# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:22:44 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 4-chloro-5-cyano-N-{2-[4-(4-fluorobenzoyl)piperidin-1-yl]ethyl}-2-methoxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(Cl)c(cc1C(=O)NCCN2CCC(CC2)C(=O)c3ccc(F)cc3)C#N
#
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
 1XP  1XP  4-chloro-5-cyano-N-{2-[4-(4-fluorobenzoyl)piperidin-1-yl]ethyl}-2-methoxybenzamide  ligand  54  31  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1XP
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
 1XP  C1   C   CR6   0  -0.158    4.5083  -0.3536  -0.4545
 1XP  C2   C   CR6   0   0.417    5.6437  -1.0398   0.0125
 1XP  C3   C   CR16  0  -0.252    4.5812   1.0047  -0.6760
 1XP  C4   C   C     0   0.523    3.2450  -1.0966  -0.7748
 1XP  C5   C   CR16  0  -0.333    6.8307  -0.3435   0.2420
 1XP  O1   O   O2    0  -0.442    5.5010  -2.3390   0.2365
 1XP  C6   C   CR6   0   0.068    5.7673   1.7107  -0.4616
 1XP  N1   N   NH1   0  -0.626    2.1633  -0.6356  -0.1342
 1XP  O2   O   O     0  -0.474    3.2304  -2.0108  -1.5829
 1XP  C7   C   CR6   0  -0.036    6.8829   1.0152  -0.0010
 1XP  C8   C   CH3   0  -0.450    6.5929  -3.0834   0.7592
 1XP  C9   C   CSP   0   0.044    5.8211   3.1079  -0.7138
 1XP  C10  C   CH2   0  -0.273    0.8244  -1.1463  -0.3400
 1XP  CL1  CL  CL    0  -0.072    8.3545   1.8590   0.2752
 1XP  N2   N   NS    0  -0.241    5.8443   4.2403  -0.9274
 1XP  C11  C   CH2   0  -0.292   -0.1816  -0.0234  -0.1124
 1XP  N3   N   NT    0  -0.422   -1.5502  -0.4522  -0.3136
 1XP  C12  C   CH2   0  -0.276   -2.4286   0.6911  -0.4952
 1XP  C13  C   CH2   0  -0.297   -2.0310  -1.3030   0.7631
 1XP  C14  C   CH2   0  -0.434   -3.8495   0.2614  -0.8217
 1XP  C15  C   CH2   0  -0.412   -3.4298  -1.8244   0.4726
 1XP  C16  C   CH1   0  -0.421   -4.3936  -0.6610   0.2796
 1XP  C17  C   C     0   0.416   -5.7978  -1.1043  -0.0610
 1XP  C18  C   CR6   0  -0.022   -6.9078  -0.1135   0.0439
 1XP  O3   O   O     0  -0.396   -6.0275  -2.2323  -0.4456
 1XP  C19  C   CR16  0  -0.246   -8.1547  -0.4417  -0.4946
 1XP  C20  C   CR16  0  -0.275   -6.7541   1.1252   0.6674
 1XP  C21  C   CR16  0  -0.398   -9.2192   0.4378  -0.4211
 1XP  C22  C   CR16  0  -0.398   -7.8114   2.0162   0.7577
 1XP  C23  C   CR6   0   0.537   -9.0261   1.6548   0.2080
 1XP  F1   F   F     0  -0.305  -10.0505   2.5112   0.2857
 1XP  H1   H   HCR6  0   0.298    3.7134   1.5399  -1.0389
 1XP  H2   H   HCR6  0   0.319    7.7150  -0.8441   0.6078
 1XP  H3   H   HNH1  0   0.410    2.2971   0.0355   0.6067
 1XP  H4   H   HCH3  0   0.245    7.4469  -3.0747   0.0795
 1XP  H5   H   HCH3  0   0.245    6.9025  -2.7073   1.7361
 1XP  H6   H   HCH3  0   0.274    6.2366  -4.1033   0.8681
 1XP  H7   H   HCH2  0   0.250    0.7373  -1.5133  -1.3616
 1XP  H8   H   HCH2  0   0.245    0.6400  -1.9912   0.3286
 1XP  H9   H   HCH2  0   0.201   -0.0319   0.4083   0.8932
 1XP  H10  H   HCH2  0   0.246    0.0379   0.7717  -0.8290
 1XP  H12  H   HCH2  0   0.193   -2.4448   1.3325   0.4039
 1XP  H13  H   HCH2  0   0.245   -2.0403   1.3026  -1.3124
 1XP  H14  H   HCH2  0   0.246   -1.3571  -2.1516   0.8843
 1XP  H15  H   HCH2  0   0.192   -2.0325  -0.7603   1.7259
 1XP  H16  H   HCH2  0   0.252   -4.4713   1.1507  -0.9369
 1XP  H17  H   HCH2  0   0.237   -3.8590  -0.2696  -1.7779
 1XP  H18  H   HCH2  0   0.228   -3.4040  -2.4470  -0.4243
 1XP  H19  H   HCH2  0   0.242   -3.7515  -2.4591   1.3005
 1XP  H20  H   HCH1  0   0.259   -4.4229  -0.0878   1.2141
 1XP  H21  H   HCR6  0   0.272   -8.2956  -1.3961  -0.9838
 1XP  H22  H   HCR6  0   0.272   -5.8081   1.4173   1.1019
 1XP  H23  H   HCR6  0   0.288  -10.1822   0.1846  -0.8447
 1XP  H24  H   HCR6  0   0.289   -7.6912   2.9734   1.2474

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
 1XP  O1   C8   single    1.421  0.020  1.421
 1XP  O1   C2   single    1.326  0.020  1.326
 1XP  C5   C2   aromatic  1.395  0.020  1.395
 1XP  C5   C7   aromatic  1.381  0.020  1.381
 1XP  C2   C1   aromatic  1.406  0.020  1.406
 1XP  CL1  C7   single    1.719  0.020  1.719
 1XP  N1   C10  single    1.448  0.020  1.448
 1XP  N1   C4   single    1.339  0.020  1.339
 1XP  C10  C11  single    1.525  0.020  1.525
 1XP  C7   C6   aromatic  1.393  0.020  1.393
 1XP  C1   C4   single    1.500  0.020  1.500
 1XP  C1   C3   aromatic  1.378  0.020  1.378
 1XP  C4   O2   double    1.220  0.020  1.220
 1XP  C6   C3   aromatic  1.397  0.020  1.397
 1XP  C6   C9   single    1.421  0.020  1.421
 1XP  C9   N2   triple    1.153  0.020  1.153
 1XP  C11  N3   single    1.448  0.020  1.448
 1XP  C13  N3   single    1.454  0.020  1.454
 1XP  C13  C15  single    1.521  0.020  1.521
 1XP  N3   C12  single    1.453  0.020  1.453
 1XP  C15  C16  single    1.523  0.020  1.523
 1XP  C12  C14  single    1.520  0.020  1.520
 1XP  C16  C14  single    1.536  0.020  1.536
 1XP  C16  C17  single    1.511  0.020  1.511
 1XP  C20  C22  aromatic  1.386  0.020  1.386
 1XP  C20  C18  aromatic  1.395  0.020  1.395
 1XP  C22  C23  aromatic  1.381  0.020  1.381
 1XP  C17  C18  single    1.492  0.020  1.492
 1XP  C17  O3   double    1.214  0.020  1.214
 1XP  C18  C19  aromatic  1.397  0.020  1.397
 1XP  C23  F1   single    1.338  0.020  1.338
 1XP  C23  C21  aromatic  1.384  0.020  1.384
 1XP  C19  C21  aromatic  1.383  0.020  1.383
 1XP  C3   H1   single    0.930  0.020  1.080
 1XP  C5   H2   single    0.930  0.020  1.080
 1XP  N1   H3   single    0.860  0.020  1.020
 1XP  C8   H4   single    0.970  0.020  1.090
 1XP  C8   H5   single    0.970  0.020  1.090
 1XP  C8   H6   single    0.970  0.020  1.090
 1XP  C10  H7   single    0.970  0.020  1.090
 1XP  C10  H8   single    0.970  0.020  1.090
 1XP  C11  H9   single    0.970  0.020  1.090
 1XP  C11  H10  single    0.970  0.020  1.090
 1XP  C12  H12  single    0.970  0.020  1.090
 1XP  C12  H13  single    0.970  0.020  1.090
 1XP  C13  H14  single    0.970  0.020  1.090
 1XP  C13  H15  single    0.970  0.020  1.090
 1XP  C14  H16  single    0.970  0.020  1.090
 1XP  C14  H17  single    0.970  0.020  1.090
 1XP  C15  H18  single    0.970  0.020  1.090
 1XP  C15  H19  single    0.970  0.020  1.090
 1XP  C16  H20  single    0.970  0.020  1.090
 1XP  C19  H21  single    0.930  0.020  1.080
 1XP  C20  H22  single    0.930  0.020  1.080
 1XP  C21  H23  single    0.930  0.020  1.080
 1XP  C22  H24  single    0.930  0.020  1.080

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
 1XP  C4   C1   C3   119.89  3.000
 1XP  C3   C1   C2   119.45  3.000
 1XP  C4   C1   C2   120.60  3.000
 1XP  O1   C2   C5   123.56  3.000
 1XP  C5   C2   C1   119.86  3.000
 1XP  O1   C2   C1   116.57  3.000
 1XP  H1   C3   C6   118.85  3.000
 1XP  H1   C3   C1   119.93  3.000
 1XP  C6   C3   C1   121.22  3.000
 1XP  O2   C4   N1   124.41  3.000
 1XP  O2   C4   C1   121.50  3.000
 1XP  N1   C4   C1   114.05  3.000
 1XP  H2   C5   C7   118.99  3.000
 1XP  H2   C5   C2   121.40  3.000
 1XP  C7   C5   C2   119.61  3.000
 1XP  C8   O1   C2   119.51  3.000
 1XP  C9   C6   C7   121.29  3.000
 1XP  C9   C6   C3   120.13  3.000
 1XP  C7   C6   C3   118.58  3.000
 1XP  H3   N1   C10  117.50  3.000
 1XP  H3   N1   C4   118.26  3.000
 1XP  C10  N1   C4   123.89  3.000
 1XP  CL1  C7   C6   119.59  3.000
 1XP  C6   C7   C5   121.27  3.000
 1XP  CL1  C7   C5   119.14  3.000
 1XP  H6   C8   H5   109.08  3.000
 1XP  H6   C8   H4   109.07  3.000
 1XP  H5   C8   H4   109.43  3.000
 1XP  H6   C8   O1   106.07  3.000
 1XP  H5   C8   O1   111.50  3.000
 1XP  H4   C8   O1   111.59  3.000
 1XP  N2   C9   C6   180.00  3.000
 1XP  H8   C10  H7   107.44  3.000
 1XP  H8   C10  C11  111.51  3.000
 1XP  H7   C10  C11  109.60  3.000
 1XP  H8   C10  N1   109.98  3.000
 1XP  H7   C10  N1   109.04  3.000
 1XP  C11  C10  N1   109.22  3.000
 1XP  H10  C11  H9   106.59  3.000
 1XP  H10  C11  N3   108.31  3.000
 1XP  H9   C11  N3   111.74  3.000
 1XP  H10  C11  C10  107.78  3.000
 1XP  H9   C11  C10  109.53  3.000
 1XP  N3   C11  C10  112.62  3.000
 1XP  C13  N3   C12  110.67  3.000
 1XP  C12  N3   C11  110.83  3.000
 1XP  C13  N3   C11  112.51  3.000
 1XP  H13  C12  H12  106.81  3.000
 1XP  H13  C12  C14  109.26  3.000
 1XP  H12  C12  C14  108.99  3.000
 1XP  H13  C12  N3   108.61  3.000
 1XP  H12  C12  N3   111.35  3.000
 1XP  C14  C12  N3   111.68  3.000
 1XP  H15  C13  H14  106.63  3.000
 1XP  H15  C13  C15  109.48  3.000
 1XP  H14  C13  C15  108.83  3.000
 1XP  H15  C13  N3   110.99  3.000
 1XP  H14  C13  N3   109.47  3.000
 1XP  C15  C13  N3   111.31  3.000
 1XP  H17  C14  H16  107.36  3.000
 1XP  H17  C14  C16  109.40  3.000
 1XP  H16  C14  C16  111.29  3.000
 1XP  H17  C14  C12  109.46  3.000
 1XP  H16  C14  C12  108.96  3.000
 1XP  C16  C14  C12  110.29  3.000
 1XP  H19  C15  H18  107.36  3.000
 1XP  H19  C15  C16  110.72  3.000
 1XP  H18  C15  C16  110.26  3.000
 1XP  H19  C15  C13  109.00  3.000
 1XP  H18  C15  C13  109.30  3.000
 1XP  C16  C15  C13  110.14  3.000
 1XP  H20  C16  C17  108.69  3.000
 1XP  H20  C16  C15  107.95  3.000
 1XP  C17  C16  C15  113.10  3.000
 1XP  H20  C16  C14  107.85  3.000
 1XP  C17  C16  C14  110.10  3.000
 1XP  C15  C16  C14  108.99  3.000
 1XP  O3   C17  C18  119.92  3.000
 1XP  O3   C17  C16  121.32  3.000
 1XP  C18  C17  C16  118.73  3.000
 1XP  C20  C18  C19  118.62  3.000
 1XP  C19  C18  C17  118.74  3.000
 1XP  C20  C18  C17  122.63  3.000
 1XP  H21  C19  C21  119.01  3.000
 1XP  H21  C19  C18  119.86  3.000
 1XP  C21  C19  C18  121.14  3.000
 1XP  H22  C20  C22  117.89  3.000
 1XP  H22  C20  C18  121.05  3.000
 1XP  C22  C20  C18  121.06  3.000
 1XP  H23  C21  C23  120.54  3.000
 1XP  H23  C21  C19  121.03  3.000
 1XP  C23  C21  C19  118.43  3.000
 1XP  H24  C22  C23  120.62  3.000
 1XP  H24  C22  C20  120.91  3.000
 1XP  C23  C22  C20  118.48  3.000
 1XP  F1   C23  C22  118.88  3.000
 1XP  F1   C23  C21  118.86  3.000
 1XP  C22  C23  C21  122.27  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
 1XP  CONST_01  C7   C5   C2   C1      0.00   0.0  0
 1XP  CONST_02  C7   C6   C3   C1      0.00   0.0  0
 1XP  CONST_03  C6   C7   C5   C2      0.00   0.0  0
 1XP  CONST_04  C6   C3   C1   C2      0.00   0.0  0
 1XP  CONST_05  C5   C2   C1   C3      0.00   0.0  0
 1XP  CONST_06  C5   C7   C6   C3      0.00   0.0  0
 1XP  CONST_07  C23  C22  C20  C18     0.00   0.0  0
 1XP  CONST_08  C23  C21  C19  C18     0.00   0.0  0
 1XP  CONST_09  C22  C20  C18  C19     0.00   0.0  0
 1XP  CONST_10  C22  C23  C21  C19     0.00   0.0  0
 1XP  CONST_11  C21  C23  C22  C20     0.00   0.0  0
 1XP  CONST_12  C21  C19  C18  C20     0.00   0.0  0
 1XP  CONST_13  C9   C6   C3   C1    180.00   0.0  0
 1XP  CONST_14  CL1  C7   C5   C2    180.00   0.0  0
 1XP  CONST_15  O1   C2   C1   C3    180.00   0.0  0
 1XP  CONST_16  CL1  C7   C6   C3    180.00   0.0  0
 1XP  CONST_17  C5   C2   C1   C4    180.00   0.0  0
 1XP  CONST_18  C6   C3   C1   C4    180.00   0.0  0
 1XP  CONST_19  C9   C6   C7   C5    180.00   0.0  0
 1XP  CONST_20  C7   C5   C2   O1    180.00   0.0  0
 1XP  CONST_21  C22  C20  C18  C17   180.00   0.0  0
 1XP  CONST_22  C21  C19  C18  C17   180.00   0.0  0
 1XP  CONST_23  F1   C23  C21  C19   180.00   0.0  0
 1XP  CONST_24  F1   C23  C22  C20   180.00   0.0  0
 1XP  CONST_25  H2   C5   C2   C1    180.00   0.0  0
 1XP  CONST_26  H1   C3   C1   C2    180.00   0.0  0
 1XP  CONST_27  H24  C22  C20  C18   180.00   0.0  0
 1XP  CONST_28  H23  C21  C19  C18   180.00   0.0  0
 1XP  CONST_29  H22  C20  C18  C19   180.00   0.0  0
 1XP  CONST_30  H21  C19  C18  C20   180.00   0.0  0
 1XP  CONST_31  C10  N1   C4   C1    180.00   0.0  0
 1XP  CONST_32  H3   N1   C4   C1      0.00   0.0  0
 1XP  CONST_33  C10  N1   C4   O2      0.00   0.0  0
 1XP  Var_01    C16  C15  C13  N3    -58.53  30.0  1
 1XP  Var_02    C16  C14  C12  N3     56.90  30.0  1
 1XP  Var_03    C15  C13  N3   C12    59.81  30.0  1
 1XP  Var_04    C14  C12  N3   C13   -59.15  30.0  1
 1XP  Var_05    C20  C18  C17  C16   -11.90  30.0  2
 1XP  Var_06    N1   C4   C1   C2    125.27  30.0  2
 1XP  Var_07    C13  N3   C11  C10    72.99  30.0  3
 1XP  Var_08    N3   C11  C10  N1    179.39  30.0  3
 1XP  Var_09    H4   C8   O1   C2    -62.11  30.0  3
 1XP  Var_10    C11  C10  N1   C4   -149.37  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
 1XP  chir_01  C16  C15  C14  C17  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
 1XP  plan-1  C1   0.020
 1XP  plan-1  C2   0.020
 1XP  plan-1  C3   0.020
 1XP  plan-1  C4   0.020
 1XP  plan-1  C5   0.020
 1XP  plan-1  O1   0.020
 1XP  plan-1  C6   0.020
 1XP  plan-1  C7   0.020
 1XP  plan-1  C9   0.020
 1XP  plan-1  CL1  0.020
 1XP  plan-1  N2   0.020
 1XP  plan-1  H1   0.020
 1XP  plan-1  H2   0.020
 1XP  plan-2  C17  0.020
 1XP  plan-2  C18  0.020
 1XP  plan-2  C19  0.020
 1XP  plan-2  C20  0.020
 1XP  plan-2  C21  0.020
 1XP  plan-2  C22  0.020
 1XP  plan-2  C23  0.020
 1XP  plan-2  F1   0.020
 1XP  plan-2  H21  0.020
 1XP  plan-2  H22  0.020
 1XP  plan-2  H23  0.020
 1XP  plan-2  H24  0.020
 1XP  plan-3  C1   0.020
 1XP  plan-3  C4   0.020
 1XP  plan-3  N1   0.020
 1XP  plan-3  O2   0.020
 1XP  plan-3  C10  0.020
 1XP  plan-3  H3   0.020
 1XP  plan-4  C16  0.020
 1XP  plan-4  C17  0.020
 1XP  plan-4  C18  0.020
 1XP  plan-4  O3   0.020

