# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:29:09 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-ethyl-N-(2-fluorophenyl)piperidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCC(CC1)Nc2ccccc2F
#
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
 NVY  NVY  1-ethyl-N-(2-fluorophenyl)piperidin-4-amine  ligand  35  16  .  2021-08-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NVY
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
 NVY  N1   N  NT    0  -0.413   3.3404  -0.0847   0.2901
 NVY  C4   C  CH2   0  -0.439   1.5681   1.1402  -0.8969
 NVY  C5   C  CH1   0  -0.092   0.5269   0.1217  -0.4547
 NVY  C6   C  CH2   0  -0.438   0.9909  -0.5298   0.8468
 NVY  C7   C  CH2   0  -0.282   2.3894  -1.1053   0.6917
 NVY  C8   C  CR6   0   0.226  -1.9344   0.0467  -0.2177
 NVY  C10  C  CR16  0  -0.259  -3.2924  -1.9571  -0.4406
 NVY  C13  C  CR6   0   0.451  -3.0997   0.6878   0.2231
 NVY  C1   C  CH3   0  -0.679   5.7657   0.4599   0.1825
 NVY  C11  C  CR16  0  -0.282  -4.4233  -1.2852  -0.0054
 NVY  C12  C  CR16  0  -0.406  -4.3173   0.0607   0.3323
 NVY  C2   C  CH2   0  -0.267   4.6931  -0.6141   0.2615
 NVY  C3   C  CH2   0  -0.287   2.9502   0.5089  -0.9757
 NVY  C9   C  CR16  0  -0.341  -2.0677  -1.3087  -0.5425
 NVY  F1   F  F     0  -0.326  -3.0016   1.9948   0.5544
 NVY  N2   N  NH1   0  -0.689  -0.7691   0.7620  -0.3570
 NVY  H2   H  HCH2  0   0.243   1.3006   1.5547  -1.8712
 NVY  H3   H  HCH2  0   0.223   1.5922   1.9714  -0.1834
 NVY  H4   H  HCH1  0   0.230   0.4678  -0.6471  -1.2335
 NVY  H5   H  HCH2  0   0.220   0.9915   0.2241   1.6406
 NVY  H6   H  HCH2  0   0.238   0.3059  -1.3235   1.1542
 NVY  H7   H  HCH2  0   0.186   2.3604  -1.9407  -0.0327
 NVY  H8   H  HCH2  0   0.237   2.7165  -1.5318   1.6431
 NVY  H9   H  HCR6  0   0.255  -3.3523  -3.0054  -0.7027
 NVY  H10  H  HCH3  0   0.226   5.7494   1.0048  -0.7615
 NVY  H11  H  HCH3  0   0.222   5.6517   1.1806   0.9928
 NVY  H12  H  HCH3  0   0.231   6.7526   0.0053   0.2721
 NVY  H13  H  HCR6  0   0.256  -5.3758  -1.7906   0.0745
 NVY  H14  H  HCR6  0   0.273  -5.1765   0.6204   0.6800
 NVY  H15  H  HCH2  0   0.225   4.8407  -1.1823   1.1834
 NVY  H16  H  HCH2  0   0.187   4.8281  -1.3339  -0.5642
 NVY  H17  H  HCH2  0   0.242   3.6706   1.2795  -1.2549
 NVY  H18  H  HCH2  0   0.186   2.9629  -0.2404  -1.7888
 NVY  H19  H  HCR6  0   0.268  -1.2079  -1.8696  -0.8828
 NVY  H20  H  HNH1  0   0.374  -0.7489   1.6346   0.1488

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
 NVY  F1   C13  single    1.352  0.020  1.352
 NVY  C12  C13  aromatic  1.374  0.020  1.374
 NVY  C12  C11  aromatic  1.392  0.020  1.392
 NVY  C13  C8   aromatic  1.401  0.020  1.401
 NVY  C11  C10  aromatic  1.386  0.020  1.386
 NVY  C8   N2   single    1.374  0.020  1.374
 NVY  C8   C9   aromatic  1.400  0.020  1.400
 NVY  C10  C9   aromatic  1.389  0.020  1.389
 NVY  N2   C5   single    1.449  0.020  1.449
 NVY  C5   C4   single    1.522  0.020  1.522
 NVY  C5   C6   single    1.528  0.020  1.528
 NVY  C4   C3   single    1.521  0.020  1.521
 NVY  C6   C7   single    1.520  0.020  1.520
 NVY  C3   N1   single    1.452  0.020  1.452
 NVY  N1   C7   single    1.452  0.020  1.452
 NVY  N1   C2   single    1.453  0.020  1.453
 NVY  C2   C1   single    1.520  0.020  1.520
 NVY  C4   H2   single    0.970  0.020  1.090
 NVY  C4   H3   single    0.970  0.020  1.090
 NVY  C5   H4   single    0.970  0.020  1.090
 NVY  C6   H5   single    0.970  0.020  1.090
 NVY  C6   H6   single    0.970  0.020  1.090
 NVY  C7   H7   single    0.970  0.020  1.090
 NVY  C7   H8   single    0.970  0.020  1.090
 NVY  C10  H9   single    0.930  0.020  1.080
 NVY  C1   H10  single    0.970  0.020  1.090
 NVY  C1   H11  single    0.970  0.020  1.090
 NVY  C1   H12  single    0.970  0.020  1.090
 NVY  C11  H13  single    0.930  0.020  1.080
 NVY  C12  H14  single    0.930  0.020  1.080
 NVY  C2   H15  single    0.970  0.020  1.090
 NVY  C2   H16  single    0.970  0.020  1.090
 NVY  C3   H17  single    0.970  0.020  1.090
 NVY  C3   H18  single    0.970  0.020  1.090
 NVY  C9   H19  single    0.930  0.020  1.080
 NVY  N2   H20  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
 NVY  C3   N1   C2   112.46  3.000
 NVY  C2   N1   C7   111.05  3.000
 NVY  C3   N1   C7   110.65  3.000
 NVY  H3   C4   H2   107.37  3.000
 NVY  H3   C4   C3   109.18  3.000
 NVY  H2   C4   C3   109.50  3.000
 NVY  H3   C4   C5   109.48  3.000
 NVY  H2   C4   C5   110.21  3.000
 NVY  C3   C4   C5   111.02  3.000
 NVY  H4   C5   N2   108.04  3.000
 NVY  H4   C5   C6   108.83  3.000
 NVY  N2   C5   C6   113.75  3.000
 NVY  H4   C5   C4   107.45  3.000
 NVY  C6   C5   C4   108.97  3.000
 NVY  N2   C5   C4   109.62  3.000
 NVY  H6   C6   H5   107.25  3.000
 NVY  H6   C6   C7   109.30  3.000
 NVY  H5   C6   C7   109.52  3.000
 NVY  H6   C6   C5   111.05  3.000
 NVY  H5   C6   C5   108.92  3.000
 NVY  C7   C6   C5   110.72  3.000
 NVY  H8   C7   H7   106.45  3.000
 NVY  H8   C7   C6   109.53  3.000
 NVY  H7   C7   C6   109.18  3.000
 NVY  H8   C7   N1   108.61  3.000
 NVY  H7   C7   N1   111.53  3.000
 NVY  C6   C7   N1   111.39  3.000
 NVY  N2   C8   C9   124.13  3.000
 NVY  C9   C8   C13  115.89  3.000
 NVY  N2   C8   C13  119.93  3.000
 NVY  H9   C10  C9   118.89  3.000
 NVY  H9   C10  C11  120.04  3.000
 NVY  C9   C10  C11  121.07  3.000
 NVY  F1   C13  C12  119.08  3.000
 NVY  C12  C13  C8   123.59  3.000
 NVY  F1   C13  C8   117.33  3.000
 NVY  H12  C1   H11  108.01  3.000
 NVY  H12  C1   H10  107.05  3.000
 NVY  H11  C1   H10  108.16  3.000
 NVY  H12  C1   C2   109.87  3.000
 NVY  H11  C1   C2   110.77  3.000
 NVY  H10  C1   C2   112.81  3.000
 NVY  H13  C11  C12  120.08  3.000
 NVY  H13  C11  C10  121.04  3.000
 NVY  C12  C11  C10  118.89  3.000
 NVY  H14  C12  C11  121.16  3.000
 NVY  H14  C12  C13  119.53  3.000
 NVY  C11  C12  C13  119.31  3.000
 NVY  H16  C2   H15  105.99  3.000
 NVY  H16  C2   C1   109.62  3.000
 NVY  H15  C2   C1   108.42  3.000
 NVY  H16  C2   N1   111.49  3.000
 NVY  H15  C2   N1   107.37  3.000
 NVY  C1   C2   N1   113.61  3.000
 NVY  H18  C3   H17  106.43  3.000
 NVY  H18  C3   C4   109.25  3.000
 NVY  H17  C3   C4   108.66  3.000
 NVY  H18  C3   N1   111.16  3.000
 NVY  H17  C3   N1   109.54  3.000
 NVY  C4   C3   N1   111.63  3.000
 NVY  H19  C9   C10  118.80  3.000
 NVY  H19  C9   C8   119.96  3.000
 NVY  C10  C9   C8   121.25  3.000
 NVY  H20  N2   C8   114.60  3.000
 NVY  H20  N2   C5   113.46  3.000
 NVY  C8   N2   C5   122.36  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
 NVY  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 NVY  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 NVY  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 NVY  CONST_04  C13  C8   C9   C10     0.00   0.0  0
 NVY  CONST_05  C9   C8   C13  C12     0.00   0.0  0
 NVY  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 NVY  CONST_07  N2   C8   C9   C10   180.00   0.0  0
 NVY  CONST_08  F1   C13  C12  C11   180.00   0.0  0
 NVY  CONST_09  N2   C8   C13  C12   180.00   0.0  0
 NVY  CONST_10  F1   C13  C8   C9    180.00   0.0  0
 NVY  CONST_13  H14  C12  C13  C8    180.00   0.0  0
 NVY  CONST_14  H9   C10  C9   C8    180.00   0.0  0
 NVY  CONST_15  H13  C11  C12  C13   180.00   0.0  0
 NVY  CONST_16  H19  C9   C8   C13   180.00   0.0  0
 NVY  Var_01    C5   C4   C3   N1    -56.78  30.0  1
 NVY  Var_02    C5   C6   C7   N1     57.68  30.0  1
 NVY  Var_03    C7   N1   C3   C4     59.02  30.0  1
 NVY  Var_04    C3   N1   C7   C6    -59.54  30.0  1
 NVY  Var_05    C1   C2   N1   C7   -165.97  30.0  3
 NVY  Var_06    H10  C1   C2   N1    -66.69  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
 NVY  chir_01  C5  N2  C4  C6  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
 NVY  plan-1  C8   0.020
 NVY  plan-1  C10  0.020
 NVY  plan-1  C13  0.020
 NVY  plan-1  C11  0.020
 NVY  plan-1  C12  0.020
 NVY  plan-1  C9   0.020
 NVY  plan-1  F1   0.020
 NVY  plan-1  N2   0.020
 NVY  plan-1  H9   0.020
 NVY  plan-1  H13  0.020
 NVY  plan-1  H14  0.020
 NVY  plan-1  H19  0.020
 NVY  plan-2  C5   0.020
 NVY  plan-2  C8   0.020
 NVY  plan-2  N2   0.020
 NVY  plan-2  H20  0.020

