# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 23:21:53 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-(1H-benzimidazol-1-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CCn1cnc2ccccc12
#
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
 2O0  2O0  3-(1H-benzimidazol-1-yl)propanamide  ligand  25  14  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2O0
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
 2O0  CAE  C  CR16  0  -0.323   3.4761   0.0611   0.4154
 2O0  CAC  C  CR16  0  -0.273   3.5317  -1.3131   0.2701
 2O0  CAD  C  CR16  0  -0.276   2.4052  -2.0545  -0.1197
 2O0  CAF  C  CR16  0  -0.305   1.1893  -1.4442  -0.3726
 2O0  CAM  C  CR56  0   0.338   1.1414  -0.0622  -0.2204
 2O0  CAL  C  CR56  0   0.125   2.2594   0.6965   0.1652
 2O0  NAJ  N  N     0  -0.471   1.9225   2.0285   0.2286
 2O0  CAG  C  CR15  0   0.106   0.6630   2.0654  -0.1007
 2O0  NAN  N  NR5   0  -0.508   0.1313   0.8506  -0.3875
 2O0  CAI  C  CH2   0  -0.305  -1.2461   0.5660  -0.7284
 2O0  CAH  C  CH2   0  -0.597  -2.0003  -0.0194   0.4574
 2O0  CAK  C  C     0   0.533  -3.4390  -0.3503   0.1157
 2O0  OAB  O  O     0  -0.493  -3.9161  -0.1242  -0.9869
 2O0  NAA  N  NH2   0  -0.803  -4.1371  -0.9033   1.1175
 2O0  H1   H  HCR6  0   0.255   4.3479   0.6289   0.7144
 2O0  H2   H  HCR6  0   0.253   4.4617  -1.8321   0.4617
 2O0  H3   H  HCR6  0   0.256   2.4898  -3.1283  -0.2235
 2O0  H4   H  HCR6  0   0.268   0.3247  -2.0223  -0.6731
 2O0  H5   H  HCR5  0   0.289   0.0611   2.9616  -0.1587
 2O0  H6   H  HCH2  0   0.280  -1.7046   1.4969  -1.0574
 2O0  H7   H  HCH2  0   0.271  -1.2578  -0.1171  -1.5781
 2O0  H8   H  HCH2  0   0.283  -1.5044  -0.9252   0.8173
 2O0  H9   H  HCH2  0   0.288  -1.9857   0.6867   1.2924
 2O0  H10  H  HNH2  0   0.408  -3.7237  -1.0867   2.0155
 2O0  H11  H  HNH2  0   0.401  -5.1019  -1.1602   0.9876

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
 2O0  CAD  CAC  aromatic  1.404  0.020  1.404
 2O0  CAD  CAF  aromatic  1.384  0.020  1.384
 2O0  CAC  CAE  aromatic  1.383  0.020  1.383
 2O0  CAF  CAM  aromatic  1.391  0.020  1.391
 2O0  CAE  CAL  aromatic  1.395  0.020  1.395
 2O0  CAM  CAL  aromatic  1.405  0.020  1.405
 2O0  CAM  NAN  aromatic  1.372  0.020  1.372
 2O0  CAI  NAN  single    1.447  0.020  1.447
 2O0  CAI  CAH  single    1.522  0.020  1.522
 2O0  CAL  NAJ  aromatic  1.375  0.020  1.375
 2O0  NAN  CAG  aromatic  1.357  0.020  1.357
 2O0  CAH  CAK  single    1.515  0.020  1.515
 2O0  NAJ  CAG  aromatic  1.302  0.020  1.302
 2O0  CAK  OAB  double    1.223  0.020  1.223
 2O0  CAK  NAA  single    1.340  0.020  1.340
 2O0  CAE  H1   single    0.930  0.020  1.080
 2O0  CAC  H2   single    0.930  0.020  1.080
 2O0  CAD  H3   single    0.930  0.020  1.080
 2O0  CAF  H4   single    0.930  0.020  1.080
 2O0  CAG  H5   single    0.930  0.020  1.080
 2O0  CAI  H6   single    0.970  0.020  1.090
 2O0  CAI  H7   single    0.970  0.020  1.090
 2O0  CAH  H8   single    0.970  0.020  1.090
 2O0  CAH  H9   single    0.970  0.020  1.090
 2O0  NAA  H10  single    0.860  0.020  1.020
 2O0  NAA  H11  single    0.860  0.020  1.020

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
 2O0  H1   CAE  CAL  120.86  3.000
 2O0  H1   CAE  CAC  121.18  3.000
 2O0  CAL  CAE  CAC  117.95  3.000
 2O0  H2   CAC  CAD  119.05  3.000
 2O0  H2   CAC  CAE  119.51  3.000
 2O0  CAD  CAC  CAE  121.45  3.000
 2O0  H3   CAD  CAF  119.27  3.000
 2O0  H3   CAD  CAC  119.21  3.000
 2O0  CAF  CAD  CAC  121.53  3.000
 2O0  H4   CAF  CAM  122.23  3.000
 2O0  H4   CAF  CAD  121.13  3.000
 2O0  CAM  CAF  CAD  116.64  3.000
 2O0  NAN  CAM  CAL  105.08  3.000
 2O0  NAN  CAM  CAF  132.30  3.000
 2O0  CAL  CAM  CAF  122.62  3.000
 2O0  NAJ  CAL  CAM  109.92  3.000
 2O0  NAJ  CAL  CAE  130.27  3.000
 2O0  CAM  CAL  CAE  119.82  3.000
 2O0  CAG  NAJ  CAL  104.63  3.000
 2O0  H5   CAG  NAN  120.84  3.000
 2O0  H5   CAG  NAJ  125.13  3.000
 2O0  NAN  CAG  NAJ  114.03  3.000
 2O0  CAI  NAN  CAG  126.79  3.000
 2O0  CAG  NAN  CAM  106.35  3.000
 2O0  CAI  NAN  CAM  126.78  3.000
 2O0  H7   CAI  H6   107.20  3.000
 2O0  H7   CAI  CAH  111.15  3.000
 2O0  H6   CAI  CAH  110.83  3.000
 2O0  H7   CAI  NAN  108.48  3.000
 2O0  H6   CAI  NAN  107.69  3.000
 2O0  CAH  CAI  NAN  111.33  3.000
 2O0  H9   CAH  H8   106.11  3.000
 2O0  H9   CAH  CAK  109.01  3.000
 2O0  H8   CAH  CAK  108.90  3.000
 2O0  H9   CAH  CAI  109.87  3.000
 2O0  H8   CAH  CAI  110.50  3.000
 2O0  CAK  CAH  CAI  112.25  3.000
 2O0  NAA  CAK  OAB  123.17  3.000
 2O0  NAA  CAK  CAH  114.59  3.000
 2O0  OAB  CAK  CAH  122.24  3.000
 2O0  H11  NAA  H10  117.56  3.000
 2O0  H11  NAA  CAK  120.53  3.000
 2O0  H10  NAA  CAK  121.91  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
 2O0  CONST_01  CAF  CAD  CAC  CAE     0.00   0.0  0
 2O0  CONST_02  CAF  CAM  CAL  CAE     0.00   0.0  0
 2O0  CONST_03  NAN  CAM  CAL  CAE   180.00   0.0  0
 2O0  CONST_04  CAG  NAJ  CAL  CAE   180.00   0.0  0
 2O0  CONST_05  CAM  CAF  CAD  CAC     0.00   0.0  0
 2O0  CONST_06  CAM  CAL  CAE  CAC     0.00   0.0  0
 2O0  CONST_07  NAJ  CAL  CAE  CAC   180.00   0.0  0
 2O0  CONST_08  CAL  CAE  CAC  CAD     0.00   0.0  0
 2O0  CONST_09  CAL  CAM  CAF  CAD     0.00   0.0  0
 2O0  CONST_10  NAN  CAM  CAF  CAD   180.00   0.0  0
 2O0  CONST_11  NAJ  CAL  CAM  CAF   180.00   0.0  0
 2O0  CONST_12  CAG  NAN  CAM  CAF   180.00   0.0  0
 2O0  CONST_13  CAG  NAJ  CAL  CAM     0.00   0.0  0
 2O0  CONST_14  NAJ  CAG  NAN  CAM     0.00   0.0  0
 2O0  CONST_15  CAG  NAN  CAM  CAL     0.00   0.0  0
 2O0  CONST_16  NAN  CAG  NAJ  CAL     0.00   0.0  0
 2O0  CONST_17  NAN  CAM  CAL  NAJ     0.00   0.0  0
 2O0  CONST_18  CAI  NAN  CAM  CAF     0.00   0.0  0
 2O0  CONST_19  CAI  NAN  CAM  CAL   180.00   0.0  0
 2O0  CONST_20  CAI  NAN  CAG  NAJ   180.00   0.0  0
 2O0  CONST_21  H3   CAD  CAC  CAE   180.00   0.0  0
 2O0  CONST_22  H4   CAF  CAD  CAC   180.00   0.0  0
 2O0  CONST_23  H1   CAE  CAC  CAD   180.00   0.0  0
 2O0  CONST_24  H2   CAC  CAD  CAF   180.00   0.0  0
 2O0  CONST_25  H5   CAG  NAN  CAM   180.00   0.0  0
 2O0  CONST_26  H10  NAA  CAK  CAH     0.00   0.0  0
 2O0  CONST_27  H11  NAA  CAK  CAH   180.00   0.0  0
 2O0  Var_01    CAH  CAI  NAN  CAM    74.16  30.0  2
 2O0  Var_02    CAK  CAH  CAI  NAN  -178.90  30.0  3
 2O0  Var_03    OAB  CAK  CAH  CAI    -1.90  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
 2O0  plan-1  CAE  0.020
 2O0  plan-1  CAC  0.020
 2O0  plan-1  CAD  0.020
 2O0  plan-1  CAF  0.020
 2O0  plan-1  CAM  0.020
 2O0  plan-1  CAL  0.020
 2O0  plan-1  NAJ  0.020
 2O0  plan-1  CAG  0.020
 2O0  plan-1  NAN  0.020
 2O0  plan-1  CAI  0.020
 2O0  plan-1  H1   0.020
 2O0  plan-1  H2   0.020
 2O0  plan-1  H3   0.020
 2O0  plan-1  H4   0.020
 2O0  plan-1  H5   0.020
 2O0  plan-2  CAH  0.020
 2O0  plan-2  CAK  0.020
 2O0  plan-2  OAB  0.020
 2O0  plan-2  NAA  0.020
 2O0  plan-2  H10  0.020
 2O0  plan-2  H11  0.020

