# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:12:05 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 1-[3-(trifluoromethyl)pyridin-2-yl]piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccnc1N2CCNCC2
#
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
 49N  49N  1-[3-(trifluoromethyl)pyridin-2-yl]piperazine  ligand  28  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_49N
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
 49N  C10  C  CR16  0  -0.330  -2.6924   2.1224  -0.0518
 49N  C5   C  CR16  0  -0.165  -2.6198   0.7504   0.1254
 49N  C9   C  CR16  0  -0.053  -1.5160   2.8133  -0.2818
 49N  C2   C  CR6   0  -0.344  -1.3793   0.1304   0.0832
 49N  C1   C  CR6   0   0.474  -0.2398   0.9236  -0.1101
 49N  C14  C  CH2   0  -0.300   3.1096  -0.1988  -1.2198
 49N  C15  C  CH2   0  -0.300   2.9265  -0.5184   1.1446
 49N  C7   C  CH2   0  -0.283   1.9063   0.7267  -1.1963
 49N  C8   C  CH2   0  -0.294   1.7166   0.3959   1.1773
 49N  C6   C  CT    0   1.079  -1.2680  -1.3627   0.1681
 49N  N4   N  N     0  -0.406  -0.3240   2.2305  -0.3018
 49N  N16  N  NH1   0  -0.602   3.8000  -0.1242   0.0549
 49N  N3   N  NT    0  -0.509   1.0270   0.3189  -0.1087
 49N  F11  F  F     0  -0.308  -2.4763  -1.9362   0.2645
 49N  F12  F  F     0  -0.304  -0.6858  -1.8883  -0.9139
 49N  F13  F  F     0  -0.310  -0.5720  -1.7796   1.2338
 49N  H1   H  HCR6  0   0.281  -3.6412   2.6389  -0.0299
 49N  H2   H  HCR6  0   0.287  -3.5277   0.1834   0.2773
 49N  H3   H  HCR6  0   0.273  -1.5341   3.8838  -0.4518
 49N  H5   H  HCH2  0   0.233   3.7886   0.1136  -2.0155
 49N  H6   H  HCH2  0   0.234   3.4683  -0.4347   2.0889
 49N  H7   H  HCH2  0   0.196   2.5716  -1.5570   1.0567
 49N  H8   H  HCH2  0   0.207   2.2454   1.7657  -1.0877
 49N  H9   H  HCH2  0   0.240   1.3659   0.6507  -2.1413
 49N  H10  H  HCH2  0   0.246   1.0440   0.0914   1.9784
 49N  H11  H  HCH2  0   0.210   2.0378   1.4265   1.3909
 49N  H12  H  HNH1  0   0.355   4.6145  -0.7235   0.0376
 49N  H4   H  HCH2  0   0.195   2.7631  -1.2159  -1.4593

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
 49N  N16  C14  single    1.452  0.020  1.452
 49N  N16  C15  single    1.451  0.020  1.451
 49N  C14  C7   single    1.518  0.020  1.518
 49N  C15  C8   single    1.517  0.020  1.517
 49N  F13  C6   single    1.339  0.020  1.339
 49N  C7   N3   single    1.457  0.020  1.457
 49N  C8   N3   single    1.461  0.020  1.461
 49N  N3   C1   single    1.404  0.020  1.404
 49N  F12  C6   single    1.336  0.020  1.336
 49N  C6   F11  single    1.341  0.020  1.341
 49N  C6   C2   single    1.500  0.020  1.500
 49N  C1   C2   aromatic  1.402  0.020  1.402
 49N  C1   N4   aromatic  1.324  0.020  1.324
 49N  C2   C5   aromatic  1.387  0.020  1.387
 49N  N4   C9   aromatic  1.327  0.020  1.327
 49N  C5   C10  aromatic  1.385  0.020  1.385
 49N  C9   C10  aromatic  1.384  0.020  1.384
 49N  C10  H1   single    0.930  0.020  1.080
 49N  C5   H2   single    0.930  0.020  1.080
 49N  C9   H3   single    0.930  0.020  1.080
 49N  C14  H4   single    0.970  0.020  1.090
 49N  C14  H5   single    0.970  0.020  1.090
 49N  C15  H6   single    0.970  0.020  1.090
 49N  C15  H7   single    0.970  0.020  1.090
 49N  C7   H8   single    0.970  0.020  1.090
 49N  C7   H9   single    0.970  0.020  1.090
 49N  C8   H10  single    0.970  0.020  1.090
 49N  C8   H11  single    0.970  0.020  1.090
 49N  N16  H12  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
 49N  H1   C10  C9   120.75  3.000
 49N  H1   C10  C5   121.12  3.000
 49N  C9   C10  C5   118.12  3.000
 49N  H2   C5   C2   121.38  3.000
 49N  H2   C5   C10  119.56  3.000
 49N  C2   C5   C10  119.05  3.000
 49N  H3   C9   N4   116.51  3.000
 49N  H3   C9   C10  120.33  3.000
 49N  N4   C9   C10  123.16  3.000
 49N  C6   C2   C1   120.72  3.000
 49N  C1   C2   C5   118.57  3.000
 49N  C6   C2   C5   120.63  3.000
 49N  N3   C1   N4   118.88  3.000
 49N  N4   C1   C2   121.80  3.000
 49N  N3   C1   C2   119.32  3.000
 49N  H5   C14  H4   107.56  3.000
 49N  H5   C14  N16  109.24  3.000
 49N  H4   C14  N16  112.85  3.000
 49N  H5   C14  C7   109.26  3.000
 49N  H4   C14  C7   108.49  3.000
 49N  N16  C14  C7   109.39  3.000
 49N  H7   C15  H6   107.54  3.000
 49N  H7   C15  N16  112.97  3.000
 49N  H6   C15  N16  109.26  3.000
 49N  H7   C15  C8   108.25  3.000
 49N  H6   C15  C8   109.32  3.000
 49N  N16  C15  C8   109.42  3.000
 49N  H9   C7   H8   107.72  3.000
 49N  H9   C7   N3   109.15  3.000
 49N  H8   C7   N3   112.17  3.000
 49N  H9   C7   C14  109.67  3.000
 49N  H8   C7   C14  109.48  3.000
 49N  N3   C7   C14  108.62  3.000
 49N  H11  C8   H10  107.41  3.000
 49N  H11  C8   N3   110.97  3.000
 49N  H10  C8   N3   109.94  3.000
 49N  H11  C8   C15  109.63  3.000
 49N  H10  C8   C15  109.87  3.000
 49N  N3   C8   C15  109.01  3.000
 49N  F13  C6   F12  107.18  3.000
 49N  F12  C6   F11  106.41  3.000
 49N  F13  C6   F11  106.14  3.000
 49N  F11  C6   C2   111.28  3.000
 49N  F12  C6   C2   112.22  3.000
 49N  F13  C6   C2   113.17  3.000
 49N  C1   N4   C9   119.25  3.000
 49N  H12  N16  C15  109.67  3.000
 49N  H12  N16  C14  109.73  3.000
 49N  C15  N16  C14  111.05  3.000
 49N  C8   N3   C7   110.94  3.000
 49N  C8   N3   C1   113.83  3.000
 49N  C7   N3   C1   115.05  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
 49N  CONST_01  C1   C2   C5   C10     0.00   0.0  0
 49N  CONST_02  C1   N4   C9   C10     0.00   0.0  0
 49N  CONST_03  N4   C1   C2   C5      0.00   0.0  0
 49N  CONST_04  N4   C9   C10  C5      0.00   0.0  0
 49N  CONST_05  C2   C1   N4   C9      0.00   0.0  0
 49N  CONST_06  C2   C5   C10  C9      0.00   0.0  0
 49N  CONST_07  N3   C1   C2   C5    180.00   0.0  0
 49N  CONST_08  N3   C1   N4   C9    180.00   0.0  0
 49N  CONST_09  C6   C2   C5   C10   180.00   0.0  0
 49N  CONST_10  N3   C1   C2   C6      0.00   0.0  0
 49N  CONST_11  N4   C1   C2   C6    180.00   0.0  0
 49N  CONST_12  H3   C9   C10  C5    180.00   0.0  0
 49N  CONST_13  H2   C5   C10  C9    180.00   0.0  0
 49N  CONST_14  H1   C10  C5   C2    180.00   0.0  0
 49N  Var_01    C7   N3   C1   C2    133.59  30.0  3
 49N  Var_02    C14  C7   N3   C1   -168.97  30.0  1
 49N  Var_03    C15  C8   N3   C1    168.62  30.0  1
 49N  Var_04    C8   C15  N16  C14   -59.34  30.0  1
 49N  Var_05    C7   C14  N16  C15    59.84  30.0  1
 49N  Var_06    N3   C7   C14  N16   -59.02  30.0  1
 49N  Var_07    N3   C8   C15  N16    58.13  30.0  1
 49N  Var_08    F13  C6   C2   C5   -118.63  30.0  2

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
 49N  plan-1  C10  0.020
 49N  plan-1  C5   0.020
 49N  plan-1  C9   0.020
 49N  plan-1  C2   0.020
 49N  plan-1  C1   0.020
 49N  plan-1  C6   0.020
 49N  plan-1  N4   0.020
 49N  plan-1  N3   0.020
 49N  plan-1  H1   0.020
 49N  plan-1  H2   0.020
 49N  plan-1  H3   0.020

