# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 09:12:23 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: ~{N}-(3-chlorophenyl)-2-[(2~{R})-1-ethanoyl-3-oxidanylidene-piperazin-2-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCNC(=O)[C@H]1CC(=O)Nc2cccc(Cl)c2
#
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
 80X  80X  "N-(3-chlorophenyl)-2-[(2R)-1-ethanoyl-3-oxidanylidene-piperazin-2-yl]ethanamide"
  ligand  37  21  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_80X
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
 80X  N1   N   NT    0  -0.468  24.1911  -3.6527   9.6835
 80X  N3   N   NH1   0  -0.745  25.4735  -2.6789  14.2223
 80X  C4   C   C     0   0.565  24.7559  -5.1915  11.5471
 80X  C5   C   CH2   0  -0.583  24.8519  -2.7239  11.8848
 80X  C6   C   C     0   0.562  24.4405  -2.6978  13.3417
 80X  C7   C   CR6   0   0.373  25.4431  -2.6344  15.6159
 80X  C8   C   CR16  0  -0.338  26.6693  -2.7410  16.2788
 80X  C10  C   CR16  0  -0.240  25.5738  -2.5490  18.4181
 80X  C13  C   C     0   0.525  23.1925  -3.0554   8.9795
 80X  C1   C   CH1   0  -0.219  24.1544  -3.8575  11.1139
 80X  C11  C   CR6   0  -0.020  24.3692  -2.4415  17.7464
 80X  C12  C   CR16  0  -0.281  24.2749  -2.4816  16.3637
 80X  C14  C   CH3   0  -0.816  21.9770  -2.6038   9.7537
 80X  C2   C   CH2   0  -0.355  25.3751  -4.1599   9.0232
 80X  C3   C   CH2   0  -0.254  25.4250  -5.6595   9.2028
 80X  C9   C   CR16  0  -0.246  26.7268  -2.6990  17.6591
 80X  N2   N   NH1   0  -0.626  25.2856  -5.9822  10.6091
 80X  O1   O   O     0  -0.481  24.7360  -5.4808  12.7358
 80X  O2   O   O     0  -0.460  23.2676  -2.6474  13.6631
 80X  O3   O   O     0  -0.482  23.2657  -2.8981   7.7711
 80X  CL1  CL  CL    0  -0.127  22.9077  -2.2429  18.6601
 80X  H1   H   HNH1  0   0.419  26.3969  -2.7565  13.8244
 80X  H2   H   HCH2  0   0.281  25.9345  -2.7806  11.7551
 80X  H3   H   HCH2  0   0.300  24.5335  -1.7711  11.4538
 80X  H4   H   HCR6  0   0.276  27.5823  -2.8584  15.7074
 80X  H5   H   HCR6  0   0.277  25.6176  -2.5163  19.4977
 80X  H6   H   HCH1  0   0.319  23.1141  -3.9024  11.4388
 80X  H7   H   HCR6  0   0.301  23.3130  -2.3920  15.8880
 80X  H8   H   HCH3  0   0.275  21.3233  -2.0470   9.0878
 80X  H9   H   HCH3  0   0.273  21.4180  -3.4584  10.1397
 80X  H10  H   HCH3  0   0.265  22.2253  -1.9670  10.6033
 80X  H11  H   HCH2  0   0.264  26.2683  -3.6955   9.4520
 80X  H12  H   HCH2  0   0.284  25.3446  -3.9064   7.9681
 80X  H13  H   HCH2  0   0.247  24.6353  -6.1360   8.6162
 80X  H14  H   HCH2  0   0.262  26.3808  -6.0466   8.8499
 80X  H15  H   HCR6  0   0.270  27.6847  -2.7844  18.1545
 80X  H16  H   HNH1  0   0.404  25.6400  -6.8738  10.9248

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
 80X  O3   C13  double    1.221  0.020  1.221
 80X  C3   C2   single    1.511  0.020  1.511
 80X  C3   N2   single    1.450  0.020  1.450
 80X  C2   N1   single    1.448  0.020  1.448
 80X  C13  N1   single    1.360  0.020  1.360
 80X  C13  C14  single    1.510  0.020  1.510
 80X  N1   C1   single    1.445  0.020  1.445
 80X  N2   C4   single    1.336  0.020  1.336
 80X  C1   C4   single    1.526  0.020  1.526
 80X  C1   C5   single    1.538  0.020  1.538
 80X  C4   O1   double    1.224  0.020  1.224
 80X  C5   C6   single    1.514  0.020  1.514
 80X  C6   O2   double    1.217  0.020  1.217
 80X  C6   N3   single    1.357  0.020  1.357
 80X  N3   C7   single    1.395  0.020  1.395
 80X  C7   C12  aromatic  1.395  0.020  1.395
 80X  C7   C8   aromatic  1.398  0.020  1.398
 80X  C12  C11  aromatic  1.387  0.020  1.387
 80X  C8   C9   aromatic  1.382  0.020  1.382
 80X  C11  C10  aromatic  1.383  0.020  1.383
 80X  C11  CL1  single    1.735  0.020  1.735
 80X  C9   C10  aromatic  1.388  0.020  1.388
 80X  N3   H1   single    0.860  0.020  1.020
 80X  C5   H2   single    0.970  0.020  1.090
 80X  C5   H3   single    0.970  0.020  1.090
 80X  C8   H4   single    0.930  0.020  1.080
 80X  C10  H5   single    0.930  0.020  1.080
 80X  C1   H6   single    0.970  0.020  1.090
 80X  C12  H7   single    0.930  0.020  1.080
 80X  C14  H8   single    0.970  0.020  1.090
 80X  C14  H9   single    0.970  0.020  1.090
 80X  C14  H10  single    0.970  0.020  1.090
 80X  C2   H11  single    0.970  0.020  1.090
 80X  C2   H12  single    0.970  0.020  1.090
 80X  C3   H13  single    0.970  0.020  1.090
 80X  C3   H14  single    0.970  0.020  1.090
 80X  C9   H15  single    0.930  0.020  1.080
 80X  N2   H16  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
 80X  C2   N1   C1   114.99  3.000
 80X  C1   N1   C13  123.78  3.000
 80X  C2   N1   C13  121.22  3.000
 80X  H1   N3   C7   114.62  3.000
 80X  H1   N3   C6   116.09  3.000
 80X  C7   N3   C6   129.20  3.000
 80X  O1   C4   N2   123.26  3.000
 80X  O1   C4   C1   118.43  3.000
 80X  N2   C4   C1   118.30  3.000
 80X  H3   C5   H2   106.69  3.000
 80X  H3   C5   C1   108.22  3.000
 80X  H2   C5   C1   110.60  3.000
 80X  H3   C5   C6   106.57  3.000
 80X  H2   C5   C6   112.62  3.000
 80X  C1   C5   C6   111.83  3.000
 80X  O2   C6   C5   121.11  3.000
 80X  O2   C6   N3   124.15  3.000
 80X  C5   C6   N3   114.69  3.000
 80X  C12  C7   C8   119.25  3.000
 80X  C8   C7   N3   116.89  3.000
 80X  C12  C7   N3   123.86  3.000
 80X  H4   C8   C9   119.67  3.000
 80X  H4   C8   C7   119.82  3.000
 80X  C9   C8   C7   120.51  3.000
 80X  H5   C10  C9   121.04  3.000
 80X  H5   C10  C11  121.19  3.000
 80X  C9   C10  C11  117.77  3.000
 80X  O3   C13  C14  121.14  3.000
 80X  C14  C13  N1   117.19  3.000
 80X  O3   C13  N1   121.67  3.000
 80X  H6   C1   C5   108.27  3.000
 80X  H6   C1   C4   104.79  3.000
 80X  C5   C1   C4   108.86  3.000
 80X  H6   C1   N1   108.95  3.000
 80X  C5   C1   N1   112.34  3.000
 80X  C4   C1   N1   113.25  3.000
 80X  CL1  C11  C12  118.11  3.000
 80X  CL1  C11  C10  119.12  3.000
 80X  C12  C11  C10  122.77  3.000
 80X  H7   C12  C11  119.92  3.000
 80X  H7   C12  C7   121.35  3.000
 80X  C11  C12  C7   118.73  3.000
 80X  H10  C14  H9   107.36  3.000
 80X  H10  C14  H8   108.37  3.000
 80X  H9   C14  H8   108.05  3.000
 80X  H10  C14  C13  113.00  3.000
 80X  H9   C14  C13  111.06  3.000
 80X  H8   C14  C13  108.86  3.000
 80X  H12  C2   H11  107.74  3.000
 80X  H12  C2   C3   110.38  3.000
 80X  H11  C2   C3   110.34  3.000
 80X  H12  C2   N1   109.79  3.000
 80X  H11  C2   N1   109.89  3.000
 80X  C3   C2   N1   108.69  3.000
 80X  H14  C3   H13  107.76  3.000
 80X  H14  C3   N2   108.63  3.000
 80X  H13  C3   N2   110.74  3.000
 80X  H14  C3   C2   110.05  3.000
 80X  H13  C3   C2   110.18  3.000
 80X  N2   C3   C2   109.45  3.000
 80X  H15  C9   C10  119.57  3.000
 80X  H15  C9   C8   119.45  3.000
 80X  C10  C9   C8   120.98  3.000
 80X  H16  N2   C3   117.78  3.000
 80X  H16  N2   C4   116.23  3.000
 80X  C3   N2   C4   125.98  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
 80X  CONST_01  C10  C11  C12  C7      0.00   0.0  0
 80X  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 80X  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 80X  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 80X  CONST_05  C9   C8   C7   C12     0.00   0.0  0
 80X  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 80X  CONST_07  C3   N2   C4   C1      0.00   0.0  0
 80X  CONST_08  C11  C12  C7   N3    180.00   0.0  0
 80X  CONST_09  C9   C8   C7   N3    180.00   0.0  0
 80X  CONST_10  CL1  C11  C12  C7    180.00   0.0  0
 80X  CONST_11  CL1  C11  C10  C9    180.00   0.0  0
 80X  CONST_12  O1   C4   N2   C3    180.00   0.0  0
 80X  CONST_13  H15  C9   C8   C7    180.00   0.0  0
 80X  CONST_14  H7   C12  C7   C8    180.00   0.0  0
 80X  CONST_15  H5   C10  C9   C8    180.00   0.0  0
 80X  CONST_16  H7   C12  C11  C10   180.00   0.0  0
 80X  CONST_17  H4   C8   C9   C10   180.00   0.0  0
 80X  CONST_18  H15  C9   C10  C11   180.00   0.0  0
 80X  CONST_19  H4   C8   C7   C12   180.00   0.0  0
 80X  CONST_20  H5   C10  C11  C12   180.00   0.0  0
 80X  CONST_21  H16  N2   C4   C1    180.00   0.0  0
 80X  CONST_22  O3   C13  N1   C1    180.00   0.0  0
 80X  CONST_23  C14  C13  N1   C1      0.00   0.0  0
 80X  CONST_24  C2   N1   C13  C14   180.00   0.0  0
 80X  CONST_25  O3   C13  N1   C2      0.00   0.0  0
 80X  CONST_26  C12  C7   N3   C6      0.00   0.0  0
 80X  CONST_27  C8   C7   N3   C6    180.00   0.0  0
 80X  CONST_28  H1   N3   C7   C8      0.00   0.0  0
 80X  CONST_29  H1   N3   C7   C12   180.00   0.0  0
 80X  CONST_30  H16  N2   C4   O1      0.00   0.0  0
 80X  CONST_31  C7   N3   C6   C5    180.00   0.0  0
 80X  CONST_32  O2   C6   N3   C7      0.00   0.0  0
 80X  CONST_33  H1   N3   C6   C5      0.00   0.0  0
 80X  CONST_34  H1   N3   C6   O2    180.00   0.0  0
 80X  Var_01    N2   C3   C2   N1    -51.99  30.0  1
 80X  Var_02    C2   C3   N2   C4     20.98  30.0  1
 80X  Var_03    C3   C2   N1   C1     62.77  30.0  1
 80X  Var_04    C3   C2   N1   C13  -116.03  30.0  1
 80X  Var_05    H13  C3   C2   N1     70.01  30.0  1
 80X  Var_06    H14  C3   C2   N1   -171.31  30.0  1
 80X  Var_07    H13  C3   N2   C4   -100.68  30.0  1
 80X  Var_08    H14  C3   N2   C4    141.17  30.0  1
 80X  Var_09    H11  C2   N1   C1    -58.07  30.0  1
 80X  Var_10    H12  C2   N1   C1   -176.40  30.0  1
 80X  Var_11    H16  N2   C3   C2   -157.28  30.0  1
 80X  Var_12    H11  C2   C3   N2     68.57  30.0  1
 80X  Var_13    H12  C2   C3   N2   -172.45  30.0  1
 80X  Var_14    H11  C2   N1   C13   123.13  30.0  1
 80X  Var_15    H12  C2   N1   C13     4.80  30.0  1
 80X  Var_16    C1   C5   C6   N3    128.50  30.0  1
 80X  Var_17    O2   C6   C5   C1    -54.09  30.0  3
 80X  Var_18    H8   C14  C13  N1    173.46  30.0  3
 80X  Var_19    H9   C14  C13  N1    -67.70  30.0  3
 80X  Var_20    H10  C14  C13  N1     53.01  30.0  3
 80X  Var_21    H2   C5   C6   N3      3.23  30.0  1
 80X  Var_22    H3   C5   C6   N3   -113.42  30.0  1
 80X  Var_23    H2   C5   C6   O2   -179.36  30.0  1
 80X  Var_24    H3   C5   C6   O2     63.98  30.0  1
 80X  Var_25    H8   C14  C13  O3     -7.11  30.0  3
 80X  Var_26    H9   C14  C13  O3    111.73  30.0  3
 80X  Var_27    H10  C14  C13  O3   -127.56  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
 80X  chir_01  C1  N1  C4  C5  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
 80X  plan-1  N3   0.020
 80X  plan-1  C7   0.020
 80X  plan-1  C8   0.020
 80X  plan-1  C10  0.020
 80X  plan-1  C11  0.020
 80X  plan-1  C12  0.020
 80X  plan-1  C9   0.020
 80X  plan-1  CL1  0.020
 80X  plan-1  H4   0.020
 80X  plan-1  H5   0.020
 80X  plan-1  H7   0.020
 80X  plan-1  H15  0.020
 80X  plan-2  N3   0.020
 80X  plan-2  C5   0.020
 80X  plan-2  C6   0.020
 80X  plan-2  C7   0.020
 80X  plan-2  O2   0.020
 80X  plan-2  H1   0.020
 80X  plan-3  N1   0.020
 80X  plan-3  C13  0.020
 80X  plan-3  C1   0.020
 80X  plan-3  C14  0.020
 80X  plan-3  C2   0.020
 80X  plan-3  O3   0.020
 80X  plan-4  C4   0.020
 80X  plan-4  C1   0.020
 80X  plan-4  C3   0.020
 80X  plan-4  N2   0.020
 80X  plan-4  O1   0.020
 80X  plan-4  H16  0.020

