# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 01:44:46 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: ~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]propan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(c1)C(=O)N[C@@H](Cc2ccc(F)cc2)C(=O)N[C@@H](C[C@@H]3CCCNC3=O)C=O
#
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
 5GI  5GI  ~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]propan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide  ligand  57  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5GI
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
 5GI  C1   C  CH1   0  -0.220   0.2724   0.4164  -0.5362
 5GI  C2   C  CH2   0  -0.519   0.7233   1.5220  -1.5178
 5GI  C3   C  C     0   0.577  -0.9620  -0.2672  -1.1099
 5GI  C4   C  CH3   0  -0.747   6.1313  -3.5573   1.5930
 5GI  C5   C  CR6   0   0.127   1.9911   2.1776  -1.0562
 5GI  C6   C  CR16  0  -0.290   3.2329   1.6854  -1.4490
 5GI  C7   C  CR16  0  -0.277   1.9532   3.2558  -0.1766
 5GI  C8   C  CR16  0  -0.396   4.4117   2.2452  -0.9767
 5GI  C9   C  CR6   0   0.510   4.3300   3.3119  -0.1040
 5GI  C10  C  CR16  0  -0.398   3.1183   3.8345   0.3045
 5GI  C12  C  CR5   0   0.139   3.2193  -1.5705   0.6668
 5GI  C13  C  C     0  -0.261  -6.3285  -1.9671   2.3758
 5GI  C14  C  CR15  0  -0.495   4.1289  -1.8974   1.6968
 5GI  C15  C  C1    0   0.199  -3.4195   0.6339  -2.8648
 5GI  C16  C  CR5   0   0.431   4.9528  -2.8028   1.1149
 5GI  C17  C  C     0  -0.468  -4.9122  -2.3443   2.0009
 5GI  C18  C  CH1   0  -0.214  -3.3516   0.0098  -1.4882
 5GI  C19  C  CH2   0  -0.464  -4.5738   0.4340  -0.6730
 5GI  C20  C  CR16  0  -0.373  -4.6291  -0.2173   0.7113
 5GI  C21  C  CR6   0   0.565  -5.8418   0.3176   1.4640
 5GI  C22  C  C     0  -0.451  -4.5637  -1.7406   0.6518
 5GI  F1   F  F     0  -0.318   5.4655   3.8633   0.3590
 5GI  N1   N  NH1   0  -0.645   1.3078  -0.5583  -0.3373
 5GI  N2   N  N     0  -0.169   3.4848  -2.2234  -0.4278
 5GI  N3   N  NR16  0  -0.629  -6.5352  -0.5384   2.2291
 5GI  N4   N  NH1   0  -0.632  -2.1251   0.3375  -0.8167
 5GI  O1   O  O     0  -0.324   4.5609  -2.9920  -0.1539
 5GI  O3   O  O     0  -0.478  -0.8730  -1.2630  -1.8079
 5GI  O4   O  O     0  -0.458   1.9521   0.0841   1.7475
 5GI  O5   O  O     0  -0.512  -6.1486   1.5035   1.3939
 5GI  H1   H  HCH1  0   0.298   0.0370   0.8690   0.4283
 5GI  H2   H  HCH2  0   0.269   0.8620   1.0797  -2.5073
 5GI  H3   H  HCH2  0   0.270  -0.0775   2.2585  -1.6110
 5GI  H4   H  HCH3  0   0.272   6.0065  -4.6291   1.4377
 5GI  H5   H  HCH3  0   0.273   7.0356  -3.2467   1.0681
 5GI  H6   H  HCH3  0   0.271   6.2750  -3.3777   2.6553
 5GI  H7   H  HCR6  0   0.260   3.2890   0.8529  -2.1393
 5GI  H8   H  HCR6  0   0.258   0.9978   3.6559   0.1412
 5GI  H9   H  HCR6  0   0.277   5.3741   1.8576  -1.2836
 5GI  H10  H  HCR6  0   0.277   3.0836   4.6748   0.9855
 5GI  H11  H  H     0   0.233  -7.0384  -2.5137   1.7471
 5GI  H12  H  H     0   0.254  -6.5423  -2.2372   3.4103
 5GI  H13  H  HCR5  0   0.287   4.1625  -1.5228   2.7049
 5GI  H14  H  H     0   0.208  -4.3490   0.4067  -3.4161
 5GI  H16  H  H     0   0.236  -4.2146  -1.9845   2.7626
 5GI  H17  H  H     0   0.253  -4.8262  -3.4312   1.9747
 5GI  H18  H  HCH1  0   0.297  -3.3953  -1.0719  -1.6525
 5GI  H19  H  HCH2  0   0.267  -4.5840   1.5209  -0.5727
 5GI  H20  H  HCH2  0   0.263  -5.4681   0.1612  -1.2397
 5GI  H21  H  HCR6  0   0.279  -3.7643   0.1326   1.2894
 5GI  H23  H  H     0   0.254  -3.5622  -2.0549   0.3528
 5GI  H24  H  H     0   0.234  -5.2548  -2.1173  -0.1103
 5GI  H25  H  HNH1  0   0.407   1.5162  -1.1797  -1.1061
 5GI  H26  H  HNR6  0   0.393  -7.3393  -0.1455   2.6969
 5GI  H28  H  HNH1  0   0.410  -2.0979   1.2029  -0.2981
 5GI  C11  C  C     0   0.553   2.0963  -0.5958   0.7469
 5GI  O2   O  O     0  -0.360  -2.5514   1.3126  -3.3451

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
 5GI  F1   C9   single    1.345  0.020  1.345
 5GI  C9   C10  aromatic  1.381  0.020  1.381
 5GI  C9   C8   aromatic  1.381  0.020  1.381
 5GI  C10  C7   aromatic  1.387  0.020  1.387
 5GI  O1   N2   aromatic  1.350  0.020  1.350
 5GI  O1   C16  aromatic  1.341  0.020  1.341
 5GI  C8   C6   aromatic  1.388  0.020  1.388
 5GI  N2   C12  aromatic  1.302  0.020  1.302
 5GI  C4   C16  single    1.479  0.020  1.479
 5GI  C16  C14  aromatic  1.355  0.020  1.355
 5GI  C7   C5   aromatic  1.392  0.020  1.392
 5GI  C12  C14  aromatic  1.412  0.020  1.412
 5GI  C12  C11  single    1.489  0.020  1.489
 5GI  C6   C5   aromatic  1.392  0.020  1.392
 5GI  C5   C2   single    1.500  0.020  1.500
 5GI  C11  N1   single    1.341  0.020  1.341
 5GI  C11  O4   double    1.218  0.020  1.218
 5GI  N1   C1   single    1.436  0.020  1.436
 5GI  C2   C1   single    1.546  0.020  1.546
 5GI  C1   C3   single    1.523  0.020  1.523
 5GI  C3   O3   double    1.219  0.020  1.219
 5GI  C3   N4   single    1.343  0.020  1.343
 5GI  C17  C13  single    1.513  0.020  1.513
 5GI  C17  C22  single    1.519  0.020  1.519
 5GI  N4   C18  single    1.436  0.020  1.436
 5GI  C13  N3   single    1.451  0.020  1.451
 5GI  C22  C20  single    1.526  0.020  1.526
 5GI  C20  C21  single    1.524  0.020  1.524
 5GI  C20  C19  single    1.531  0.020  1.531
 5GI  N3   C21  single    1.341  0.020  1.341
 5GI  C18  C19  single    1.529  0.020  1.529
 5GI  C18  C15  single    1.513  0.020  1.513
 5GI  O5   C21  double    1.227  0.020  1.227
 5GI  C15  O2   double    1.202  0.020  1.202
 5GI  C1   H1   single    0.970  0.020  1.090
 5GI  C2   H2   single    0.970  0.020  1.090
 5GI  C2   H3   single    0.970  0.020  1.090
 5GI  C4   H4   single    0.970  0.020  1.090
 5GI  C4   H5   single    0.970  0.020  1.090
 5GI  C4   H6   single    0.970  0.020  1.090
 5GI  C6   H7   single    0.930  0.020  1.080
 5GI  C7   H8   single    0.930  0.020  1.080
 5GI  C8   H9   single    0.930  0.020  1.080
 5GI  C10  H10  single    0.930  0.020  1.080
 5GI  C13  H11  single    0.970  0.020  1.090
 5GI  C13  H12  single    0.970  0.020  1.090
 5GI  C14  H13  single    0.930  0.020  1.080
 5GI  C15  H14  single    0.930  0.020  1.080
 5GI  C17  H16  single    0.970  0.020  1.090
 5GI  C17  H17  single    0.970  0.020  1.090
 5GI  C18  H18  single    0.970  0.020  1.090
 5GI  C19  H19  single    0.970  0.020  1.090
 5GI  C19  H20  single    0.970  0.020  1.090
 5GI  C20  H21  single    0.970  0.020  1.090
 5GI  C22  H23  single    0.970  0.020  1.090
 5GI  C22  H24  single    0.970  0.020  1.090
 5GI  N1   H25  single    0.860  0.020  1.020
 5GI  N3   H26  single    0.860  0.020  1.020
 5GI  N4   H28  single    0.860  0.020  1.020

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
 5GI  H1   C1   N1   108.34  3.000
 5GI  H1   C1   C3   110.13  3.000
 5GI  N1   C1   C3   109.39  3.000
 5GI  H1   C1   C2   109.12  3.000
 5GI  C3   C1   C2   108.56  3.000
 5GI  N1   C1   C2   111.30  3.000
 5GI  H3   C2   H2   106.79  3.000
 5GI  H3   C2   C5   110.57  3.000
 5GI  H2   C2   C5   110.38  3.000
 5GI  H3   C2   C1   108.83  3.000
 5GI  H2   C2   C1   108.82  3.000
 5GI  C5   C2   C1   111.33  3.000
 5GI  O3   C3   N4   123.76  3.000
 5GI  N4   C3   C1   114.68  3.000
 5GI  O3   C3   C1   121.53  3.000
 5GI  H6   C4   H5   108.28  3.000
 5GI  H6   C4   H4   108.47  3.000
 5GI  H5   C4   H4   107.84  3.000
 5GI  H6   C4   C16  109.70  3.000
 5GI  H5   C4   C16  111.09  3.000
 5GI  H4   C4   C16  111.37  3.000
 5GI  C7   C5   C6   118.45  3.000
 5GI  C6   C5   C2   120.83  3.000
 5GI  C7   C5   C2   120.66  3.000
 5GI  H7   C6   C8   118.89  3.000
 5GI  H7   C6   C5   119.85  3.000
 5GI  C8   C6   C5   121.26  3.000
 5GI  H8   C7   C10  119.01  3.000
 5GI  H8   C7   C5   119.69  3.000
 5GI  C10  C7   C5   121.30  3.000
 5GI  H9   C8   C9   120.58  3.000
 5GI  H9   C8   C6   120.97  3.000
 5GI  C9   C8   C6   118.46  3.000
 5GI  F1   C9   C10  118.93  3.000
 5GI  C10  C9   C8   122.08  3.000
 5GI  F1   C9   C8   118.98  3.000
 5GI  H10  C10  C9   120.53  3.000
 5GI  H10  C10  C7   121.02  3.000
 5GI  C9   C10  C7   118.45  3.000
 5GI  N2   C12  C14  111.45  3.000
 5GI  C14  C12  C11  126.72  3.000
 5GI  N2   C12  C11  121.82  3.000
 5GI  H12  C13  H11  107.11  3.000
 5GI  H12  C13  N3   108.17  3.000
 5GI  H11  C13  N3   109.95  3.000
 5GI  H12  C13  C17  110.91  3.000
 5GI  H11  C13  C17  109.90  3.000
 5GI  N3   C13  C17  110.72  3.000
 5GI  H13  C14  C16  128.01  3.000
 5GI  H13  C14  C12  128.52  3.000
 5GI  C16  C14  C12  103.47  3.000
 5GI  H14  C15  O2   121.63  3.000
 5GI  H14  C15  C18  114.02  3.000
 5GI  O2   C15  C18  124.34  3.000
 5GI  O1   C16  C14  108.83  3.000
 5GI  C14  C16  C4   133.35  3.000
 5GI  O1   C16  C4   117.82  3.000
 5GI  H17  C17  H16  107.11  3.000
 5GI  H17  C17  C22  110.90  3.000
 5GI  H16  C17  C22  109.97  3.000
 5GI  H17  C17  C13  109.16  3.000
 5GI  H16  C17  C13  110.03  3.000
 5GI  C22  C17  C13  109.63  3.000
 5GI  H18  C18  N4   109.24  3.000
 5GI  H18  C18  C19  108.80  3.000
 5GI  N4   C18  C19  111.72  3.000
 5GI  H18  C18  C15  105.62  3.000
 5GI  C19  C18  C15  109.56  3.000
 5GI  N4   C18  C15  111.69  3.000
 5GI  H20  C19  H19  106.77  3.000
 5GI  H20  C19  C20  109.45  3.000
 5GI  H19  C19  C20  109.89  3.000
 5GI  H20  C19  C18  107.95  3.000
 5GI  H19  C19  C18  109.43  3.000
 5GI  C20  C19  C18  113.13  3.000
 5GI  H21  C20  C22  107.76  3.000
 5GI  H21  C20  C21  104.77  3.000
 5GI  C22  C20  C21  113.81  3.000
 5GI  H21  C20  C19  108.20  3.000
 5GI  C21  C20  C19  109.03  3.000
 5GI  C22  C20  C19  112.83  3.000
 5GI  O5   C21  N3   121.34  3.000
 5GI  O5   C21  C20  120.66  3.000
 5GI  N3   C21  C20  117.98  3.000
 5GI  H24  C22  H23  106.81  3.000
 5GI  H24  C22  C20  110.08  3.000
 5GI  H23  C22  C20  109.73  3.000
 5GI  H24  C22  C17  109.66  3.000
 5GI  H23  C22  C17  109.84  3.000
 5GI  C20  C22  C17  110.63  3.000
 5GI  H25  N1   C11  118.47  3.000
 5GI  H25  N1   C1   117.44  3.000
 5GI  C11  N1   C1   123.71  3.000
 5GI  O1   N2   C12  106.10  3.000
 5GI  H26  N3   C21  115.32  3.000
 5GI  H26  N3   C13  116.72  3.000
 5GI  C21  N3   C13  127.76  3.000
 5GI  H28  N4   C18  117.32  3.000
 5GI  H28  N4   C3   118.34  3.000
 5GI  C18  N4   C3   122.33  3.000
 5GI  N2   O1   C16  110.14  3.000
 5GI  O4   C11  N1   125.36  3.000
 5GI  O4   C11  C12  119.92  3.000
 5GI  N1   C11  C12  114.72  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
 5GI  CONST_01  C9   C10  C7   C5      0.00   0.0  0
 5GI  CONST_02  C9   C8   C6   C5      0.00   0.0  0
 5GI  CONST_03  C10  C9   C8   C6      0.00   0.0  0
 5GI  CONST_04  C10  C7   C5   C6      0.00   0.0  0
 5GI  CONST_05  C8   C9   C10  C7      0.00   0.0  0
 5GI  CONST_06  C8   C6   C5   C7      0.00   0.0  0
 5GI  CONST_07  C16  O1   N2   C12     0.00   0.0  0
 5GI  CONST_08  O1   C16  C14  C12     0.00   0.0  0
 5GI  CONST_09  N2   O1   C16  C14     0.00   0.0  0
 5GI  CONST_10  O1   N2   C12  C14     0.00   0.0  0
 5GI  CONST_11  N2   C12  C14  C16     0.00   0.0  0
 5GI  CONST_12  C20  C21  N3   C13     0.00   0.0  0
 5GI  CONST_13  C10  C7   C5   C2    180.00   0.0  0
 5GI  CONST_14  C8   C6   C5   C2    180.00   0.0  0
 5GI  CONST_15  N2   O1   C16  C4    180.00   0.0  0
 5GI  CONST_16  C12  C14  C16  C4    180.00   0.0  0
 5GI  CONST_17  F1   C9   C8   C6    180.00   0.0  0
 5GI  CONST_18  F1   C9   C10  C7    180.00   0.0  0
 5GI  CONST_19  O1   N2   C12  C11   180.00   0.0  0
 5GI  CONST_20  C16  C14  C12  C11   180.00   0.0  0
 5GI  CONST_21  O5   C21  N3   C13   180.00   0.0  0
 5GI  CONST_22  H10  C10  C7   C5    180.00   0.0  0
 5GI  CONST_23  H9   C8   C6   C5    180.00   0.0  0
 5GI  CONST_24  H8   C7   C5   C6    180.00   0.0  0
 5GI  CONST_25  H7   C6   C5   C7    180.00   0.0  0
 5GI  CONST_26  H13  C14  C12  N2    180.00   0.0  0
 5GI  CONST_27  H26  N3   C21  C20   180.00   0.0  0
 5GI  CONST_28  C12  C11  N1   C1    180.00   0.0  0
 5GI  CONST_29  H25  N1   C11  C12     0.00   0.0  0
 5GI  CONST_30  O4   C11  N1   C1      0.00   0.0  0
 5GI  CONST_31  C18  N4   C3   C1    180.00   0.0  0
 5GI  CONST_32  O3   C3   N4   C18     0.00   0.0  0
 5GI  CONST_33  H28  N4   C3   C1      0.00   0.0  0
 5GI  Var_01    C20  C22  C17  C13    61.76  30.0  1
 5GI  Var_02    C21  N3   C13  C17    22.53  30.0  1
 5GI  Var_03    N3   C13  C17  C22   -49.90  30.0  1
 5GI  Var_04    C7   C5   C2   C1    -87.09  30.0  2
 5GI  Var_05    N1   C11  C12  C14  -174.33  30.0  2
 5GI  Var_06    H4   C4   C16  C14   126.02  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
 5GI  chir_01  C1   N1   C2   C3   negativ
 5GI  chir_02  C18  N4   C19  C15  negativ
 5GI  chir_03  C20  C22  C21  C19  positiv

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
 5GI  plan-1  C4   0.020
 5GI  plan-1  C12  0.020
 5GI  plan-1  C14  0.020
 5GI  plan-1  C16  0.020
 5GI  plan-1  N2   0.020
 5GI  plan-1  O1   0.020
 5GI  plan-1  H13  0.020
 5GI  plan-1  C11  0.020
 5GI  plan-2  C15  0.020
 5GI  plan-2  C18  0.020
 5GI  plan-2  H14  0.020
 5GI  plan-2  O2   0.020
 5GI  plan-3  C2   0.020
 5GI  plan-3  C5   0.020
 5GI  plan-3  C6   0.020
 5GI  plan-3  C7   0.020
 5GI  plan-3  C8   0.020
 5GI  plan-3  C9   0.020
 5GI  plan-3  C10  0.020
 5GI  plan-3  F1   0.020
 5GI  plan-3  H7   0.020
 5GI  plan-3  H8   0.020
 5GI  plan-3  H9   0.020
 5GI  plan-3  H10  0.020
 5GI  plan-4  C1   0.020
 5GI  plan-4  C3   0.020
 5GI  plan-4  C18  0.020
 5GI  plan-4  N4   0.020
 5GI  plan-4  O3   0.020
 5GI  plan-4  H28  0.020
 5GI  plan-5  C1   0.020
 5GI  plan-5  C12  0.020
 5GI  plan-5  N1   0.020
 5GI  plan-5  O4   0.020
 5GI  plan-5  H25  0.020
 5GI  plan-5  C11  0.020
 5GI  plan-6  C13  0.020
 5GI  plan-6  C20  0.020
 5GI  plan-6  C21  0.020
 5GI  plan-6  N3   0.020
 5GI  plan-6  O5   0.020
 5GI  plan-6  H26  0.020

