# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:34:19 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-(5-chlorofuran-2-carbonyl)-N-(2,2,2-trifluoroethyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)CNC(=O)N1CCN(CC1)C(=O)c2oc(Cl)cc2
#
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
 XZY  XZY  4-(5-chlorofuran-2-carbonyl)-N-(2,2,2-trifluoroethyl)piperazine-1-carboxamide  ligand  35  22  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XZY
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
 XZY  N1   N   NH1   0  -0.697  -15.7615  16.8559  25.6885
 XZY  N3   N   NT    0  -0.472  -18.9701  13.0318  25.3500
 XZY  C4   C   CH2   0  -0.281  -18.4620  14.7770  26.9680
 XZY  C5   C   CH2   0  -0.325  -18.7367  13.3011  26.7576
 XZY  C6   C   C     0   0.497  -20.0059  12.3632  24.8015
 XZY  C7   C   CR5   0   0.217  -21.2645  12.2304  25.5624
 XZY  C8   C   CR15  0  -0.305  -22.2242  11.2752  25.4601
 XZY  C10  C   CR5   0   0.273  -22.8734  12.8270  26.8807
 XZY  C1   C   C     0   0.757  -16.5244  16.1849  26.6028
 XZY  C11  C   CH2   0  -0.306  -17.8216  13.3963  24.5457
 XZY  C12  C   CH2   0  -0.310  -17.5138  14.8788  24.7162
 XZY  C2   C   CH2   0  -0.475  -14.8125  17.8479  26.0959
 XZY  C3   C   CT    0   0.971  -15.4018  19.2448  26.1240
 XZY  C9   C   CR15  0  -0.287  -23.2782  11.6563  26.3340
 XZY  F1   F   F     0  -0.301  -16.4627  19.3457  26.9306
 XZY  F2   F   F     0  -0.310  -14.4941  20.1370  26.5448
 XZY  F3   F   F     0  -0.312  -15.8105  19.6406  24.9092
 XZY  N2   N   NT    0  -0.512  -17.3684  15.2222  26.1188
 XZY  O1   O   O     0  -0.527  -16.4278  16.4179  27.8003
 XZY  O2   O   O     0  -0.468  -19.9680  11.8710  23.6819
 XZY  O3   O   O     0  -0.402  -21.6695  13.1906  26.4344
 XZY  CL1  CL  CL    0  -0.077  -23.6197  13.8693  27.9826
 XZY  H1   H   HNH1  0   0.412  -15.9392  16.7836  24.7016
 XZY  H4   H   HCH2  0   0.271  -18.2048  14.9487  28.0091
 XZY  H5   H   HCH2  0   0.237  -19.3707  15.3481  26.7438
 XZY  H7   H   HCH2  0   0.258  -17.8650  12.7184  27.0737
 XZY  H6   H   HCH2  0   0.281  -19.5694  12.9867  27.3773
 XZY  H8   H   HCR5  0   0.281  -22.1857  10.3941  24.8404
 XZY  H10  H   HCH2  0   0.251  -16.9552  12.8025  24.8536
 XZY  H11  H   HCH2  0   0.279  -18.0150  13.1897  23.4966
 XZY  H13  H   HCH2  0   0.261  -16.5871  15.0625  24.1755
 XZY  H12  H   HCH2  0   0.246  -18.3053  15.4723  24.2446
 XZY  H2   H   HCH2  0   0.289  -14.4196  17.6124  27.0838
 XZY  H3   H   HCH2  0   0.297  -13.9687  17.8507  25.4034
 XZY  H9   H   HCR5  0   0.289  -24.2041  11.1401  26.5237

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
 XZY  O1   C1   double    1.224  0.020  1.224
 XZY  C1   N1   single    1.367  0.020  1.367
 XZY  N1   C2   single    1.432  0.020  1.432
 XZY  C2   C3   single    1.516  0.020  1.516
 XZY  C3   F1   single    1.337  0.020  1.337
 XZY  C3   F2   single    1.341  0.020  1.341
 XZY  C3   F3   single    1.341  0.020  1.341
 XZY  C1   N2   single    1.369  0.020  1.369
 XZY  N2   C4   single    1.454  0.020  1.454
 XZY  C4   C5   single    1.516  0.020  1.516
 XZY  C5   N3   single    1.452  0.020  1.452
 XZY  N3   C6   single    1.349  0.020  1.349
 XZY  C6   O2   double    1.224  0.020  1.224
 XZY  C6   C7   single    1.477  0.020  1.477
 XZY  C7   C8   aromatic  1.358  0.020  1.358
 XZY  C8   C9   aromatic  1.421  0.020  1.421
 XZY  C9   C10  aromatic  1.354  0.020  1.354
 XZY  C10  CL1  single    1.690  0.020  1.690
 XZY  C10  O3   aromatic  1.334  0.020  1.334
 XZY  N3   C11  single    1.449  0.020  1.449
 XZY  C11  C12  single    1.524  0.020  1.524
 XZY  N2   C12  single    1.451  0.020  1.451
 XZY  C7   O3   aromatic  1.359  0.020  1.359
 XZY  N1   H1   single    0.860  0.020  1.020
 XZY  C4   H4   single    0.970  0.020  1.090
 XZY  C4   H5   single    0.970  0.020  1.090
 XZY  C5   H7   single    0.970  0.020  1.090
 XZY  C5   H6   single    0.970  0.020  1.090
 XZY  C8   H8   single    0.930  0.020  1.080
 XZY  C11  H10  single    0.970  0.020  1.090
 XZY  C11  H11  single    0.970  0.020  1.090
 XZY  C12  H13  single    0.970  0.020  1.090
 XZY  C12  H12  single    0.970  0.020  1.090
 XZY  C2   H2   single    0.970  0.020  1.090
 XZY  C2   H3   single    0.970  0.020  1.090
 XZY  C9   H9   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
 XZY  H1   N1   C2   116.50  3.000
 XZY  H1   N1   C1   121.51  3.000
 XZY  C2   N1   C1   121.31  3.000
 XZY  C11  N3   C6   120.50  3.000
 XZY  C11  N3   C5   111.36  3.000
 XZY  C6   N3   C5   127.54  3.000
 XZY  H5   C4   H4   108.06  3.000
 XZY  H5   C4   N2   110.14  3.000
 XZY  H4   C4   N2   109.47  3.000
 XZY  H5   C4   C5   109.18  3.000
 XZY  H4   C4   C5   109.26  3.000
 XZY  N2   C4   C5   110.69  3.000
 XZY  H6   C5   H7   106.98  3.000
 XZY  H6   C5   C4   110.00  3.000
 XZY  H7   C5   C4   109.49  3.000
 XZY  H6   C5   N3   112.13  3.000
 XZY  H7   C5   N3   108.00  3.000
 XZY  C4   C5   N3   110.14  3.000
 XZY  O2   C6   C7   117.49  3.000
 XZY  C7   C6   N3   119.30  3.000
 XZY  O2   C6   N3   123.20  3.000
 XZY  O3   C7   C8   109.56  3.000
 XZY  O3   C7   C6   121.41  3.000
 XZY  C8   C7   C6   128.82  3.000
 XZY  H8   C8   C9   126.82  3.000
 XZY  H8   C8   C7   126.37  3.000
 XZY  C9   C8   C7   106.81  3.000
 XZY  CL1  C10  O3   116.63  3.000
 XZY  O3   C10  C9   111.74  3.000
 XZY  CL1  C10  C9   131.63  3.000
 XZY  O1   C1   N2   121.91  3.000
 XZY  N2   C1   N1   116.93  3.000
 XZY  O1   C1   N1   121.14  3.000
 XZY  H11  C11  H10  108.02  3.000
 XZY  H11  C11  C12  109.21  3.000
 XZY  H10  C11  C12  109.66  3.000
 XZY  H11  C11  N3   110.31  3.000
 XZY  H10  C11  N3   109.56  3.000
 XZY  C12  C11  N3   110.05  3.000
 XZY  H12  C12  H13  108.03  3.000
 XZY  H12  C12  N2   111.10  3.000
 XZY  H13  C12  N2   110.79  3.000
 XZY  H12  C12  C11  109.44  3.000
 XZY  H13  C12  C11  106.30  3.000
 XZY  N2   C12  C11  111.02  3.000
 XZY  H3   C2   H2   107.29  3.000
 XZY  H3   C2   C3   108.05  3.000
 XZY  H2   C2   C3   108.83  3.000
 XZY  H3   C2   N1   109.48  3.000
 XZY  H2   C2   N1   110.33  3.000
 XZY  C3   C2   N1   112.70  3.000
 XZY  F3   C3   F2   107.10  3.000
 XZY  F3   C3   F1   106.41  3.000
 XZY  F2   C3   F1   107.33  3.000
 XZY  F3   C3   C2   111.93  3.000
 XZY  F2   C3   C2   110.84  3.000
 XZY  F1   C3   C2   112.91  3.000
 XZY  H9   C9   C10  126.90  3.000
 XZY  H9   C9   C8   128.12  3.000
 XZY  C10  C9   C8   104.98  3.000
 XZY  C12  N2   C1   124.74  3.000
 XZY  C12  N2   C4   114.61  3.000
 XZY  C1   N2   C4   118.20  3.000
 XZY  C10  O3   C7   106.91  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
 XZY  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 XZY  CONST_02  C9   C10  O3   C7      0.00   0.0  0
 XZY  CONST_03  C10  O3   C7   C8      0.00   0.0  0
 XZY  CONST_04  O3   C10  C9   C8      0.00   0.0  0
 XZY  CONST_05  O3   C7   C8   C9      0.00   0.0  0
 XZY  CONST_06  C9   C8   C7   C6    180.00   0.0  0
 XZY  CONST_07  C10  O3   C7   C6    180.00   0.0  0
 XZY  CONST_08  CL1  C10  O3   C7    180.00   0.0  0
 XZY  CONST_09  CL1  C10  C9   C8    180.00   0.0  0
 XZY  CONST_11  C11  N3   C6   C7    180.00   0.0  0
 XZY  CONST_12  H9   C9   C8   C7    180.00   0.0  0
 XZY  CONST_13  H8   C8   C9   C10   180.00   0.0  0
 XZY  CONST_16  O2   C6   N3   C11     0.00   0.0  0
 XZY  CONST_17  O1   C1   N2   C12   180.00   0.0  0
 XZY  CONST_19  C12  N2   C1   N1      0.00   0.0  0
 XZY  CONST_20  N2   C1   N1   C2    180.00   0.0  0
 XZY  CONST_21  H1   N1   C1   N2      0.00   0.0  0
 XZY  CONST_22  O1   C1   N1   C2      0.00   0.0  0
 XZY  Var_01    N2   C4   C5   N3    -54.50  30.0  1
 XZY  Var_02    N2   C12  C11  N3     53.58  30.0  1
 XZY  Var_03    C11  C12  N2   C4    -51.02  30.0  1
 XZY  Var_04    C11  N3   C5   C4     60.02  30.0  1
 XZY  Var_05    C12  N2   C4   C5     51.47  30.0  1
 XZY  Var_06    C12  C11  N3   C5    -59.33  30.0  1
 XZY  Var_07    C8   C7   C6   N3   -154.83  30.0  2
 XZY  Var_08    F1   C3   C2   N1     57.85  30.0  3
 XZY  Var_09    C3   C2   N1   C1    -91.63  30.0  3

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
 XZY  plan-1  C6   0.020
 XZY  plan-1  C7   0.020
 XZY  plan-1  C8   0.020
 XZY  plan-1  C10  0.020
 XZY  plan-1  C9   0.020
 XZY  plan-1  O3   0.020
 XZY  plan-1  CL1  0.020
 XZY  plan-1  H8   0.020
 XZY  plan-1  H9   0.020
 XZY  plan-2  N3   0.020
 XZY  plan-2  C5   0.020
 XZY  plan-2  C6   0.020
 XZY  plan-2  C7   0.020
 XZY  plan-2  C11  0.020
 XZY  plan-2  O2   0.020
 XZY  plan-3  N1   0.020
 XZY  plan-3  C4   0.020
 XZY  plan-3  C1   0.020
 XZY  plan-3  C12  0.020
 XZY  plan-3  C2   0.020
 XZY  plan-3  N2   0.020
 XZY  plan-3  O1   0.020
 XZY  plan-3  H1   0.020

