# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:15:52 2022
#   Inital geometry file: a 60 line input string
#   Ligand name: 5-methoxy-6-(trifluoromethyl)-1~{H}-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2cc[nH]c2cc1C(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
 98Q  98Q  5-methoxy-6-(trifluoromethyl)-1~{H}-indole  ligand  23  15  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_98Q
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
 98Q  C10  C  CR16  0  -0.330  184.8143  282.7394  109.2502
 98Q  C01  C  CH3   0  -0.435  182.4362  286.8234  108.3674
 98Q  O02  O  O2    0  -0.473  182.9210  285.5546  107.9826
 98Q  C03  C  CR6   0   0.401  183.6327  284.8381  108.8751
 98Q  C04  C  CR16  0  -0.490  183.9245  285.2707  110.1534
 98Q  C05  C  CR56  0   0.094  184.6665  284.4371  111.0019
 98Q  C06  C  CR15  0  -0.421  185.1297  284.5589  112.3435
 98Q  C07  C  CR15  0  -0.016  185.8047  283.4023  112.6290
 98Q  N08  N  NR15  0  -0.681  185.7867  282.5754  111.5498
 98Q  C09  C  CR56  0   0.352  185.0978  283.1802  110.5350
 98Q  C11  C  CR6   0  -0.335  184.0824  283.5693  108.4214
 98Q  C12  C  CT    0   1.056  183.7568  283.1299  107.0307
 98Q  F13  F  F     0  -0.316  182.4358  283.0393  106.8101
 98Q  F14  F  F     0  -0.306  184.2633  281.9199  106.7565
 98Q  F15  F  F     0  -0.316  184.2442  283.9625  106.0974
 98Q  H1   H  HCR6  0   0.276  185.1613  281.7708  108.9168
 98Q  H2   H  HCH3  0   0.261  181.8841  287.2132  107.5158
 98Q  H3   H  HCH3  0   0.228  181.7623  286.7593  109.2256
 98Q  H4   H  HCH3  0   0.228  183.2481  287.5154  108.6074
 98Q  H5   H  HCR6  0   0.278  183.5918  286.2352  110.5128
 98Q  H6   H  HCR5  0   0.249  184.9837  285.3909  113.0133
 98Q  H7   H  HCR5  0   0.284  186.3028  283.1049  113.5380
 98Q  H8   H  HNR5  0   0.412  186.2122  281.6639  111.5089

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
 98Q  F15  C12  single    1.342  0.020  1.342
 98Q  F13  C12  single    1.342  0.020  1.342
 98Q  F14  C12  single    1.340  0.020  1.340
 98Q  C12  C11  single    1.494  0.020  1.494
 98Q  O02  C01  single    1.412  0.020  1.412
 98Q  O02  C03  single    1.348  0.020  1.348
 98Q  C11  C03  aromatic  1.421  0.020  1.421
 98Q  C11  C10  aromatic  1.383  0.020  1.383
 98Q  C03  C04  aromatic  1.381  0.020  1.381
 98Q  C10  C09  aromatic  1.388  0.020  1.388
 98Q  C04  C05  aromatic  1.402  0.020  1.402
 98Q  C09  C05  aromatic  1.408  0.020  1.408
 98Q  C09  N08  aromatic  1.368  0.020  1.368
 98Q  C05  C06  aromatic  1.425  0.020  1.425
 98Q  N08  C07  aromatic  1.360  0.020  1.360
 98Q  C06  C07  aromatic  1.369  0.020  1.369
 98Q  C10  H1   single    0.930  0.020  1.080
 98Q  C01  H2   single    0.970  0.020  1.090
 98Q  C01  H3   single    0.970  0.020  1.090
 98Q  C01  H4   single    0.970  0.020  1.090
 98Q  C04  H5   single    0.930  0.020  1.080
 98Q  C06  H6   single    0.930  0.020  1.080
 98Q  C07  H7   single    0.930  0.020  1.080
 98Q  N08  H8   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
 98Q  H1   C10  C11  121.51  3.000
 98Q  H1   C10  C09  120.29  3.000
 98Q  C11  C10  C09  118.20  3.000
 98Q  H4   C01  H3   108.82  3.000
 98Q  H4   C01  H2   108.79  3.000
 98Q  H3   C01  H2   108.84  3.000
 98Q  H4   C01  O02  111.94  3.000
 98Q  H3   C01  O02  111.90  3.000
 98Q  H2   C01  O02  106.45  3.000
 98Q  C03  O02  C01  118.59  3.000
 98Q  C11  C03  C04  120.58  3.000
 98Q  C04  C03  O02  123.93  3.000
 98Q  C11  C03  O02  115.49  3.000
 98Q  H5   C04  C05  119.47  3.000
 98Q  H5   C04  C03  121.46  3.000
 98Q  C05  C04  C03  119.07  3.000
 98Q  C09  C05  C06  106.79  3.000
 98Q  C06  C05  C04  133.73  3.000
 98Q  C09  C05  C04  119.48  3.000
 98Q  H6   C06  C07  126.10  3.000
 98Q  H6   C06  C05  127.38  3.000
 98Q  C07  C06  C05  106.53  3.000
 98Q  H7   C07  N08  120.49  3.000
 98Q  H7   C07  C06  129.53  3.000
 98Q  N08  C07  C06  109.98  3.000
 98Q  H8   N08  C09  125.67  3.000
 98Q  H8   N08  C07  125.26  3.000
 98Q  C09  N08  C07  109.07  3.000
 98Q  N08  C09  C05  107.64  3.000
 98Q  N08  C09  C10  130.50  3.000
 98Q  C05  C09  C10  121.86  3.000
 98Q  C12  C11  C03  119.40  3.000
 98Q  C03  C11  C10  120.82  3.000
 98Q  C12  C11  C10  119.78  3.000
 98Q  F15  C12  F14  106.29  3.000
 98Q  F14  C12  F13  106.10  3.000
 98Q  F15  C12  F13  106.56  3.000
 98Q  F14  C12  C11  111.93  3.000
 98Q  F13  C12  C11  112.78  3.000
 98Q  F15  C12  C11  112.68  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
 98Q  CONST_01  C04  C03  C11  C10     0.00   0.0  0
 98Q  CONST_02  C04  C05  C09  C10     0.00   0.0  0
 98Q  CONST_03  C06  C05  C09  C10   180.00   0.0  0
 98Q  CONST_04  C07  N08  C09  C10   180.00   0.0  0
 98Q  CONST_05  C09  C10  C11  C03     0.00   0.0  0
 98Q  CONST_06  C09  C05  C04  C03     0.00   0.0  0
 98Q  CONST_07  C06  C05  C04  C03   180.00   0.0  0
 98Q  CONST_08  N08  C09  C05  C04   180.00   0.0  0
 98Q  CONST_09  C07  C06  C05  C04   180.00   0.0  0
 98Q  CONST_10  C11  C03  C04  C05     0.00   0.0  0
 98Q  CONST_11  C11  C10  C09  C05     0.00   0.0  0
 98Q  CONST_12  C07  N08  C09  C05     0.00   0.0  0
 98Q  CONST_13  N08  C07  C06  C05     0.00   0.0  0
 98Q  CONST_14  N08  C09  C05  C06     0.00   0.0  0
 98Q  CONST_15  C09  N08  C07  C06     0.00   0.0  0
 98Q  CONST_16  C09  C05  C06  C07     0.00   0.0  0
 98Q  CONST_17  C11  C10  C09  N08   180.00   0.0  0
 98Q  CONST_18  O02  C03  C11  C10   180.00   0.0  0
 98Q  CONST_19  C05  C04  C03  O02   180.00   0.0  0
 98Q  CONST_20  C12  C11  C03  C04   180.00   0.0  0
 98Q  CONST_21  C12  C11  C10  C09   180.00   0.0  0
 98Q  CONST_22  H8   N08  C09  C10     0.00   0.0  0
 98Q  CONST_23  H1   C10  C11  C03   180.00   0.0  0
 98Q  CONST_24  H6   C06  C05  C04     0.00   0.0  0
 98Q  CONST_25  H7   C07  C06  C05   180.00   0.0  0
 98Q  CONST_26  H5   C04  C05  C06     0.00   0.0  0
 98Q  Var_01    F15  C12  C11  C10  -120.41  30.0  3
 98Q  Var_02    C11  C03  O02  C01   179.70  30.0  2
 98Q  Var_03    H2   C01  O02  C03  -179.05  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
 98Q  plan-1  C10  0.020
 98Q  plan-1  O02  0.020
 98Q  plan-1  C03  0.020
 98Q  plan-1  C04  0.020
 98Q  plan-1  C05  0.020
 98Q  plan-1  C06  0.020
 98Q  plan-1  C07  0.020
 98Q  plan-1  N08  0.020
 98Q  plan-1  C09  0.020
 98Q  plan-1  C11  0.020
 98Q  plan-1  C12  0.020
 98Q  plan-1  H1   0.020
 98Q  plan-1  H5   0.020
 98Q  plan-1  H6   0.020
 98Q  plan-1  H7   0.020
 98Q  plan-1  H8   0.020

