# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 13:22:32 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 2-(benzimidazol-1-yl)-~{N}-(2-phenylethyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Cn1cnc2ccccc12)NCCc3ccccc3
#
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
 JRT  JRT  2-(benzimidazol-1-yl)-~{N}-(2-phenylethyl)ethanamide  ligand  38  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JRT
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
 JRT  N1   N  NR5   0  -0.491  -2.8365   1.2098   0.3565
 JRT  N3   N  NH1   0  -0.644   0.7113   0.7721   0.7747
 JRT  C4   C  CR56  0   0.124  -4.5666   0.1493  -0.4973
 JRT  C5   C  CR56  0   0.347  -3.4297  -0.0256   0.3081
 JRT  C6   C  CR16  0  -0.305  -3.0957  -1.2464   0.8829
 JRT  C7   C  CR16  0  -0.275  -3.9489  -2.3054   0.6253
 JRT  C8   C  CR16  0  -0.273  -5.0913  -2.1498  -0.1751
 JRT  C10  C  CH2   0  -0.231   1.9410   0.3681   0.1224
 JRT  C13  C  CR16  0  -0.305   4.7074  -1.4495   0.3421
 JRT  C15  C  CR16  0  -0.271   6.7069  -0.8663  -0.8639
 JRT  C17  C  CR16  0  -0.305   5.2096   0.8523  -0.0933
 JRT  O1   O  O     0  -0.479  -0.5416   0.8401  -1.1017
 JRT  C1   C  C     0   0.546  -0.4201   0.9975   0.1012
 JRT  C2   C  CH2   0  -0.461  -1.5729   1.5216   0.9536
 JRT  C3   C  CR15  0   0.111  -3.5940   2.0315  -0.4140
 JRT  N2   N  N     0  -0.468  -4.6376   1.4537  -0.9319
 JRT  C9   C  CR16  0  -0.322  -5.4145  -0.9301  -0.7424
 JRT  C11  C  CH2   0  -0.563   3.0817   0.3030   1.1325
 JRT  C12  C  CR6   0   0.123   4.3632  -0.1050   0.4615
 JRT  C14  C  CR16  0  -0.240   5.8702  -1.8294  -0.3149
 JRT  C16  C  CR16  0  -0.240   6.3740   0.4774  -0.7500
 JRT  H8   H  HNH1  0   0.410   0.7212   0.9047   1.7739
 JRT  H4   H  HCR6  0   0.268  -2.2166  -1.3727   1.5022
 JRT  H5   H  HCR6  0   0.257  -3.7304  -3.2763   1.0502
 JRT  H6   H  HCR6  0   0.254  -5.7301  -3.0055  -0.3510
 JRT  H9   H  HCH2  0   0.245   1.8118  -0.6093  -0.3503
 JRT  H10  H  HCH2  0   0.245   2.1891   1.0785  -0.6702
 JRT  H15  H  HCR6  0   0.255   7.6152  -1.1614  -1.3732
 JRT  H17  H  HCR6  0   0.249   4.9560   1.9026  -0.0060
 JRT  H2   H  HCH2  0   0.321  -1.4796   2.6068   1.0263
 JRT  H1   H  HCH2  0   0.297  -1.5335   1.1357   1.9735
 JRT  H3   H  HCR5  0   0.290  -3.3238   3.0694  -0.5484
 JRT  H7   H  HCR6  0   0.256  -6.2962  -0.8143  -1.3596
 JRT  H11  H  HCH2  0   0.260   3.2015   1.2800   1.6075
 JRT  H12  H  HCH2  0   0.260   2.8294  -0.4111   1.9207
 JRT  H14  H  HCR6  0   0.255   6.1254  -2.8783  -0.3953
 JRT  H16  H  HCR6  0   0.254   7.0236   1.2350  -1.1698
 JRT  H13  H  HCR6  0   0.249   4.0616  -2.2071   0.7716

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
 JRT  N2   C3   aromatic  1.300  0.020  1.300
 JRT  N2   C4   aromatic  1.377  0.020  1.377
 JRT  C3   N1   aromatic  1.357  0.020  1.357
 JRT  C4   C9   aromatic  1.394  0.020  1.394
 JRT  C4   C5   aromatic  1.404  0.020  1.404
 JRT  C9   C8   aromatic  1.383  0.020  1.383
 JRT  N1   C5   aromatic  1.371  0.020  1.371
 JRT  N1   C2   single    1.432  0.020  1.432
 JRT  C5   C6   aromatic  1.390  0.020  1.390
 JRT  C8   C7   aromatic  1.404  0.020  1.404
 JRT  C2   C1   single    1.527  0.020  1.527
 JRT  C6   C7   aromatic  1.384  0.020  1.384
 JRT  C1   N3   single    1.336  0.020  1.336
 JRT  C1   O1   double    1.219  0.020  1.219
 JRT  N3   C10  single    1.449  0.020  1.449
 JRT  C10  C11  single    1.525  0.020  1.525
 JRT  C17  C16  aromatic  1.388  0.020  1.388
 JRT  C17  C12  aromatic  1.393  0.020  1.393
 JRT  C16  C15  aromatic  1.389  0.020  1.389
 JRT  C11  C12  single    1.503  0.020  1.503
 JRT  C12  C13  aromatic  1.393  0.020  1.393
 JRT  C15  C14  aromatic  1.389  0.020  1.389
 JRT  C13  C14  aromatic  1.389  0.020  1.389
 JRT  N3   H8   single    0.860  0.020  1.020
 JRT  C6   H4   single    0.930  0.020  1.080
 JRT  C7   H5   single    0.930  0.020  1.080
 JRT  C8   H6   single    0.930  0.020  1.080
 JRT  C10  H9   single    0.970  0.020  1.090
 JRT  C10  H10  single    0.970  0.020  1.090
 JRT  C13  H13  single    0.930  0.020  1.080
 JRT  C15  H15  single    0.930  0.020  1.080
 JRT  C17  H17  single    0.930  0.020  1.080
 JRT  C2   H2   single    0.970  0.020  1.090
 JRT  C2   H1   single    0.970  0.020  1.090
 JRT  C3   H3   single    0.930  0.020  1.080
 JRT  C9   H7   single    0.930  0.020  1.080
 JRT  C11  H11  single    0.970  0.020  1.090
 JRT  C11  H12  single    0.970  0.020  1.090
 JRT  C14  H14  single    0.930  0.020  1.080
 JRT  C16  H16  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
 JRT  C3   N1   C2   126.68  3.000
 JRT  C2   N1   C5   126.34  3.000
 JRT  C3   N1   C5   106.49  3.000
 JRT  H8   N3   C1   119.08  3.000
 JRT  H8   N3   C10  118.32  3.000
 JRT  C1   N3   C10  122.59  3.000
 JRT  C9   C4   N2   130.28  3.000
 JRT  C9   C4   C5   119.79  3.000
 JRT  N2   C4   C5   109.93  3.000
 JRT  C6   C5   C4   122.76  3.000
 JRT  C6   C5   N1   132.27  3.000
 JRT  C4   C5   N1   104.97  3.000
 JRT  H4   C6   C7   121.17  3.000
 JRT  H4   C6   C5   122.28  3.000
 JRT  C7   C6   C5   116.54  3.000
 JRT  H5   C7   C8   119.19  3.000
 JRT  H5   C7   C6   119.27  3.000
 JRT  C8   C7   C6   121.54  3.000
 JRT  H6   C8   C9   119.51  3.000
 JRT  H6   C8   C7   119.04  3.000
 JRT  C9   C8   C7   121.45  3.000
 JRT  H10  C10  H9   107.12  3.000
 JRT  H10  C10  C11  109.77  3.000
 JRT  H9   C10  C11  109.67  3.000
 JRT  H10  C10  N3   109.74  3.000
 JRT  H9   C10  N3   110.09  3.000
 JRT  C11  C10  N3   110.39  3.000
 JRT  H13  C13  C14  119.67  3.000
 JRT  H13  C13  C12  119.56  3.000
 JRT  C14  C13  C12  120.77  3.000
 JRT  H15  C15  C16  120.23  3.000
 JRT  H15  C15  C14  120.17  3.000
 JRT  C16  C15  C14  119.61  3.000
 JRT  H17  C17  C16  119.73  3.000
 JRT  H17  C17  C12  119.45  3.000
 JRT  C16  C17  C12  120.82  3.000
 JRT  C2   C1   O1   121.33  3.000
 JRT  O1   C1   N3   124.06  3.000
 JRT  C2   C1   N3   114.58  3.000
 JRT  H1   C2   H2   106.64  3.000
 JRT  H1   C2   C1   111.92  3.000
 JRT  H2   C2   C1   108.30  3.000
 JRT  H1   C2   N1   110.16  3.000
 JRT  H2   C2   N1   108.64  3.000
 JRT  C1   C2   N1   111.03  3.000
 JRT  H3   C3   N2   125.29  3.000
 JRT  H3   C3   N1   120.82  3.000
 JRT  N2   C3   N1   113.89  3.000
 JRT  C3   N2   C4   104.70  3.000
 JRT  H7   C9   C8   121.23  3.000
 JRT  H7   C9   C4   120.84  3.000
 JRT  C8   C9   C4   117.93  3.000
 JRT  H12  C11  H11  107.21  3.000
 JRT  H12  C11  C12  109.96  3.000
 JRT  H11  C11  C12  110.07  3.000
 JRT  H12  C11  C10  109.44  3.000
 JRT  H11  C11  C10  109.37  3.000
 JRT  C12  C11  C10  110.71  3.000
 JRT  C11  C12  C17  120.62  3.000
 JRT  C11  C12  C13  120.73  3.000
 JRT  C17  C12  C13  118.62  3.000
 JRT  H14  C14  C15  120.04  3.000
 JRT  H14  C14  C13  119.84  3.000
 JRT  C15  C14  C13  120.12  3.000
 JRT  H16  C16  C17  119.84  3.000
 JRT  H16  C16  C15  120.09  3.000
 JRT  C17  C16  C15  120.07  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
 JRT  CONST_01  C4   N2   C3   N1      0.00   0.0  0
 JRT  CONST_02  N2   C4   C5   N1      0.00   0.0  0
 JRT  CONST_03  C9   C4   C5   N1    180.00   0.0  0
 JRT  CONST_04  C7   C6   C5   N1    180.00   0.0  0
 JRT  CONST_05  C7   C8   C9   C4      0.00   0.0  0
 JRT  CONST_06  C3   N1   C5   C4      0.00   0.0  0
 JRT  CONST_07  C7   C6   C5   C4      0.00   0.0  0
 JRT  CONST_08  C3   N2   C4   C5      0.00   0.0  0
 JRT  CONST_09  C8   C9   C4   C5      0.00   0.0  0
 JRT  CONST_10  N2   C3   N1   C5      0.00   0.0  0
 JRT  CONST_11  C8   C7   C6   C5      0.00   0.0  0
 JRT  CONST_12  N2   C4   C5   C6    180.00   0.0  0
 JRT  CONST_13  C9   C4   C5   C6      0.00   0.0  0
 JRT  CONST_14  C3   N1   C5   C6    180.00   0.0  0
 JRT  CONST_15  C9   C8   C7   C6      0.00   0.0  0
 JRT  CONST_16  N2   C4   C9   C8    180.00   0.0  0
 JRT  CONST_17  C16  C17  C12  C13     0.00   0.0  0
 JRT  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 JRT  CONST_19  C12  C17  C16  C15     0.00   0.0  0
 JRT  CONST_20  C12  C13  C14  C15     0.00   0.0  0
 JRT  CONST_21  C14  C15  C16  C17     0.00   0.0  0
 JRT  CONST_22  C14  C13  C12  C17     0.00   0.0  0
 JRT  CONST_23  C9   C4   N2   C3    180.00   0.0  0
 JRT  CONST_24  C2   N1   C5   C4    180.00   0.0  0
 JRT  CONST_25  C2   N1   C5   C6      0.00   0.0  0
 JRT  CONST_26  N2   C3   N1   C2    180.00   0.0  0
 JRT  CONST_27  C16  C17  C12  C11   180.00   0.0  0
 JRT  CONST_28  C14  C13  C12  C11   180.00   0.0  0
 JRT  CONST_29  H4   C6   C5   N1      0.00   0.0  0
 JRT  CONST_30  H3   C3   N2   C4    180.00   0.0  0
 JRT  CONST_31  H6   C8   C9   C4    180.00   0.0  0
 JRT  CONST_32  H7   C9   C4   C5    180.00   0.0  0
 JRT  CONST_33  H5   C7   C6   C5    180.00   0.0  0
 JRT  CONST_34  H17  C17  C12  C13   180.00   0.0  0
 JRT  CONST_35  H15  C15  C14  C13   180.00   0.0  0
 JRT  CONST_36  H13  C13  C14  C15   180.00   0.0  0
 JRT  CONST_37  H16  C16  C17  C12   180.00   0.0  0
 JRT  CONST_38  H14  C14  C13  C12   180.00   0.0  0
 JRT  CONST_39  C2   C1   N3   C10   180.00   0.0  0
 JRT  CONST_40  O1   C1   N3   C10     0.00   0.0  0
 JRT  CONST_41  H8   N3   C1   O1    180.00   0.0  0
 JRT  Var_01    C1   C2   N1   C5     73.39  30.0  2
 JRT  Var_02    C17  C12  C11  C10    88.67  30.0  2
 JRT  Var_03    N3   C1   C2   N1   -155.38  30.0  3
 JRT  Var_04    C12  C11  C10  N3   -179.56  30.0  3
 JRT  Var_05    C11  C10  N3   C1    175.22  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
 JRT  plan-1  C13  0.020
 JRT  plan-1  C15  0.020
 JRT  plan-1  C17  0.020
 JRT  plan-1  C11  0.020
 JRT  plan-1  C12  0.020
 JRT  plan-1  C14  0.020
 JRT  plan-1  C16  0.020
 JRT  plan-1  H15  0.020
 JRT  plan-1  H17  0.020
 JRT  plan-1  H14  0.020
 JRT  plan-1  H16  0.020
 JRT  plan-1  H13  0.020
 JRT  plan-2  N1   0.020
 JRT  plan-2  C4   0.020
 JRT  plan-2  C5   0.020
 JRT  plan-2  C6   0.020
 JRT  plan-2  C7   0.020
 JRT  plan-2  C8   0.020
 JRT  plan-2  C2   0.020
 JRT  plan-2  C3   0.020
 JRT  plan-2  N2   0.020
 JRT  plan-2  C9   0.020
 JRT  plan-2  H4   0.020
 JRT  plan-2  H5   0.020
 JRT  plan-2  H6   0.020
 JRT  plan-2  H3   0.020
 JRT  plan-2  H7   0.020
 JRT  plan-3  N3   0.020
 JRT  plan-3  C10  0.020
 JRT  plan-3  O1   0.020
 JRT  plan-3  C1   0.020
 JRT  plan-3  C2   0.020
 JRT  plan-3  H8   0.020

