# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:31:15 2021
#   Inital geometry file: a 96 line input string
#   Ligand name: 2,6-dichloro-N-[1-(propan-2-yl)piperidin-4-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N1CCC(CC1)NC(=O)c2c(Cl)cccc2Cl
#
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
 R3P  R3P  2,6-dichloro-N-[1-(propan-2-yl)piperidin-4-yl]benzamide  ligand  40  20  .  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_R3P
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
 R3P  CL1  CL  CL    0  -0.103  -11.2578  -16.5799  -4.9211
 R3P  C14  C   CR6   0  -0.092   -9.6918  -16.9903  -5.5321
 R3P  C13  C   CR16  0  -0.192   -9.4201  -16.8083  -6.8783
 R3P  C12  C   CR16  0  -0.278   -8.1632  -17.1407  -7.3598
 R3P  C11  C   CR16  0  -0.192   -7.1906  -17.6505  -6.5134
 R3P  C10  C   CR6   0  -0.090   -7.4926  -17.8213  -5.1725
 R3P  CL   CL  CL    0  -0.103   -6.2864  -18.4575  -4.1070
 R3P  C9   C   CR6   0   0.105   -8.7423  -17.5016  -4.6572
 R3P  C8   C   C     0   0.486   -9.0252  -17.6304  -3.1830
 R3P  O    O   O     0  -0.462   -8.7959  -16.6994  -2.4297
 R3P  N1   N   NH1   0  -0.618   -9.5232  -18.8169  -2.8340
 R3P  C5   C   CH1   0  -0.033   -9.8159  -19.2460  -1.4743
 R3P  C4   C   CH2   0  -0.491  -10.8524  -18.3873  -0.7592
 R3P  C3   C   CH2   0  -0.285  -11.2769  -19.0824   0.5436
 R3P  C6   C   CH2   0  -0.458   -8.5519  -19.3880  -0.6096
 R3P  C7   C   CH2   0  -0.344   -8.9024  -19.1815   0.8684
 R3P  N    N   NT    0  -0.419  -10.1798  -19.7460   1.2591
 R3P  C1   C   CH1   0  -0.072  -10.2766  -21.2087   1.2580
 R3P  C2   C   CH3   0  -0.649  -11.4458  -21.6489   2.1364
 R3P  C    C   CH3   0  -0.691   -9.0052  -21.8753   1.7721
 R3P  H1   H   HCR6  0   0.290  -10.1774  -16.4128  -7.5407
 R3P  H2   H   HCR6  0   0.284   -7.9396  -17.0018  -8.4086
 R3P  H3   H   HCR6  0   0.291   -6.2117  -17.9107  -6.8910
 R3P  H4   H   HNH1  0   0.411   -9.6279  -19.5072  -3.5600
 R3P  H5   H   HCH1  0   0.254  -10.2603  -20.2359  -1.6021
 R3P  H6   H   HCH2  0   0.240  -10.4496  -17.3946  -0.5576
 R3P  H7   H   HCH2  0   0.244  -11.7314  -18.2488  -1.3920
 R3P  H8   H   HCH2  0   0.225  -11.7666  -18.3482   1.1922
 R3P  H9   H   HCH2  0   0.226  -12.0404  -19.8245   0.3005
 R3P  H10  H   HCH2  0   0.230   -8.1110  -20.3734  -0.7758
 R3P  H11  H   HCH2  0   0.242   -7.7969  -18.6558  -0.9009
 R3P  H12  H   HCH2  0   0.250   -8.1066  -19.5662   1.5060
 R3P  H13  H   HCH2  0   0.241   -8.9431  -18.1094   1.0795
 R3P  H15  H   HCH1  0   0.192  -10.4604  -21.5944   0.2393
 R3P  H16  H   HCH3  0   0.221  -11.5636  -22.7328   2.0966
 R3P  H17  H   HCH3  0   0.215  -11.2686  -21.3624   3.1752
 R3P  H18  H   HCH3  0   0.230  -12.3940  -21.2089   1.8273
 R3P  H19  H   HCH3  0   0.234   -8.1569  -21.7499   1.0994
 R3P  H20  H   HCH3  0   0.224   -8.7259  -21.4863   2.7535
 R3P  H21  H   HCH3  0   0.237   -9.1758  -22.9471   1.8758

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
 R3P  C12  C11  aromatic  1.387  0.020  1.387
 R3P  C12  C13  aromatic  1.386  0.020  1.386
 R3P  C11  C10  aromatic  1.385  0.020  1.385
 R3P  C13  C14  aromatic  1.385  0.020  1.385
 R3P  C10  CL   single    1.731  0.020  1.731
 R3P  C10  C9   aromatic  1.389  0.020  1.389
 R3P  C14  C9   aromatic  1.389  0.020  1.389
 R3P  C14  CL1  single    1.730  0.020  1.730
 R3P  C9   C8   single    1.507  0.020  1.507
 R3P  C8   N1   single    1.333  0.020  1.333
 R3P  C8   O    double    1.219  0.020  1.219
 R3P  N1   C5   single    1.455  0.020  1.455
 R3P  C5   C4   single    1.524  0.020  1.524
 R3P  C5   C6   single    1.538  0.020  1.538
 R3P  C4   C3   single    1.536  0.020  1.536
 R3P  C6   C7   single    1.533  0.020  1.533
 R3P  C3   N    single    1.468  0.020  1.468
 R3P  C7   N    single    1.450  0.020  1.450
 R3P  C2   C1   single    1.527  0.020  1.527
 R3P  N    C1   single    1.466  0.020  1.466
 R3P  C1   C    single    1.525  0.020  1.525
 R3P  C13  H1   single    0.930  0.020  1.080
 R3P  C12  H2   single    0.930  0.020  1.080
 R3P  C11  H3   single    0.930  0.020  1.080
 R3P  N1   H4   single    0.860  0.020  1.020
 R3P  C5   H5   single    0.970  0.020  1.090
 R3P  C4   H6   single    0.970  0.020  1.090
 R3P  C4   H7   single    0.970  0.020  1.090
 R3P  C3   H8   single    0.970  0.020  1.090
 R3P  C3   H9   single    0.970  0.020  1.090
 R3P  C6   H10  single    0.970  0.020  1.090
 R3P  C6   H11  single    0.970  0.020  1.090
 R3P  C7   H12  single    0.970  0.020  1.090
 R3P  C7   H13  single    0.970  0.020  1.090
 R3P  C1   H15  single    0.970  0.020  1.090
 R3P  C2   H16  single    0.970  0.020  1.090
 R3P  C2   H17  single    0.970  0.020  1.090
 R3P  C2   H18  single    0.970  0.020  1.090
 R3P  C    H19  single    0.970  0.020  1.090
 R3P  C    H20  single    0.970  0.020  1.090
 R3P  C    H21  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
 R3P  C9   C14  C13  121.77  3.000
 R3P  C9   C14  CL1  118.92  3.000
 R3P  C13  C14  CL1  119.31  3.000
 R3P  H1   C13  C12  120.66  3.000
 R3P  H1   C13  C14  120.40  3.000
 R3P  C12  C13  C14  118.94  3.000
 R3P  H2   C12  C11  119.62  3.000
 R3P  H2   C12  C13  119.58  3.000
 R3P  C11  C12  C13  120.80  3.000
 R3P  H3   C11  C10  120.40  3.000
 R3P  H3   C11  C12  120.70  3.000
 R3P  C10  C11  C12  118.90  3.000
 R3P  C9   C10  CL   118.89  3.000
 R3P  C9   C10  C11  121.81  3.000
 R3P  CL   C10  C11  119.30  3.000
 R3P  C8   C9   C10  120.82  3.000
 R3P  C8   C9   C14  121.30  3.000
 R3P  C10  C9   C14  117.78  3.000
 R3P  N1   C8   O    126.02  3.000
 R3P  O    C8   C9   120.26  3.000
 R3P  N1   C8   C9   113.73  3.000
 R3P  H4   N1   C5   116.76  3.000
 R3P  H4   N1   C8   117.39  3.000
 R3P  C5   N1   C8   125.59  3.000
 R3P  H5   C5   C6   108.45  3.000
 R3P  H5   C5   C4   106.78  3.000
 R3P  C6   C5   C4   110.31  3.000
 R3P  H5   C5   N1   103.87  3.000
 R3P  C6   C5   N1   112.78  3.000
 R3P  C4   C5   N1   114.14  3.000
 R3P  H7   C4   H6   106.80  3.000
 R3P  H7   C4   C3   109.05  3.000
 R3P  H6   C4   C3   110.94  3.000
 R3P  H7   C4   C5   110.30  3.000
 R3P  H6   C4   C5   110.40  3.000
 R3P  C3   C4   C5   109.32  3.000
 R3P  H9   C3   H8   105.95  3.000
 R3P  H9   C3   N    108.89  3.000
 R3P  H8   C3   N    110.39  3.000
 R3P  H9   C3   C4   108.17  3.000
 R3P  H8   C3   C4   108.80  3.000
 R3P  N    C3   C4   114.28  3.000
 R3P  H11  C6   H10  106.58  3.000
 R3P  H11  C6   C7   108.98  3.000
 R3P  H10  C6   C7   111.14  3.000
 R3P  H11  C6   C5   110.89  3.000
 R3P  H10  C6   C5   109.23  3.000
 R3P  C7   C6   C5   109.98  3.000
 R3P  H13  C7   H12  105.09  3.000
 R3P  H13  C7   N    107.27  3.000
 R3P  H12  C7   N    110.37  3.000
 R3P  H13  C7   C6   109.08  3.000
 R3P  H12  C7   C6   110.46  3.000
 R3P  N    C7   C6   114.13  3.000
 R3P  C1   N    C7   116.51  3.000
 R3P  C1   N    C3   113.66  3.000
 R3P  C7   N    C3   110.54  3.000
 R3P  H15  C1   C    107.28  3.000
 R3P  H15  C1   C2   107.60  3.000
 R3P  C    C1   C2   108.57  3.000
 R3P  H15  C1   N    111.10  3.000
 R3P  C    C1   N    112.39  3.000
 R3P  C2   C1   N    109.74  3.000
 R3P  H18  C2   H17  107.76  3.000
 R3P  H18  C2   H16  107.26  3.000
 R3P  H17  C2   H16  108.23  3.000
 R3P  H18  C2   C1   112.74  3.000
 R3P  H17  C2   C1   110.32  3.000
 R3P  H16  C2   C1   110.37  3.000
 R3P  H21  C    H20  107.74  3.000
 R3P  H21  C    H19  107.07  3.000
 R3P  H20  C    H19  108.34  3.000
 R3P  H21  C    C1   109.35  3.000
 R3P  H20  C    C1   111.13  3.000
 R3P  H19  C    C1   112.99  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
 R3P  CONST_01  C11  C12  C13  C14    0.00   0.0  0
 R3P  CONST_02  C11  C10  C9   C14    0.00   0.0  0
 R3P  CONST_03  C10  C11  C12  C13    0.00   0.0  0
 R3P  CONST_04  C10  C9   C14  C13    0.00   0.0  0
 R3P  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 R3P  CONST_06  C9   C14  C13  C12    0.00   0.0  0
 R3P  CONST_07  C12  C13  C14  CL1  180.00   0.0  0
 R3P  CONST_08  C10  C9   C14  CL1  180.00   0.0  0
 R3P  CONST_09  CL   C10  C9   C14  180.00   0.0  0
 R3P  CONST_10  C8   C9   C14  C13  180.00   0.0  0
 R3P  CONST_11  CL   C10  C11  C12  180.00   0.0  0
 R3P  CONST_12  C8   C9   C10  C11  180.00   0.0  0
 R3P  CONST_13  H2   C12  C13  C14  180.00   0.0  0
 R3P  CONST_14  H3   C11  C12  C13  180.00   0.0  0
 R3P  CONST_15  H1   C13  C12  C11  180.00   0.0  0
 R3P  CONST_16  C5   N1   C8   C9   180.00   0.0  0
 R3P  CONST_17  C5   N1   C8   O      0.00   0.0  0
 R3P  CONST_18  H4   N1   C8   C9     0.00   0.0  0
 R3P  Var_01    N    C3   C4   C5    38.83  30.0  1
 R3P  Var_02    N    C7   C6   C5    37.98  30.0  1
 R3P  Var_03    C7   N    C3   C4    21.85  30.0  1
 R3P  Var_04    C6   C7   N    C3   -63.49  30.0  1
 R3P  Var_05    N1   C8   C9   C14   92.06  30.0  2
 R3P  Var_06    C2   C1   N    C3   -69.85  30.0  3
 R3P  Var_07    H16  C2   C1   N    176.70  30.0  3
 R3P  Var_08    H19  C    C1   N    -68.32  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
 R3P  chir_01  C5  N1  C4  C6  positiv

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
 R3P  plan-1  CL1  0.020
 R3P  plan-1  C14  0.020
 R3P  plan-1  C13  0.020
 R3P  plan-1  C12  0.020
 R3P  plan-1  C11  0.020
 R3P  plan-1  C10  0.020
 R3P  plan-1  CL   0.020
 R3P  plan-1  C9   0.020
 R3P  plan-1  C8   0.020
 R3P  plan-1  H1   0.020
 R3P  plan-1  H2   0.020
 R3P  plan-1  H3   0.020
 R3P  plan-2  C9   0.020
 R3P  plan-2  C8   0.020
 R3P  plan-2  O    0.020
 R3P  plan-2  N1   0.020
 R3P  plan-2  C5   0.020
 R3P  plan-2  H4   0.020

