# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 07:18:08 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 3-[3-chloro-5-(trifluoromethyl)pyridin-2-yl]-2-methyl-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c2ccccc2c1c3ncc(cc3Cl)C(F)(F)F
#
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
 OJ7  OJ7  3-[3-chloro-5-(trifluoromethyl)pyridin-2-yl]-2-methyl-1H-indole  ligand  31  21  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OJ7
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
 OJ7  C4   C   CR56  0   0.343  -2.4775   0.1812   0.2507
 OJ7  C14  C   CR6   0  -0.081   0.5853   0.6384  -0.7315
 OJ7  C5   C   CR56  0   0.223  -3.6857  -0.5298   0.1701
 OJ7  C6   C   CR16  0  -0.414  -4.9127   0.0397   0.4919
 OJ7  C11  C   CR16  0  -0.031   2.0777  -1.1930   0.5703
 OJ7  C7   C   CR16  0  -0.138  -4.9132   1.3371   0.9115
 OJ7  C8   C   CR16  0  -0.313  -3.7180   2.0623   1.0536
 OJ7  C9   C   CR16  0  -0.431  -2.4999   1.4955   0.7324
 OJ7  C10  C   CR6   0   0.205   0.0046  -0.4913  -0.1325
 OJ7  C12  C   CR6   0  -0.295   2.6989  -0.0274   0.1410
 OJ7  C13  C   CR16  0  -0.137   1.9313   0.8932  -0.5554
 OJ7  N1   N   NR15  0  -0.716  -3.3806  -1.8053  -0.2208
 OJ7  N2   N   N     0  -0.484   0.7823  -1.4046   0.4446
 OJ7  C3   C   CR5   0  -0.182  -1.4319  -0.7325  -0.1330
 OJ7  C2   C   CR5   0   0.523  -2.0370  -1.9381  -0.4035
 OJ7  CL1  CL  CL    0  -0.107  -0.3262   1.6732  -1.7625
 OJ7  C15  C   CT    0   0.963   4.1417   0.2372   0.4319
 OJ7  F1   F   F     0  -0.282   4.2951   0.9435   1.5546
 OJ7  F2   F   F     0  -0.179   4.8337  -0.8968   0.5765
 OJ7  F3   F   F     0  -0.406   4.7206   0.9350  -0.5524
 OJ7  H1   H   HCR6  0   0.250  -5.8399  -0.5107   0.4083
 OJ7  H2   H   HCR6  0   0.310   2.6391  -1.9907   1.0409
 OJ7  H3   H   HCR6  0   0.259  -5.8493   1.8196   1.1607
 OJ7  H4   H   HCR6  0   0.224  -3.7657   3.0755   1.4286
 OJ7  H5   H   HCR6  0   0.217  -1.5832   2.0542   0.8622
 OJ7  H6   H   HCR6  0   0.302   2.3716   1.7826  -0.9863
 OJ7  H7   H   HNR5  0   0.397  -4.0453  -2.5137  -0.4742
 OJ7  H8   H   HCH3  0   0.267  -1.4161  -3.9136   0.0869
 OJ7  H9   H   HCH3  0   0.251  -2.0219  -3.7452  -1.5621
 OJ7  H10  H   HCH3  0   0.265  -0.4250  -3.1295  -1.1198
 OJ7  C1   C   CH3   0  -0.804  -1.4478  -3.2489  -0.7780

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
 OJ7  F1   C15  single    1.335  0.020  1.335
 OJ7  F2   C15  single    1.336  0.020  1.336
 OJ7  F3   C15  single    1.338  0.020  1.338
 OJ7  C15  C12  single    1.495  0.020  1.495
 OJ7  C12  C13  aromatic  1.386  0.020  1.386
 OJ7  C12  C11  aromatic  1.389  0.020  1.389
 OJ7  C13  C14  aromatic  1.381  0.020  1.381
 OJ7  C11  N2   aromatic  1.319  0.020  1.319
 OJ7  C14  C10  aromatic  1.404  0.020  1.404
 OJ7  C14  CL1  single    1.722  0.020  1.722
 OJ7  N2   C10  aromatic  1.331  0.020  1.331
 OJ7  C10  C3   single    1.457  0.020  1.457
 OJ7  C3   C4   aromatic  1.441  0.020  1.441
 OJ7  C3   C2   aromatic  1.376  0.020  1.376
 OJ7  C9   C4   aromatic  1.400  0.020  1.400
 OJ7  C9   C8   aromatic  1.381  0.020  1.381
 OJ7  C4   C5   aromatic  1.404  0.020  1.404
 OJ7  C1   C2   single    1.485  0.020  1.485
 OJ7  C2   N1   aromatic  1.362  0.020  1.362
 OJ7  C8   C7   aromatic  1.405  0.020  1.405
 OJ7  C5   N1   aromatic  1.369  0.020  1.369
 OJ7  C5   C6   aromatic  1.390  0.020  1.390
 OJ7  C7   C6   aromatic  1.364  0.020  1.364
 OJ7  C6   H1   single    0.930  0.020  1.080
 OJ7  C11  H2   single    0.930  0.020  1.080
 OJ7  C7   H3   single    0.930  0.020  1.080
 OJ7  C8   H4   single    0.930  0.020  1.080
 OJ7  C9   H5   single    0.930  0.020  1.080
 OJ7  C13  H6   single    0.930  0.020  1.080
 OJ7  N1   H7   single    0.860  0.020  1.020
 OJ7  C1   H8   single    0.970  0.020  1.090
 OJ7  C1   H9   single    0.970  0.020  1.090
 OJ7  C1   H10  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
 OJ7  C3   C4   C9   134.32  3.000
 OJ7  C9   C4   C5   118.77  3.000
 OJ7  C3   C4   C5   106.74  3.000
 OJ7  CL1  C14  C13  118.78  3.000
 OJ7  CL1  C14  C10  121.33  3.000
 OJ7  C13  C14  C10  119.80  3.000
 OJ7  N1   C5   C6   130.14  3.000
 OJ7  C6   C5   C4   122.59  3.000
 OJ7  N1   C5   C4   107.24  3.000
 OJ7  H1   C6   C7   120.51  3.000
 OJ7  H1   C6   C5   122.02  3.000
 OJ7  C7   C6   C5   117.47  3.000
 OJ7  H2   C11  N2   115.62  3.000
 OJ7  H2   C11  C12  121.38  3.000
 OJ7  N2   C11  C12  123.00  3.000
 OJ7  H3   C7   C8   118.84  3.000
 OJ7  H3   C7   C6   119.69  3.000
 OJ7  C8   C7   C6   121.46  3.000
 OJ7  H4   C8   C9   120.26  3.000
 OJ7  H4   C8   C7   118.75  3.000
 OJ7  C9   C8   C7   120.98  3.000
 OJ7  H5   C9   C8   120.50  3.000
 OJ7  H5   C9   C4   120.85  3.000
 OJ7  C8   C9   C4   118.64  3.000
 OJ7  C3   C10  N2   117.56  3.000
 OJ7  C3   C10  C14  122.74  3.000
 OJ7  N2   C10  C14  119.68  3.000
 OJ7  C15  C12  C13  120.96  3.000
 OJ7  C13  C12  C11  117.71  3.000
 OJ7  C15  C12  C11  121.32  3.000
 OJ7  H6   C13  C12  121.37  3.000
 OJ7  H6   C13  C14  119.83  3.000
 OJ7  C12  C13  C14  118.76  3.000
 OJ7  H7   N1   C2   123.39  3.000
 OJ7  H7   N1   C5   125.60  3.000
 OJ7  C2   N1   C5   110.43  3.000
 OJ7  C10  N2   C11  120.34  3.000
 OJ7  C2   C3   C10  125.38  3.000
 OJ7  C2   C3   C4   106.79  3.000
 OJ7  C10  C3   C4   127.64  3.000
 OJ7  C1   C2   C3   130.43  3.000
 OJ7  C1   C2   N1   120.73  3.000
 OJ7  C3   C2   N1   108.78  3.000
 OJ7  F3   C15  F2   107.34  3.000
 OJ7  F3   C15  F1   107.03  3.000
 OJ7  F2   C15  F1   107.36  3.000
 OJ7  F3   C15  C12  111.50  3.000
 OJ7  F2   C15  C12  111.75  3.000
 OJ7  F1   C15  C12  111.59  3.000
 OJ7  H10  C1   H9   108.64  3.000
 OJ7  H10  C1   H8   106.82  3.000
 OJ7  H9   C1   H8   107.93  3.000
 OJ7  H10  C1   C2   110.87  3.000
 OJ7  H9   C1   C2   111.96  3.000
 OJ7  H8   C1   C2   110.44  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
 OJ7  CONST_03  N1   C2   C3   C4     0.00   0.0  0
 OJ7  CONST_04  C7   C8   C9   C4     0.00   0.0  0
 OJ7  CONST_05  C2   N1   C5   C4     0.00   0.0  0
 OJ7  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 OJ7  CONST_07  C11  C12  C13  C14    0.00   0.0  0
 OJ7  CONST_08  C11  N2   C10  C14    0.00   0.0  0
 OJ7  CONST_10  C10  C3   C4   C5   180.00   0.0  0
 OJ7  CONST_11  C2   C3   C4   C5     0.00   0.0  0
 OJ7  CONST_12  C8   C9   C4   C5     0.00   0.0  0
 OJ7  CONST_13  C3   C2   N1   C5     0.00   0.0  0
 OJ7  CONST_14  C8   C7   C6   C5     0.00   0.0  0
 OJ7  CONST_15  C3   C4   C5   C6   180.00   0.0  0
 OJ7  CONST_16  C9   C4   C5   C6     0.00   0.0  0
 OJ7  CONST_17  C2   N1   C5   C6   180.00   0.0  0
 OJ7  CONST_18  C9   C8   C7   C6     0.00   0.0  0
 OJ7  CONST_19  C3   C10  N2   C11  180.00   0.0  0
 OJ7  CONST_20  N1   C5   C6   C7   180.00   0.0  0
 OJ7  CONST_21  C3   C4   C9   C8   180.00   0.0  0
 OJ7  CONST_22  C10  C3   C4   C9     0.00   0.0  0
 OJ7  CONST_23  C2   C3   C4   C9   180.00   0.0  0
 OJ7  CONST_24  N1   C5   C4   C9   180.00   0.0  0
 OJ7  CONST_25  C12  C13  C14  C10    0.00   0.0  0
 OJ7  CONST_26  C12  C11  N2   C10    0.00   0.0  0
 OJ7  CONST_27  N1   C2   C3   C10  180.00   0.0  0
 OJ7  CONST_28  N2   C11  C12  C13    0.00   0.0  0
 OJ7  CONST_29  N2   C10  C14  C13    0.00   0.0  0
 OJ7  CONST_30  C3   C10  C14  C13  180.00   0.0  0
 OJ7  CONST_31  C3   C4   C5   N1     0.00   0.0  0
 OJ7  CONST_33  C1   C2   C3   C4   180.00   0.0  0
 OJ7  CONST_34  C15  C12  C13  C14  180.00   0.0  0
 OJ7  CONST_35  C1   C2   N1   C5   180.00   0.0  0
 OJ7  CONST_36  C1   C2   C3   C10    0.00   0.0  0
 OJ7  CONST_37  CL1  C14  C13  C12  180.00   0.0  0
 OJ7  CONST_38  C15  C12  C11  N2   180.00   0.0  0
 OJ7  CONST_39  CL1  C14  C10  N2   180.00   0.0  0
 OJ7  CONST_40  CL1  C14  C10  C3     0.00   0.0  0
 OJ7  CONST_41  H4   C8   C9   C4   180.00   0.0  0
 OJ7  CONST_42  H7   N1   C5   C4   180.00   0.0  0
 OJ7  CONST_43  H1   C6   C5   C4   180.00   0.0  0
 OJ7  CONST_44  H5   C9   C4   C5   180.00   0.0  0
 OJ7  CONST_45  H3   C7   C6   C5   180.00   0.0  0
 OJ7  CONST_46  H6   C13  C12  C11  180.00   0.0  0
 OJ7  CONST_47  H2   C11  N2   C10  180.00   0.0  0
 OJ7  Var_01    F1   C15  C12  C11  -93.19  30.0  3
 OJ7  Var_02    H8   C1   C2   N1   -75.86  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
 OJ7  plan-1  C14  0.020
 OJ7  plan-1  C11  0.020
 OJ7  plan-1  C10  0.020
 OJ7  plan-1  C12  0.020
 OJ7  plan-1  C13  0.020
 OJ7  plan-1  N2   0.020
 OJ7  plan-1  C3   0.020
 OJ7  plan-1  CL1  0.020
 OJ7  plan-1  C15  0.020
 OJ7  plan-1  H2   0.020
 OJ7  plan-1  H6   0.020
 OJ7  plan-2  C4   0.020
 OJ7  plan-2  C5   0.020
 OJ7  plan-2  C6   0.020
 OJ7  plan-2  C7   0.020
 OJ7  plan-2  C8   0.020
 OJ7  plan-2  C9   0.020
 OJ7  plan-2  C10  0.020
 OJ7  plan-2  N1   0.020
 OJ7  plan-2  C3   0.020
 OJ7  plan-2  C2   0.020
 OJ7  plan-2  H1   0.020
 OJ7  plan-2  H3   0.020
 OJ7  plan-2  H4   0.020
 OJ7  plan-2  H5   0.020
 OJ7  plan-2  H7   0.020
 OJ7  plan-2  C1   0.020

