# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:15:40 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: N-[3-(difluoromethoxy)-4-(1,3-oxazol-5-yl)phenyl]-D-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@H](N)C(=O)Nc1ccc(c2ocnc2)c(OC(F)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
 5QI  5QI  "N-[3-(difluoromethoxy)-4-(1,3-oxazol-5-yl)phenyl]-D-leucinamide"
  ligand  43  24  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5QI
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
 5QI  C13  C  CH2   0  -0.418  -31.6270  35.3478  34.5157
 5QI  C16  C  CH3   0  -0.656  -29.4204  34.5574  33.5362
 5QI  C15  C  CH3   0  -0.646  -30.4512  36.7116  32.7834
 5QI  C11  C  C     0   0.561  -32.9733  33.3087  33.9894
 5QI  C12  C  CH1   0  -0.234  -32.1332  34.0039  35.0532
 5QI  C1   C  CR6   0  -0.111  -33.8294  29.4884  30.5462
 5QI  C2   C  CR16  0  -0.279  -32.6666  29.2567  31.2865
 5QI  C3   C  CR16  0  -0.344  -32.2283  30.1419  32.2478
 5QI  C4   C  CR6   0   0.394  -32.9371  31.3161  32.5043
 5QI  C5   C  CR16  0  -0.440  -34.0861  31.5873  31.7625
 5QI  C6   C  CR6   0   0.359  -34.5173  30.6757  30.8123
 5QI  C7   C  CR5   0   0.387  -34.2902  28.5285  29.5589
 5QI  N1   N  NH1   0  -0.749  -32.4332  32.1685  33.4829
 5QI  O1   O  O2    0  -0.488  -35.6308  30.9061  30.0557
 5QI  C8   C  CH1   0   0.640  -36.6568  31.6517  30.5498
 5QI  O2   O  O     0  -0.404  -33.5216  27.4196  29.3852
 5QI  C9   C  CR15  0   0.166  -34.1349  26.6911  28.4506
 5QI  N2   N  N     0  -0.408  -35.2181  27.2195  28.0080
 5QI  C10  C  CR15  0  -0.246  -35.3415  28.4008  28.7039
 5QI  O3   O  O     0  -0.457  -34.0435  33.7683  33.6351
 5QI  C14  C  CH1   0  -0.252  -30.7309  35.2945  33.2757
 5QI  N3   N  NH2   0  -0.781  -32.9607  34.1149  36.2466
 5QI  F1   F  F     0  -0.306  -37.7524  31.2825  29.8701
 5QI  F2   F  F     0  -0.328  -36.4575  32.9613  30.2724
 5QI  H10  H  HCH2  0   0.229  -31.0791  35.8415  35.3261
 5QI  H9   H  HCH2  0   0.226  -32.4978  35.9769  34.3037
 5QI  H16  H  HCH3  0   0.227  -29.5680  33.5096  33.8013
 5QI  H17  H  HCH3  0   0.229  -28.7833  34.5779  32.6507
 5QI  H15  H  HCH3  0   0.216  -28.8666  35.0286  34.3520
 5QI  H12  H  HCH3  0   0.225  -31.3755  37.2426  32.5499
 5QI  H14  H  HCH3  0   0.214  -29.9179  37.2901  33.5416
 5QI  H13  H  HCH3  0   0.226  -29.8367  36.7023  31.8817
 5QI  H8   H  HCH1  0   0.258  -31.2772  33.3771  35.3191
 5QI  H2   H  HCR6  0   0.279  -31.3258  29.9177  32.8030
 5QI  H3   H  HCR6  0   0.315  -34.6143  32.5126  31.9208
 5QI  H4   H  HNH1  0   0.424  -31.5604  31.8720  33.8930
 5QI  H5   H  HCH1  0   0.213  -36.8155  31.5315  31.6243
 5QI  H6   H  HCR5  0   0.296  -33.6765  25.7566  28.1639
 5QI  H7   H  HCR5  0   0.272  -36.1719  29.0630  28.5372
 5QI  H11  H  HCH1  0   0.221  -31.2659  34.7710  32.4743
 5QI  H20  H  HNH2  0   0.355  -32.3978  34.4959  36.9973
 5QI  H18  H  HNH2  0   0.343  -33.6968  34.7920  36.0822
 5QI  H1   H  HCR6  0   0.270  -32.0887  28.3583  31.1202

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
 5QI  N2   C10  aromatic  1.377  0.020  1.377
 5QI  N2   C9   aromatic  1.284  0.020  1.284
 5QI  C10  C7   aromatic  1.361  0.020  1.361
 5QI  C9   O2   aromatic  1.334  0.020  1.334
 5QI  C7   O2   aromatic  1.360  0.020  1.360
 5QI  C7   C1   single    1.452  0.020  1.452
 5QI  F1   C8   single    1.341  0.020  1.341
 5QI  F2   C8   single    1.353  0.020  1.353
 5QI  O1   C8   single    1.361  0.020  1.361
 5QI  O1   C6   single    1.366  0.020  1.366
 5QI  C1   C6   aromatic  1.398  0.020  1.398
 5QI  C1   C2   aromatic  1.398  0.020  1.398
 5QI  C6   C5   aromatic  1.386  0.020  1.386
 5QI  C2   C3   aromatic  1.378  0.020  1.378
 5QI  C5   C4   aromatic  1.394  0.020  1.394
 5QI  C3   C4   aromatic  1.395  0.020  1.395
 5QI  C4   N1   single    1.392  0.020  1.392
 5QI  C15  C14  single    1.526  0.020  1.526
 5QI  C14  C16  single    1.526  0.020  1.526
 5QI  C14  C13  single    1.531  0.020  1.531
 5QI  N1   C11  single    1.360  0.020  1.360
 5QI  O3   C11  double    1.217  0.020  1.217
 5QI  C11  C12  single    1.523  0.020  1.523
 5QI  C13  C12  single    1.533  0.020  1.533
 5QI  C12  N3   single    1.456  0.020  1.456
 5QI  C13  H10  single    0.970  0.020  1.090
 5QI  C13  H9   single    0.970  0.020  1.090
 5QI  C16  H16  single    0.970  0.020  1.090
 5QI  C16  H17  single    0.970  0.020  1.090
 5QI  C16  H15  single    0.970  0.020  1.090
 5QI  C15  H12  single    0.970  0.020  1.090
 5QI  C15  H14  single    0.970  0.020  1.090
 5QI  C15  H13  single    0.970  0.020  1.090
 5QI  C12  H8   single    0.970  0.020  1.090
 5QI  C2   H1   single    0.930  0.020  1.080
 5QI  C3   H2   single    0.930  0.020  1.080
 5QI  C5   H3   single    0.930  0.020  1.080
 5QI  N1   H4   single    0.860  0.020  1.020
 5QI  C8   H5   single    0.970  0.020  1.090
 5QI  C9   H6   single    0.930  0.020  1.080
 5QI  C10  H7   single    0.930  0.020  1.080
 5QI  C14  H11  single    0.970  0.020  1.090
 5QI  N3   H20  single    0.890  0.020  1.040
 5QI  N3   H18  single    0.890  0.020  1.040

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
 5QI  H9   C13  H10  106.38  3.000
 5QI  H9   C13  C14  109.19  3.000
 5QI  H10  C13  C14  108.79  3.000
 5QI  H9   C13  C12  107.99  3.000
 5QI  H10  C13  C12  107.50  3.000
 5QI  C14  C13  C12  116.53  3.000
 5QI  H15  C16  H17  107.57  3.000
 5QI  H15  C16  H16  107.54  3.000
 5QI  H17  C16  H16  107.12  3.000
 5QI  H15  C16  C14  110.75  3.000
 5QI  H17  C16  C14  110.72  3.000
 5QI  H16  C16  C14  112.91  3.000
 5QI  H13  C15  H14  107.64  3.000
 5QI  H13  C15  H12  107.71  3.000
 5QI  H14  C15  H12  107.72  3.000
 5QI  H13  C15  C14  111.22  3.000
 5QI  H14  C15  C14  110.93  3.000
 5QI  H12  C15  C14  111.44  3.000
 5QI  O3   C11  N1   123.87  3.000
 5QI  O3   C11  C12  121.05  3.000
 5QI  N1   C11  C12  115.08  3.000
 5QI  H8   C12  N3   106.80  3.000
 5QI  H8   C12  C11  109.87  3.000
 5QI  N3   C12  C11  107.08  3.000
 5QI  H8   C12  C13  109.22  3.000
 5QI  N3   C12  C13  114.08  3.000
 5QI  C11  C12  C13  109.71  3.000
 5QI  C7   C1   C6   122.33  3.000
 5QI  C6   C1   C2   116.71  3.000
 5QI  C7   C1   C2   120.96  3.000
 5QI  H1   C2   C3   118.10  3.000
 5QI  H1   C2   C1   120.06  3.000
 5QI  C3   C2   C1   121.83  3.000
 5QI  H2   C3   C4   120.22  3.000
 5QI  H2   C3   C2   119.31  3.000
 5QI  C4   C3   C2   120.48  3.000
 5QI  N1   C4   C5   123.58  3.000
 5QI  N1   C4   C3   117.43  3.000
 5QI  C5   C4   C3   118.98  3.000
 5QI  H3   C5   C6   120.89  3.000
 5QI  H3   C5   C4   119.53  3.000
 5QI  C6   C5   C4   119.56  3.000
 5QI  O1   C6   C5   121.51  3.000
 5QI  C5   C6   C1   122.43  3.000
 5QI  O1   C6   C1   116.05  3.000
 5QI  C10  C7   O2   106.24  3.000
 5QI  O2   C7   C1   116.51  3.000
 5QI  C10  C7   C1   137.25  3.000
 5QI  H4   N1   C4   114.77  3.000
 5QI  H4   N1   C11  116.01  3.000
 5QI  C4   N1   C11  129.17  3.000
 5QI  C8   O1   C6   120.38  3.000
 5QI  H5   C8   F2   109.24  3.000
 5QI  H5   C8   F1   110.45  3.000
 5QI  F2   C8   F1   106.43  3.000
 5QI  H5   C8   O1   113.96  3.000
 5QI  F2   C8   O1   110.16  3.000
 5QI  F1   C8   O1   106.31  3.000
 5QI  C9   O2   C7   105.95  3.000
 5QI  H6   C9   N2   128.53  3.000
 5QI  H6   C9   O2   117.61  3.000
 5QI  N2   C9   O2   113.86  3.000
 5QI  C10  N2   C9   104.75  3.000
 5QI  H7   C10  N2   121.29  3.000
 5QI  H7   C10  C7   129.50  3.000
 5QI  N2   C10  C7   109.20  3.000
 5QI  H11  C14  C15  107.28  3.000
 5QI  H11  C14  C16  108.25  3.000
 5QI  C15  C14  C16  110.25  3.000
 5QI  H11  C14  C13  108.85  3.000
 5QI  C16  C14  C13  112.41  3.000
 5QI  C15  C14  C13  109.65  3.000
 5QI  H18  N3   H20  105.82  3.000
 5QI  H18  N3   C12  109.30  3.000
 5QI  H20  N3   C12  108.68  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
 5QI  CONST_01  N2   C10  C7   C1    180.00   0.0  0
 5QI  CONST_02  C9   O2   C7   C1    180.00   0.0  0
 5QI  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 5QI  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 5QI  CONST_05  C10  C7   C1   C2    180.00   0.0  0
 5QI  CONST_06  O2   C7   C1   C2      0.00   0.0  0
 5QI  CONST_07  C5   C6   C1   C2      0.00   0.0  0
 5QI  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 5QI  CONST_09  C7   C1   C2   C3    180.00   0.0  0
 5QI  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 5QI  CONST_11  C6   C5   C4   C3      0.00   0.0  0
 5QI  CONST_12  C7   C1   C6   C5    180.00   0.0  0
 5QI  CONST_13  C10  C7   C1   C6      0.00   0.0  0
 5QI  CONST_14  O2   C7   C1   C6    180.00   0.0  0
 5QI  CONST_15  C9   N2   C10  C7      0.00   0.0  0
 5QI  CONST_16  N2   C9   O2   C7      0.00   0.0  0
 5QI  CONST_17  C10  N2   C9   O2      0.00   0.0  0
 5QI  CONST_18  N2   C10  C7   O2      0.00   0.0  0
 5QI  CONST_19  C10  C7   O2   C9      0.00   0.0  0
 5QI  CONST_20  O1   C6   C1   C2    180.00   0.0  0
 5QI  CONST_21  N1   C4   C3   C2    180.00   0.0  0
 5QI  CONST_22  O1   C6   C5   C4    180.00   0.0  0
 5QI  CONST_23  N1   C4   C5   C6    180.00   0.0  0
 5QI  CONST_24  O1   C6   C1   C7      0.00   0.0  0
 5QI  CONST_25  H7   C10  C7   C1      0.00   0.0  0
 5QI  CONST_26  H3   C5   C6   C1    180.00   0.0  0
 5QI  CONST_27  H2   C3   C2   C1    180.00   0.0  0
 5QI  CONST_28  H3   C5   C4   C3    180.00   0.0  0
 5QI  CONST_29  H1   C2   C3   C4    180.00   0.0  0
 5QI  CONST_30  H2   C3   C4   C5    180.00   0.0  0
 5QI  CONST_31  H1   C2   C1   C6    180.00   0.0  0
 5QI  CONST_32  H6   C9   O2   C7    180.00   0.0  0
 5QI  CONST_33  H1   C2   C1   C7      0.00   0.0  0
 5QI  CONST_34  H7   C10  C7   O2    180.00   0.0  0
 5QI  CONST_35  H7   C10  N2   C9    180.00   0.0  0
 5QI  CONST_36  H6   C9   N2   C10   180.00   0.0  0
 5QI  CONST_37  C5   C4   N1   C11     0.00   0.0  0
 5QI  CONST_38  C3   C4   N1   C11   180.00   0.0  0
 5QI  CONST_39  H4   N1   C4   C3      0.00   0.0  0
 5QI  CONST_40  H4   N1   C4   C5    180.00   0.0  0
 5QI  CONST_41  C4   N1   C11  C12   180.00   0.0  0
 5QI  CONST_42  O3   C11  N1   C4      0.00   0.0  0
 5QI  CONST_43  H4   N1   C11  C12     0.00   0.0  0
 5QI  CONST_44  H4   N1   C11  O3    180.00   0.0  0
 5QI  Var_01    C8   O1   C6   C1    151.84  30.0  2
 5QI  Var_02    C8   O1   C6   C5    -29.66  30.0  2
 5QI  Var_03    F1   C8   O1   C6   -156.32  30.0  3
 5QI  Var_04    F2   C8   O1   C6     88.76  30.0  3
 5QI  Var_05    H5   C8   O1   C6    -34.42  30.0  3
 5QI  Var_06    C12  C13  C14  C16   -63.43  30.0  3
 5QI  Var_07    C12  C13  C14  C15   173.55  30.0  3
 5QI  Var_08    H12  C15  C14  C13   -58.17  30.0  3
 5QI  Var_09    H14  C15  C14  C13    61.85  30.0  3
 5QI  Var_10    H13  C15  C14  C13  -178.37  30.0  3
 5QI  Var_11    H16  C16  C14  C13    62.67  30.0  3
 5QI  Var_12    H17  C16  C14  C13  -177.23  30.0  3
 5QI  Var_13    H15  C16  C14  C13   -57.99  30.0  3
 5QI  Var_14    H12  C15  C14  C16   177.55  30.0  3
 5QI  Var_15    H14  C15  C14  C16   -62.43  30.0  3
 5QI  Var_16    H13  C15  C14  C16    57.34  30.0  3
 5QI  Var_17    H10  C13  C14  C16    58.23  30.0  3
 5QI  Var_18    H9   C13  C14  C16   173.94  30.0  3
 5QI  Var_19    H16  C16  C14  C15  -174.66  30.0  3
 5QI  Var_20    H17  C16  C14  C15   -54.56  30.0  3
 5QI  Var_21    H15  C16  C14  C15    64.68  30.0  3
 5QI  Var_22    H10  C13  C14  C15   -64.79  30.0  3
 5QI  Var_23    H9   C13  C14  C15    50.92  30.0  3
 5QI  Var_24    H11  C14  C13  C12    56.48  30.0  1

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
 5QI  chir_01  C12  C11  C13  N3  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
 5QI  plan-1  C1   0.020
 5QI  plan-1  C7   0.020
 5QI  plan-1  O2   0.020
 5QI  plan-1  C9   0.020
 5QI  plan-1  N2   0.020
 5QI  plan-1  C10  0.020
 5QI  plan-1  H6   0.020
 5QI  plan-1  H7   0.020
 5QI  plan-2  C1   0.020
 5QI  plan-2  C2   0.020
 5QI  plan-2  C3   0.020
 5QI  plan-2  C4   0.020
 5QI  plan-2  C5   0.020
 5QI  plan-2  C6   0.020
 5QI  plan-2  C7   0.020
 5QI  plan-2  N1   0.020
 5QI  plan-2  O1   0.020
 5QI  plan-2  H2   0.020
 5QI  plan-2  H3   0.020
 5QI  plan-2  H1   0.020
 5QI  plan-3  C11  0.020
 5QI  plan-3  C12  0.020
 5QI  plan-3  C4   0.020
 5QI  plan-3  N1   0.020
 5QI  plan-3  O3   0.020
 5QI  plan-3  H4   0.020

