# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 16:35:15 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 1-[3-chloro-4-(trifluoromethoxy)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(OC(F)(F)F)c(Cl)c1
#
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
 54Z  54Z  1-[3-chloro-4-(trifluoromethoxy)phenyl]methanamine  ligand  21  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_54Z
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
 54Z  C6  C   CR6   0  -0.187   0.4747  -0.9137  -0.4512
 54Z  C2  C   CR16  0  -0.370   1.6119   1.6049  -0.3481
 54Z  C4  C   CR6   0   0.549  -0.3280   0.2145  -0.5688
 54Z  C5  C   CT    0   1.140  -2.5089   0.1636   0.2615
 54Z  C1  C   CR6   0   0.223   2.4254   0.4846  -0.2229
 54Z  CL  CL  CL    0  -0.079  -0.2308  -2.4846  -0.5382
 54Z  O   O   O2    0  -0.531  -1.6833   0.0580  -0.7916
 54Z  F2  F   F     0  -0.345  -2.5609   1.4042   0.7492
 54Z  F1  F   F     0  -0.279  -3.7209  -0.1725  -0.1462
 54Z  F   F   F     0  -0.357  -2.1606  -0.6335   1.2699
 54Z  C3  C   CR16  0  -0.314   0.2420   1.4730  -0.5215
 54Z  C7  C   CR16  0  -0.295   1.8407  -0.7778  -0.2781
 54Z  C   C   CH2   0  -0.388   3.9223   0.5965  -0.0706
 54Z  N   N   NH2   0  -0.787   4.3369   1.9055   0.3902
 54Z  H1  H   HCR6  0   0.255   2.0520   2.5915  -0.3071
 54Z  H2  H   HCR6  0   0.330  -0.3787   2.3516  -0.6377
 54Z  H3  H   HCR6  0   0.295   2.4537  -1.6651  -0.1793
 54Z  H4  H   HCH2  0   0.257   4.2696  -0.2316   0.5615
 54Z  H5  H   HCH2  0   0.190   4.3713   0.4242  -1.0529
 54Z  H6  H   HNH2  0   0.325   4.1251   2.0055   1.3749
 54Z  H7  H   HNH2  0   0.369   5.3417   1.9840   0.3088

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
 54Z  F   C5  single    1.332  0.020  1.332
 54Z  F2  C5  single    1.334  0.020  1.334
 54Z  F1  C5  single    1.322  0.020  1.322
 54Z  C5  O   single    1.342  0.020  1.342
 54Z  O   C4  single    1.382  0.020  1.382
 54Z  C3  C4  aromatic  1.382  0.020  1.382
 54Z  C3  C2  aromatic  1.387  0.020  1.387
 54Z  C4  C6  aromatic  1.390  0.020  1.390
 54Z  C2  C1  aromatic  1.390  0.020  1.390
 54Z  C6  CL  single    1.724  0.020  1.724
 54Z  C6  C7  aromatic  1.384  0.020  1.384
 54Z  C1  C7  aromatic  1.392  0.020  1.392
 54Z  C1  C   single    1.509  0.020  1.509
 54Z  C   N   single    1.448  0.020  1.448
 54Z  C2  H1  single    0.930  0.020  1.080
 54Z  C3  H2  single    0.930  0.020  1.080
 54Z  C7  H3  single    0.930  0.020  1.080
 54Z  C   H4  single    0.970  0.020  1.090
 54Z  C   H5  single    0.970  0.020  1.090
 54Z  N   H6  single    0.890  0.020  1.040
 54Z  N   H7  single    0.890  0.020  1.040

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
 54Z  C7  C6  CL  119.99  3.000
 54Z  C7  C6  C4  120.07  3.000
 54Z  CL  C6  C4  119.94  3.000
 54Z  H1  C2  C3  119.57  3.000
 54Z  H1  C2  C1  119.60  3.000
 54Z  C3  C2  C1  120.83  3.000
 54Z  C3  C4  O   120.85  3.000
 54Z  C3  C4  C6  119.87  3.000
 54Z  O   C4  C6  119.21  3.000
 54Z  F   C5  F1  108.73  3.000
 54Z  F1  C5  F2  108.26  3.000
 54Z  F   C5  F2  106.86  3.000
 54Z  F1  C5  O   107.58  3.000
 54Z  F2  C5  O   112.58  3.000
 54Z  F   C5  O   112.71  3.000
 54Z  C   C1  C7  119.21  3.000
 54Z  C   C1  C2  122.00  3.000
 54Z  C7  C1  C2  118.77  3.000
 54Z  C5  O   C4  117.89  3.000
 54Z  H2  C3  C4  119.93  3.000
 54Z  H2  C3  C2  120.18  3.000
 54Z  C4  C3  C2  119.87  3.000
 54Z  H3  C7  C1  120.10  3.000
 54Z  H3  C7  C6  119.32  3.000
 54Z  C1  C7  C6  120.58  3.000
 54Z  H5  C   H4  105.57  3.000
 54Z  H5  C   N   108.09  3.000
 54Z  H4  C   N   114.08  3.000
 54Z  H5  C   C1  107.75  3.000
 54Z  H4  C   C1  108.41  3.000
 54Z  N   C   C1  112.53  3.000
 54Z  H7  N   H6  106.17  3.000
 54Z  H7  N   C   109.21  3.000
 54Z  H6  N   C   109.81  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
 54Z  CONST_01  C2  C3  C4  C6    0.00   0.0  0
 54Z  CONST_02  C2  C1  C7  C6    0.00   0.0  0
 54Z  CONST_03  C1  C2  C3  C4    0.00   0.0  0
 54Z  CONST_04  C1  C7  C6  C4    0.00   0.0  0
 54Z  CONST_05  C7  C6  C4  C3    0.00   0.0  0
 54Z  CONST_06  C7  C1  C2  C3    0.00   0.0  0
 54Z  CONST_07  C   C1  C7  C6  180.00   0.0  0
 54Z  CONST_08  O   C4  C3  C2  180.00   0.0  0
 54Z  CONST_09  CL  C6  C7  C1  180.00   0.0  0
 54Z  CONST_10  C3  C4  C6  CL  180.00   0.0  0
 54Z  CONST_11  C7  C6  C4  O   180.00   0.0  0
 54Z  CONST_12  C   C1  C2  C3  180.00   0.0  0
 54Z  CONST_13  H2  C3  C4  C6  180.00   0.0  0
 54Z  CONST_14  H3  C7  C1  C2  180.00   0.0  0
 54Z  CONST_15  H1  C2  C3  C4  180.00   0.0  0
 54Z  Var_01    N   C   C1  C2   20.18  30.0  2
 54Z  Var_02    C3  C4  O   C5  -83.59  30.0  2
 54Z  Var_03    F   C5  O   C4  -52.95  30.0  3
 54Z  Var_04    H6  N   C   C1   74.52  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
 54Z  plan-1  C6  0.020
 54Z  plan-1  C2  0.020
 54Z  plan-1  C4  0.020
 54Z  plan-1  C1  0.020
 54Z  plan-1  CL  0.020
 54Z  plan-1  O   0.020
 54Z  plan-1  C3  0.020
 54Z  plan-1  C7  0.020
 54Z  plan-1  C   0.020
 54Z  plan-1  H1  0.020
 54Z  plan-1  H2  0.020
 54Z  plan-1  H3  0.020

