# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:37:24 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-(furan-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)c2occc2
#
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
 Y1S  Y1S  4-(furan-2-carbonyl)-N-(2,2,2-trifluoroethyl)piperazine-1-carboxamide  ligand  35  21  .  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_Y1S
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
 Y1S  N1   N  NT    0  -0.514  -17.5550  15.5140  26.2656
 Y1S  C4   C  CH2   0  -0.303  -18.0805  13.7742  24.6165
 Y1S  C5   C  C     0   0.498  -20.2182  12.6568  24.9125
 Y1S  C6   C  CR5   0   0.211  -21.4429  12.4430  25.7102
 Y1S  C7   C  CR15  0  -0.315  -22.3464  11.4316  25.6199
 Y1S  C8   C  CR15  0  -0.334  -23.3811  11.7371  26.5461
 Y1S  C10  C  CH2   0  -0.320  -18.9297  13.5918  26.8535
 Y1S  N    N  NH1   0  -0.698  -15.7589  16.9606  25.9197
 Y1S  C    C  C     0   0.757  -16.7202  16.4788  26.7619
 Y1S  O    O  O     0  -0.526  -16.8053  16.8782  27.9157
 Y1S  C1   C  CH2   0  -0.475  -14.7913  17.9172  26.3679
 Y1S  C11  C  CH2   0  -0.284  -18.6469  15.0593  27.1114
 Y1S  C2   C  CT    0   0.975  -15.1629  19.3259  25.9573
 Y1S  C3   C  CH2   0  -0.308  -17.7694  15.2453  24.8535
 Y1S  C9   C  CR15  0   0.014  -23.0355  12.9190  27.1130
 Y1S  F    F  F     0  -0.310  -14.2672  20.2122  26.4145
 Y1S  F1   F  F     0  -0.312  -15.2100  19.4616  24.6243
 Y1S  F2   F  F     0  -0.304  -16.3621  19.6965  26.4215
 Y1S  N2   N  NT    0  -0.473  -19.1982  13.3661  25.4446
 Y1S  O1   O  O     0  -0.472  -20.1868  12.1938  23.7800
 Y1S  O2   O  O     0  -0.404  -21.8661  13.3543  26.6148
 Y1S  H6   H  HCH2  0   0.276  -18.3185  13.6236  23.5669
 Y1S  H5   H  HCH2  0   0.249  -17.2017  13.1662  24.8550
 Y1S  H7   H  HCR5  0   0.271  -22.2778  10.5686  24.9780
 Y1S  H8   H  HCR5  0   0.271  -24.2648  11.1580  26.7578
 Y1S  H10  H  HCH2  0   0.281  -19.7478  13.2587  27.4820
 Y1S  H11  H  HCH2  0   0.253  -18.0499  13.0015  27.1324
 Y1S  H    H  HNH1  0   0.411  -15.5917  16.5437  25.0213
 Y1S  H1   H  HCH2  0   0.288  -14.6894  17.8825  27.4519
 Y1S  H2   H  HCH2  0   0.297  -13.8155  17.6829  25.9397
 Y1S  H13  H  HCH2  0   0.235  -19.5531  15.6474  26.9226
 Y1S  H12  H  HCH2  0   0.270  -18.3766  15.1883  28.1555
 Y1S  H3   H  HCH2  0   0.247  -18.5973  15.8557  24.4744
 Y1S  H4   H  HCH2  0   0.262  -16.8945  15.4839  24.2545
 Y1S  H9   H  HCR5  0   0.286  -23.5092  13.5454  27.8516

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
 Y1S  O    C    double    1.224  0.020  1.224
 Y1S  N    C    single    1.366  0.020  1.366
 Y1S  C1   N    single    1.433  0.020  1.433
 Y1S  C2   C1   single    1.514  0.020  1.514
 Y1S  F    C2   single    1.340  0.020  1.340
 Y1S  F1   C2   single    1.341  0.020  1.341
 Y1S  F2   C2   single    1.338  0.020  1.338
 Y1S  C    N1   single    1.369  0.020  1.369
 Y1S  N1   C3   single    1.453  0.020  1.453
 Y1S  C3   C4   single    1.522  0.020  1.522
 Y1S  C4   N2   single    1.450  0.020  1.450
 Y1S  N2   C5   single    1.351  0.020  1.351
 Y1S  C5   O1   double    1.224  0.020  1.224
 Y1S  C6   C5   single    1.477  0.020  1.477
 Y1S  C6   C7   aromatic  1.359  0.020  1.359
 Y1S  C7   C8   aromatic  1.422  0.020  1.422
 Y1S  C8   C9   aromatic  1.356  0.020  1.356
 Y1S  C9   O2   aromatic  1.344  0.020  1.344
 Y1S  O2   C6   aromatic  1.352  0.020  1.352
 Y1S  C10  N2   single    1.452  0.020  1.452
 Y1S  C11  C10  single    1.517  0.020  1.517
 Y1S  N1   C11  single    1.454  0.020  1.454
 Y1S  C4   H6   single    0.970  0.020  1.090
 Y1S  C4   H5   single    0.970  0.020  1.090
 Y1S  C7   H7   single    0.930  0.020  1.080
 Y1S  C8   H8   single    0.930  0.020  1.080
 Y1S  C10  H10  single    0.970  0.020  1.090
 Y1S  C10  H11  single    0.970  0.020  1.090
 Y1S  N    H    single    0.860  0.020  1.020
 Y1S  C1   H1   single    0.970  0.020  1.090
 Y1S  C1   H2   single    0.970  0.020  1.090
 Y1S  C11  H13  single    0.970  0.020  1.090
 Y1S  C11  H12  single    0.970  0.020  1.090
 Y1S  C3   H3   single    0.970  0.020  1.090
 Y1S  C3   H4   single    0.970  0.020  1.090
 Y1S  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
 Y1S  C3   N1   C11  113.37  3.000
 Y1S  C11  N1   C    117.87  3.000
 Y1S  C3   N1   C    124.93  3.000
 Y1S  H5   C4   H6   108.02  3.000
 Y1S  H5   C4   N2   109.76  3.000
 Y1S  H6   C4   N2   110.11  3.000
 Y1S  H5   C4   C3   109.80  3.000
 Y1S  H6   C4   C3   109.21  3.000
 Y1S  N2   C4   C3   109.92  3.000
 Y1S  O1   C5   N2   122.92  3.000
 Y1S  O1   C5   C6   117.79  3.000
 Y1S  N2   C5   C6   119.28  3.000
 Y1S  O2   C6   C7   109.75  3.000
 Y1S  O2   C6   C5   121.55  3.000
 Y1S  C7   C6   C5   128.53  3.000
 Y1S  H7   C7   C8   127.33  3.000
 Y1S  H7   C7   C6   126.38  3.000
 Y1S  C8   C7   C6   106.29  3.000
 Y1S  H8   C8   C9   126.55  3.000
 Y1S  H8   C8   C7   127.54  3.000
 Y1S  C9   C8   C7   105.91  3.000
 Y1S  H11  C10  H10  107.03  3.000
 Y1S  H11  C10  N2   108.17  3.000
 Y1S  H10  C10  N2   112.04  3.000
 Y1S  H11  C10  C11  109.17  3.000
 Y1S  H10  C10  C11  109.84  3.000
 Y1S  N2   C10  C11  110.48  3.000
 Y1S  H    N    C1   116.39  3.000
 Y1S  H    N    C    121.49  3.000
 Y1S  C1   N    C    121.20  3.000
 Y1S  O    C    N    121.00  3.000
 Y1S  N    C    N1   117.02  3.000
 Y1S  O    C    N1   121.96  3.000
 Y1S  H2   C1   H1   107.45  3.000
 Y1S  H2   C1   C2   108.24  3.000
 Y1S  H1   C1   C2   108.82  3.000
 Y1S  H2   C1   N    109.75  3.000
 Y1S  H1   C1   N    110.68  3.000
 Y1S  C2   C1   N    111.77  3.000
 Y1S  H12  C11  H13  107.91  3.000
 Y1S  H12  C11  C10  108.95  3.000
 Y1S  H13  C11  C10  109.60  3.000
 Y1S  H12  C11  N1   109.58  3.000
 Y1S  H13  C11  N1   110.65  3.000
 Y1S  C10  C11  N1   110.10  3.000
 Y1S  F2   C2   F1   106.58  3.000
 Y1S  F2   C2   F    107.31  3.000
 Y1S  F1   C2   F    107.19  3.000
 Y1S  F2   C2   C1   112.56  3.000
 Y1S  F1   C2   C1   111.87  3.000
 Y1S  F    C2   C1   111.03  3.000
 Y1S  H4   C3   H3   107.17  3.000
 Y1S  H4   C3   C4   106.91  3.000
 Y1S  H3   C3   C4   109.27  3.000
 Y1S  H4   C3   N1   112.09  3.000
 Y1S  H3   C3   N1   110.15  3.000
 Y1S  C4   C3   N1   111.11  3.000
 Y1S  H9   C9   O2   116.63  3.000
 Y1S  H9   C9   C8   132.92  3.000
 Y1S  O2   C9   C8   110.45  3.000
 Y1S  C10  N2   C5   127.10  3.000
 Y1S  C10  N2   C4   111.59  3.000
 Y1S  C5   N2   C4   120.31  3.000
 Y1S  C9   O2   C6   107.58  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
 Y1S  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 Y1S  CONST_02  C8   C9   O2   C6      0.00   0.0  0
 Y1S  CONST_03  C9   O2   C6   C7      0.00   0.0  0
 Y1S  CONST_04  O2   C9   C8   C7      0.00   0.0  0
 Y1S  CONST_05  O2   C6   C7   C8      0.00   0.0  0
 Y1S  CONST_06  C8   C7   C6   C5    180.00   0.0  0
 Y1S  CONST_07  C9   O2   C6   C5    180.00   0.0  0
 Y1S  CONST_08  C6   C5   N2   C4    180.00   0.0  0
 Y1S  CONST_10  H8   C8   C7   C6    180.00   0.0  0
 Y1S  CONST_11  H9   C9   O2   C6    180.00   0.0  0
 Y1S  CONST_12  H7   C7   C8   C9    180.00   0.0  0
 Y1S  CONST_13  O1   C5   N2   C4      0.00   0.0  0
 Y1S  CONST_16  C11  N1   C    O       0.00   0.0  0
 Y1S  CONST_18  C11  N1   C    N     180.00   0.0  0
 Y1S  CONST_19  C1   N    C    N1    180.00   0.0  0
 Y1S  CONST_20  H    N    C    N1      0.00   0.0  0
 Y1S  CONST_21  C1   N    C    O       0.00   0.0  0
 Y1S  Var_01    N2   C4   C3   N1     54.30  30.0  1
 Y1S  Var_02    N2   C10  C11  N1    -55.58  30.0  1
 Y1S  Var_03    C11  N1   C3   C4    -53.62  30.0  1
 Y1S  Var_04    C11  C10  N2   C4     59.07  30.0  1
 Y1S  Var_05    C3   C4   N2   C10   -57.91  30.0  1
 Y1S  Var_06    C3   N1   C11  C10    53.90  30.0  1
 Y1S  Var_07    N2   C5   C6   C7   -154.08  30.0  2
 Y1S  Var_08    F    C2   C1   N     178.35  30.0  2
 Y1S  Var_09    C2   C1   N    C     -99.47  30.0  1

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
 Y1S  plan-1  C5   0.020
 Y1S  plan-1  C6   0.020
 Y1S  plan-1  C7   0.020
 Y1S  plan-1  C8   0.020
 Y1S  plan-1  C9   0.020
 Y1S  plan-1  O2   0.020
 Y1S  plan-1  H7   0.020
 Y1S  plan-1  H8   0.020
 Y1S  plan-1  H9   0.020
 Y1S  plan-2  C4   0.020
 Y1S  plan-2  C5   0.020
 Y1S  plan-2  C6   0.020
 Y1S  plan-2  C10  0.020
 Y1S  plan-2  N2   0.020
 Y1S  plan-2  O1   0.020
 Y1S  plan-3  N1   0.020
 Y1S  plan-3  N    0.020
 Y1S  plan-3  C    0.020
 Y1S  plan-3  O    0.020
 Y1S  plan-3  C1   0.020
 Y1S  plan-3  C11  0.020
 Y1S  plan-3  C3   0.020
 Y1S  plan-3  H    0.020

