  HCR5  0   0.291   0.8827   2.7900   0.3767

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
 2NZ  CAG  NAI  aromatic  1.300  0.020  1.300
 2NZ  CAG  N    aromatic  1.358  0.020  1.358
 2NZ  NAI  CAK  aromatic  1.376  0.020  1.376
 2NZ  O    C    double    1.206  0.020  1.206
 2NZ  C    CAA  single    1.498  0.020  1.498
 2NZ  C    CA   single    1.520  0.020  1.520
 2NZ  N    CA   single    1.432  0.020  1.432
 2NZ  N    CAL  aromatic  1.372  0.020  1.372
 2NZ  CAK  CAL  aromatic  1.404  0.020  1.404
 2NZ  CAK  CAE  aromatic  1.394  0.020  1.394
 2NZ  CAL  CAF  aromatic  1.390  0.020  1.390
 2NZ  CAE  CAC  aromatic  1.383  0.020  1.383
 2NZ  CAF  CAD  aromatic  1.384  0.020  1.384
 2NZ  CAC  CAD  aromatic  1.403  0.020  1.403
 2NZ  CAA  H1   single    0.970  0.020  1.090
 2NZ  CAA  H2   single    0.970  0.020  1.090
 2NZ  CAA  H3   single    0.970  0.020  1.090
 2NZ  CA   H4   single    0.970  0.020  1.090
 2NZ  CA   H5   single    0.970  0.020  1.090
 2NZ  CAF  H6   single    0.930  0.020  1.080
 2NZ  CAD  H7   single    0.930  0.020  1.080
 2NZ  CAC  H8   single    0.930  0.020  1.080
 2NZ  CAE  H9   single    0.930  0.020  1.080
 2NZ  CAG  H10  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
 2NZ  H3   CAA  H2   109.68  3.000
 2NZ  H3   CAA  H1   106.77  3.000
 2NZ  H2   CAA  H1   108.71  3.000
 2NZ  H3   CAA  C    111.12  3.000
 2NZ  H2   CAA  C    111.32  3.000
 2NZ  H1   CAA  C    109.10  3.000
 2NZ  CA   C    O    121.15  3.000
 2NZ  CA   C    CAA  114.85  3.000
 2NZ  O    C    CAA  124.00  3.000
 2NZ  H5   CA   H4   105.83  3.000
 2NZ  H5   CA   N    109.36  3.000
 2NZ  H4   CA   N    110.33  3.000
 2NZ  H5   CA   C    108.61  3.000
 2NZ  H4   CA   C    109.75  3.000
 2NZ  N    CA   C    112.71  3.000
 2NZ  CAG  N    CAL  106.46  3.000
 2NZ  CAL  N    CA   126.62  3.000
 2NZ  CAG  N    CA   126.58  3.000
 2NZ  CAK  CAL  CAF  122.64  3.000
 2NZ  CAF  CAL  N    132.39  3.000
 2NZ  CAK  CAL  N    104.97  3.000
 2NZ  H6   CAF  CAD  121.00  3.000
 2NZ  H6   CAF  CAL  122.39  3.000
 2NZ  CAD  CAF  CAL  116.61  3.000
 2NZ  H7   CAD  CAC  119.23  3.000
 2NZ  H7   CAD  CAF  119.22  3.000
 2NZ  CAC  CAD  CAF  121.55  3.000
 2NZ  H8   CAC  CAE  119.50  3.000
 2NZ  H8   CAC  CAD  119.09  3.000
 2NZ  CAE  CAC  CAD  121.42  3.000
 2NZ  H9   CAE  CAK  120.84  3.000
 2NZ  H9   CAE  CAC  121.24  3.000
 2NZ  CAK  CAE  CAC  117.93  3.000
 2NZ  NAI  CAK  CAE  130.19  3.000
 2NZ  CAE  CAK  CAL  119.86  3.000
 2NZ  NAI  CAK  CAL  109.95  3.000
 2NZ  CAG  NAI  CAK  104.73  3.000
 2NZ  H10  CAG  NAI  125.27  3.000
 2NZ  H10  CAG  N    120.85  3.000
 2NZ  NAI  CAG  N    113.87  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
 2NZ  CONST_01  CAK  NAI  CAG  N       0.00   0.0  0
 2NZ  CONST_02  NAI  CAK  CAL  N       0.00   0.0  0
 2NZ  CONST_03  CAE  CAK  CAL  N     180.00   0.0  0
 2NZ  CONST_04  CAD  CAF  CAL  N     180.00   0.0  0
 2NZ  CONST_05  NAI  CAG  N    CAL     0.00   0.0  0
 2NZ  CONST_06  CAG  NAI  CAK  CAL     0.00   0.0  0
 2NZ  CONST_07  CAC  CAE  CAK  CAL     0.00   0.0  0
 2NZ  CONST_08  CAC  CAD  CAF  CAL     0.00   0.0  0
 2NZ  CONST_09  CAG  N    CAL  CAF   180.00   0.0  0
 2NZ  CONST_10  NAI  CAK  CAL  CAF   180.00   0.0  0
 2NZ  CONST_11  CAE  CAK  CAL  CAF     0.00   0.0  0
 2NZ  CONST_12  CAE  CAC  CAD  CAF     0.00   0.0  0
 2NZ  CONST_13  CAK  CAL  CAF  CAD     0.00   0.0  0
 2NZ  CONST_14  CAK  CAE  CAC  CAD     0.00   0.0  0
 2NZ  CONST_15  NAI  CAK  CAE  CAC   180.00   0.0  0
 2NZ  CONST_16  CAG  NAI  CAK  CAE   180.00   0.0  0
 2NZ  CONST_17  CAG  N    CAL  CAK     0.00   0.0  0
 2NZ  CONST_18  NAI  CAG  N    CA    180.00   0.0  0
 2NZ  CONST_19  CAK  CAL  N    CA    180.00   0.0  0
 2NZ  CONST_20  CAF  CAL  N    CA      0.00   0.0  0
 2NZ  CONST_21  H6   CAF  CAL  N       0.00   0.0  0
 2NZ  CONST_22  H10  CAG  N    CAL   180.00   0.0  0
 2NZ  CONST_23  H9   CAE  CAK  CAL   180.00   0.0  0
 2NZ  CONST_24  H7   CAD  CAF  CAL   180.00   0.0  0
 2NZ  CONST_25  H8   CAC  CAD  CAF   180.00   0.0  0
 2NZ  Var_01    CAG  N    CA   C     -95.78  30.0  2
 2NZ  Var_02    N    CA   C    CAA  -175.05  30.0  3
 2NZ  Var_03    H1   CAA  C    O    -107.42  30.0  3

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
 2NZ  plan-1  CA   0.020
 2NZ  plan-1  N    0.020
 2NZ  plan-1  CAL  0.020
 2NZ  plan-1  CAF  0.020
 2NZ  plan-1  CAD  0.020
 2NZ  plan-1  CAC  0.020
 2NZ  plan-1  CAE  0.020
 2NZ  plan-1  CAK  0.020
 2NZ  plan-1  NAI  0.020
 2NZ  plan-1  CAG  0.020
 2NZ  plan-1  H6   0.020
 2NZ  plan-1  H7   0.020
 2NZ  plan-1  H8   0.020
 2NZ  plan-1  H9   0.020
 2NZ  plan-1  H10  0.020
 2NZ  plan-2  CAA  0.020
 2NZ  plan-2  C    0.020
 2NZ  plan-2  O    0.020
 2NZ  plan-2  CA   0.020

