# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 05:08:40 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-(4-fluorophenyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)N1CCN(CC1)c2ccc(F)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
 O1M  O1M  4-(4-fluorophenyl)piperazine-1-carboxamide  ligand  30  16  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O1M
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
 O1M  N1   N  NT    0  -0.482  -2.8069  -0.0709  -0.1457
 O1M  C4   C  CH2   0  -0.287  -2.1044   0.9863  -0.8446
 O1M  C5   C  CR6   0   0.346   1.4097  -0.0268  -0.1736
 O1M  C6   C  CR16  0  -0.301   2.1720  -1.1674  -0.4588
 O1M  C7   C  CR16  0  -0.399   3.5508  -1.1614  -0.3452
 O1M  C8   C  CR6   0   0.496   4.1866   0.0030   0.0446
 O1M  C10  C  CR16  0  -0.335   2.0888   1.1277   0.2238
 O1M  N    N  NH2   0  -0.846  -4.7770  -1.0129   0.6603
 O1M  C    C  C     0   0.665  -4.1233   0.0837   0.1761
 O1M  O    O  O     0  -0.546  -4.6907   1.1694   0.0909
 O1M  C1   C  CH2   0  -0.311  -2.0790  -1.3227  -0.1137
 O1M  C2   C  CH2   0  -0.297  -0.6773  -1.1054   0.4270
 O1M  C3   C  CH2   0  -0.315  -0.7070   1.1789  -0.2838
 O1M  C9   C  CR16  0  -0.401   3.4752   1.1486   0.3246
 O1M  F    F  F     0  -0.323   5.5294   0.0151   0.1493
 O1M  N2   N  NT    0  -0.517   0.0186  -0.0733  -0.3265
 O1M  H1   H  HCH2  0   0.231  -2.0301   0.7403  -1.9107
 O1M  H2   H  HCH2  0   0.266  -2.6598   1.9157  -0.7556
 O1M  H3   H  HCR6  0   0.271   1.6840  -2.0724  -0.7966
 O1M  H4   H  HCR6  0   0.277   4.1228  -2.0508  -0.5771
 O1M  H5   H  HCR6  0   0.277   1.5480   2.0310   0.4703
 O1M  H6   H  HNH2  0   0.400  -4.4905  -1.9439   0.4124
 O1M  H7   H  HNH2  0   0.395  -5.7741  -0.9046   0.7427
 O1M  H8   H  HCH2  0   0.258  -2.5654  -2.0448   0.5372
 O1M  H9   H  HCH2  0   0.240  -2.0225  -1.7580  -1.1181
 O1M  H10  H  HCH2  0   0.223  -0.7400  -0.8342   1.4916
 O1M  H11  H  HCH2  0   0.262  -0.1383  -2.0491   0.3629
 O1M  H12  H  HCH2  0   0.258  -0.1963   1.9187  -0.9019
 O1M  H13  H  HCH2  0   0.217  -0.7751   1.5849   0.7372
 O1M  H14  H  HCR6  0   0.277   3.9849   2.0515   0.6351

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
 O1M  F    C8   single    1.347  0.020  1.347
 O1M  C8   C9   aromatic  1.377  0.020  1.377
 O1M  C8   C7   aromatic  1.383  0.020  1.383
 O1M  C9   C10  aromatic  1.390  0.020  1.390
 O1M  C7   C6   aromatic  1.383  0.020  1.383
 O1M  C10  C5   aromatic  1.397  0.020  1.397
 O1M  C6   C5   aromatic  1.401  0.020  1.401
 O1M  C5   N2   single    1.400  0.020  1.400
 O1M  N2   C3   single    1.448  0.020  1.448
 O1M  N2   C2   single    1.455  0.020  1.455
 O1M  C3   C4   single    1.518  0.020  1.518
 O1M  C2   C1   single    1.518  0.020  1.518
 O1M  C4   N1   single    1.449  0.020  1.449
 O1M  C1   N1   single    1.448  0.020  1.448
 O1M  N1   C    single    1.364  0.020  1.364
 O1M  C    N    single    1.365  0.020  1.365
 O1M  C    O    double    1.228  0.020  1.228
 O1M  C4   H1   single    0.970  0.020  1.090
 O1M  C4   H2   single    0.970  0.020  1.090
 O1M  C6   H3   single    0.930  0.020  1.080
 O1M  C7   H4   single    0.930  0.020  1.080
 O1M  C10  H5   single    0.930  0.020  1.080
 O1M  N    H6   single    0.890  0.020  1.040
 O1M  N    H7   single    0.890  0.020  1.040
 O1M  C1   H8   single    0.970  0.020  1.090
 O1M  C1   H9   single    0.970  0.020  1.090
 O1M  C2   H10  single    0.970  0.020  1.090
 O1M  C2   H11  single    0.970  0.020  1.090
 O1M  C3   H12  single    0.970  0.020  1.090
 O1M  C3   H13  single    0.970  0.020  1.090
 O1M  C9   H14  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
 O1M  C1   N1   C    125.29  3.000
 O1M  C    N1   C4   119.93  3.000
 O1M  C1   N1   C4   113.43  3.000
 O1M  H2   C4   H1   107.83  3.000
 O1M  H2   C4   C3   109.39  3.000
 O1M  H1   C4   C3   108.98  3.000
 O1M  H2   C4   N1   109.68  3.000
 O1M  H1   C4   N1   109.75  3.000
 O1M  C3   C4   N1   111.14  3.000
 O1M  N2   C5   C10  122.77  3.000
 O1M  N2   C5   C6   119.43  3.000
 O1M  C10  C5   C6   117.78  3.000
 O1M  H3   C6   C7   118.60  3.000
 O1M  H3   C6   C5   119.93  3.000
 O1M  C7   C6   C5   121.47  3.000
 O1M  H4   C7   C8   120.61  3.000
 O1M  H4   C7   C6   120.36  3.000
 O1M  C8   C7   C6   119.01  3.000
 O1M  F    C8   C9   119.45  3.000
 O1M  C9   C8   C7   121.35  3.000
 O1M  F    C8   C7   119.20  3.000
 O1M  H5   C10  C9   118.01  3.000
 O1M  H5   C10  C5   120.81  3.000
 O1M  C9   C10  C5   121.18  3.000
 O1M  H7   N    H6   113.72  3.000
 O1M  H7   N    C    114.64  3.000
 O1M  H6   N    C    121.33  3.000
 O1M  O    C    N    120.89  3.000
 O1M  O    C    N1   121.99  3.000
 O1M  N    C    N1   117.05  3.000
 O1M  H9   C1   H8   107.94  3.000
 O1M  H9   C1   C2   109.61  3.000
 O1M  H8   C1   C2   107.15  3.000
 O1M  H9   C1   N1   110.42  3.000
 O1M  H8   C1   N1   111.25  3.000
 O1M  C2   C1   N1   110.38  3.000
 O1M  H11  C2   H10  107.39  3.000
 O1M  H11  C2   N2   110.34  3.000
 O1M  H10  C2   N2   110.70  3.000
 O1M  H11  C2   C1   108.19  3.000
 O1M  H10  C2   C1   109.10  3.000
 O1M  N2   C2   C1   111.02  3.000
 O1M  H13  C3   H12  107.71  3.000
 O1M  H13  C3   N2   112.17  3.000
 O1M  H12  C3   N2   109.58  3.000
 O1M  H13  C3   C4   109.42  3.000
 O1M  H12  C3   C4   107.92  3.000
 O1M  N2   C3   C4   109.93  3.000
 O1M  H14  C9   C10  120.20  3.000
 O1M  H14  C9   C8   120.60  3.000
 O1M  C10  C9   C8   119.20  3.000
 O1M  C3   N2   C2   111.01  3.000
 O1M  C2   N2   C5   116.24  3.000
 O1M  C3   N2   C5   117.78  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
 O1M  CONST_01  C8   C9   C10  C5      0.00   0.0  0
 O1M  CONST_02  C8   C7   C6   C5      0.00   0.0  0
 O1M  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 O1M  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 O1M  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 O1M  CONST_06  C10  C5   C6   C7      0.00   0.0  0
 O1M  CONST_07  N2   C5   C6   C7    180.00   0.0  0
 O1M  CONST_08  N2   C5   C10  C9    180.00   0.0  0
 O1M  CONST_09  F    C8   C7   C6    180.00   0.0  0
 O1M  CONST_10  F    C8   C9   C10   180.00   0.0  0
 O1M  CONST_11  H14  C9   C10  C5    180.00   0.0  0
 O1M  CONST_12  H4   C7   C6   C5    180.00   0.0  0
 O1M  CONST_13  H5   C10  C5   C6    180.00   0.0  0
 O1M  CONST_14  H3   C6   C7   C8    180.00   0.0  0
 O1M  CONST_15  O    C    N1   C4      0.00   0.0  0
 O1M  CONST_16  C1   N1   C    O     180.00   0.0  0
 O1M  CONST_17  N    C    N1   C4    180.00   0.0  0
 O1M  CONST_18  C1   N1   C    N       0.00   0.0  0
 O1M  CONST_20  H7   N    C    N1    180.00   0.0  0
 O1M  Var_01    N2   C3   C4   N1     55.50  30.0  1
 O1M  Var_02    N2   C2   C1   N1    -54.43  30.0  1
 O1M  Var_03    C5   N2   C3   C4    164.17  30.0  1
 O1M  Var_04    C2   C1   N1   C4     52.91  30.0  1
 O1M  Var_05    C1   C2   N2   C5   -163.41  30.0  1
 O1M  Var_06    C3   N2   C5   C6   -167.96  30.0  2
 O1M  Var_07    C3   C4   N1   C1    -53.87  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
 O1M  plan-1  C5   0.020
 O1M  plan-1  C6   0.020
 O1M  plan-1  C7   0.020
 O1M  plan-1  C8   0.020
 O1M  plan-1  C10  0.020
 O1M  plan-1  C9   0.020
 O1M  plan-1  F    0.020
 O1M  plan-1  N2   0.020
 O1M  plan-1  H3   0.020
 O1M  plan-1  H4   0.020
 O1M  plan-1  H5   0.020
 O1M  plan-1  H14  0.020
 O1M  plan-2  N1   0.020
 O1M  plan-2  C4   0.020
 O1M  plan-2  N    0.020
 O1M  plan-2  C    0.020
 O1M  plan-2  O    0.020
 O1M  plan-2  C1   0.020
 O1M  plan-2  H6   0.020
 O1M  plan-2  H7   0.020

