# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:46:33 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-(5-methylfuran-2-carbonyl)-N-(2,2,2-trifluoroethyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(cc1)C(=O)N2CCN(CC2)C(=O)NCC(F)(F)F
#
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
 Y2V  Y2V  4-(5-methylfuran-2-carbonyl)-N-(2,2,2-trifluoroethyl)piperazine-1-carboxamide  ligand  38  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 PERFECT
;

data_comp_Y2V
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
 Y2V  N1   N  NT    0  -0.512  -17.3686  15.2936  26.2492
 Y2V  C4   C  CR5   0   0.198  -21.2874  12.3887  25.6672
 Y2V  C5   C  C     0   0.484  -20.0400  12.4937  24.8905
 Y2V  C6   C  CH2   0  -0.324  -18.7151  13.3452  26.8498
 Y2V  C7   C  CH2   0  -0.280  -18.4410  14.8131  27.1077
 Y2V  C8   C  C     0   0.757  -16.5405  16.2659  26.7419
 Y2V  C10  C  CT    0   0.971  -15.4482  19.3518  26.3001
 Y2V  N    N  NT    0  -0.472  -18.9772  13.1234  25.4403
 Y2V  O    O  O     0  -0.474  -20.0224  12.0273  23.7581
 Y2V  C1   C  CR5   0   0.367  -22.8480  13.0336  27.0588
 Y2V  C11  C  CH2   0  -0.309  -17.5393  14.9923  24.8391
 Y2V  C12  C  CH2   0  -0.306  -17.8456  13.5144  24.6270
 Y2V  C2   C  CR15  0  -0.377  -23.3038  11.8981  26.4658
 Y2V  C3   C  CR15  0  -0.298  -22.2960  11.4861  25.5531
 Y2V  F    F  F     0  -0.312  -15.8892  19.7495  25.0974
 Y2V  F1   F  F     0  -0.301  -16.4874  19.4444  27.1358
 Y2V  F2   F  F     0  -0.310  -14.5353  20.2475  26.7021
 Y2V  N2   N  NH1   0  -0.698  -15.7991  16.9683  25.8345
 Y2V  O1   O  O     0  -0.528  -16.4393  16.4819  27.9424
 Y2V  O2   O  O     0  -0.427  -21.6260  13.3330  26.5781
 Y2V  H5   H  HCH2  0   0.280  -19.5331  13.0047  27.4749
 Y2V  H6   H  HCH2  0   0.255  -17.8339  12.7565  27.1268
 Y2V  H8   H  HCH2  0   0.235  -19.3564  15.3895  26.9289
 Y2V  H7   H  HCH2  0   0.269  -18.1581  14.9469  28.1477
 Y2V  H2   H  HCH3  0   0.260  -23.5378  14.9598  27.6755
 Y2V  H1   H  HCH3  0   0.261  -24.4141  13.5916  28.3604
 Y2V  H    H  HCH3  0   0.259  -22.8087  14.0052  28.9639
 Y2V  H12  H  HCH2  0   0.245  -18.3423  15.5964  24.4012
 Y2V  H13  H  HCH2  0   0.259  -16.6241  15.1973  24.2864
 Y2V  H15  H  HCH2  0   0.277  -18.0582  13.3402  23.5757
 Y2V  H14  H  HCH2  0   0.249  -16.9713  12.9147  24.8994
 Y2V  H3   H  HCR5  0   0.265  -24.2508  11.4194  26.6560
 Y2V  H4   H  HCR5  0   0.268  -22.3144  10.6266  24.9027
 Y2V  H10  H  HCH2  0   0.289  -14.4532  17.7119  27.2337
 Y2V  H11  H  HCH2  0   0.297  -14.0124  17.9748  25.5536
 Y2V  H9   H  HNH1  0   0.412  -15.9671  16.8942  24.8464
 Y2V  C    C  CH3   0  -0.753  -23.4287  13.9471  28.0677
 Y2V  C9   C  CH2   0  -0.475  -14.8521  17.9584  26.2509

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
 Y2V  C    C1   single    1.480  0.020  1.480
 Y2V  C1   C2   aromatic  1.360  0.020  1.360
 Y2V  C2   C3   aromatic  1.421  0.020  1.421
 Y2V  C3   C4   aromatic  1.358  0.020  1.358
 Y2V  C4   C5   single    1.473  0.020  1.473
 Y2V  O    C5   double    1.225  0.020  1.225
 Y2V  C5   N    single    1.352  0.020  1.352
 Y2V  N    C6   single    1.451  0.020  1.451
 Y2V  C6   C7   single    1.515  0.020  1.515
 Y2V  C7   N1   single    1.455  0.020  1.455
 Y2V  N1   C8   single    1.369  0.020  1.369
 Y2V  O1   C8   double    1.224  0.020  1.224
 Y2V  C8   N2   single    1.366  0.020  1.366
 Y2V  N2   C9   single    1.432  0.020  1.432
 Y2V  C9   C10  single    1.516  0.020  1.516
 Y2V  F    C10  single    1.341  0.020  1.341
 Y2V  F1   C10  single    1.337  0.020  1.337
 Y2V  C10  F2   single    1.341  0.020  1.341
 Y2V  C11  N1   single    1.452  0.020  1.452
 Y2V  C12  C11  single    1.524  0.020  1.524
 Y2V  N    C12  single    1.447  0.020  1.447
 Y2V  O2   C4   aromatic  1.355  0.020  1.355
 Y2V  C1   O2   aromatic  1.347  0.020  1.347
 Y2V  C6   H5   single    0.970  0.020  1.090
 Y2V  C6   H6   single    0.970  0.020  1.090
 Y2V  C7   H8   single    0.970  0.020  1.090
 Y2V  C7   H7   single    0.970  0.020  1.090
 Y2V  C    H2   single    0.970  0.020  1.090
 Y2V  C    H1   single    0.970  0.020  1.090
 Y2V  C    H    single    0.970  0.020  1.090
 Y2V  C11  H12  single    0.970  0.020  1.090
 Y2V  C11  H13  single    0.970  0.020  1.090
 Y2V  C12  H15  single    0.970  0.020  1.090
 Y2V  C12  H14  single    0.970  0.020  1.090
 Y2V  C2   H3   single    0.930  0.020  1.080
 Y2V  C3   H4   single    0.930  0.020  1.080
 Y2V  C9   H10  single    0.970  0.020  1.090
 Y2V  C9   H11  single    0.970  0.020  1.090
 Y2V  N2   H9   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
 Y2V  C11  N1   C8   124.61  3.000
 Y2V  C11  N1   C7   114.69  3.000
 Y2V  C8   N1   C7   117.91  3.000
 Y2V  O2   C4   C3   109.51  3.000
 Y2V  O2   C4   C5   121.09  3.000
 Y2V  C3   C4   C5   129.18  3.000
 Y2V  O    C5   N    122.82  3.000
 Y2V  N    C5   C4   118.97  3.000
 Y2V  O    C5   C4   118.20  3.000
 Y2V  H6   C6   H5   106.99  3.000
 Y2V  H6   C6   N    108.00  3.000
 Y2V  H5   C6   N    112.08  3.000
 Y2V  H6   C6   C7   109.39  3.000
 Y2V  H5   C6   C7   110.03  3.000
 Y2V  N    C6   C7   110.25  3.000
 Y2V  H7   C7   H8   107.99  3.000
 Y2V  H7   C7   C6   109.23  3.000
 Y2V  H8   C7   C6   109.30  3.000
 Y2V  H7   C7   N1   109.40  3.000
 Y2V  H8   C7   N1   110.21  3.000
 Y2V  C6   C7   N1   110.65  3.000
 Y2V  O1   C8   N2   121.05  3.000
 Y2V  N2   C8   N1   117.03  3.000
 Y2V  O1   C8   N1   121.90  3.000
 Y2V  F2   C10  F1   107.20  3.000
 Y2V  F2   C10  F    107.13  3.000
 Y2V  F1   C10  F    106.53  3.000
 Y2V  F2   C10  C9   110.85  3.000
 Y2V  F1   C10  C9   112.93  3.000
 Y2V  F    C10  C9   111.88  3.000
 Y2V  C12  N    C6   111.31  3.000
 Y2V  C12  N    C5   120.79  3.000
 Y2V  C6   N    C5   127.46  3.000
 Y2V  O2   C1   C2   109.52  3.000
 Y2V  O2   C1   C    117.53  3.000
 Y2V  C2   C1   C    132.95  3.000
 Y2V  H13  C11  H12  108.01  3.000
 Y2V  H13  C11  C12  106.32  3.000
 Y2V  H12  C11  C12  109.36  3.000
 Y2V  H13  C11  N1   110.81  3.000
 Y2V  H12  C11  N1   111.08  3.000
 Y2V  C12  C11  N1   111.10  3.000
 Y2V  H14  C12  H15  108.01  3.000
 Y2V  H14  C12  C11  109.63  3.000
 Y2V  H15  C12  C11  109.23  3.000
 Y2V  H14  C12  N    109.67  3.000
 Y2V  H15  C12  N    110.33  3.000
 Y2V  C11  C12  N    109.93  3.000
 Y2V  H3   C2   C3   127.43  3.000
 Y2V  H3   C2   C1   126.04  3.000
 Y2V  C3   C2   C1   106.53  3.000
 Y2V  H4   C3   C2   127.35  3.000
 Y2V  H4   C3   C4   126.39  3.000
 Y2V  C2   C3   C4   106.26  3.000
 Y2V  H9   N2   C9   116.58  3.000
 Y2V  H9   N2   C8   121.62  3.000
 Y2V  C9   N2   C8   121.42  3.000
 Y2V  C1   O2   C4   108.17  3.000
 Y2V  H    C    H1   108.13  3.000
 Y2V  H    C    H2   107.61  3.000
 Y2V  H1   C    H2   108.03  3.000
 Y2V  H    C    C1   111.70  3.000
 Y2V  H1   C    C1   109.71  3.000
 Y2V  H2   C    C1   111.53  3.000
 Y2V  H11  C9   H10  107.35  3.000
 Y2V  H11  C9   N2   109.47  3.000
 Y2V  H10  C9   N2   110.37  3.000
 Y2V  H11  C9   C10  108.02  3.000
 Y2V  H10  C9   C10  108.83  3.000
 Y2V  N2   C9   C10  112.63  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
 Y2V  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 Y2V  CONST_02  C2   C1   O2   C4      0.00   0.0  0
 Y2V  CONST_03  C3   C4   O2   C1      0.00   0.0  0
 Y2V  CONST_04  O2   C4   C3   C2      0.00   0.0  0
 Y2V  CONST_05  O2   C1   C2   C3      0.00   0.0  0
 Y2V  CONST_06  C    C1   O2   C4    180.00   0.0  0
 Y2V  CONST_07  C2   C3   C4   C5    180.00   0.0  0
 Y2V  CONST_08  C1   O2   C4   C5    180.00   0.0  0
 Y2V  CONST_09  C3   C2   C1   C     180.00   0.0  0
 Y2V  CONST_11  C12  N    C5   C4    180.00   0.0  0
 Y2V  CONST_12  H3   C2   C3   C4    180.00   0.0  0
 Y2V  CONST_13  H4   C3   C2   C1    180.00   0.0  0
 Y2V  CONST_16  C12  N    C5   O       0.00   0.0  0
 Y2V  CONST_17  O1   C8   N1   C11   180.00   0.0  0
 Y2V  CONST_19  N2   C8   N1   C11     0.00   0.0  0
 Y2V  CONST_20  C9   N2   C8   N1    180.00   0.0  0
 Y2V  CONST_21  H9   N2   C8   N1      0.00   0.0  0
 Y2V  CONST_22  O1   C8   N2   C9      0.00   0.0  0
 Y2V  Var_01    N    C6   C7   N1    -54.36  30.0  1
 Y2V  Var_02    N    C12  C11  N1     53.60  30.0  1
 Y2V  Var_03    C11  C12  N    C6    -59.57  30.0  1
 Y2V  Var_04    C11  N1   C7   C6     51.01  30.0  1
 Y2V  Var_05    C12  N    C6   C7     60.29  30.0  1
 Y2V  Var_06    C12  C11  N1   C7    -50.73  30.0  1
 Y2V  Var_07    C3   C4   C5   N    -156.37  30.0  3
 Y2V  Var_08    H2   C    C1   C2   -119.43  30.0  2
 Y2V  Var_09    C10  C9   N2   C8    -92.69  30.0  3
 Y2V  Var_10    N2   C9   C10  F     -60.91  30.0  2

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
 Y2V  plan-1  C4   0.020
 Y2V  plan-1  C5   0.020
 Y2V  plan-1  C1   0.020
 Y2V  plan-1  C2   0.020
 Y2V  plan-1  C3   0.020
 Y2V  plan-1  O2   0.020
 Y2V  plan-1  H3   0.020
 Y2V  plan-1  H4   0.020
 Y2V  plan-1  C    0.020
 Y2V  plan-2  C4   0.020
 Y2V  plan-2  C5   0.020
 Y2V  plan-2  C6   0.020
 Y2V  plan-2  N    0.020
 Y2V  plan-2  O    0.020
 Y2V  plan-2  C12  0.020
 Y2V  plan-3  N1   0.020
 Y2V  plan-3  C7   0.020
 Y2V  plan-3  C8   0.020
 Y2V  plan-3  C11  0.020
 Y2V  plan-3  N2   0.020
 Y2V  plan-3  O1   0.020
 Y2V  plan-3  H9   0.020
 Y2V  plan-3  C9   0.020

