# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 20:54:56 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (3R)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC[C@@H](Oc1ccc(cc1)C(F)(F)F)c2ccccc2
#
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
 RFX  RFX  (3R)-N-methyl-3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine  ligand  40  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RFX
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
 RFX  F14   F  F     0  -0.317  -4.8872  -2.1886  -0.0471
 RFX  C12   C  CT    0   1.050  -3.7070  -2.8230   0.0502
 RFX  F15   F  F     0  -0.304  -3.7096  -3.4695   1.2203
 RFX  F13   F  F     0  -0.317  -3.7101  -3.7604  -0.9121
 RFX  C9    C  CR6   0  -0.224  -2.5579  -1.8835  -0.0899
 RFX  C10   C  CR16  0  -0.272  -1.6031  -1.7422   0.9038
 RFX  C11   C  CR16  0  -0.344  -0.5404  -0.8615   0.7495
 RFX  C6    C  CR6   0   0.408  -0.4309  -0.1051  -0.4139
 RFX  C7    C  CR16  0  -0.344  -1.3923  -0.2505  -1.4191
 RFX  C8    C  CR16  0  -0.251  -2.4419  -1.1284  -1.2573
 RFX  O5    O  O2    0  -0.485   0.5411   0.7859  -0.6642
 RFX  C3    C  CH1   0  -0.048   1.5734   1.0069   0.2883
 RFX  C2    C  CH2   0  -0.457   2.2699   2.3008  -0.1090
 RFX  C1    C  CH2   0  -0.256   1.3423   3.5085  -0.1130
 RFX  N4    N  NH1   0  -0.594   2.0906   4.7257  -0.3513
 RFX  C22   C  CH3   0  -0.517   1.2419   5.8986  -0.3970
 RFX  C16   C  CR6   0   0.092   2.5440  -0.1492   0.3350
 RFX  C21   C  CR16  0  -0.295   2.9029  -0.8354  -0.8216
 RFX  C20   C  CR16  0  -0.239   3.8287  -1.8682  -0.7639
 RFX  C19   C  CR16  0  -0.265   4.4125  -2.2199   0.4467
 RFX  C18   C  CR16  0  -0.241   4.0630  -1.5343   1.6022
 RFX  C17   C  CR16  0  -0.302   3.1305  -0.5071   1.5442
 RFX  H10   H  HCR6  0   0.273  -1.6603  -2.3143   1.8196
 RFX  H11   H  HCR6  0   0.288   0.1836  -0.7889   1.5478
 RFX  H7    H  HCR6  0   0.274  -1.3090   0.3358  -2.3252
 RFX  H8    H  HCR6  0   0.275  -3.1719  -1.2186  -2.0517
 RFX  H3    H  HCH1  0   0.249   1.1311   1.1468   1.2838
 RFX  H2    H  HCH2  0   0.245   3.0735   2.4634   0.6148
 RFX  H2A   H  HCH2  0   0.242   2.7458   2.1861  -1.0871
 RFX  H1    H  HCH2  0   0.226   0.6012   3.4056  -0.9098
 RFX  H1A   H  HCH2  0   0.189   0.7755   3.5365   0.8334
 RFX  H22   H  HCH3  0   0.192   0.6045   6.0269   0.4895
 RFX  H22A  H  HCH3  0   0.231   1.8527   6.7953  -0.5015
 RFX  H21   H  HCR6  0   0.253   2.4603  -0.5704  -1.7739
 RFX  H20   H  HCR6  0   0.257   4.0948  -2.4003  -1.6682
 RFX  H19   H  HCR6  0   0.257   5.1336  -3.0255   0.4886
 RFX  H18   H  HCR6  0   0.257   4.5098  -1.8023   2.5509
 RFX  H17   H  HCR6  0   0.254   2.8519   0.0176   2.4514
 RFX  H171  H  HNH1  0   0.341   2.7723   4.8430   0.3882
 RFX  H181  H  HCH3  0   0.221   0.5833   5.8458  -1.2662

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
 RFX  F14  C12   single    1.343  0.020  1.343
 RFX  C12  F15   single    1.337  0.020  1.337
 RFX  C12  C9    single    1.491  0.020  1.491
 RFX  F13  C12   single    1.343  0.020  1.343
 RFX  C9   C10   aromatic  1.385  0.020  1.385
 RFX  C10  C11   aromatic  1.389  0.020  1.389
 RFX  C10  H10   single    0.930  0.020  1.080
 RFX  C11  H11   single    0.930  0.020  1.080
 RFX  C6   C11   aromatic  1.392  0.020  1.392
 RFX  C6   O5    single    1.342  0.020  1.342
 RFX  C7   C6    aromatic  1.399  0.020  1.399
 RFX  C7   H7    single    0.930  0.020  1.080
 RFX  C8   C9    aromatic  1.395  0.020  1.395
 RFX  C8   C7    aromatic  1.378  0.020  1.378
 RFX  C8   H8    single    0.930  0.020  1.080
 RFX  O5   C3    single    1.422  0.020  1.422
 RFX  C3   C16   single    1.510  0.020  1.510
 RFX  C3   C2    single    1.522  0.020  1.522
 RFX  C3   H3    single    0.970  0.020  1.090
 RFX  C2   H2    single    0.970  0.020  1.090
 RFX  C2   H2A   single    0.970  0.020  1.090
 RFX  C1   C2    single    1.523  0.020  1.523
 RFX  C1   N4    single    1.449  0.020  1.449
 RFX  C1   H1    single    0.970  0.020  1.090
 RFX  C1   H1A   single    0.970  0.020  1.090
 RFX  N4   C22   single    1.448  0.020  1.448
 RFX  C22  H22   single    0.970  0.020  1.090
 RFX  C22  H22A  single    0.970  0.020  1.090
 RFX  C16  C17   aromatic  1.391  0.020  1.391
 RFX  C21  C16   aromatic  1.392  0.020  1.392
 RFX  C21  C20   aromatic  1.388  0.020  1.388
 RFX  C21  H21   single    0.930  0.020  1.080
 RFX  C20  C19   aromatic  1.389  0.020  1.389
 RFX  C20  H20   single    0.930  0.020  1.080
 RFX  C19  C18   aromatic  1.388  0.020  1.388
 RFX  C19  H19   single    0.930  0.020  1.080
 RFX  C18  H18   single    0.930  0.020  1.080
 RFX  C17  C18   aromatic  1.388  0.020  1.388
 RFX  C17  H17   single    0.930  0.020  1.080
 RFX  N4   H171  single    0.890  0.020  1.040
 RFX  C22  H181  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
 RFX  C9    C12  F13   111.98  3.000
 RFX  F13   C12  F15   106.83  3.000
 RFX  C9    C12  F15   112.86  3.000
 RFX  F13   C12  F14   106.00  3.000
 RFX  C9    C12  F14   111.88  3.000
 RFX  F15   C12  F14   106.86  3.000
 RFX  C8    C9   C10   119.19  3.000
 RFX  C8    C9   C12   118.93  3.000
 RFX  C10   C9   C12   121.88  3.000
 RFX  H10   C10  C11   118.04  3.000
 RFX  H10   C10  C9    121.14  3.000
 RFX  C11   C10  C9    120.82  3.000
 RFX  H11   C11  C6    121.89  3.000
 RFX  C6    C11  C10   119.84  3.000
 RFX  H11   C11  C10   118.26  3.000
 RFX  O5    C6   C7    115.65  3.000
 RFX  C7    C6   C11   119.35  3.000
 RFX  O5    C6   C11   125.00  3.000
 RFX  H7    C7   C8    120.13  3.000
 RFX  C8    C7   C6    120.37  3.000
 RFX  H7    C7   C6    119.50  3.000
 RFX  H8    C8   C7    118.72  3.000
 RFX  H8    C8   C9    120.85  3.000
 RFX  C7    C8   C9    120.42  3.000
 RFX  C3    O5   C6    120.27  3.000
 RFX  H3    C3   C16   109.17  3.000
 RFX  H3    C3   C2    108.22  3.000
 RFX  C16   C3   C2    111.39  3.000
 RFX  H3    C3   O5    109.55  3.000
 RFX  C2    C3   O5    106.83  3.000
 RFX  C16   C3   O5    111.61  3.000
 RFX  H2A   C2   H2    106.72  3.000
 RFX  H2A   C2   C1    110.23  3.000
 RFX  H2    C2   C1    109.35  3.000
 RFX  C1    C2   C3    113.33  3.000
 RFX  H2A   C2   C3    110.08  3.000
 RFX  H2    C2   C3    106.85  3.000
 RFX  H1A   C1   H1    106.22  3.000
 RFX  H1A   C1   N4    112.65  3.000
 RFX  H1    C1   N4    108.02  3.000
 RFX  H1A   C1   C2    109.31  3.000
 RFX  H1    C1   C2    109.89  3.000
 RFX  N4    C1   C2    110.62  3.000
 RFX  H171  N4   C22   108.89  3.000
 RFX  H171  N4   C1    108.96  3.000
 RFX  C22   N4   C1    112.52  3.000
 RFX  H181  C22  H22A  107.54  3.000
 RFX  H181  C22  H22   107.33  3.000
 RFX  H22A  C22  H22   107.83  3.000
 RFX  H181  C22  N4    109.84  3.000
 RFX  H22A  C22  N4    109.93  3.000
 RFX  H22   C22  N4    114.13  3.000
 RFX  C17   C16  C21   119.13  3.000
 RFX  C21   C16  C3    121.16  3.000
 RFX  C17   C16  C3    119.66  3.000
 RFX  H21   C21  C20   119.41  3.000
 RFX  H21   C21  C16   120.31  3.000
 RFX  C20   C21  C16   120.28  3.000
 RFX  H20   C20  C19   120.02  3.000
 RFX  H20   C20  C21   119.66  3.000
 RFX  C19   C20  C21   120.32  3.000
 RFX  H19   C19  C18   120.21  3.000
 RFX  H19   C19  C20   120.16  3.000
 RFX  C18   C19  C20   119.63  3.000
 RFX  H18   C18  C17   119.81  3.000
 RFX  C17   C18  C19   119.98  3.000
 RFX  H18   C18  C19   120.22  3.000
 RFX  H17   C17  C18   119.71  3.000
 RFX  H17   C17  C16   119.64  3.000
 RFX  C18   C17  C16   120.66  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
 RFX  CONST_01  C6   C11  C10  C9     0.00   0.0  0
 RFX  CONST_02  C6   C7   C8   C9     0.00   0.0  0
 RFX  CONST_03  C7   C8   C9   C10    0.00   0.0  0
 RFX  CONST_04  C7   C6   C11  C10    0.00   0.0  0
 RFX  CONST_05  C8   C9   C10  C11    0.00   0.0  0
 RFX  CONST_06  C8   C7   C6   C11    0.00   0.0  0
 RFX  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 RFX  CONST_08  C19  C20  C21  C16    0.00   0.0  0
 RFX  CONST_09  C18  C17  C16  C21    0.00   0.0  0
 RFX  CONST_10  C18  C19  C20  C21    0.00   0.0  0
 RFX  CONST_11  C17  C16  C21  C20    0.00   0.0  0
 RFX  CONST_12  C17  C18  C19  C20    0.00   0.0  0
 RFX  CONST_13  C11  C10  C9   C12  180.00   0.0  0
 RFX  CONST_14  C7   C8   C9   C12  180.00   0.0  0
 RFX  CONST_15  O5   C6   C11  C10  180.00   0.0  0
 RFX  CONST_16  O5   C6   C7   C8   180.00   0.0  0
 RFX  CONST_17  C18  C17  C16  C3   180.00   0.0  0
 RFX  CONST_18  C20  C21  C16  C3   180.00   0.0  0
 RFX  CONST_19  H11  C11  C10  C9   180.00   0.0  0
 RFX  CONST_20  H7   C7   C8   C9   180.00   0.0  0
 RFX  CONST_21  H8   C8   C9   C10  180.00   0.0  0
 RFX  CONST_22  H10  C10  C11  C6   180.00   0.0  0
 RFX  CONST_23  H18  C18  C17  C16  180.00   0.0  0
 RFX  CONST_24  H20  C20  C21  C16  180.00   0.0  0
 RFX  CONST_25  H17  C17  C16  C21  180.00   0.0  0
 RFX  CONST_26  H19  C19  C20  C21  180.00   0.0  0
 RFX  CONST_27  H21  C21  C20  C19  180.00   0.0  0
 RFX  Var_01    C10  C9   C12  F14  121.56  30.0  2
 RFX  Var_02    N4   C1   C2   C3   173.62  30.0  1
 RFX  Var_03    C22  N4   C1   C2   178.54  30.0  3
 RFX  Var_04    H22  C22  N4   C1    54.41  30.0  3

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
 RFX  chir_01  C3  O5  C16  C2  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
 RFX  plan-1  C12  0.020
 RFX  plan-1  C9   0.020
 RFX  plan-1  C10  0.020
 RFX  plan-1  C11  0.020
 RFX  plan-1  C6   0.020
 RFX  plan-1  C7   0.020
 RFX  plan-1  C8   0.020
 RFX  plan-1  O5   0.020
 RFX  plan-1  H10  0.020
 RFX  plan-1  H11  0.020
 RFX  plan-1  H7   0.020
 RFX  plan-1  H8   0.020
 RFX  plan-2  C3   0.020
 RFX  plan-2  C16  0.020
 RFX  plan-2  C21  0.020
 RFX  plan-2  C20  0.020
 RFX  plan-2  C19  0.020
 RFX  plan-2  C18  0.020
 RFX  plan-2  C17  0.020
 RFX  plan-2  H21  0.020
 RFX  plan-2  H20  0.020
 RFX  plan-2  H19  0.020
 RFX  plan-2  H18  0.020
 RFX  plan-2  H17  0.020

