# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 07:47:40 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H]([C@H](O)C(=O)NO)C(=O)N[C@H](C(O)=O)c1ccccc1
#
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
 TOD  TOD  '(2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid'  ligand  45  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TOD
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
 TOD  C2   C  CH1    0  -0.261   1.5207   2.1018   0.8430
 TOD  C3   C  CH3    0  -0.671   2.6119   2.5397  -0.1279
 TOD  C4   C  CH2    0  -0.409   1.6282   0.6395   1.2854
 TOD  C5   C  CH1    0  -0.442   1.4459  -0.4774   0.2355
 TOD  C6   C  CH1    0  -0.060   2.6651  -0.8310  -0.6181
 TOD  C7   C  C      0   0.503   3.8706  -1.1318   0.2676
 TOD  C10  C  C      0   0.073  -3.3397  -0.6327  -0.0575
 TOD  C11  C  C1     0  -0.294  -3.4681  -0.2257   1.2705
 TOD  C12  C  C1     0  -0.240  -4.5731  -0.6038   2.0198
 TOD  C14  C  C1     0  -0.242  -5.4604  -1.7787   0.1249
 TOD  C16  C  C      0   0.418  -2.3469   1.3126  -1.2072
 TOD  O6   O  OC    -1  -0.603  -2.9885   1.5464  -2.2470
 TOD  O5   O  O      0  -0.577  -1.9125   2.1249  -0.3765
 TOD  C9   C  CH1    0  -0.195  -2.1579  -0.2017  -0.8847
 TOD  C15  C  C1     0  -0.321  -4.3488  -1.4079  -0.6207
 TOD  C13  C  C1     0  -0.270  -5.5741  -1.3813   1.4501
 TOD  N2   N  NH1    0  -0.647  -0.9313  -0.4878  -0.1776
 TOD  C8   C  C      0   0.617   0.2673  -0.1657  -0.6776
 TOD  O4   O  O      0  -0.506   0.4039   0.3521  -1.7777
 TOD  C1   C  CH3    0  -0.652   1.5501   2.9871   2.0869
 TOD  O3   O  OH1    0  -0.656   2.4092  -1.9603  -1.4181
 TOD  O1   O  O      0  -0.471   3.8740  -2.0691   1.0465
 TOD  N1   N  NH1    0  -0.374   4.8920  -0.2768   0.1102
 TOD  O2   O  OH1    0  -0.539   6.0855  -0.5209   0.7183
 TOD  H1   H  HCH1   0   0.254   0.5458   2.2421   0.3671
 TOD  H2   H  HCH3   0   0.228   2.5325   3.6083  -0.3369
 TOD  H3   H  HCH3   0   0.206   3.6055   2.3641   0.2925
 TOD  H4   H  HCH3   0   0.232   2.5480   2.0232  -1.0852
 TOD  H5   H  HCH2   0   0.231   2.5800   0.4932   1.8072
 TOD  H6   H  HCH2   0   0.240   0.8609   0.4749   2.0466
 TOD  H7   H  HCH1   0   0.266   1.2065  -1.3820   0.8073
 TOD  H8   H  HCH1   0   0.259   2.8858  -0.0205  -1.3136
 TOD  H9   H  H      0   0.253  -2.7042   0.3965   1.7207
 TOD  H10  H  H      0   0.253  -4.6571  -0.2849   3.0509
 TOD  H11  H  H      0   0.254  -6.2345  -2.3839  -0.3294
 TOD  H13  H  HCH1   0   0.241  -2.1716  -0.7591  -1.8256
 TOD  H14  H  H      0   0.249  -4.2596  -1.7316  -1.6508
 TOD  H15  H  H      0   0.253  -6.4348  -1.6768   2.0361
 TOD  H16  H  HNH1   0   0.395  -0.9777  -0.9476   0.7179
 TOD  H17  H  HCH3   0   0.211   2.4927   2.8790   2.6303
 TOD  H18  H  HCH3   0   0.225   1.4416   4.0403   1.8219
 TOD  H19  H  HCH3   0   0.223   0.7426   2.7358   2.7774
 TOD  H20  H  HOH1   0   0.447   2.2439  -2.7129  -0.8379
 TOD  H21  H  HNH1   0   0.419   4.9378   0.3657  -0.6680
 TOD  H22  H  HOH1   0   0.480   6.1066   0.0398   1.5046

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
 TOD  C12  C13  aromatic  1.390  0.020  1.390
 TOD  C12  C11  aromatic  1.388  0.020  1.388
 TOD  C13  C14  aromatic  1.388  0.020  1.388
 TOD  O1   C7   double    1.219  0.020  1.219
 TOD  C11  C10  aromatic  1.395  0.020  1.395
 TOD  C14  C15  aromatic  1.389  0.020  1.389
 TOD  C3   C2   single    1.525  0.020  1.525
 TOD  O2   N1   single    1.361  0.020  1.361
 TOD  C10  C15  aromatic  1.391  0.020  1.391
 TOD  C10  C9   single    1.506  0.020  1.506
 TOD  C7   N1   single    1.341  0.020  1.341
 TOD  C7   C6   single    1.526  0.020  1.526
 TOD  O3   C6   single    1.407  0.020  1.407
 TOD  C2   C1   single    1.527  0.020  1.527
 TOD  C2   C4   single    1.532  0.020  1.532
 TOD  N2   C9   single    1.444  0.020  1.444
 TOD  N2   C8   single    1.338  0.020  1.338
 TOD  C5   C6   single    1.530  0.020  1.530
 TOD  C5   C4   single    1.544  0.020  1.544
 TOD  C5   C8   single    1.523  0.020  1.523
 TOD  C9   C16  single    1.560  0.020  1.560
 TOD  C8   O4   double    1.223  0.020  1.223
 TOD  O5   C16  deloc     1.240  0.020  1.240
 TOD  C16  O6   deloc     1.244  0.020  1.244
 TOD  C2   H1   single    0.970  0.020  1.090
 TOD  C3   H2   single    0.970  0.020  1.090
 TOD  C3   H3   single    0.970  0.020  1.090
 TOD  C3   H4   single    0.970  0.020  1.090
 TOD  C4   H5   single    0.970  0.020  1.090
 TOD  C4   H6   single    0.970  0.020  1.090
 TOD  C5   H7   single    0.970  0.020  1.090
 TOD  C6   H8   single    0.970  0.020  1.090
 TOD  C11  H9   single    0.930  0.020  1.080
 TOD  C12  H10  single    0.930  0.020  1.080
 TOD  C14  H11  single    0.930  0.020  1.080
 TOD  C9   H13  single    0.970  0.020  1.090
 TOD  C15  H14  single    0.930  0.020  1.080
 TOD  C13  H15  single    0.930  0.020  1.080
 TOD  N2   H16  single    0.860  0.020  1.020
 TOD  C1   H17  single    0.970  0.020  1.090
 TOD  C1   H18  single    0.970  0.020  1.090
 TOD  C1   H19  single    0.970  0.020  1.090
 TOD  O3   H20  single    0.850  0.020  0.980
 TOD  N1   H21  single    0.890  0.020  1.040
 TOD  O2   H22  single    0.850  0.020  0.980

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
 TOD  H1   C2   C1   107.29  3.000
 TOD  H1   C2   C4   108.10  3.000
 TOD  C1   C2   C4   108.48  3.000
 TOD  H1   C2   C3   108.90  3.000
 TOD  C4   C2   C3   114.07  3.000
 TOD  C1   C2   C3   109.78  3.000
 TOD  H4   C3   H3   108.37  3.000
 TOD  H4   C3   H2   106.95  3.000
 TOD  H3   C3   H2   107.27  3.000
 TOD  H4   C3   C2   112.42  3.000
 TOD  H3   C3   C2   111.06  3.000
 TOD  H2   C3   C2   110.55  3.000
 TOD  H6   C4   H5   104.96  3.000
 TOD  H6   C4   C5   106.36  3.000
 TOD  H5   C4   C5   109.27  3.000
 TOD  H6   C4   C2   107.19  3.000
 TOD  H5   C4   C2   109.03  3.000
 TOD  C5   C4   C2   119.08  3.000
 TOD  H7   C5   C8   108.22  3.000
 TOD  H7   C5   C6   105.92  3.000
 TOD  C8   C5   C6   109.24  3.000
 TOD  H7   C5   C4   105.54  3.000
 TOD  C8   C5   C4   110.55  3.000
 TOD  C6   C5   C4   116.91  3.000
 TOD  H8   C6   O3   105.70  3.000
 TOD  H8   C6   C7   110.91  3.000
 TOD  O3   C6   C7   108.38  3.000
 TOD  H8   C6   C5   110.21  3.000
 TOD  O3   C6   C5   110.96  3.000
 TOD  C7   C6   C5   110.57  3.000
 TOD  N1   C7   O1   124.27  3.000
 TOD  N1   C7   C6   114.07  3.000
 TOD  O1   C7   C6   121.66  3.000
 TOD  C15  C10  C9   120.42  3.000
 TOD  C9   C10  C11  120.78  3.000
 TOD  C15  C10  C11  118.76  3.000
 TOD  H9   C11  C12  119.58  3.000
 TOD  H9   C11  C10  119.89  3.000
 TOD  C12  C11  C10  120.52  3.000
 TOD  H10  C12  C13  119.96  3.000
 TOD  H10  C12  C11  119.73  3.000
 TOD  C13  C12  C11  120.31  3.000
 TOD  H11  C14  C13  120.14  3.000
 TOD  H11  C14  C15  119.76  3.000
 TOD  C13  C14  C15  120.10  3.000
 TOD  C9   C16  O5   117.06  3.000
 TOD  O5   C16  O6   128.12  3.000
 TOD  C9   C16  O6   114.70  3.000
 TOD  H13  C9   N2   109.32  3.000
 TOD  H13  C9   C16  108.38  3.000
 TOD  N2   C9   C16  113.36  3.000
 TOD  H13  C9   C10  108.47  3.000
 TOD  C16  C9   C10  107.24  3.000
 TOD  N2   C9   C10  109.93  3.000
 TOD  H14  C15  C14  119.76  3.000
 TOD  H14  C15  C10  119.45  3.000
 TOD  C14  C15  C10  120.79  3.000
 TOD  H15  C13  C14  120.25  3.000
 TOD  H15  C13  C12  120.24  3.000
 TOD  C14  C13  C12  119.51  3.000
 TOD  H16  N2   C8   118.90  3.000
 TOD  H16  N2   C9   119.10  3.000
 TOD  C8   N2   C9   122.01  3.000
 TOD  O4   C8   N2   122.54  3.000
 TOD  O4   C8   C5   122.63  3.000
 TOD  N2   C8   C5   114.82  3.000
 TOD  H19  C1   H18  107.58  3.000
 TOD  H19  C1   H17  107.50  3.000
 TOD  H18  C1   H17  107.57  3.000
 TOD  H19  C1   C2   111.56  3.000
 TOD  H18  C1   C2   111.08  3.000
 TOD  H17  C1   C2   111.35  3.000
 TOD  H20  O3   C6   108.38  3.000
 TOD  H21  N1   O2   114.73  3.000
 TOD  H21  N1   C7   122.02  3.000
 TOD  O2   N1   C7   120.06  3.000
 TOD  H22  O2   N1   106.18  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
 TOD  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 TOD  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 TOD  CONST_03  C14  C13  C12  C11     0.00   0.0  0
 TOD  CONST_04  C14  C15  C10  C11     0.00   0.0  0
 TOD  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 TOD  CONST_06  C15  C10  C11  C12     0.00   0.0  0
 TOD  CONST_07  C9   C10  C11  C12   180.00   0.0  0
 TOD  CONST_08  C9   C10  C15  C14   180.00   0.0  0
 TOD  CONST_09  H10  C12  C11  C10   180.00   0.0  0
 TOD  CONST_10  H11  C14  C15  C10   180.00   0.0  0
 TOD  CONST_11  H15  C13  C12  C11   180.00   0.0  0
 TOD  CONST_12  H14  C15  C10  C11   180.00   0.0  0
 TOD  CONST_13  H9   C11  C10  C15   180.00   0.0  0
 TOD  CONST_14  C9   N2   C8   C5    180.00   0.0  0
 TOD  CONST_15  O2   N1   C7   C6    180.00   0.0  0
 TOD  CONST_16  O4   C8   N2   C9      0.00   0.0  0
 TOD  CONST_17  O2   N1   C7   O1      0.00   0.0  0
 TOD  CONST_18  H16  N2   C8   C5      0.00   0.0  0
 TOD  CONST_19  H21  N1   C7   C6      0.00   0.0  0
 TOD  Var_01    C5   C4   C2   C3    -64.86  30.0  3
 TOD  Var_02    H17  C1   C2   C3    -63.19  30.0  3
 TOD  Var_03    H2   C3   C2   C4   -175.09  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
 TOD  chir_01  C5  C6  C4   C8   negativ
 TOD  chir_02  C6  O3  C5   C7   negativ
 TOD  chir_03  C9  N2  C10  C16  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
 TOD  plan-1  C10  0.020
 TOD  plan-1  C11  0.020
 TOD  plan-1  C12  0.020
 TOD  plan-1  C14  0.020
 TOD  plan-1  C9   0.020
 TOD  plan-1  C15  0.020
 TOD  plan-1  C13  0.020
 TOD  plan-1  H9   0.020
 TOD  plan-1  H10  0.020
 TOD  plan-1  H11  0.020
 TOD  plan-1  H14  0.020
 TOD  plan-1  H15  0.020
 TOD  plan-2  C6   0.020
 TOD  plan-2  C7   0.020
 TOD  plan-2  O1   0.020
 TOD  plan-2  N1   0.020
 TOD  plan-2  O2   0.020
 TOD  plan-2  H21  0.020
 TOD  plan-3  C5   0.020
 TOD  plan-3  C9   0.020
 TOD  plan-3  N2   0.020
 TOD  plan-3  C8   0.020
 TOD  plan-3  O4   0.020
 TOD  plan-3  H16  0.020
 TOD  plan-4  C16  0.020
 TOD  plan-4  O6   0.020
 TOD  plan-4  O5   0.020
 TOD  plan-4  C9   0.020

