# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 12:30:06 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: N-(2,4-difluorophenyl)-4-(furan-2-carbonyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(NC(=O)N2CCN(CC2)C(=O)c3occc3)c(F)c1
#
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
 Y1D  Y1D  N-(2,4-difluorophenyl)-4-(furan-2-carbonyl)piperazine-1-carboxamide  ligand  39  24  .  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_Y1D
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
 Y1D  N1   N  NT    0  -0.494  -17.0827  14.4784  26.7074
 Y1D  C4   C  CR6   0   0.535  -14.6399  20.3049  26.9928
 Y1D  C5   C  CR16  0  -0.568  -14.1276  19.2233  27.6850
 Y1D  C6   C  CR6   0   0.538  -14.6188  17.9713  27.3770
 Y1D  C7   C  CH2   0  -0.243  -17.9747  13.7171  27.5695
 Y1D  C8   C  CH2   0  -0.380  -18.7039  12.6807  26.7193
 Y1D  C10  C  CR5   0   0.215  -21.4698  13.3297  25.7763
 Y1D  C13  C  CR15  0   0.016  -22.6517  13.6352  27.5769
 Y1D  C15  C  CH2   0  -0.395  -16.6878  13.7932  25.4941
 Y1D  C    C  C     0   0.718  -16.7147  15.7269  27.0842
 Y1D  O    O  O     0  -0.512  -16.9282  16.1620  28.2051
 Y1D  C1   C  CR6   0   0.165  -15.6174  17.7725  26.4296
 Y1D  C11  C  CR15  0  -0.315  -22.7503  13.0107  25.4514
 Y1D  C12  C  CR15  0  -0.335  -23.5205  13.2013  26.6314
 Y1D  C14  C  CH2   0  -0.249  -17.9017  13.5747  24.5938
 Y1D  C2   C  CR16  0  -0.282  -16.1034  18.8917  25.7643
 Y1D  C3   C  CR16  0  -0.421  -15.6141  20.1635  26.0261
 Y1D  F1   F  F     0  -0.299  -14.0982  16.9124  28.0023
 Y1D  N2   N  NT    0  -0.467  -19.0504  13.2510  25.4311
 Y1D  O2   O  O     0  -0.405  -21.4097  13.7168  27.0703
 Y1D  H3   H  HCR6  0   0.302  -13.3534  19.3463  28.4314
 Y1D  H5   H  HCH2  0   0.241  -17.4310  13.2124  28.3737
 Y1D  H4   H  HCH2  0   0.251  -18.6972  14.3915  28.0273
 Y1D  H7   H  HCH2  0   0.272  -18.0726  11.8048  26.5478
 Y1D  H6   H  HCH2  0   0.294  -19.5765  12.3138  27.2482
 Y1D  H10  H  HCR5  0   0.286  -22.7713  13.9183  28.6103
 Y1D  H14  H  HCH2  0   0.275  -16.2278  12.8394  25.7638
 Y1D  H13  H  HCH2  0   0.285  -15.9196  14.3420  24.9553
 Y1D  H    H  HNH1  0   0.413  -16.3100  16.3342  25.1535
 Y1D  H8   H  HCR5  0   0.271  -23.1004  12.6756  24.4887
 Y1D  H9   H  HCR5  0   0.271  -24.5785  13.0412  26.7584
 Y1D  H12  H  HCH2  0   0.248  -17.6893  12.7808  23.8716
 Y1D  H11  H  HCH2  0   0.255  -18.1191  14.4835  24.0322
 Y1D  H1   H  HCR6  0   0.284  -16.8798  18.7618  25.0210
 Y1D  H2   H  HCR6  0   0.285  -15.9976  21.0247  25.4962
 Y1D  C9   C  C     0   0.501  -20.2832  13.3835  24.9007
 Y1D  N    N  NH1   0  -0.773  -16.0711  16.4832  26.1224
 Y1D  F    F  F     0  -0.310  -14.1656  21.5260  27.2747
 Y1D  O1   O  O     0  -0.477  -20.4579  13.5744  23.7034

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
 Y1D  O    C    double    1.221  0.020  1.221
 Y1D  N    C    single    1.383  0.020  1.383
 Y1D  C1   N    single    1.401  0.020  1.401
 Y1D  C1   C2   aromatic  1.390  0.020  1.390
 Y1D  C2   C3   aromatic  1.388  0.020  1.388
 Y1D  C3   C4   aromatic  1.380  0.020  1.380
 Y1D  F    C4   single    1.340  0.020  1.340
 Y1D  C4   C5   aromatic  1.383  0.020  1.383
 Y1D  C5   C6   aromatic  1.380  0.020  1.380
 Y1D  C6   C1   aromatic  1.391  0.020  1.391
 Y1D  F1   C6   single    1.335  0.020  1.335
 Y1D  C    N1   single    1.355  0.020  1.355
 Y1D  N1   C7   single    1.455  0.020  1.455
 Y1D  C7   C8   single    1.526  0.020  1.526
 Y1D  C8   N2   single    1.451  0.020  1.451
 Y1D  N2   C9   single    1.349  0.020  1.349
 Y1D  C9   O1   double    1.225  0.020  1.225
 Y1D  C10  C9   single    1.476  0.020  1.476
 Y1D  C10  C11  aromatic  1.359  0.020  1.359
 Y1D  C11  C12  aromatic  1.422  0.020  1.422
 Y1D  C12  C13  aromatic  1.355  0.020  1.355
 Y1D  C13  O2   aromatic  1.344  0.020  1.344
 Y1D  O2   C10  aromatic  1.352  0.020  1.352
 Y1D  C14  N2   single    1.458  0.020  1.458
 Y1D  C15  C14  single    1.527  0.020  1.527
 Y1D  N1   C15  single    1.448  0.020  1.448
 Y1D  C5   H3   single    0.930  0.020  1.080
 Y1D  C7   H5   single    0.970  0.020  1.090
 Y1D  C7   H4   single    0.970  0.020  1.090
 Y1D  C8   H7   single    0.970  0.020  1.090
 Y1D  C8   H6   single    0.970  0.020  1.090
 Y1D  C13  H10  single    0.930  0.020  1.080
 Y1D  C15  H14  single    0.970  0.020  1.090
 Y1D  C15  H13  single    0.970  0.020  1.090
 Y1D  N    H    single    0.860  0.020  1.020
 Y1D  C11  H8   single    0.930  0.020  1.080
 Y1D  C12  H9   single    0.930  0.020  1.080
 Y1D  C14  H12  single    0.970  0.020  1.090
 Y1D  C14  H11  single    0.970  0.020  1.090
 Y1D  C2   H1   single    0.930  0.020  1.080
 Y1D  C3   H2   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
 Y1D  C    N1   C15  126.50  3.000
 Y1D  C15  N1   C7   114.58  3.000
 Y1D  C    N1   C7   118.92  3.000
 Y1D  F    C4   C3   119.39  3.000
 Y1D  F    C4   C5   118.45  3.000
 Y1D  C3   C4   C5   122.16  3.000
 Y1D  H3   C5   C6   120.78  3.000
 Y1D  H3   C5   C4   121.42  3.000
 Y1D  C6   C5   C4   117.79  3.000
 Y1D  F1   C6   C1   119.05  3.000
 Y1D  F1   C6   C5   118.44  3.000
 Y1D  C1   C6   C5   122.51  3.000
 Y1D  H4   C7   H5   107.84  3.000
 Y1D  H4   C7   C8   109.73  3.000
 Y1D  H5   C7   C8   109.49  3.000
 Y1D  H4   C7   N1   109.37  3.000
 Y1D  H5   C7   N1   111.85  3.000
 Y1D  C8   C7   N1   108.55  3.000
 Y1D  H6   C8   H7   105.67  3.000
 Y1D  H6   C8   N2   111.96  3.000
 Y1D  H7   C8   N2   108.27  3.000
 Y1D  H6   C8   C7   110.04  3.000
 Y1D  H7   C8   C7   110.83  3.000
 Y1D  N2   C8   C7   109.99  3.000
 Y1D  O2   C10  C9   121.45  3.000
 Y1D  O2   C10  C11  109.75  3.000
 Y1D  C9   C10  C11  128.63  3.000
 Y1D  H10  C13  O2   116.62  3.000
 Y1D  H10  C13  C12  132.96  3.000
 Y1D  O2   C13  C12  110.42  3.000
 Y1D  H13  C15  H14  105.39  3.000
 Y1D  H13  C15  C14  109.99  3.000
 Y1D  H14  C15  C14  110.81  3.000
 Y1D  H13  C15  N1   111.66  3.000
 Y1D  H14  C15  N1   108.72  3.000
 Y1D  C14  C15  N1   110.17  3.000
 Y1D  O    C    N    121.67  3.000
 Y1D  N    C    N1   115.91  3.000
 Y1D  O    C    N1   122.42  3.000
 Y1D  C2   C1   N    121.53  3.000
 Y1D  C2   C1   C6   117.52  3.000
 Y1D  N    C1   C6   120.90  3.000
 Y1D  H8   C11  C12  127.36  3.000
 Y1D  H8   C11  C10  126.34  3.000
 Y1D  C12  C11  C10  106.29  3.000
 Y1D  H9   C12  C11  127.58  3.000
 Y1D  H9   C12  C13  126.49  3.000
 Y1D  C11  C12  C13  105.93  3.000
 Y1D  H11  C14  H12  107.67  3.000
 Y1D  H11  C14  N2   108.89  3.000
 Y1D  H12  C14  N2   111.77  3.000
 Y1D  H11  C14  C15  110.06  3.000
 Y1D  H12  C14  C15  109.80  3.000
 Y1D  N2   C14  C15  108.63  3.000
 Y1D  H1   C2   C3   119.49  3.000
 Y1D  H1   C2   C1   118.87  3.000
 Y1D  C3   C2   C1   121.64  3.000
 Y1D  H2   C3   C2   120.83  3.000
 Y1D  H2   C3   C4   120.80  3.000
 Y1D  C2   C3   C4   118.37  3.000
 Y1D  C9   N2   C14  118.20  3.000
 Y1D  C14  N2   C8   114.15  3.000
 Y1D  C9   N2   C8   127.31  3.000
 Y1D  C13  O2   C10  107.60  3.000
 Y1D  O1   C9   N2   122.01  3.000
 Y1D  O1   C9   C10  118.10  3.000
 Y1D  N2   C9   C10  119.87  3.000
 Y1D  H    N    C1   115.03  3.000
 Y1D  H    N    C    118.49  3.000
 Y1D  C1   N    C    120.11  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
 Y1D  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 Y1D  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 Y1D  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 Y1D  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 Y1D  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 Y1D  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 Y1D  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 Y1D  CONST_08  C12  C13  O2   C10     0.00   0.0  0
 Y1D  CONST_09  C11  C10  O2   C13     0.00   0.0  0
 Y1D  CONST_10  O2   C13  C12  C11     0.00   0.0  0
 Y1D  CONST_11  O2   C10  C11  C12     0.00   0.0  0
 Y1D  CONST_12  F1   C6   C5   C4    180.00   0.0  0
 Y1D  CONST_13  N    C1   C6   C5    180.00   0.0  0
 Y1D  CONST_14  F    C4   C5   C6    180.00   0.0  0
 Y1D  CONST_15  C9   C10  O2   C13   180.00   0.0  0
 Y1D  CONST_16  C3   C2   C1   N     180.00   0.0  0
 Y1D  CONST_17  C9   C10  C11  C12   180.00   0.0  0
 Y1D  CONST_18  F1   C6   C1   C2    180.00   0.0  0
 Y1D  CONST_19  F    C4   C3   C2    180.00   0.0  0
 Y1D  CONST_21  C14  N2   C9   C10   180.00   0.0  0
 Y1D  CONST_22  H1   C2   C3   C4    180.00   0.0  0
 Y1D  CONST_23  H2   C3   C4   C5    180.00   0.0  0
 Y1D  CONST_24  H9   C12  C11  C10   180.00   0.0  0
 Y1D  CONST_25  H10  C13  O2   C10   180.00   0.0  0
 Y1D  CONST_26  H8   C11  C12  C13   180.00   0.0  0
 Y1D  CONST_27  H3   C5   C6   C1    180.00   0.0  0
 Y1D  CONST_28  O    C    N1   C7      0.00   0.0  0
 Y1D  CONST_30  O    C    N1   C15   180.00   0.0  0
 Y1D  CONST_31  O1   C9   N2   C14     0.00   0.0  0
 Y1D  CONST_32  C1   N    C    N1    180.00   0.0  0
 Y1D  CONST_35  N    C    N1   C7    180.00   0.0  0
 Y1D  CONST_36  N    C    N1   C15     0.00   0.0  0
 Y1D  CONST_38  C1   N    C    O       0.00   0.0  0
 Y1D  Var_01    N2   C8   C7   N1    -38.84  30.0  1
 Y1D  Var_02    N2   C14  C15  N1    -37.98  30.0  1
 Y1D  Var_03    C14  C15  N1   C7     65.34  30.0  1
 Y1D  Var_04    C14  N2   C8   C7     66.11  30.0  1
 Y1D  Var_05    C15  N1   C7   C8    -23.61  30.0  1
 Y1D  Var_06    C15  C14  N2   C8    -24.33  30.0  1
 Y1D  Var_07    N2   C9   C10  C11  -156.52  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
 Y1D  plan-1  C10  0.020
 Y1D  plan-1  C13  0.020
 Y1D  plan-1  C11  0.020
 Y1D  plan-1  C12  0.020
 Y1D  plan-1  O2   0.020
 Y1D  plan-1  H10  0.020
 Y1D  plan-1  H8   0.020
 Y1D  plan-1  H9   0.020
 Y1D  plan-1  C9   0.020
 Y1D  plan-2  C4   0.020
 Y1D  plan-2  C5   0.020
 Y1D  plan-2  C6   0.020
 Y1D  plan-2  C1   0.020
 Y1D  plan-2  C2   0.020
 Y1D  plan-2  C3   0.020
 Y1D  plan-2  F1   0.020
 Y1D  plan-2  H3   0.020
 Y1D  plan-2  H1   0.020
 Y1D  plan-2  H2   0.020
 Y1D  plan-2  N    0.020
 Y1D  plan-2  F    0.020
 Y1D  plan-3  C8   0.020
 Y1D  plan-3  C10  0.020
 Y1D  plan-3  C14  0.020
 Y1D  plan-3  N2   0.020
 Y1D  plan-3  C9   0.020
 Y1D  plan-3  O1   0.020
 Y1D  plan-4  N1   0.020
 Y1D  plan-4  C7   0.020
 Y1D  plan-4  C15  0.020
 Y1D  plan-4  C    0.020
 Y1D  plan-4  O    0.020
 Y1D  plan-4  C1   0.020
 Y1D  plan-4  H    0.020
 Y1D  plan-4  N    0.020

