# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:51:34 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(cn1)c2ccc(cc2)[C@H](C(=O)NO)c3ccccc3F
#
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
 EBE  EBE  (2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide  ligand  41  25  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EBE
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
 EBE  C4   C  CR16  0  -0.276  -0.0968   0.0557  -0.8354
 EBE  C5   C  CR16  0  -0.299   1.2830   0.1523  -0.9060
 EBE  C6   C  CR6   0   0.080   2.0788  -0.1344   0.2039
 EBE  C7   C  CR6   0  -0.044   3.5420  -0.0197   0.1319
 EBE  C8   C  CR16  0  -0.054   4.2695  -0.3597  -1.0045
 EBE  C3   C  CR6   0   0.177  -0.7217  -0.3218   0.3480
 EBE  C2   C  CR16  0  -0.283   0.0683  -0.6091   1.4549
 EBE  C10  C  CR6   0   0.350   6.2241   0.2080  -0.0030
 EBE  C1   C  CR16  0  -0.299   1.4495  -0.5206   1.3866
 EBE  C19  C  CR16  0  -0.288  -3.5950   0.5584  -1.4883
 EBE  C12  C  CR16  0  -0.054   4.3119   0.4444   1.1938
 EBE  C13  C  CH1   0  -0.562  -2.2241  -0.4461   0.4412
 EBE  C14  C  CR6   0  -0.066  -2.9382   0.6851  -0.2680
 EBE  C18  C  CR16  0  -0.254  -4.2163   1.6468  -2.0877
 EBE  N9   N  N     0  -0.404   5.5856  -0.2465  -1.0778
 EBE  C20  C  C     0   0.547  -2.6687  -1.8051  -0.0968
 EBE  C24  C  CH3   0  -0.729   7.7131   0.3108  -0.0701
 EBE  O21  O  O     0  -0.452  -2.1322  -2.3616  -1.0341
 EBE  N22  N  NH1   0  -0.360  -3.7051  -2.3148   0.5907
 EBE  O23  O  OH1   0  -0.539  -4.3647  -3.4028   0.1077
 EBE  C17  C  CR16  0  -0.248  -4.1874   2.8900  -1.4750
 EBE  C16  C  CR16  0  -0.407  -3.5339   3.0476  -0.2602
 EBE  C15  C  CR6   0   0.548  -2.9272   1.9483   0.3103
 EBE  F25  F  F     0  -0.309  -2.2885   2.1050   1.4818
 EBE  N11  N  N     0  -0.404   5.6290   0.5558   1.1344
 EBE  H1   H  HCR6  0   0.256  -0.6849   0.3031  -1.7097
 EBE  H2   H  HCR6  0   0.258   1.7393   0.4788  -1.8322
 EBE  H3   H  HCR6  0   0.272   3.7679  -0.7492  -1.8846
 EBE  H4   H  HCR6  0   0.259  -0.3977  -0.9114   2.3850
 EBE  H5   H  HCR6  0   0.258   2.0381  -0.7681   2.2613
 EBE  H7   H  HCR6  0   0.272   3.8415   0.7537   2.1218
 EBE  H8   H  HCH1  0   0.303  -2.4969  -0.4004   1.5004
 EBE  H9   H  HCR6  0   0.264  -4.7216   1.5175  -3.0351
 EBE  H10  H  HCH3  0   0.262   8.1678  -0.6346   0.2349
 EBE  H11  H  HCH3  0   0.253   8.0456   0.5218  -1.0842
 EBE  H12  H  HCH3  0   0.252   8.0825   1.0839   0.6002
 EBE  H13  H  HNH1  0   0.422  -4.2257  -1.7650   1.2603
 EBE  H14  H  HOH1  0   0.481  -4.0486  -4.1572   0.6217
 EBE  H15  H  HCR6  0   0.270  -4.6699   3.7408  -1.9368
 EBE  H16  H  HCR6  0   0.281  -3.4928   4.0083   0.2364
 EBE  H6   H  HCR6  0   0.266  -3.6246  -0.3974  -1.9949

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
 EBE  F25  C15  single    1.343  0.020  1.343
 EBE  C16  C15  aromatic  1.379  0.020  1.379
 EBE  C16  C17  aromatic  1.388  0.020  1.388
 EBE  C15  C14  aromatic  1.389  0.020  1.389
 EBE  C17  C18  aromatic  1.386  0.020  1.386
 EBE  C14  C13  single    1.514  0.020  1.514
 EBE  C14  C19  aromatic  1.392  0.020  1.392
 EBE  C13  C20  single    1.528  0.020  1.528
 EBE  C13  C3   single    1.510  0.020  1.510
 EBE  C18  C19  aromatic  1.389  0.020  1.389
 EBE  N22  C20  single    1.344  0.020  1.344
 EBE  N22  O23  single    1.361  0.020  1.361
 EBE  C20  O21  double    1.215  0.020  1.215
 EBE  C4   C3   aromatic  1.391  0.020  1.391
 EBE  C4   C5   aromatic  1.385  0.020  1.385
 EBE  C3   C2   aromatic  1.390  0.020  1.390
 EBE  C5   C6   aromatic  1.395  0.020  1.395
 EBE  C2   C1   aromatic  1.386  0.020  1.386
 EBE  C6   C1   aromatic  1.394  0.020  1.394
 EBE  C6   C7   single    1.469  0.020  1.469
 EBE  C8   C7   aromatic  1.391  0.020  1.391
 EBE  C8   N9   aromatic  1.323  0.020  1.323
 EBE  C7   C12  aromatic  1.391  0.020  1.391
 EBE  N9   C10  aromatic  1.330  0.020  1.330
 EBE  C12  N11  aromatic  1.323  0.020  1.323
 EBE  C10  N11  aromatic  1.330  0.020  1.330
 EBE  C10  C24  single    1.494  0.020  1.494
 EBE  C4   H1   single    0.930  0.020  1.080
 EBE  C5   H2   single    0.930  0.020  1.080
 EBE  C8   H3   single    0.930  0.020  1.080
 EBE  C2   H4   single    0.930  0.020  1.080
 EBE  C1   H5   single    0.930  0.020  1.080
 EBE  C19  H6   single    0.930  0.020  1.080
 EBE  C12  H7   single    0.930  0.020  1.080
 EBE  C13  H8   single    0.970  0.020  1.090
 EBE  C18  H9   single    0.930  0.020  1.080
 EBE  C24  H10  single    0.970  0.020  1.090
 EBE  C24  H11  single    0.970  0.020  1.090
 EBE  C24  H12  single    0.970  0.020  1.090
 EBE  N22  H13  single    0.890  0.020  1.040
 EBE  O23  H14  single    0.850  0.020  0.980
 EBE  C17  H15  single    0.930  0.020  1.080
 EBE  C16  H16  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
 EBE  H1   C4   C3   120.35  3.000
 EBE  H1   C4   C5   118.96  3.000
 EBE  C3   C4   C5   120.67  3.000
 EBE  H2   C5   C6   120.13  3.000
 EBE  H2   C5   C4   118.98  3.000
 EBE  C6   C5   C4   120.88  3.000
 EBE  C1   C6   C7   120.84  3.000
 EBE  C7   C6   C5   120.85  3.000
 EBE  C1   C6   C5   118.31  3.000
 EBE  C12  C7   C8   114.56  3.000
 EBE  C12  C7   C6   122.66  3.000
 EBE  C8   C7   C6   122.79  3.000
 EBE  H3   C8   N9   116.46  3.000
 EBE  H3   C8   C7   120.55  3.000
 EBE  N9   C8   C7   122.98  3.000
 EBE  C13  C3   C2   119.95  3.000
 EBE  C2   C3   C4   118.58  3.000
 EBE  C13  C3   C4   121.46  3.000
 EBE  H4   C2   C1   119.27  3.000
 EBE  H4   C2   C3   119.80  3.000
 EBE  C1   C2   C3   120.93  3.000
 EBE  N11  C10  C24  117.80  3.000
 EBE  C24  C10  N9   117.75  3.000
 EBE  N11  C10  N9   124.44  3.000
 EBE  H5   C1   C2   119.16  3.000
 EBE  H5   C1   C6   120.21  3.000
 EBE  C2   C1   C6   120.62  3.000
 EBE  H6   C19  C18  118.54  3.000
 EBE  H6   C19  C14  120.26  3.000
 EBE  C18  C19  C14  121.21  3.000
 EBE  H7   C12  N11  116.47  3.000
 EBE  H7   C12  C7   120.52  3.000
 EBE  N11  C12  C7   123.00  3.000
 EBE  H8   C13  C20  107.78  3.000
 EBE  H8   C13  C14  107.73  3.000
 EBE  C20  C13  C14  111.25  3.000
 EBE  H8   C13  C3   107.70  3.000
 EBE  C20  C13  C3   109.94  3.000
 EBE  C14  C13  C3   112.25  3.000
 EBE  C15  C14  C13  118.73  3.000
 EBE  C13  C14  C19  124.42  3.000
 EBE  C15  C14  C19  116.84  3.000
 EBE  H9   C18  C17  120.27  3.000
 EBE  H9   C18  C19  119.56  3.000
 EBE  C17  C18  C19  120.17  3.000
 EBE  C10  N9   C8   117.52  3.000
 EBE  N22  C20  O21  124.15  3.000
 EBE  O21  C20  C13  123.41  3.000
 EBE  N22  C20  C13  112.43  3.000
 EBE  H12  C24  H11  109.43  3.000
 EBE  H12  C24  H10  107.56  3.000
 EBE  H11  C24  H10  107.50  3.000
 EBE  H12  C24  C10  111.08  3.000
 EBE  H11  C24  C10  111.09  3.000
 EBE  H10  C24  C10  110.05  3.000
 EBE  H13  N22  O23  114.85  3.000
 EBE  H13  N22  C20  121.99  3.000
 EBE  O23  N22  C20  119.69  3.000
 EBE  H14  O23  N22  106.07  3.000
 EBE  H15  C17  C16  119.62  3.000
 EBE  H15  C17  C18  120.49  3.000
 EBE  C16  C17  C18  119.89  3.000
 EBE  H16  C16  C15  120.07  3.000
 EBE  H16  C16  C17  121.34  3.000
 EBE  C15  C16  C17  118.59  3.000
 EBE  F25  C15  C16  118.48  3.000
 EBE  C16  C15  C14  123.30  3.000
 EBE  F25  C15  C14  118.21  3.000
 EBE  C12  N11  C10  117.50  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
 EBE  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 EBE  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 EBE  CONST_03  C7   C6   C5   C4   180.00   0.0  0
 EBE  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 EBE  CONST_05  C2   C1   C6   C5     0.00   0.0  0
 EBE  CONST_08  C3   C4   C5   C6     0.00   0.0  0
 EBE  CONST_09  C3   C2   C1   C6     0.00   0.0  0
 EBE  CONST_10  N9   C8   C7   C6   180.00   0.0  0
 EBE  CONST_11  N11  C12  C7   C6   180.00   0.0  0
 EBE  CONST_12  C2   C1   C6   C7   180.00   0.0  0
 EBE  CONST_13  C10  N9   C8   C7     0.00   0.0  0
 EBE  CONST_14  C10  N11  C12  C7     0.00   0.0  0
 EBE  CONST_16  N11  C12  C7   C8     0.00   0.0  0
 EBE  CONST_17  N11  C10  N9   C8     0.00   0.0  0
 EBE  CONST_19  C16  C15  C14  C19    0.00   0.0  0
 EBE  CONST_20  C16  C17  C18  C19    0.00   0.0  0
 EBE  CONST_21  N9   C8   C7   C12    0.00   0.0  0
 EBE  CONST_22  N9   C10  N11  C12    0.00   0.0  0
 EBE  CONST_23  C17  C16  C15  C14    0.00   0.0  0
 EBE  CONST_24  C17  C18  C19  C14    0.00   0.0  0
 EBE  CONST_25  C15  C16  C17  C18    0.00   0.0  0
 EBE  CONST_26  C15  C14  C19  C18    0.00   0.0  0
 EBE  CONST_27  C13  C3   C4   C5   180.00   0.0  0
 EBE  CONST_28  C24  C10  N9   C8   180.00   0.0  0
 EBE  CONST_29  C13  C3   C2   C1   180.00   0.0  0
 EBE  CONST_30  F25  C15  C14  C19  180.00   0.0  0
 EBE  CONST_31  C24  C10  N11  C12  180.00   0.0  0
 EBE  CONST_32  C16  C15  C14  C13  180.00   0.0  0
 EBE  CONST_33  C18  C19  C14  C13  180.00   0.0  0
 EBE  CONST_34  F25  C15  C16  C17  180.00   0.0  0
 EBE  CONST_35  H4   C2   C3   C4   180.00   0.0  0
 EBE  CONST_36  H5   C1   C6   C5   180.00   0.0  0
 EBE  CONST_37  H1   C4   C5   C6   180.00   0.0  0
 EBE  CONST_38  H3   C8   C7   C6     0.00   0.0  0
 EBE  CONST_39  H7   C12  C7   C6     0.00   0.0  0
 EBE  CONST_40  H2   C5   C6   C7     0.00   0.0  0
 EBE  CONST_41  H15  C17  C18  C19  180.00   0.0  0
 EBE  CONST_42  H16  C16  C15  C14  180.00   0.0  0
 EBE  CONST_43  H9   C18  C19  C14  180.00   0.0  0
 EBE  CONST_44  H6   C19  C18  C17  180.00   0.0  0
 EBE  CONST_45  O23  N22  C20  C13  180.00   0.0  0
 EBE  CONST_46  O23  N22  C20  O21    0.00   0.0  0
 EBE  CONST_47  H13  N22  C20  C13    0.00   0.0  0
 EBE  Var_01    H10  C24  C10  N9   -87.94  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 EBE  chir_01  C13  C14  C20  C3  negativ

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
 EBE  plan-1  C4   0.020
 EBE  plan-1  C5   0.020
 EBE  plan-1  C6   0.020
 EBE  plan-1  C7   0.020
 EBE  plan-1  C3   0.020
 EBE  plan-1  C2   0.020
 EBE  plan-1  C1   0.020
 EBE  plan-1  C13  0.020
 EBE  plan-1  H1   0.020
 EBE  plan-1  H2   0.020
 EBE  plan-1  H4   0.020
 EBE  plan-1  H5   0.020
 EBE  plan-2  C6   0.020
 EBE  plan-2  C7   0.020
 EBE  plan-2  C8   0.020
 EBE  plan-2  C10  0.020
 EBE  plan-2  C12  0.020
 EBE  plan-2  N9   0.020
 EBE  plan-2  C24  0.020
 EBE  plan-2  N11  0.020
 EBE  plan-2  H3   0.020
 EBE  plan-2  H7   0.020
 EBE  plan-3  C19  0.020
 EBE  plan-3  C13  0.020
 EBE  plan-3  C14  0.020
 EBE  plan-3  C18  0.020
 EBE  plan-3  C17  0.020
 EBE  plan-3  C16  0.020
 EBE  plan-3  C15  0.020
 EBE  plan-3  F25  0.020
 EBE  plan-3  H9   0.020
 EBE  plan-3  H15  0.020
 EBE  plan-3  H16  0.020
 EBE  plan-3  H6   0.020
 EBE  plan-4  C13  0.020
 EBE  plan-4  C20  0.020
 EBE  plan-4  O21  0.020
 EBE  plan-4  N22  0.020
 EBE  plan-4  O23  0.020
 EBE  plan-4  H13  0.020

