# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 12:46:20 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: ~{N}-(1-propylbenzimidazol-2-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCn1c(NC(=O)CC)nc2ccccc12
#
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
 GTJ  GTJ  ~{N}-(1-propylbenzimidazol-2-yl)propanamide  ligand  34  17  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GTJ
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
 GTJ  N1   N  NR5   0  -0.569  -0.6590   0.5329  -0.2537
 GTJ  N3   N  NH1   0  -0.769   1.6528   0.1576   0.1110
 GTJ  C4   C  CR56  0   0.351  -1.8131  -0.2089  -0.1571
 GTJ  C5   C  CR16  0  -0.312  -3.1477   0.1177  -0.3502
 GTJ  C6   C  CR16  0  -0.280  -4.0701  -0.9030  -0.1743
 GTJ  C7   C  CR16  0  -0.273  -3.6683  -2.1969   0.1816
 GTJ  C8   C  CR16  0  -0.337  -2.3323  -2.5113   0.3723
 GTJ  C10  C  CR5   0   0.699   0.3603  -0.3144   0.0761
 GTJ  C13  C  CH3   0  -0.659   5.3266  -0.5717  -0.1315
 GTJ  C1   C  CH3   0  -0.668  -0.6797   4.3181   0.2240
 GTJ  C2   C  CH2   0  -0.435  -0.7462   2.8508   0.6189
 GTJ  C3   C  CH2   0  -0.348  -0.5825   1.9399  -0.5915
 GTJ  C9   C  CR56  0   0.146  -1.3919  -1.4982   0.2022
 GTJ  N2   N  N     0  -0.484  -0.0255  -1.5278   0.3473
 GTJ  C11  C  C     0   0.549   2.7972  -0.5931  -0.0338
 GTJ  O1   O  O     0  -0.433   2.7841  -1.7815  -0.2543
 GTJ  C12  C  CH2   0  -0.597   4.0590   0.2273   0.1049
 GTJ  H1   H  HNH1  0   0.430   1.7803   1.1456   0.2711
 GTJ  H2   H  HCR6  0   0.267  -3.4638   1.1161  -0.6239
 GTJ  H3   H  HCR6  0   0.254  -5.1225  -0.6936  -0.3132
 GTJ  H4   H  HCR6  0   0.251  -4.4199  -2.9645   0.3113
 GTJ  H5   H  HCR6  0   0.253  -2.0244  -3.5116   0.6485
 GTJ  H6   H  HCH3  0   0.232   5.4351  -1.3804   0.5897
 GTJ  H7   H  HCH3  0   0.232   5.3468  -1.0063  -1.1302
 GTJ  H8   H  HCH3  0   0.238   6.1955   0.0780  -0.0351
 GTJ  H9   H  HCH3  0   0.227   0.2891   4.5694  -0.2100
 GTJ  H10  H  HCH3  0   0.226  -1.4476   4.5671  -0.5102
 GTJ  H11  H  HCH3  0   0.240  -0.8306   4.9605   1.0908
 GTJ  H12  H  HCH2  0   0.234   0.0312   2.6285   1.3548
 GTJ  H13  H  HCH2  0   0.239  -1.7025   2.6353   1.1012
 GTJ  H14  H  HCH2  0   0.268   0.3657   2.1276  -1.0985
 GTJ  H15  H  HCH2  0   0.276  -1.3602   2.1442  -1.3290
 GTJ  H16  H  HCH2  0   0.279   4.0651   0.6736   1.1042
 GTJ  H17  H  HCH2  0   0.273   4.0037   1.0697  -0.5913

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
 GTJ  C13  C12  single    1.517  0.020  1.517
 GTJ  O1   C11  double    1.209  0.020  1.209
 GTJ  C12  C11  single    1.511  0.020  1.511
 GTJ  C11  N3   single    1.376  0.020  1.376
 GTJ  N3   C10  single    1.376  0.020  1.376
 GTJ  N2   C10  aromatic  1.302  0.020  1.302
 GTJ  N2   C9   aromatic  1.374  0.020  1.374
 GTJ  C10  N1   aromatic  1.366  0.020  1.366
 GTJ  C8   C9   aromatic  1.393  0.020  1.393
 GTJ  C8   C7   aromatic  1.386  0.020  1.386
 GTJ  C9   C4   aromatic  1.403  0.020  1.403
 GTJ  N1   C4   aromatic  1.375  0.020  1.375
 GTJ  N1   C3   single    1.449  0.020  1.449
 GTJ  C7   C6   aromatic  1.401  0.020  1.401
 GTJ  C4   C5   aromatic  1.388  0.020  1.388
 GTJ  C3   C2   single    1.524  0.020  1.524
 GTJ  C6   C5   aromatic  1.387  0.020  1.387
 GTJ  C2   C1   single    1.521  0.020  1.521
 GTJ  N3   H1   single    0.860  0.020  1.020
 GTJ  C5   H2   single    0.930  0.020  1.080
 GTJ  C6   H3   single    0.930  0.020  1.080
 GTJ  C7   H4   single    0.930  0.020  1.080
 GTJ  C8   H5   single    0.930  0.020  1.080
 GTJ  C13  H6   single    0.970  0.020  1.090
 GTJ  C13  H7   single    0.970  0.020  1.090
 GTJ  C13  H8   single    0.970  0.020  1.090
 GTJ  C1   H9   single    0.970  0.020  1.090
 GTJ  C1   H10  single    0.970  0.020  1.090
 GTJ  C1   H11  single    0.970  0.020  1.090
 GTJ  C2   H12  single    0.970  0.020  1.090
 GTJ  C2   H13  single    0.970  0.020  1.090
 GTJ  C3   H14  single    0.970  0.020  1.090
 GTJ  C3   H15  single    0.970  0.020  1.090
 GTJ  C12  H16  single    0.970  0.020  1.090
 GTJ  C12  H17  single    0.970  0.020  1.090

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
 GTJ  C3   N1   C10  128.26  3.000
 GTJ  C3   N1   C4   125.76  3.000
 GTJ  C10  N1   C4   105.94  3.000
 GTJ  H1   N3   C11  116.47  3.000
 GTJ  H1   N3   C10  117.28  3.000
 GTJ  C11  N3   C10  126.24  3.000
 GTJ  C9   C4   C5   122.73  3.000
 GTJ  C5   C4   N1   132.10  3.000
 GTJ  C9   C4   N1   105.17  3.000
 GTJ  H2   C5   C6   121.11  3.000
 GTJ  H2   C5   C4   122.22  3.000
 GTJ  C6   C5   C4   116.67  3.000
 GTJ  H3   C6   C7   119.36  3.000
 GTJ  H3   C6   C5   119.22  3.000
 GTJ  C7   C6   C5   121.42  3.000
 GTJ  H4   C7   C8   119.48  3.000
 GTJ  H4   C7   C6   119.11  3.000
 GTJ  C8   C7   C6   121.40  3.000
 GTJ  H5   C8   C9   120.75  3.000
 GTJ  H5   C8   C7   121.27  3.000
 GTJ  C9   C8   C7   117.98  3.000
 GTJ  N2   C10  N3   126.34  3.000
 GTJ  N2   C10  N1   114.04  3.000
 GTJ  N3   C10  N1   119.62  3.000
 GTJ  H8   C13  H7   107.72  3.000
 GTJ  H8   C13  H6   107.76  3.000
 GTJ  H7   C13  H6   108.00  3.000
 GTJ  H8   C13  C12  109.79  3.000
 GTJ  H7   C13  C12  111.62  3.000
 GTJ  H6   C13  C12  111.79  3.000
 GTJ  H11  C1   H10  107.66  3.000
 GTJ  H11  C1   H9   107.68  3.000
 GTJ  H10  C1   H9   107.74  3.000
 GTJ  H11  C1   C2   110.87  3.000
 GTJ  H10  C1   C2   111.35  3.000
 GTJ  H9   C1   C2   111.36  3.000
 GTJ  H13  C2   H12  106.56  3.000
 GTJ  H13  C2   C3   109.08  3.000
 GTJ  H12  C2   C3   109.68  3.000
 GTJ  H13  C2   C1   110.07  3.000
 GTJ  H12  C2   C1   109.87  3.000
 GTJ  C3   C2   C1   111.46  3.000
 GTJ  H15  C3   H14  105.84  3.000
 GTJ  H15  C3   C2   110.39  3.000
 GTJ  H14  C3   C2   111.07  3.000
 GTJ  H15  C3   N1   107.56  3.000
 GTJ  H14  C3   N1   108.73  3.000
 GTJ  C2   C3   N1   112.93  3.000
 GTJ  N2   C9   C8   130.00  3.000
 GTJ  C8   C9   C4   119.80  3.000
 GTJ  N2   C9   C4   110.19  3.000
 GTJ  C9   N2   C10  104.63  3.000
 GTJ  C12  C11  O1   124.02  3.000
 GTJ  C12  C11  N3   112.86  3.000
 GTJ  O1   C11  N3   123.12  3.000
 GTJ  H17  C12  H16  105.50  3.000
 GTJ  H17  C12  C11  108.50  3.000
 GTJ  H16  C12  C11  108.04  3.000
 GTJ  H17  C12  C13  110.40  3.000
 GTJ  H16  C12  C13  110.64  3.000
 GTJ  C11  C12  C13  113.42  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
 GTJ  CONST_01  C9   N2   C10  N1      0.00   0.0  0
 GTJ  CONST_02  N2   C9   C4   N1      0.00   0.0  0
 GTJ  CONST_03  C8   C9   C4   N1    180.00   0.0  0
 GTJ  CONST_04  C6   C5   C4   N1    180.00   0.0  0
 GTJ  CONST_05  C10  N2   C9   C4      0.00   0.0  0
 GTJ  CONST_06  C7   C8   C9   C4      0.00   0.0  0
 GTJ  CONST_07  N2   C10  N1   C4      0.00   0.0  0
 GTJ  CONST_08  C7   C6   C5   C4      0.00   0.0  0
 GTJ  CONST_09  N2   C9   C4   C5    180.00   0.0  0
 GTJ  CONST_10  C8   C9   C4   C5      0.00   0.0  0
 GTJ  CONST_11  C10  N1   C4   C5    180.00   0.0  0
 GTJ  CONST_12  C8   C7   C6   C5      0.00   0.0  0
 GTJ  CONST_13  C9   C8   C7   C6      0.00   0.0  0
 GTJ  CONST_14  C9   C4   C5   C6      0.00   0.0  0
 GTJ  CONST_15  N2   C9   C8   C7    180.00   0.0  0
 GTJ  CONST_16  C10  N2   C9   C8    180.00   0.0  0
 GTJ  CONST_17  C9   C4   N1   C10     0.00   0.0  0
 GTJ  CONST_18  C9   N2   C10  N3    180.00   0.0  0
 GTJ  CONST_19  C4   N1   C10  N3    180.00   0.0  0
 GTJ  CONST_20  C3   N1   C4   C5      0.00   0.0  0
 GTJ  CONST_21  N2   C10  N1   C3    180.00   0.0  0
 GTJ  CONST_22  C9   C4   N1   C3    180.00   0.0  0
 GTJ  CONST_23  H2   C5   C4   N1      0.00   0.0  0
 GTJ  CONST_24  H5   C8   C9   C4    180.00   0.0  0
 GTJ  CONST_25  H3   C6   C5   C4    180.00   0.0  0
 GTJ  CONST_26  H4   C7   C6   C5    180.00   0.0  0
 GTJ  CONST_30  O1   C11  N3   C10     0.00   0.0  0
 GTJ  CONST_31  C12  C11  N3   C10   180.00   0.0  0
 GTJ  Var_01    C2   C3   N1   C4     86.07  30.0  2
 GTJ  Var_02    C1   C2   C3   N1   -179.21  30.0  3
 GTJ  Var_03    C13  C12  C11  N3   -176.68  30.0  1
 GTJ  Var_04    H9   C1   C2   C3    -61.99  30.0  3
 GTJ  Var_05    H6   C13  C12  C11   -61.49  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
 GTJ  plan-1  N1   0.020
 GTJ  plan-1  N3   0.020
 GTJ  plan-1  C4   0.020
 GTJ  plan-1  C5   0.020
 GTJ  plan-1  C6   0.020
 GTJ  plan-1  C7   0.020
 GTJ  plan-1  C8   0.020
 GTJ  plan-1  C10  0.020
 GTJ  plan-1  C3   0.020
 GTJ  plan-1  C9   0.020
 GTJ  plan-1  N2   0.020
 GTJ  plan-1  H2   0.020
 GTJ  plan-1  H3   0.020
 GTJ  plan-1  H4   0.020
 GTJ  plan-1  H5   0.020
 GTJ  plan-2  N3   0.020
 GTJ  plan-2  C10  0.020
 GTJ  plan-2  C11  0.020
 GTJ  plan-2  O1   0.020
 GTJ  plan-2  C12  0.020
 GTJ  plan-2  H1   0.020

