# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 14:36:46 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 3-fluoro-N-1H-indol-5-yl-5-morpholin-4-ylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(cc(c1)C(=O)Nc2ccc3[nH]ccc3c2)N4CCOCC4
#
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
 LI3  LI3  3-fluoro-N-1H-indol-5-yl-5-morpholin-4-ylbenzamide  ligand  43  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LI3
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
 LI3  F1    F  F     0  -0.317  -3.7181   1.0419   2.2849
 LI3  C2    C  CR6   0   0.584  -2.4245   0.7346   2.0992
 LI3  C3    C  CR16  0  -0.534  -1.6603   0.4700   3.2169
 LI3  C4    C  CR6   0   0.439  -0.3006   0.1599   3.0670
 LI3  C5    C  CR16  0  -0.388   0.2270   0.1689   1.7648
 LI3  C6    C  CR6   0  -0.010  -0.5738   0.4310   0.6656
 LI3  C7    C  CR16  0  -0.507  -1.9290   0.7228   0.8139
 LI3  C8    C  C     0   0.519   0.0792   0.4155  -0.6825
 LI3  O9    O  O     0  -0.465   1.2472   0.7354  -0.8238
 LI3  N10   N  NH1   0  -0.753  -0.7230   0.0130  -1.6947
 LI3  C11   C  CR6   0   0.355  -0.3651  -0.1237  -3.0504
 LI3  C12   C  CR16  0  -0.357  -0.9769  -1.1748  -3.7640
 LI3  C13   C  CR16  0  -0.293  -0.7245  -1.3817  -5.1031
 LI3  C14   C  CR56  0   0.338   0.1719  -0.5217  -5.7328
 LI3  N15   N  NR15  0  -0.679   0.6164  -0.4819  -7.0225
 LI3  C17   C  CR15  0  -0.025   1.4899   0.5564  -7.1673
 LI3  C18   C  CR15  0  -0.421   1.6313   1.2122  -5.9777
 LI3  C19   C  CR56  0   0.067   0.7939   0.5372  -5.0365
 LI3  C20   C  CR16  0  -0.397   0.5138   0.7394  -3.6805
 LI3  N21   N  NT    0  -0.531   0.4891  -0.1709   4.1512
 LI3  C22   C  CH2   0  -0.329  -0.1081  -0.1791   5.4737
 LI3  C23   C  CH2   0  -0.186   0.7788  -0.9297   6.4505
 LI3  O24   O  O2    0  -0.480   2.0889  -0.4164   6.4798
 LI3  C25   C  CH2   0  -0.189   2.6693  -0.5168   5.2010
 LI3  C26   C  CH2   0  -0.323   1.8816   0.2584   4.1635
 LI3  H3    H  HCR6  0   0.294  -2.1341   0.5307   4.1864
 LI3  H5    H  HCR6  0   0.273   1.2683  -0.0613   1.5939
 LI3  H7    H  HCR6  0   0.279  -2.5714   0.9705  -0.0209
 LI3  H10   H  HNH1  0   0.417  -1.6123  -0.3887  -1.4401
 LI3  H12   H  HCR6  0   0.264  -1.6605  -1.8364  -3.2455
 LI3  H13   H  HCR6  0   0.264  -1.2042  -2.1917  -5.6368
 LI3  H15   H  HNR5  0   0.411   0.3478  -1.1159  -7.7562
 LI3  H17   H  HCR5  0   0.282   1.9535   0.7511  -8.1210
 LI3  H18   H  HCR5  0   0.248   2.2552   2.0723  -5.7947
 LI3  H20   H  HCR6  0   0.259   0.9697   1.5628  -3.1513
 LI3  H221  H  HCH2  0   0.230  -0.2979   0.8408   5.8386
 LI3  H222  H  HCH2  0   0.261  -1.0650  -0.7013   5.4447
 LI3  H231  H  HCH2  0   0.246   0.3633  -0.8440   7.4552
 LI3  H232  H  HCH2  0   0.208   0.7928  -1.9943   6.1774
 LI3  H251  H  HCH2  0   0.246   3.6816  -0.1157   5.2619
 LI3  H252  H  HCH2  0   0.209   2.7382  -1.5698   4.8934
 LI3  H261  H  HCH2  0   0.263   2.3502   0.0776   3.1991
 LI3  H262  H  HCH2  0   0.232   1.9517   1.3360   4.3659

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
 LI3  F1   C2    single    1.343  0.020  1.343
 LI3  C2   C3    aromatic  1.380  0.020  1.380
 LI3  C2   C7    aromatic  1.378  0.020  1.378
 LI3  C3   C4    aromatic  1.403  0.020  1.403
 LI3  C3   H3    single    0.930  0.020  1.080
 LI3  C4   C5    aromatic  1.405  0.020  1.405
 LI3  C4   N21   single    1.381  0.020  1.381
 LI3  C5   C6    aromatic  1.385  0.020  1.385
 LI3  C5   H5    single    0.930  0.020  1.080
 LI3  C6   C7    aromatic  1.394  0.020  1.394
 LI3  C6   C8    single    1.498  0.020  1.498
 LI3  C7   H7    single    0.930  0.020  1.080
 LI3  C8   O9    double    1.219  0.020  1.219
 LI3  C8   N10   single    1.353  0.020  1.353
 LI3  N10  C11   single    1.409  0.020  1.409
 LI3  N10  H10   single    0.860  0.020  1.020
 LI3  C11  C12   aromatic  1.410  0.020  1.410
 LI3  C11  C20   aromatic  1.384  0.020  1.384
 LI3  C12  C13   aromatic  1.378  0.020  1.378
 LI3  C12  H12   single    0.930  0.020  1.080
 LI3  C13  C14   aromatic  1.393  0.020  1.393
 LI3  C13  H13   single    0.930  0.020  1.080
 LI3  C14  N15   aromatic  1.365  0.020  1.365
 LI3  C14  C19   aromatic  1.412  0.020  1.412
 LI3  N15  C17   aromatic  1.365  0.020  1.365
 LI3  N15  H15   single    0.860  0.020  1.020
 LI3  C17  C18   aromatic  1.366  0.020  1.366
 LI3  C17  H17   single    0.930  0.020  1.080
 LI3  C18  C19   aromatic  1.429  0.020  1.429
 LI3  C18  H18   single    0.930  0.020  1.080
 LI3  C19  C20   aromatic  1.399  0.020  1.399
 LI3  C20  H20   single    0.930  0.020  1.080
 LI3  N21  C22   single    1.451  0.020  1.451
 LI3  N21  C26   single    1.457  0.020  1.457
 LI3  C22  C23   single    1.518  0.020  1.518
 LI3  C22  H221  single    0.970  0.020  1.090
 LI3  C22  H222  single    0.970  0.020  1.090
 LI3  C23  O24   single    1.407  0.020  1.407
 LI3  C23  H231  single    0.970  0.020  1.090
 LI3  C23  H232  single    0.970  0.020  1.090
 LI3  O24  C25   single    1.408  0.020  1.408
 LI3  C25  C26   single    1.516  0.020  1.516
 LI3  C25  H251  single    0.970  0.020  1.090
 LI3  C25  H252  single    0.970  0.020  1.090
 LI3  C26  H261  single    0.970  0.020  1.090
 LI3  C26  H262  single    0.970  0.020  1.090

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
 LI3  C7    C2   C3    123.72  3.000
 LI3  C7    C2   F1    118.52  3.000
 LI3  C3    C2   F1    117.75  3.000
 LI3  H3    C3   C4    122.22  3.000
 LI3  H3    C3   C2    118.24  3.000
 LI3  C4    C3   C2    119.52  3.000
 LI3  N21   C4   C5    120.95  3.000
 LI3  N21   C4   C3    121.55  3.000
 LI3  C5    C4   C3    117.49  3.000
 LI3  H5    C5   C6    118.18  3.000
 LI3  H5    C5   C4    120.48  3.000
 LI3  C6    C5   C4    121.31  3.000
 LI3  C8    C6   C7    121.44  3.000
 LI3  C8    C6   C5    117.40  3.000
 LI3  C7    C6   C5    121.14  3.000
 LI3  H7    C7   C6    122.88  3.000
 LI3  H7    C7   C2    120.29  3.000
 LI3  C6    C7   C2    116.78  3.000
 LI3  N10   C8   O9    124.02  3.000
 LI3  N10   C8   C6    114.70  3.000
 LI3  O9    C8   C6    121.28  3.000
 LI3  H10   N10  C11   115.36  3.000
 LI3  H10   N10  C8    116.90  3.000
 LI3  C11   N10  C8    126.74  3.000
 LI3  C20   C11  C12   120.67  3.000
 LI3  C20   C11  N10   122.62  3.000
 LI3  C12   C11  N10   116.68  3.000
 LI3  H12   C12  C13   119.27  3.000
 LI3  H12   C12  C11   119.13  3.000
 LI3  C13   C12  C11   121.60  3.000
 LI3  H13   C13  C14   121.64  3.000
 LI3  H13   C13  C12   120.68  3.000
 LI3  C14   C13  C12   117.68  3.000
 LI3  C19   C14  N15   107.50  3.000
 LI3  C19   C14  C13   121.58  3.000
 LI3  N15   C14  C13   130.91  3.000
 LI3  H15   N15  C17   124.95  3.000
 LI3  H15   N15  C14   125.72  3.000
 LI3  C17   N15  C14   109.33  3.000
 LI3  H17   C17  C18   129.74  3.000
 LI3  H17   C17  N15   120.44  3.000
 LI3  C18   C17  N15   109.83  3.000
 LI3  H18   C18  C19   127.16  3.000
 LI3  H18   C18  C17   126.21  3.000
 LI3  C19   C18  C17   106.63  3.000
 LI3  C20   C19  C18   133.41  3.000
 LI3  C20   C19  C14   119.88  3.000
 LI3  C18   C19  C14   106.72  3.000
 LI3  H20   C20  C19   120.04  3.000
 LI3  H20   C20  C11   121.38  3.000
 LI3  C19   C20  C11   118.57  3.000
 LI3  C26   N21  C22   112.78  3.000
 LI3  C26   N21  C4    118.84  3.000
 LI3  C22   N21  C4    118.77  3.000
 LI3  H222  C22  H221  107.54  3.000
 LI3  H222  C22  C23   107.04  3.000
 LI3  H221  C22  C23   110.24  3.000
 LI3  H222  C22  N21   109.85  3.000
 LI3  H221  C22  N21   111.61  3.000
 LI3  C23   C22  N21   110.42  3.000
 LI3  H232  C23  H231  108.05  3.000
 LI3  H232  C23  O24   110.28  3.000
 LI3  H231  C23  O24   107.87  3.000
 LI3  H232  C23  C22   109.06  3.000
 LI3  H231  C23  C22   109.35  3.000
 LI3  O24   C23  C22   112.14  3.000
 LI3  C25   O24  C23   109.80  3.000
 LI3  H252  C25  H251  108.04  3.000
 LI3  H252  C25  C26   109.33  3.000
 LI3  H251  C25  C26   109.42  3.000
 LI3  H252  C25  O24   110.39  3.000
 LI3  H251  C25  O24   107.80  3.000
 LI3  C26   C25  O24   111.78  3.000
 LI3  H262  C26  H261  107.40  3.000
 LI3  H262  C26  C25   110.01  3.000
 LI3  H261  C26  C25   107.35  3.000
 LI3  H262  C26  N21   110.58  3.000
 LI3  H261  C26  N21   110.81  3.000
 LI3  C25   C26  N21   110.59  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
 LI3  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 LI3  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 LI3  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 LI3  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 LI3  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 LI3  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 LI3  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 LI3  CONST_08  C14  C19  C20  C11     0.00   0.0  0
 LI3  CONST_09  C18  C19  C20  C11   180.00   0.0  0
 LI3  CONST_10  C19  C20  C11  C12     0.00   0.0  0
 LI3  CONST_11  N15  C14  C13  C12   180.00   0.0  0
 LI3  CONST_12  C19  C14  C13  C12     0.00   0.0  0
 LI3  CONST_13  C20  C11  C12  C13     0.00   0.0  0
 LI3  CONST_14  C17  N15  C14  C13   180.00   0.0  0
 LI3  CONST_15  C18  C19  C14  C13   180.00   0.0  0
 LI3  CONST_16  C20  C19  C14  C13     0.00   0.0  0
 LI3  CONST_17  C18  C17  N15  C14     0.00   0.0  0
 LI3  CONST_18  C17  C18  C19  C14     0.00   0.0  0
 LI3  CONST_19  C18  C19  C14  N15     0.00   0.0  0
 LI3  CONST_20  C20  C19  C14  N15   180.00   0.0  0
 LI3  CONST_21  C19  C18  C17  N15     0.00   0.0  0
 LI3  CONST_22  C19  C14  N15  C17     0.00   0.0  0
 LI3  CONST_23  C20  C19  C18  C17   180.00   0.0  0
 LI3  CONST_24  N21  C4   C3   C2    180.00   0.0  0
 LI3  CONST_25  N21  C4   C5   C6    180.00   0.0  0
 LI3  CONST_26  C4   C3   C2   F1    180.00   0.0  0
 LI3  CONST_27  C6   C7   C2   F1    180.00   0.0  0
 LI3  CONST_28  C8   C6   C7   C2    180.00   0.0  0
 LI3  CONST_29  C8   C6   C5   C4    180.00   0.0  0
 LI3  CONST_30  C13  C12  C11  N10   180.00   0.0  0
 LI3  CONST_31  C19  C20  C11  N10   180.00   0.0  0
 LI3  CONST_32  H7   C7   C2   C3    180.00   0.0  0
 LI3  CONST_33  H5   C5   C4   C3    180.00   0.0  0
 LI3  CONST_34  H3   C3   C4   C5    180.00   0.0  0
 LI3  CONST_35  H13  C13  C12  C11   180.00   0.0  0
 LI3  CONST_36  H20  C20  C11  C12   180.00   0.0  0
 LI3  CONST_37  H15  N15  C14  C13     0.00   0.0  0
 LI3  CONST_38  H12  C12  C13  C14   180.00   0.0  0
 LI3  CONST_39  H17  C17  N15  C14   180.00   0.0  0
 LI3  CONST_40  H18  C18  C19  C14   180.00   0.0  0
 LI3  CONST_41  C11  N10  C8   C6    180.00   0.0  0
 LI3  CONST_45  C11  N10  C8   O9      0.00   0.0  0
 LI3  Var_01    C22  N21  C4   C3     -0.75  30.0  2
 LI3  Var_02    C23  C22  N21  C4    163.97  30.0  1
 LI3  Var_03    C25  C26  N21  C4   -163.69  30.0  1
 LI3  Var_04    O24  C23  C22  N21    55.02  30.0  1
 LI3  Var_05    O24  C25  C26  N21   -55.23  30.0  1
 LI3  Var_06    C26  C25  O24  C23    59.98  30.0  1
 LI3  Var_07    O9   C8   C6   C5    -30.89  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
 LI3  plan-1  F1   0.020
 LI3  plan-1  C2   0.020
 LI3  plan-1  C3   0.020
 LI3  plan-1  C4   0.020
 LI3  plan-1  C5   0.020
 LI3  plan-1  C6   0.020
 LI3  plan-1  C7   0.020
 LI3  plan-1  C8   0.020
 LI3  plan-1  N21  0.020
 LI3  plan-1  H3   0.020
 LI3  plan-1  H5   0.020
 LI3  plan-1  H7   0.020
 LI3  plan-2  N10  0.020
 LI3  plan-2  C11  0.020
 LI3  plan-2  C12  0.020
 LI3  plan-2  C13  0.020
 LI3  plan-2  C14  0.020
 LI3  plan-2  N15  0.020
 LI3  plan-2  C17  0.020
 LI3  plan-2  C18  0.020
 LI3  plan-2  C19  0.020
 LI3  plan-2  C20  0.020
 LI3  plan-2  H12  0.020
 LI3  plan-2  H13  0.020
 LI3  plan-2  H15  0.020
 LI3  plan-2  H17  0.020
 LI3  plan-2  H18  0.020
 LI3  plan-2  H20  0.020
 LI3  plan-3  C6   0.020
 LI3  plan-3  C8   0.020
 LI3  plan-3  O9   0.020
 LI3  plan-3  N10  0.020
 LI3  plan-3  C11  0.020
 LI3  plan-3  H10  0.020

