# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 21:49:13 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-{[6-methoxy-5-(trifluoromethyl)naphthalen-1-yl]carbonothioyl}-N-methylglycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2c(cccc2c1C(F)(F)F)C(=S)N(C)CC(O)=O
#
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
 TOL  TOL  N-{[6-methoxy-5-(trifluoromethyl)naphthalen-1-yl]carbonothioyl}-N-methylglycine  ligand  38  24  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TOL
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
 TOL  C1    C  CT    0   1.063  -0.7636   0.0546   3.9136
 TOL  F1    F  F     0  -0.324  -1.5242  -1.0464   4.0637
 TOL  F2    F  F     0  -0.286  -0.0224   0.1336   5.0143
 TOL  F3    F  F     0  -0.325  -1.6027   1.1070   3.9584
 TOL  C2    C  CR6   0  -0.377   0.0003   0.0170   2.6197
 TOL  C3    C  CR6   0   0.381   1.3861   0.0984   2.5774
 TOL  O1    O  O2    0  -0.454   2.0718   0.2321   3.7137
 TOL  C4    C  CH3   0  -0.445   3.4876   0.3141   3.6871
 TOL  C5    C  CR16  0  -0.390   2.0521   0.0378   1.3298
 TOL  C6    C  CR16  0  -0.302   1.3533  -0.0877   0.1711
 TOL  C7    C  CR66  0   0.077  -0.0555  -0.1552   0.1650
 TOL  C8    C  CR6   0   0.010  -0.7736  -0.2730  -1.0543
 TOL  C9    C  CR16  0  -0.287  -2.1395  -0.3434  -1.0553
 TOL  C10   C  CR16  0  -0.228  -2.8303  -0.2850   0.1643
 TOL  C11   C  CR16  0  -0.355  -2.1677  -0.1701   1.3556
 TOL  C12   C  CR66  0   0.187  -0.7494  -0.1027   1.4046
 TOL  C13   C  C     0   0.096  -0.0408  -0.3593  -2.3460
 TOL  S1    S  S1    0  -0.314   0.2911  -1.8658  -2.9661
 TOL  N1    N  NT    0  -0.336   0.3165   0.7763  -2.9302
 TOL  C14   C  CH3   0  -0.531  -0.0439   2.1017  -2.4515
 TOL  C15   C  CH2   0  -0.448   1.0065   0.7328  -4.1947
 TOL  C16   C  C     0   0.555   0.0641   0.3645  -5.3222
 TOL  O2    O  O     0  -0.426  -1.1340   0.4246  -5.2525
 TOL  O3    O  OH1   0  -0.587   0.7397   0.0246  -6.4079
 TOL  H41   H  HCH3  0   0.269   3.7965   0.4274   4.7226
 TOL  H42   H  HCH3  0   0.239   3.9428  -0.5919   3.2817
 TOL  H43   H  HCH3  0   0.239   3.8364   1.1792   3.1198
 TOL  H5    H  HCR6  0   0.301   3.1297   0.0875   1.2813
 TOL  H6    H  HCR6  0   0.272   1.9071  -0.1436  -0.7569
 TOL  H9    H  HCR6  0   0.267  -2.6854  -0.4394  -1.9847
 TOL  H10   H  HCR6  0   0.270  -3.9110  -0.3318   0.1632
 TOL  H11   H  HCR6  0   0.258  -2.7720  -0.1315   2.2470
 TOL  H141  H  HCH3  0   0.278  -0.5518   2.0505  -1.4952
 TOL  H142  H  HCH3  0   0.269   0.8550   2.7055  -2.3368
 TOL  H143  H  HCH3  0   0.268  -0.7033   2.5867  -3.1713
 TOL  H151  H  HCH2  0   0.322   1.4195   1.7220  -4.4040
 TOL  H152  H  HCH2  0   0.308   1.8411   0.0323  -4.1556
 TOL  HO3   H  HOH1  0   0.486   0.1305  -0.1521  -7.1409

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
 TOL  C1   F1    single    1.347  0.020  1.347
 TOL  C1   F2    single    1.329  0.020  1.329
 TOL  C1   F3    single    1.347  0.020  1.347
 TOL  C1   C2    single    1.503  0.020  1.503
 TOL  C2   C3    aromatic  1.389  0.020  1.389
 TOL  C2   C12   aromatic  1.433  0.020  1.433
 TOL  C3   O1    single    1.334  0.020  1.334
 TOL  C3   C5    aromatic  1.416  0.020  1.416
 TOL  O1   C4    single    1.418  0.020  1.418
 TOL  C4   H41   single    0.970  0.020  1.090
 TOL  C4   H42   single    0.970  0.020  1.090
 TOL  C4   H43   single    0.970  0.020  1.090
 TOL  C5   C6    aromatic  1.359  0.020  1.359
 TOL  C5   H5    single    0.930  0.020  1.080
 TOL  C6   C7    aromatic  1.411  0.020  1.411
 TOL  C6   H6    single    0.930  0.020  1.080
 TOL  C7   C8    aromatic  1.420  0.020  1.420
 TOL  C7   C12   aromatic  1.422  0.020  1.422
 TOL  C8   C9    aromatic  1.368  0.020  1.368
 TOL  C8   C13   single    1.488  0.020  1.488
 TOL  C9   C10   aromatic  1.403  0.020  1.403
 TOL  C9   H9    single    0.930  0.020  1.080
 TOL  C10  C11   aromatic  1.368  0.020  1.368
 TOL  C10  H10   single    0.930  0.020  1.080
 TOL  C11  C12   aromatic  1.421  0.020  1.421
 TOL  C11  H11   single    0.930  0.020  1.080
 TOL  C13  S1    double    1.663  0.020  1.663
 TOL  C13  N1    single    1.326  0.020  1.326
 TOL  N1   C14   single    1.455  0.020  1.455
 TOL  N1   C15   single    1.441  0.020  1.441
 TOL  C14  H141  single    0.970  0.020  1.090
 TOL  C14  H142  single    0.970  0.020  1.090
 TOL  C14  H143  single    0.970  0.020  1.090
 TOL  C15  C16   single    1.515  0.020  1.515
 TOL  C15  H151  single    0.970  0.020  1.090
 TOL  C15  H152  single    0.970  0.020  1.090
 TOL  C16  O2    double    1.202  0.020  1.202
 TOL  C16  O3    single    1.323  0.020  1.323
 TOL  O3   HO3   single    0.850  0.020  0.980

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
 TOL  C2    C1   F3    111.39  3.000
 TOL  C2    C1   F2    115.53  3.000
 TOL  F3    C1   F2    105.87  3.000
 TOL  C2    C1   F1    111.26  3.000
 TOL  F3    C1   F1    106.46  3.000
 TOL  F2    C1   F1    105.74  3.000
 TOL  C12   C2   C3    120.08  3.000
 TOL  C12   C2   C1    117.79  3.000
 TOL  C3    C2   C1    122.13  3.000
 TOL  C5    C3   O1    120.88  3.000
 TOL  C5    C3   C2    119.59  3.000
 TOL  O1    C3   C2    119.53  3.000
 TOL  C4    O1   C3    120.20  3.000
 TOL  H43   C4   H42   109.35  3.000
 TOL  H43   C4   H41   108.77  3.000
 TOL  H42   C4   H41   108.77  3.000
 TOL  H43   C4   O1    111.99  3.000
 TOL  H42   C4   O1    112.03  3.000
 TOL  H41   C4   O1    105.78  3.000
 TOL  H5    C5   C6    118.63  3.000
 TOL  H5    C5   C3    120.47  3.000
 TOL  C6    C5   C3    120.90  3.000
 TOL  H6    C6   C7    120.33  3.000
 TOL  H6    C6   C5    118.22  3.000
 TOL  C7    C6   C5    121.45  3.000
 TOL  C12   C7   C8    120.33  3.000
 TOL  C12   C7   C6    118.82  3.000
 TOL  C8    C7   C6    120.85  3.000
 TOL  C13   C8   C9    119.23  3.000
 TOL  C13   C8   C7    120.09  3.000
 TOL  C9    C8   C7    120.66  3.000
 TOL  H9    C9   C10   120.13  3.000
 TOL  H9    C9   C8    120.60  3.000
 TOL  C10   C9   C8    119.28  3.000
 TOL  H10   C10  C11   119.24  3.000
 TOL  H10   C10  C9    119.30  3.000
 TOL  C11   C10  C9    121.47  3.000
 TOL  H11   C11  C12   121.97  3.000
 TOL  H11   C11  C10   116.86  3.000
 TOL  C12   C11  C10   121.17  3.000
 TOL  C11   C12  C7    117.09  3.000
 TOL  C11   C12  C2    123.75  3.000
 TOL  C7    C12  C2    119.16  3.000
 TOL  N1    C13  S1    123.91  3.000
 TOL  N1    C13  C8    117.74  3.000
 TOL  S1    C13  C8    118.34  3.000
 TOL  C15   N1   C14   115.78  3.000
 TOL  C15   N1   C13   119.32  3.000
 TOL  C14   N1   C13   124.65  3.000
 TOL  H143  C14  H142  108.80  3.000
 TOL  H143  C14  H141  108.68  3.000
 TOL  H142  C14  H141  108.66  3.000
 TOL  H143  C14  N1    109.75  3.000
 TOL  H142  C14  N1    109.59  3.000
 TOL  H141  C14  N1    111.31  3.000
 TOL  H152  C15  H151  107.41  3.000
 TOL  H152  C15  C16   110.29  3.000
 TOL  H151  C15  C16   108.23  3.000
 TOL  H152  C15  N1    110.76  3.000
 TOL  H151  C15  N1    108.77  3.000
 TOL  C16   C15  N1    111.26  3.000
 TOL  O3    C16  O2    124.72  3.000
 TOL  O3    C16  C15   110.83  3.000
 TOL  O2    C16  C15   124.40  3.000
 TOL  HO3   O3   C16   110.27  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
 TOL  CONST_01  C6    C5   C3   C2      0.00   0.0  0
 TOL  CONST_02  C6    C7   C12  C2      0.00   0.0  0
 TOL  CONST_03  C8    C7   C12  C2    180.00   0.0  0
 TOL  CONST_04  C10   C11  C12  C2    180.00   0.0  0
 TOL  CONST_05  C7    C12  C2   C3      0.00   0.0  0
 TOL  CONST_06  C11   C12  C2   C3    180.00   0.0  0
 TOL  CONST_07  C7    C6   C5   C3      0.00   0.0  0
 TOL  CONST_08  C12   C2   C3   C5      0.00   0.0  0
 TOL  CONST_09  C8    C7   C6   C5    180.00   0.0  0
 TOL  CONST_10  C12   C7   C6   C5      0.00   0.0  0
 TOL  CONST_11  C9    C8   C7   C6    180.00   0.0  0
 TOL  CONST_12  C11   C12  C7   C6    180.00   0.0  0
 TOL  CONST_13  C10   C9   C8   C7      0.00   0.0  0
 TOL  CONST_14  C10   C11  C12  C7      0.00   0.0  0
 TOL  CONST_15  C11   C12  C7   C8      0.00   0.0  0
 TOL  CONST_16  C11   C10  C9   C8      0.00   0.0  0
 TOL  CONST_17  C12   C7   C8   C9      0.00   0.0  0
 TOL  CONST_18  C12   C11  C10  C9      0.00   0.0  0
 TOL  CONST_19  C5    C3   C2   C1    180.00   0.0  0
 TOL  CONST_20  C7    C12  C2   C1    180.00   0.0  0
 TOL  CONST_21  C11   C12  C2   C1      0.00   0.0  0
 TOL  CONST_22  C12   C2   C3   O1    180.00   0.0  0
 TOL  CONST_23  C6    C5   C3   O1    180.00   0.0  0
 TOL  CONST_24  C13   C8   C7   C6      0.00   0.0  0
 TOL  CONST_25  C13   C8   C9   C10   180.00   0.0  0
 TOL  CONST_26  C13   C8   C7   C12   180.00   0.0  0
 TOL  CONST_27  H5    C5   C3   C2    180.00   0.0  0
 TOL  CONST_28  H11   C11  C12  C2      0.00   0.0  0
 TOL  CONST_29  H6    C6   C5   C3    180.00   0.0  0
 TOL  CONST_30  H9    C9   C8   C7    180.00   0.0  0
 TOL  CONST_31  H10   C10  C9   C8    180.00   0.0  0
 TOL  CONST_32  HO3   O3   C16  C15   180.00   0.0  0
 TOL  Var_01    C3    C2   C1   F1   -122.33  30.0  2
 TOL  Var_02    C5    C3   O1   C4     -0.09  30.0  3
 TOL  Var_03    S1    C13  C8   C7     94.25  30.0  2
 TOL  Var_04    C14   N1   C13  C8     -4.90  30.0  2
 TOL  Var_05    H41   C4   O1   C3    179.44  30.0  3
 TOL  Var_06    C16   C15  N1   C13    73.89  30.0  3
 TOL  Var_07    O2    C16  C15  N1     17.21  30.0  3
 TOL  Var_08    H141  C14  N1   C13     6.20  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
 TOL  plan-1  C1   0.020
 TOL  plan-1  C2   0.020
 TOL  plan-1  C3   0.020
 TOL  plan-1  O1   0.020
 TOL  plan-1  C5   0.020
 TOL  plan-1  C6   0.020
 TOL  plan-1  C7   0.020
 TOL  plan-1  C8   0.020
 TOL  plan-1  C9   0.020
 TOL  plan-1  C10  0.020
 TOL  plan-1  C11  0.020
 TOL  plan-1  C12  0.020
 TOL  plan-1  C13  0.020
 TOL  plan-1  H5   0.020
 TOL  plan-1  H6   0.020
 TOL  plan-1  H9   0.020
 TOL  plan-1  H10  0.020
 TOL  plan-1  H11  0.020
 TOL  plan-2  C15  0.020
 TOL  plan-2  C16  0.020
 TOL  plan-2  O2   0.020
 TOL  plan-2  O3   0.020
 TOL  plan-2  HO3  0.020
 TOL  plan-3  C8   0.020
 TOL  plan-3  C13  0.020
 TOL  plan-3  S1   0.020
 TOL  plan-3  N1   0.020

