# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:15:16 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-[2-(piperidin-1-yl)-5-(trifluoromethyl)phenyl]pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc(N2CCCCC2)c(NC(=O)c3ccncc3)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
 3UL  3UL  N-[2-(piperidin-1-yl)-5-(trifluoromethyl)phenyl]pyridine-4-carboxamide  ligand  43  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3UL
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
 3UL  C1   C  CR6   0   0.051   2.7803  -1.3274   0.0244
 3UL  C2   C  CR16  0  -0.335   3.5652  -2.2787   0.6645
 3UL  C3   C  CR16  0  -0.053   4.9439  -2.1852   0.5620
 3UL  C4   C  CR16  0  -0.051   4.8132  -0.3404  -0.7542
 3UL  C5   C  CR16  0  -0.372   3.4266  -0.3373  -0.7078
 3UL  C6   C  CR6   0   0.362  -0.7502  -0.0449  -0.0442
 3UL  C8   C  CR6   0  -0.185  -3.0755  -0.6433  -0.0689
 3UL  C9   C  CT    0   1.050  -4.1042  -1.7291  -0.0440
 3UL  C12  C  CR6   0   0.247  -1.1085   1.3190  -0.0948
 3UL  F2   F  F     0  -0.315  -3.9735  -2.5630  -1.0871
 3UL  F    F  F     0  -0.315  -3.9991  -2.4861   1.0587
 3UL  F1   F  F     0  -0.302  -5.3537  -1.2588  -0.0758
 3UL  C7   C  CR16  0  -0.346  -1.7355  -1.0210  -0.0218
 3UL  C10  C  CR16  0  -0.306  -3.4384   0.6902  -0.1467
 3UL  C11  C  CR16  0  -0.276  -2.4476   1.6637  -0.1564
 3UL  N2   N  NT    0  -0.533  -0.0546   2.2570  -0.0916
 3UL  C17  C  CH2   0  -0.293  -0.2052   3.3914  -0.9940
 3UL  C16  C  CH2   0  -0.439   1.1226   4.1213  -1.1245
 3UL  C15  C  CH2   0  -0.442   1.6328   4.5679   0.2402
 3UL  C14  C  CH2   0  -0.438   1.6908   3.3884   1.2030
 3UL  C13  C  CH2   0  -0.312   0.3557   2.6647   1.2562
 3UL  N1   N  NH1   0  -0.760   0.6189  -0.2888  -0.0628
 3UL  C    C  C     0   0.547   1.2900  -1.4418   0.1413
 3UL  O    O  O     0  -0.450   0.7647  -2.5040   0.4217
 3UL  N    N  N     0  -0.395   5.5648  -1.2378  -0.1313
 3UL  H1   H  HCR6  0   0.279   3.1180  -3.0772   1.2393
 3UL  H2   H  HCR6  0   0.274   5.5724  -2.9125   1.0627
 3UL  H3   H  HCR6  0   0.277   5.3327   0.4187  -1.3271
 3UL  H4   H  HCR6  0   0.271   2.8946   0.4192  -1.2705
 3UL  H5   H  HCR6  0   0.293  -1.4623  -2.0644   0.0171
 3UL  H6   H  HCR6  0   0.272  -4.4749   0.9930  -0.1909
 3UL  H7   H  HCR6  0   0.269  -2.7335   2.7064  -0.2072
 3UL  H8   H  HCH2  0   0.252  -0.5324   3.0196  -1.9661
 3UL  H9   H  HCH2  0   0.208  -0.9703   4.0978  -0.6383
 3UL  H10  H  HCH2  0   0.220   1.8511   3.4543  -1.5955
 3UL  H11  H  HCH2  0   0.239   0.9959   4.9778  -1.7897
 3UL  H12  H  HCH2  0   0.238   2.6156   5.0348   0.1486
 3UL  H13  H  HCH2  0   0.216   0.9594   5.3310   0.6447
 3UL  H14  H  HCH2  0   0.213   2.4688   2.6851   0.8879
 3UL  H15  H  HCH2  0   0.241   1.9562   3.7211   2.2086
 3UL  H16  H  HCH2  0   0.227  -0.4068   3.3162   1.7096
 3UL  H17  H  HCH2  0   0.256   0.4276   1.7781   1.8895
 3UL  H18  H  HNH1  0   0.413   1.1352   0.5691  -0.2308

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
 3UL  F    C9   single    1.342  0.020  1.342
 3UL  F2   C9   single    1.342  0.020  1.342
 3UL  C9   C8   single    1.496  0.020  1.496
 3UL  C9   F1   single    1.335  0.020  1.335
 3UL  C13  C14  single    1.520  0.020  1.520
 3UL  C13  N2   single    1.467  0.020  1.467
 3UL  C8   C10  aromatic  1.384  0.020  1.384
 3UL  C8   C7   aromatic  1.393  0.020  1.393
 3UL  C10  C11  aromatic  1.389  0.020  1.389
 3UL  C14  C15  single    1.524  0.020  1.524
 3UL  C7   C6   aromatic  1.387  0.020  1.387
 3UL  C11  C12  aromatic  1.384  0.020  1.384
 3UL  O    C    double    1.218  0.020  1.218
 3UL  C6   C12  aromatic  1.411  0.020  1.411
 3UL  C6   N1   single    1.391  0.020  1.391
 3UL  C12  N2   single    1.411  0.020  1.411
 3UL  C    N1   single    1.350  0.020  1.350
 3UL  C    C1   single    1.499  0.020  1.499
 3UL  N2   C17  single    1.457  0.020  1.457
 3UL  C5   C1   aromatic  1.391  0.020  1.391
 3UL  C5   C4   aromatic  1.387  0.020  1.387
 3UL  C15  C16  single    1.524  0.020  1.524
 3UL  C1   C2   aromatic  1.390  0.020  1.390
 3UL  C4   N    aromatic  1.326  0.020  1.326
 3UL  C2   C3   aromatic  1.386  0.020  1.386
 3UL  N    C3   aromatic  1.328  0.020  1.328
 3UL  C17  C16  single    1.521  0.020  1.521
 3UL  C2   H1   single    0.930  0.020  1.080
 3UL  C3   H2   single    0.930  0.020  1.080
 3UL  C4   H3   single    0.930  0.020  1.080
 3UL  C5   H4   single    0.930  0.020  1.080
 3UL  C7   H5   single    0.930  0.020  1.080
 3UL  C10  H6   single    0.930  0.020  1.080
 3UL  C11  H7   single    0.930  0.020  1.080
 3UL  C17  H8   single    0.970  0.020  1.090
 3UL  C17  H9   single    0.970  0.020  1.090
 3UL  C16  H10  single    0.970  0.020  1.090
 3UL  C16  H11  single    0.970  0.020  1.090
 3UL  C15  H12  single    0.970  0.020  1.090
 3UL  C15  H13  single    0.970  0.020  1.090
 3UL  C14  H14  single    0.970  0.020  1.090
 3UL  C14  H15  single    0.970  0.020  1.090
 3UL  C13  H16  single    0.970  0.020  1.090
 3UL  C13  H17  single    0.970  0.020  1.090
 3UL  N1   H18  single    0.860  0.020  1.020

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
 3UL  C    C1   C5   123.87  3.000
 3UL  C5   C1   C2   117.87  3.000
 3UL  C    C1   C2   118.25  3.000
 3UL  H1   C2   C3   120.06  3.000
 3UL  H1   C2   C1   121.13  3.000
 3UL  C3   C2   C1   118.80  3.000
 3UL  H2   C3   N    116.66  3.000
 3UL  H2   C3   C2   119.84  3.000
 3UL  N    C3   C2   123.50  3.000
 3UL  H3   C4   N    116.78  3.000
 3UL  H3   C4   C5   119.69  3.000
 3UL  N    C4   C5   123.53  3.000
 3UL  H4   C5   C4   118.38  3.000
 3UL  H4   C5   C1   122.88  3.000
 3UL  C4   C5   C1   118.72  3.000
 3UL  N1   C6   C7   125.17  3.000
 3UL  N1   C6   C12  114.77  3.000
 3UL  C7   C6   C12  120.02  3.000
 3UL  C10  C8   C7   121.02  3.000
 3UL  C7   C8   C9   117.65  3.000
 3UL  C10  C8   C9   121.33  3.000
 3UL  F1   C9   F    106.95  3.000
 3UL  F1   C9   F2   106.94  3.000
 3UL  F    C9   F2   106.29  3.000
 3UL  F1   C9   C8   112.80  3.000
 3UL  F2   C9   C8   111.79  3.000
 3UL  F    C9   C8   111.68  3.000
 3UL  N2   C12  C11  123.87  3.000
 3UL  N2   C12  C6   116.92  3.000
 3UL  C11  C12  C6   119.21  3.000
 3UL  H5   C7   C8   120.46  3.000
 3UL  H5   C7   C6   120.07  3.000
 3UL  C8   C7   C6   119.47  3.000
 3UL  H6   C10  C11  119.17  3.000
 3UL  H6   C10  C8   121.58  3.000
 3UL  C11  C10  C8   119.25  3.000
 3UL  H7   C11  C10  119.15  3.000
 3UL  H7   C11  C12  119.84  3.000
 3UL  C10  C11  C12  121.02  3.000
 3UL  C13  N2   C17  112.43  3.000
 3UL  C17  N2   C12  116.04  3.000
 3UL  C13  N2   C12  113.32  3.000
 3UL  H9   C17  H8   107.35  3.000
 3UL  H9   C17  C16  109.07  3.000
 3UL  H8   C17  C16  110.42  3.000
 3UL  H9   C17  N2   111.80  3.000
 3UL  H8   C17  N2   108.51  3.000
 3UL  C16  C17  N2   109.67  3.000
 3UL  H11  C16  H10  107.05  3.000
 3UL  H11  C16  C15  110.76  3.000
 3UL  H10  C16  C15  109.95  3.000
 3UL  H11  C16  C17  109.12  3.000
 3UL  H10  C16  C17  109.00  3.000
 3UL  C15  C16  C17  110.86  3.000
 3UL  H13  C15  H12  106.65  3.000
 3UL  H13  C15  C14  109.23  3.000
 3UL  H12  C15  C14  110.48  3.000
 3UL  H13  C15  C16  109.21  3.000
 3UL  H12  C15  C16  110.58  3.000
 3UL  C14  C15  C16  110.60  3.000
 3UL  H15  C14  H14  106.74  3.000
 3UL  H15  C14  C13  109.05  3.000
 3UL  H14  C14  C13  109.17  3.000
 3UL  H15  C14  C15  110.82  3.000
 3UL  H14  C14  C15  110.02  3.000
 3UL  C13  C14  C15  110.94  3.000
 3UL  H17  C13  H16  106.70  3.000
 3UL  H17  C13  C14  110.44  3.000
 3UL  H16  C13  C14  109.94  3.000
 3UL  H17  C13  N2   109.01  3.000
 3UL  H16  C13  N2   110.45  3.000
 3UL  C14  C13  N2   110.25  3.000
 3UL  H18  N1   C    119.60  3.000
 3UL  H18  N1   C6   110.77  3.000
 3UL  C    N1   C6   129.59  3.000
 3UL  O    C    N1   124.44  3.000
 3UL  N1   C    C1   114.67  3.000
 3UL  O    C    C1   120.88  3.000
 3UL  C4   N    C3   117.58  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
 3UL  CONST_01  N    C4   C5   C1      0.00   0.0  0
 3UL  CONST_02  N    C3   C2   C1      0.00   0.0  0
 3UL  CONST_03  C4   C5   C1   C2      0.00   0.0  0
 3UL  CONST_04  C4   N    C3   C2      0.00   0.0  0
 3UL  CONST_05  C5   C1   C2   C3      0.00   0.0  0
 3UL  CONST_06  C5   C4   N    C3      0.00   0.0  0
 3UL  CONST_07  C10  C8   C7   C6      0.00   0.0  0
 3UL  CONST_08  C10  C11  C12  C6      0.00   0.0  0
 3UL  CONST_09  C12  C11  C10  C8      0.00   0.0  0
 3UL  CONST_10  C12  C6   C7   C8      0.00   0.0  0
 3UL  CONST_11  C11  C10  C8   C7      0.00   0.0  0
 3UL  CONST_12  C11  C12  C6   C7      0.00   0.0  0
 3UL  CONST_13  N2   C12  C6   C7    180.00   0.0  0
 3UL  CONST_14  N2   C12  C11  C10   180.00   0.0  0
 3UL  CONST_15  C    C1   C2   C3    180.00   0.0  0
 3UL  CONST_16  C    C1   C5   C4    180.00   0.0  0
 3UL  CONST_17  C9   C8   C7   C6    180.00   0.0  0
 3UL  CONST_18  N1   C6   C7   C8    180.00   0.0  0
 3UL  CONST_19  C11  C10  C8   C9    180.00   0.0  0
 3UL  CONST_20  N1   C6   C12  C11   180.00   0.0  0
 3UL  CONST_21  N1   C6   C12  N2      0.00   0.0  0
 3UL  CONST_22  H3   C4   C5   C1    180.00   0.0  0
 3UL  CONST_23  H2   C3   C2   C1    180.00   0.0  0
 3UL  CONST_24  H4   C5   C1   C2    180.00   0.0  0
 3UL  CONST_25  H1   C2   C1   C5    180.00   0.0  0
 3UL  CONST_26  H7   C11  C12  C6    180.00   0.0  0
 3UL  CONST_27  H6   C10  C11  C12   180.00   0.0  0
 3UL  CONST_28  H5   C7   C6   C12   180.00   0.0  0
 3UL  CONST_29  C6   N1   C    C1    180.00   0.0  0
 3UL  CONST_30  C    N1   C6   C12   180.00   0.0  0
 3UL  CONST_31  C    N1   C6   C7      0.00   0.0  0
 3UL  CONST_32  H18  N1   C6   C12     0.00   0.0  0
 3UL  CONST_33  O    C    N1   C6      0.00   0.0  0
 3UL  Var_01    C13  N2   C12  C6    -88.98  30.0  2
 3UL  Var_02    C14  C13  N2   C12   165.97  30.0  1
 3UL  Var_03    C16  C17  N2   C12  -166.69  30.0  1
 3UL  Var_04    C15  C14  C13  N2     55.22  30.0  1
 3UL  Var_05    C15  C16  C17  N2    -56.88  30.0  1
 3UL  Var_06    C14  C15  C16  C17    53.70  30.0  1
 3UL  Var_07    C13  C14  C15  C16   -52.84  30.0  1
 3UL  Var_08    O    C    C1   C2    -21.66  30.0  2
 3UL  Var_09    C10  C8   C9   F2    119.25  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
 3UL  plan-1  C1   0.020
 3UL  plan-1  C2   0.020
 3UL  plan-1  C3   0.020
 3UL  plan-1  C4   0.020
 3UL  plan-1  C5   0.020
 3UL  plan-1  C    0.020
 3UL  plan-1  N    0.020
 3UL  plan-1  H1   0.020
 3UL  plan-1  H2   0.020
 3UL  plan-1  H3   0.020
 3UL  plan-1  H4   0.020
 3UL  plan-2  C6   0.020
 3UL  plan-2  C8   0.020
 3UL  plan-2  C9   0.020
 3UL  plan-2  C12  0.020
 3UL  plan-2  C7   0.020
 3UL  plan-2  C10  0.020
 3UL  plan-2  C11  0.020
 3UL  plan-2  N2   0.020
 3UL  plan-2  N1   0.020
 3UL  plan-2  H5   0.020
 3UL  plan-2  H6   0.020
 3UL  plan-2  H7   0.020
 3UL  plan-3  C1   0.020
 3UL  plan-3  C6   0.020
 3UL  plan-3  N1   0.020
 3UL  plan-3  C    0.020
 3UL  plan-3  O    0.020
 3UL  plan-3  H18  0.020

