# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 14:03:09 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: N-[3-methoxy-4-(1,3-oxazol-5-yl)phenyl]-D-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(NC(=O)[C@H](N)CC(C)C)ccc1c2ocnc2
#
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
 YFS  YFS  N-[3-methoxy-4-(1,3-oxazol-5-yl)phenyl]-D-leucinamide  ligand  43  22  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YFS
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
 YFS  C13  C  CR6   0  -0.128  36.9611   6.4087  17.4607
 YFS  C18  C  CR15  0   0.162  38.6705   3.7832  15.8763
 YFS  C16  C  CR5   0   0.381  37.3603   5.3562  16.5451
 YFS  C15  C  CR16  0  -0.362  37.3962   7.7394  19.4416
 YFS  C20  C  CR15  0  -0.252  36.8960   4.8113  15.3869
 YFS  C22  C  CH3   0  -0.440  33.8448   7.5133  15.9295
 YFS  C11  C  CR16  0  -0.478  35.3944   8.1367  18.1658
 YFS  C12  C  CR6   0   0.391  35.7702   7.1333  17.2789
 YFS  N1   N  NH2   0  -0.782  33.7394  10.8461  22.3857
 YFS  C2   C  CH1   0  -0.233  34.8074  11.1966  21.4592
 YFS  C3   C  CH2   0  -0.417  34.6932  12.6100  20.8780
 YFS  C4   C  CH1   0  -0.252  35.7866  13.0341  19.8951
 YFS  C5   C  CH3   0  -0.645  35.4527  14.4073  19.3198
 YFS  C6   C  CH3   0  -0.656  37.1706  13.0503  20.5366
 YFS  C7   C  C     0   0.559  34.7733  10.1710  20.3332
 YFS  O8   O  O     0  -0.460  33.7793  10.0352  19.6426
 YFS  C10  C  CR6   0   0.399  36.2088   8.4465  19.2539
 YFS  C14  C  CR16  0  -0.272  37.7554   6.7425  18.5586
 YFS  O17  O  O     0  -0.406  38.5041   4.6830  16.8486
 YFS  N19  N  N     0  -0.410  37.7514   3.8102  14.9809
 YFS  O21  O  O2    0  -0.470  35.0323   6.7971  16.2121
 YFS  H39  H  HCR5  0   0.293  39.5355   3.1398  15.9337
 YFS  H38  H  HCR6  0   0.270  38.0428   7.9698  20.2791
 YFS  H40  H  HCR5  0   0.271  36.0192   5.0646  14.8188
 YFS  H41  H  HCH3  0   0.264  33.4435   7.0872  15.0137
 YFS  H42  H  HCH3  0   0.234  33.1037   7.4024  16.7244
 YFS  H43  H  HCH3  0   0.234  34.0407   8.5760  15.7695
 YFS  H36  H  HCR6  0   0.310  34.4756   8.6774  18.0165
 YFS  H25  H  HNH2  0   0.354  33.7865  11.4633  23.1874
 YFS  H24  H  HNH2  0   0.343  32.8434  11.0289  21.9483
 YFS  H23  H  HCH1  0   0.256  35.7463  11.1099  22.0122
 YFS  H26  H  HCH2  0   0.228  34.6802  13.3122  21.7192
 YFS  H27  H  HCH2  0   0.225  33.7166  12.6955  20.3901
 YFS  H28  H  HCH1  0   0.221  35.8057  12.3246  19.0587
 YFS  H31  H  HCH3  0   0.225  34.4833  14.4055  18.8185
 YFS  H30  H  HCH3  0   0.214  35.4160  15.1618  20.1094
 YFS  H29  H  HCH3  0   0.225  36.2031  14.7245  18.5941
 YFS  H33  H  HCH3  0   0.226  37.4877  12.0638  20.8766
 YFS  H34  H  HCH3  0   0.228  37.9222  13.4025  19.8285
 YFS  H32  H  HCH3  0   0.215  37.1889  13.7190  21.4005
 YFS  H35  H  HNH1  0   0.421  36.6427   9.6266  20.8532
 YFS  H37  H  HCR6  0   0.263  38.6827   6.2150  18.7351
 YFS  N9   N  NH1   0  -0.749  35.9132   9.4487  20.1786

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
 YFS  N19  C20  aromatic  1.378  0.020  1.378
 YFS  N19  C18  aromatic  1.283  0.020  1.283
 YFS  C20  C16  aromatic  1.362  0.020  1.362
 YFS  C18  O17  aromatic  1.335  0.020  1.335
 YFS  C22  O21  single    1.415  0.020  1.415
 YFS  O21  C12  single    1.340  0.020  1.340
 YFS  C16  O17  aromatic  1.361  0.020  1.361
 YFS  C16  C13  single    1.451  0.020  1.451
 YFS  C12  C13  aromatic  1.406  0.020  1.406
 YFS  C12  C11  aromatic  1.391  0.020  1.391
 YFS  C13  C14  aromatic  1.396  0.020  1.396
 YFS  C11  C10  aromatic  1.394  0.020  1.394
 YFS  C14  C15  aromatic  1.379  0.020  1.379
 YFS  C5   C4   single    1.526  0.020  1.526
 YFS  C10  C15  aromatic  1.395  0.020  1.395
 YFS  C10  N9   single    1.395  0.020  1.395
 YFS  O8   C7   double    1.218  0.020  1.218
 YFS  C4   C6   single    1.526  0.020  1.526
 YFS  C4   C3   single    1.530  0.020  1.530
 YFS  N9   C7   single    1.358  0.020  1.358
 YFS  C7   C2   single    1.524  0.020  1.524
 YFS  C3   C2   single    1.533  0.020  1.533
 YFS  C2   N1   single    1.457  0.020  1.457
 YFS  C18  H39  single    0.930  0.020  1.080
 YFS  C15  H38  single    0.930  0.020  1.080
 YFS  C20  H40  single    0.930  0.020  1.080
 YFS  C22  H41  single    0.970  0.020  1.090
 YFS  C22  H42  single    0.970  0.020  1.090
 YFS  C22  H43  single    0.970  0.020  1.090
 YFS  C11  H36  single    0.930  0.020  1.080
 YFS  N1   H25  single    0.890  0.020  1.040
 YFS  N1   H24  single    0.890  0.020  1.040
 YFS  C2   H23  single    0.970  0.020  1.090
 YFS  C3   H26  single    0.970  0.020  1.090
 YFS  C3   H27  single    0.970  0.020  1.090
 YFS  C4   H28  single    0.970  0.020  1.090
 YFS  C5   H31  single    0.970  0.020  1.090
 YFS  C5   H30  single    0.970  0.020  1.090
 YFS  C5   H29  single    0.970  0.020  1.090
 YFS  C6   H33  single    0.970  0.020  1.090
 YFS  C6   H34  single    0.970  0.020  1.090
 YFS  C6   H32  single    0.970  0.020  1.090
 YFS  N9   H35  single    0.860  0.020  1.020
 YFS  C14  H37  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
 YFS  C14  C13  C12  117.42  3.000
 YFS  C14  C13  C16  120.89  3.000
 YFS  C12  C13  C16  121.69  3.000
 YFS  H39  C18  N19  128.57  3.000
 YFS  H39  C18  O17  117.56  3.000
 YFS  N19  C18  O17  113.86  3.000
 YFS  O17  C16  C20  106.15  3.000
 YFS  O17  C16  C13  116.69  3.000
 YFS  C20  C16  C13  137.16  3.000
 YFS  H38  C15  C14  119.57  3.000
 YFS  H38  C15  C10  120.30  3.000
 YFS  C14  C15  C10  120.13  3.000
 YFS  H40  C20  N19  121.45  3.000
 YFS  H40  C20  C16  129.30  3.000
 YFS  N19  C20  C16  109.25  3.000
 YFS  H43  C22  H42  109.08  3.000
 YFS  H43  C22  H41  108.91  3.000
 YFS  H42  C22  H41  108.84  3.000
 YFS  H43  C22  O21  111.78  3.000
 YFS  H42  C22  O21  111.88  3.000
 YFS  H41  C22  O21  106.24  3.000
 YFS  H36  C11  C10  119.68  3.000
 YFS  H36  C11  C12  120.30  3.000
 YFS  C10  C11  C12  120.02  3.000
 YFS  O21  C12  C11  122.68  3.000
 YFS  C11  C12  C13  121.21  3.000
 YFS  O21  C12  C13  116.11  3.000
 YFS  H24  N1   H25  105.83  3.000
 YFS  H24  N1   C2   109.28  3.000
 YFS  H25  N1   C2   108.83  3.000
 YFS  H23  C2   C7   109.86  3.000
 YFS  H23  C2   C3   109.21  3.000
 YFS  C7   C2   C3   109.81  3.000
 YFS  H23  C2   N1   106.80  3.000
 YFS  C3   C2   N1   114.11  3.000
 YFS  C7   C2   N1   106.96  3.000
 YFS  H27  C3   H26  106.35  3.000
 YFS  H27  C3   C4   109.23  3.000
 YFS  H26  C3   C4   108.90  3.000
 YFS  H27  C3   C2   107.91  3.000
 YFS  H26  C3   C2   107.50  3.000
 YFS  C4   C3   C2   116.48  3.000
 YFS  H28  C4   C6   108.16  3.000
 YFS  H28  C4   C5   107.36  3.000
 YFS  C6   C4   C5   110.33  3.000
 YFS  H28  C4   C3   108.85  3.000
 YFS  C6   C4   C3   112.41  3.000
 YFS  C5   C4   C3   109.59  3.000
 YFS  H29  C5   H30  107.64  3.000
 YFS  H29  C5   H31  107.81  3.000
 YFS  H30  C5   H31  107.65  3.000
 YFS  H29  C5   C4   111.22  3.000
 YFS  H30  C5   C4   110.88  3.000
 YFS  H31  C5   C4   111.47  3.000
 YFS  H32  C6   H34  107.70  3.000
 YFS  H32  C6   H33  107.59  3.000
 YFS  H34  C6   H33  107.11  3.000
 YFS  H32  C6   C4   110.74  3.000
 YFS  H34  C6   C4   110.83  3.000
 YFS  H33  C6   C4   112.66  3.000
 YFS  N9   C7   O8   124.14  3.000
 YFS  N9   C7   C2   115.04  3.000
 YFS  O8   C7   C2   120.82  3.000
 YFS  N9   C10  C11  123.58  3.000
 YFS  N9   C10  C15  117.09  3.000
 YFS  C11  C10  C15  119.32  3.000
 YFS  H37  C14  C15  118.12  3.000
 YFS  H37  C14  C13  119.98  3.000
 YFS  C15  C14  C13  121.89  3.000
 YFS  C16  O17  C18  106.00  3.000
 YFS  C20  N19  C18  104.73  3.000
 YFS  C12  O21  C22  119.61  3.000
 YFS  H35  N9   C10  114.60  3.000
 YFS  H35  N9   C7   115.90  3.000
 YFS  C10  N9   C7   129.43  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
 YFS  CONST_01  N19  C20  C16  C13  180.00   0.0  0
 YFS  CONST_02  C18  O17  C16  C13  180.00   0.0  0
 YFS  CONST_03  C10  C11  C12  C13    0.00   0.0  0
 YFS  CONST_04  C10  C15  C14  C13    0.00   0.0  0
 YFS  CONST_05  C16  C20  N19  C18    0.00   0.0  0
 YFS  CONST_06  C20  C16  O17  C18    0.00   0.0  0
 YFS  CONST_07  N19  C18  O17  C16    0.00   0.0  0
 YFS  CONST_08  C11  C12  C13  C16  180.00   0.0  0
 YFS  CONST_09  C15  C14  C13  C16  180.00   0.0  0
 YFS  CONST_10  C12  C13  C14  C15    0.00   0.0  0
 YFS  CONST_11  C12  C11  C10  C15    0.00   0.0  0
 YFS  CONST_12  O17  C18  N19  C20    0.00   0.0  0
 YFS  CONST_13  C12  C13  C16  C20    0.00   0.0  0
 YFS  CONST_14  C14  C13  C16  C20  180.00   0.0  0
 YFS  CONST_15  C14  C13  C12  C11    0.00   0.0  0
 YFS  CONST_16  C14  C15  C10  C11    0.00   0.0  0
 YFS  CONST_17  O17  C16  C13  C12  180.00   0.0  0
 YFS  CONST_18  O17  C16  C13  C14    0.00   0.0  0
 YFS  CONST_19  N19  C20  C16  O17    0.00   0.0  0
 YFS  CONST_20  O21  C12  C13  C16    0.00   0.0  0
 YFS  CONST_21  N9   C10  C11  C12  180.00   0.0  0
 YFS  CONST_22  C14  C15  C10  N9   180.00   0.0  0
 YFS  CONST_23  O21  C12  C11  C10  180.00   0.0  0
 YFS  CONST_24  O21  C12  C13  C14  180.00   0.0  0
 YFS  CONST_25  H40  C20  C16  C13    0.00   0.0  0
 YFS  CONST_26  H36  C11  C12  C13  180.00   0.0  0
 YFS  CONST_27  H38  C15  C14  C13  180.00   0.0  0
 YFS  CONST_28  H39  C18  O17  C16  180.00   0.0  0
 YFS  CONST_29  H37  C14  C13  C16    0.00   0.0  0
 YFS  CONST_30  C7   N9   C10  C15  180.00   0.0  0
 YFS  CONST_31  C7   N9   C10  C11    0.00   0.0  0
 YFS  CONST_32  H35  N9   C10  C15    0.00   0.0  0
 YFS  CONST_33  C10  N9   C7   C2   180.00   0.0  0
 YFS  CONST_34  C10  N9   C7   O8     0.00   0.0  0
 YFS  Var_01    C11  C12  O21  C22    2.49  30.0  2
 YFS  Var_02    H41  C22  O21  C12  178.20  30.0  3
 YFS  Var_03    C5   C4   C3   C2   174.84  30.0  2
 YFS  Var_04    H31  C5   C4   C3   -58.14  30.0  3
 YFS  Var_05    H33  C6   C4   C3    62.79  30.0  3

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
 YFS  chir_01  C2  C7  C3  N1  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
 YFS  plan-1  C13  0.020
 YFS  plan-1  C18  0.020
 YFS  plan-1  C16  0.020
 YFS  plan-1  C20  0.020
 YFS  plan-1  O17  0.020
 YFS  plan-1  N19  0.020
 YFS  plan-1  H39  0.020
 YFS  plan-1  H40  0.020
 YFS  plan-2  C13  0.020
 YFS  plan-2  C16  0.020
 YFS  plan-2  C15  0.020
 YFS  plan-2  C11  0.020
 YFS  plan-2  C12  0.020
 YFS  plan-2  C10  0.020
 YFS  plan-2  C14  0.020
 YFS  plan-2  O21  0.020
 YFS  plan-2  H38  0.020
 YFS  plan-2  H36  0.020
 YFS  plan-2  H37  0.020
 YFS  plan-2  N9   0.020
 YFS  plan-3  C2   0.020
 YFS  plan-3  C7   0.020
 YFS  plan-3  O8   0.020
 YFS  plan-3  C10  0.020
 YFS  plan-3  H35  0.020
 YFS  plan-3  N9   0.020

