# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 10:13:10 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2S)-3-(4-cyanophenoxy)-N-[4-cyano-3-(trifluoromethyl)phenyl]-2-hydroxy-2-methylpropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](O)(COc1ccc(cc1)C#N)C(=O)Nc2ccc(C#N)c(c2)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
 RLJ  RLJ  (2S)-3-(4-cyanophenoxy)-N-[4-cyano-3-(trifluoromethyl)phenyl]-2-hydroxy-2-methylpropanamide  ligand  42  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RLJ
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
 RLJ  C1    C  CR16  0  -0.301  -2.6052  -0.9767  -1.4174
 RLJ  F1    F  F     0  -0.291  -5.1947   1.6950   1.8633
 RLJ  C2    C  CR16  0  -0.229  -3.9121  -1.4202  -1.5037
 RLJ  F2    F  F     0  -0.310  -6.2211  -0.1950   1.8398
 RLJ  C3    C  CR6   0   0.027  -4.9141  -0.8747  -0.7097
 RLJ  F3    F  F     0  -0.310  -6.6370   1.2727   0.3244
 RLJ  C4    C  CR6   0  -0.150  -4.5869   0.1437   0.1954
 RLJ  C5    C  CR6   0   0.445  -2.2796   0.0382  -0.5179
 RLJ  C6    C  CR16  0  -0.417  -3.2883   0.5882   0.2854
 RLJ  C7    C  CT    0   1.079  -5.6581   0.7381   1.0631
 RLJ  C8    C  CSP   0   0.015  -6.2426  -1.3720  -0.8444
 RLJ  N8    N  NS    0  -0.237  -7.3065  -1.7934  -0.9772
 RLJ  N9    N  NH1   0  -0.748  -1.0085   0.5598  -0.3480
 RLJ  C10   C  C     0   0.539   0.1405   0.2318  -0.9910
 RLJ  O10   O  O     0  -0.445   0.2363  -0.6262  -1.8453
 RLJ  C11   C  CT    0   0.049   1.3490   1.0955  -0.5807
 RLJ  O11   O  OH1   0  -0.654   1.1190   1.7715   0.6308
 RLJ  C12   C  CH3   0  -0.662   1.5260   2.1590  -1.6627
 RLJ  C13   C  CH2   0  -0.198   2.5597   0.1667  -0.4799
 RLJ  O14   O  O2    0  -0.462   3.6752   0.9665  -0.1431
 RLJ  C16   C  CR6   0   0.419   4.8632   0.3837   0.0505
 RLJ  C17   C  CR16  0  -0.338   5.9153   1.2392   0.3960
 RLJ  C18   C  CR16  0  -0.222   7.1759   0.7332   0.6186
 RLJ  C19   C  CR6   0  -0.024   7.4105  -0.6407   0.5004
 RLJ  C20   C  CR16  0  -0.222   6.3633  -1.4917   0.1558
 RLJ  C21   C  CR16  0  -0.371   5.0945  -0.9875  -0.0700
 RLJ  C22   C  CSP   0   0.051   8.7124  -1.1676   0.7321
 RLJ  N22   N  NS    0  -0.261   9.7668  -1.5946   0.9215
 RLJ  H1    H  HCR6  0   0.306  -1.8603  -1.4264  -2.0511
 RLJ  H2    H  HCR6  0   0.297  -4.1548  -2.2076  -2.2037
 RLJ  H6    H  HCR6  0   0.302  -3.0284   1.3728   0.9838
 RLJ  HN9   H  HNH1  0   0.427  -0.9181   1.2977   0.3385
 RLJ  HO11  H  HOH1  0   0.465   1.2273   1.1651   1.3737
 RLJ  H12   H  HCH3  0   0.254   0.6405   2.7932  -1.7232
 RLJ  H12A  H  HCH3  0   0.260   2.3821   2.7957  -1.4435
 RLJ  H12B  H  HCH3  0   0.248   1.6817   1.6992  -2.6373
 RLJ  H13   H  HCH2  0   0.261   2.3838  -0.5915   0.2937
 RLJ  H13A  H  HCH2  0   0.260   2.7221  -0.3483  -1.4294
 RLJ  H17   H  HCR6  0   0.282   5.7305   2.3016   0.4872
 RLJ  H18   H  HCR6  0   0.283   7.9839   1.4014   0.8841
 RLJ  H20   H  HCR6  0   0.286   6.5357  -2.5552   0.0628
 RLJ  H21   H  HCR6  0   0.298   4.3048  -1.6756  -0.3370

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
 RLJ  C1   C2    aromatic  1.383  0.020  1.383
 RLJ  C1   C5    aromatic  1.395  0.020  1.395
 RLJ  F1   C7    single    1.331  0.020  1.331
 RLJ  C2   C3    aromatic  1.390  0.020  1.390
 RLJ  F2   C7    single    1.338  0.020  1.338
 RLJ  C3   C4    aromatic  1.401  0.020  1.401
 RLJ  C3   C8    single    1.425  0.020  1.425
 RLJ  F3   C7    single    1.338  0.020  1.338
 RLJ  C4   C6    aromatic  1.376  0.020  1.376
 RLJ  C4   C7    single    1.501  0.020  1.501
 RLJ  C5   C6    aromatic  1.402  0.020  1.402
 RLJ  C5   N9    single    1.384  0.020  1.384
 RLJ  C8   N8    triple    1.152  0.020  1.152
 RLJ  N9   C10   single    1.357  0.020  1.357
 RLJ  C10  O10   double    1.215  0.020  1.215
 RLJ  C10  C11   single    1.541  0.020  1.541
 RLJ  C11  O11   single    1.406  0.020  1.406
 RLJ  C11  C12   single    1.527  0.020  1.527
 RLJ  C11  C13   single    1.529  0.020  1.529
 RLJ  C13  O14   single    1.413  0.020  1.413
 RLJ  O14  C16   single    1.337  0.020  1.337
 RLJ  C16  C17   aromatic  1.399  0.020  1.399
 RLJ  C16  C21   aromatic  1.396  0.020  1.396
 RLJ  C17  C18   aromatic  1.376  0.020  1.376
 RLJ  C18  C19   aromatic  1.399  0.020  1.399
 RLJ  C19  C20   aromatic  1.393  0.020  1.393
 RLJ  C19  C22   single    1.423  0.020  1.423
 RLJ  C20  C21   aromatic  1.384  0.020  1.384
 RLJ  C22  N22   triple    1.153  0.020  1.153
 RLJ  C1   H1    single    0.930  0.020  1.080
 RLJ  C2   H2    single    0.930  0.020  1.080
 RLJ  C6   H6    single    0.930  0.020  1.080
 RLJ  N9   HN9   single    0.860  0.020  1.020
 RLJ  O11  HO11  single    0.850  0.020  0.980
 RLJ  C12  H12   single    0.970  0.020  1.090
 RLJ  C12  H12A  single    0.970  0.020  1.090
 RLJ  C12  H12B  single    0.970  0.020  1.090
 RLJ  C13  H13   single    0.970  0.020  1.090
 RLJ  C13  H13A  single    0.970  0.020  1.090
 RLJ  C17  H17   single    0.930  0.020  1.080
 RLJ  C18  H18   single    0.930  0.020  1.080
 RLJ  C20  H20   single    0.930  0.020  1.080
 RLJ  C21  H21   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
 RLJ  H1    C1   C5    121.47  3.000
 RLJ  H1    C1   C2    118.90  3.000
 RLJ  C5    C1   C2    119.63  3.000
 RLJ  H2    C2   C3    119.59  3.000
 RLJ  H2    C2   C1    119.09  3.000
 RLJ  C3    C2   C1    121.32  3.000
 RLJ  C8    C3   C4    122.17  3.000
 RLJ  C8    C3   C2    118.76  3.000
 RLJ  C4    C3   C2    119.07  3.000
 RLJ  C7    C4   C6    120.52  3.000
 RLJ  C7    C4   C3    119.64  3.000
 RLJ  C6    C4   C3    119.84  3.000
 RLJ  N9    C5   C6    116.26  3.000
 RLJ  N9    C5   C1    124.59  3.000
 RLJ  C6    C5   C1    119.14  3.000
 RLJ  H6    C6   C5    118.78  3.000
 RLJ  H6    C6   C4    120.22  3.000
 RLJ  C5    C6   C4    121.00  3.000
 RLJ  C4    C7   F3    111.18  3.000
 RLJ  C4    C7   F2    111.07  3.000
 RLJ  F3    C7   F2    106.93  3.000
 RLJ  C4    C7   F1    112.57  3.000
 RLJ  F3    C7   F1    107.43  3.000
 RLJ  F2    C7   F1    107.39  3.000
 RLJ  N8    C8   C3    180.00  3.000
 RLJ  HN9   N9   C10   114.97  3.000
 RLJ  HN9   N9   C5    116.10  3.000
 RLJ  C10   N9   C5    128.92  3.000
 RLJ  C11   C10  O10   121.42  3.000
 RLJ  C11   C10  N9    113.73  3.000
 RLJ  O10   C10  N9    124.81  3.000
 RLJ  C13   C11  C12   112.20  3.000
 RLJ  C13   C11  O11   111.38  3.000
 RLJ  C12   C11  O11   107.13  3.000
 RLJ  C13   C11  C10   107.34  3.000
 RLJ  C12   C11  C10   107.01  3.000
 RLJ  O11   C11  C10   111.75  3.000
 RLJ  HO11  O11  C11   110.05  3.000
 RLJ  H12B  C12  H12A  108.33  3.000
 RLJ  H12B  C12  H12   108.17  3.000
 RLJ  H12A  C12  H12   108.02  3.000
 RLJ  H12B  C12  C11   110.89  3.000
 RLJ  H12A  C12  C11   110.83  3.000
 RLJ  H12   C12  C11   110.49  3.000
 RLJ  H13A  C13  H13   108.11  3.000
 RLJ  H13A  C13  O14   110.89  3.000
 RLJ  H13   C13  O14   110.46  3.000
 RLJ  H13A  C13  C11   110.29  3.000
 RLJ  H13   C13  C11   109.83  3.000
 RLJ  O14   C13  C11   107.27  3.000
 RLJ  C16   O14  C13   119.27  3.000
 RLJ  C21   C16  C17   119.83  3.000
 RLJ  C21   C16  O14   124.25  3.000
 RLJ  C17   C16  O14   115.92  3.000
 RLJ  H17   C17  C18   120.24  3.000
 RLJ  H17   C17  C16   119.51  3.000
 RLJ  C18   C17  C16   120.25  3.000
 RLJ  H18   C18  C19   120.15  3.000
 RLJ  H18   C18  C17   119.79  3.000
 RLJ  C19   C18  C17   120.06  3.000
 RLJ  C22   C19  C20   120.12  3.000
 RLJ  C22   C19  C18   120.21  3.000
 RLJ  C20   C19  C18   119.67  3.000
 RLJ  H20   C20  C21   119.37  3.000
 RLJ  H20   C20  C19   120.16  3.000
 RLJ  C21   C20  C19   120.48  3.000
 RLJ  H21   C21  C20   118.57  3.000
 RLJ  H21   C21  C16   121.72  3.000
 RLJ  C20   C21  C16   119.72  3.000
 RLJ  N22   C22  C19   180.00  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
 RLJ  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 RLJ  CONST_02  C4   C6   C5   C1      0.00   0.0  0
 RLJ  CONST_03  C6   C5   C1   C2      0.00   0.0  0
 RLJ  CONST_04  C6   C4   C3   C2      0.00   0.0  0
 RLJ  CONST_05  C5   C1   C2   C3      0.00   0.0  0
 RLJ  CONST_06  C5   C6   C4   C3      0.00   0.0  0
 RLJ  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 RLJ  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 RLJ  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 RLJ  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 RLJ  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 RLJ  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 RLJ  CONST_13  C8   C3   C2   C1    180.00   0.0  0
 RLJ  CONST_14  N9   C5   C1   C2    180.00   0.0  0
 RLJ  CONST_15  C7   C4   C3   C2    180.00   0.0  0
 RLJ  CONST_16  N9   C5   C6   C4    180.00   0.0  0
 RLJ  CONST_17  C7   C4   C6   C5    180.00   0.0  0
 RLJ  CONST_18  C8   C3   C4   C6    180.00   0.0  0
 RLJ  CONST_19  C18  C17  C16  O14   180.00   0.0  0
 RLJ  CONST_20  C20  C21  C16  O14   180.00   0.0  0
 RLJ  CONST_21  C22  C19  C18  C17   180.00   0.0  0
 RLJ  CONST_22  C22  C19  C20  C21   180.00   0.0  0
 RLJ  CONST_23  H6   C6   C5   C1    180.00   0.0  0
 RLJ  CONST_24  H1   C1   C2   C3    180.00   0.0  0
 RLJ  CONST_25  H2   C2   C3   C4    180.00   0.0  0
 RLJ  CONST_26  H18  C18  C17  C16   180.00   0.0  0
 RLJ  CONST_27  H20  C20  C21  C16   180.00   0.0  0
 RLJ  CONST_28  H21  C21  C16  C17   180.00   0.0  0
 RLJ  CONST_29  H17  C17  C18  C19   180.00   0.0  0
 RLJ  CONST_30  C10  N9   C5   C1      0.00   0.0  0
 RLJ  CONST_31  C10  N9   C5   C6    180.00   0.0  0
 RLJ  CONST_32  HN9  N9   C5   C1    180.00   0.0  0
 RLJ  CONST_33  O10  C10  N9   C5      0.00   0.0  0
 RLJ  CONST_34  C11  C10  N9   C5    180.00   0.0  0
 RLJ  Var_01    C3   C4   C7   F1   -179.73  30.0  2
 RLJ  Var_02    C17  C16  O14  C13  -179.28  30.0  2
 RLJ  Var_03    H13  C13  O14  C16    58.11  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 RLJ  chir_01  C11  O11  C12  C13  negativ

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
 RLJ  plan-1  C1   0.020
 RLJ  plan-1  C2   0.020
 RLJ  plan-1  C3   0.020
 RLJ  plan-1  C4   0.020
 RLJ  plan-1  C5   0.020
 RLJ  plan-1  C6   0.020
 RLJ  plan-1  C7   0.020
 RLJ  plan-1  C8   0.020
 RLJ  plan-1  N8   0.020
 RLJ  plan-1  N9   0.020
 RLJ  plan-1  H1   0.020
 RLJ  plan-1  H2   0.020
 RLJ  plan-1  H6   0.020
 RLJ  plan-2  O14  0.020
 RLJ  plan-2  C16  0.020
 RLJ  plan-2  C17  0.020
 RLJ  plan-2  C18  0.020
 RLJ  plan-2  C19  0.020
 RLJ  plan-2  C20  0.020
 RLJ  plan-2  C21  0.020
 RLJ  plan-2  C22  0.020
 RLJ  plan-2  N22  0.020
 RLJ  plan-2  H17  0.020
 RLJ  plan-2  H18  0.020
 RLJ  plan-2  H20  0.020
 RLJ  plan-2  H21  0.020
 RLJ  plan-3  C5   0.020
 RLJ  plan-3  N9   0.020
 RLJ  plan-3  C10  0.020
 RLJ  plan-3  O10  0.020
 RLJ  plan-3  C11  0.020
 RLJ  plan-3  HN9  0.020

