# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 08:26:57 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-(phenylethynyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](NC(=O)c1ccc(cc1)C#Cc2ccccc2)C(=O)NO
#
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
 L59  L59  N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-(phenylethynyl)benzamide  ligand  43  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L59
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
 L59  O2   O  O     0  -0.466   4.6309  -2.1123   0.0866
 L59  C17  C  C     0   0.529   4.9537  -1.0533  -0.4211
 L59  N2   N  NH1   0  -0.368   5.8390  -0.9278  -1.4187
 L59  O3   O  OH1   0  -0.536   6.3434  -2.0345  -2.0263
 L59  C16  C  CH1   0  -0.234   4.3966   0.2730   0.0767
 L59  C18  C  CH1   0   0.059   4.9704   0.6120   1.4693
 L59  O4   O  OH1   0  -0.660   4.3759   1.7906   1.9538
 L59  C19  C  CH3   0  -0.692   6.4698   0.8299   1.4148
 L59  N1   N  NH1   0  -0.671   2.9576   0.1672   0.1298
 L59  C1   C  C     0   0.541   2.1268   1.0151  -0.5132
 L59  O1   O  O     0  -0.470   2.5211   1.9535  -1.1873
 L59  C2   C  CR6   0  -0.042   0.6650   0.7414  -0.3613
 L59  C7   C  CR16  0  -0.257  -0.1997   1.2853  -1.3096
 L59  C6   C  CR16  0  -0.283  -1.5624   1.0750  -1.2260
 L59  C5   C  CR6   0  -0.109  -2.0970   0.3225  -0.1748
 L59  C4   C  CR16  0  -0.280  -1.2330  -0.2078   0.7872
 L59  C3   C  CR16  0  -0.285   0.1313   0.0005   0.6916
 L59  C8   C  CSP   0   0.145  -3.4986   0.1044  -0.0879
 L59  C9   C  CSP   0   0.145  -4.6906  -0.0785  -0.0231
 L59  C10  C  CR6   0  -0.116  -6.0951  -0.2927   0.0473
 L59  C15  C  CR16  0  -0.292  -6.9646   0.4772  -0.7327
 L59  C14  C  CR16  0  -0.247  -8.3317   0.2646  -0.6644
 L59  C13  C  CR16  0  -0.251  -8.8464  -0.7142   0.1772
 L59  C12  C  CR16  0  -0.247  -7.9876  -1.4825   0.9541
 L59  C11  C  CR16  0  -0.293  -6.6191  -1.2760   0.8935
 L59  H13  H  HNH1  0   0.422   5.9732  -0.0624  -1.9224
 L59  H14  H  HOH1  0   0.481   7.2071  -2.1957  -1.6237
 L59  H1   H  HCH1  0   0.283   4.6460   1.0890  -0.6050
 L59  H2   H  HCH1  0   0.217   4.7577  -0.2325   2.1392
 L59  H18  H  HOH1  0   0.451   3.4486   1.6113   2.1385
 L59  H17  H  HCH3  0   0.234   6.7312   1.6095   0.6968
 L59  H16  H  HCH3  0   0.251   6.8453   1.1241   2.3945
 L59  H15  H  HCH3  0   0.239   6.9931  -0.0811   1.1271
 L59  H3   H  HNH1  0   0.412   2.5842  -0.6703   0.5504
 L59  H7   H  HCR6  0   0.268   0.1973   1.8701  -2.1280
 L59  H6   H  HCR6  0   0.267  -2.2199   1.4932  -1.9763
 L59  H5   H  HCR6  0   0.270  -1.6332  -0.7784   1.6143
 L59  H4   H  HCR6  0   0.265   0.7626  -0.4111   1.4685
 L59  H12  H  HCR6  0   0.263  -6.5628   1.2391  -1.3878
 L59  H11  H  HCR6  0   0.265  -8.9971   0.8641  -1.2713
 L59  H10  H  HCR6  0   0.265  -9.9147  -0.8791   0.2271
 L59  H9   H  HCR6  0   0.265  -8.3859  -2.2466   1.6087
 L59  H8   H  HCR6  0   0.263  -5.9490  -1.8750   1.4949

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
 L59  C19  C18  single    1.516  0.020  1.516
 L59  O4   C18  single    1.406  0.020  1.406
 L59  C18  C16  single    1.544  0.020  1.544
 L59  O2   C17  double    1.218  0.020  1.218
 L59  O3   N2   single    1.360  0.020  1.360
 L59  C17  N2   single    1.340  0.020  1.340
 L59  C17  C16  single    1.522  0.020  1.522
 L59  C16  N1   single    1.444  0.020  1.444
 L59  N1   C1   single    1.350  0.020  1.350
 L59  C1   O1   double    1.221  0.020  1.221
 L59  C1   C2   single    1.495  0.020  1.495
 L59  C3   C2   aromatic  1.394  0.020  1.394
 L59  C3   C4   aromatic  1.383  0.020  1.383
 L59  C2   C7   aromatic  1.394  0.020  1.394
 L59  C4   C5   aromatic  1.398  0.020  1.398
 L59  C7   C6   aromatic  1.381  0.020  1.381
 L59  C5   C6   aromatic  1.399  0.020  1.399
 L59  C5   C8   single    1.421  0.020  1.421
 L59  C8   C9   triple    1.208  0.020  1.208
 L59  C9   C10  single    1.423  0.020  1.423
 L59  C15  C14  aromatic  1.385  0.020  1.385
 L59  C15  C10  aromatic  1.399  0.020  1.399
 L59  C14  C13  aromatic  1.390  0.020  1.390
 L59  C10  C11  aromatic  1.399  0.020  1.399
 L59  C13  C12  aromatic  1.390  0.020  1.390
 L59  C11  C12  aromatic  1.385  0.020  1.385
 L59  N2   H13  single    0.860  0.020  1.020
 L59  O3   H14  single    0.850  0.020  0.980
 L59  C16  H1   single    0.970  0.020  1.090
 L59  C18  H2   single    0.970  0.020  1.090
 L59  O4   H18  single    0.850  0.020  0.980
 L59  C19  H17  single    0.970  0.020  1.090
 L59  C19  H16  single    0.970  0.020  1.090
 L59  C19  H15  single    0.970  0.020  1.090
 L59  N1   H3   single    0.860  0.020  1.020
 L59  C7   H7   single    0.930  0.020  1.080
 L59  C6   H6   single    0.930  0.020  1.080
 L59  C4   H5   single    0.930  0.020  1.080
 L59  C3   H4   single    0.930  0.020  1.080
 L59  C15  H12  single    0.930  0.020  1.080
 L59  C14  H11  single    0.930  0.020  1.080
 L59  C13  H10  single    0.930  0.020  1.080
 L59  C12  H9   single    0.930  0.020  1.080
 L59  C11  H8   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
 L59  C16  C17  N2   113.81  3.000
 L59  C16  C17  O2   121.62  3.000
 L59  N2   C17  O2   124.54  3.000
 L59  H13  N2   O3   115.16  3.000
 L59  H13  N2   C17  122.64  3.000
 L59  O3   N2   C17  120.12  3.000
 L59  H14  O3   N2   106.33  3.000
 L59  H1   C16  N1   107.77  3.000
 L59  H1   C16  C18  108.31  3.000
 L59  N1   C16  C18  110.69  3.000
 L59  H1   C16  C17  111.31  3.000
 L59  N1   C16  C17  108.24  3.000
 L59  C18  C16  C17  110.50  3.000
 L59  H2   C18  C19  108.90  3.000
 L59  H2   C18  O4   110.63  3.000
 L59  C19  C18  O4   108.06  3.000
 L59  H2   C18  C16  108.02  3.000
 L59  O4   C18  C16  109.74  3.000
 L59  C19  C18  C16  111.51  3.000
 L59  H18  O4   C18  108.50  3.000
 L59  H15  C19  H16  107.32  3.000
 L59  H15  C19  H17  107.97  3.000
 L59  H16  C19  H17  108.43  3.000
 L59  H15  C19  C18  111.37  3.000
 L59  H16  C19  C18  110.32  3.000
 L59  H17  C19  C18  111.30  3.000
 L59  H3   N1   C1   119.48  3.000
 L59  H3   N1   C16  116.43  3.000
 L59  C1   N1   C16  123.36  3.000
 L59  C2   C1   O1   120.84  3.000
 L59  C2   C1   N1   116.00  3.000
 L59  O1   C1   N1   123.15  3.000
 L59  C3   C2   C7   118.94  3.000
 L59  C7   C2   C1   117.78  3.000
 L59  C3   C2   C1   123.27  3.000
 L59  H7   C7   C6   119.36  3.000
 L59  H7   C7   C2   119.88  3.000
 L59  C6   C7   C2   120.76  3.000
 L59  H6   C6   C5   119.80  3.000
 L59  H6   C6   C7   119.91  3.000
 L59  C5   C6   C7   120.29  3.000
 L59  C8   C5   C4   120.62  3.000
 L59  C8   C5   C6   120.36  3.000
 L59  C4   C5   C6   119.02  3.000
 L59  H5   C4   C3   119.82  3.000
 L59  H5   C4   C5   119.86  3.000
 L59  C3   C4   C5   120.33  3.000
 L59  H4   C3   C4   117.92  3.000
 L59  H4   C3   C2   121.40  3.000
 L59  C4   C3   C2   120.66  3.000
 L59  C9   C8   C5   180.00  3.000
 L59  C10  C9   C8   180.00  3.000
 L59  C11  C10  C15  119.42  3.000
 L59  C11  C10  C9   120.37  3.000
 L59  C15  C10  C9   120.21  3.000
 L59  H12  C15  C14  120.28  3.000
 L59  H12  C15  C10  119.62  3.000
 L59  C14  C15  C10  120.09  3.000
 L59  H11  C14  C13  120.15  3.000
 L59  H11  C14  C15  119.62  3.000
 L59  C13  C14  C15  120.23  3.000
 L59  H10  C13  C12  120.00  3.000
 L59  H10  C13  C14  120.06  3.000
 L59  C12  C13  C14  119.94  3.000
 L59  H9   C12  C11  119.69  3.000
 L59  H9   C12  C13  120.07  3.000
 L59  C11  C12  C13  120.24  3.000
 L59  H8   C11  C12  120.34  3.000
 L59  H8   C11  C10  119.57  3.000
 L59  C12  C11  C10  120.08  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
 L59  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 L59  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 L59  CONST_03  C4   C3   C2   C7     0.00   0.0  0
 L59  CONST_04  C4   C5   C6   C7     0.00   0.0  0
 L59  CONST_05  C3   C2   C7   C6     0.00   0.0  0
 L59  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 L59  CONST_07  C13  C14  C15  C10    0.00   0.0  0
 L59  CONST_08  C13  C12  C11  C10    0.00   0.0  0
 L59  CONST_09  C12  C13  C14  C15    0.00   0.0  0
 L59  CONST_10  C12  C11  C10  C15    0.00   0.0  0
 L59  CONST_11  C11  C10  C15  C14    0.00   0.0  0
 L59  CONST_12  C11  C12  C13  C14    0.00   0.0  0
 L59  CONST_13  C4   C3   C2   C1   180.00   0.0  0
 L59  CONST_14  C6   C7   C2   C1   180.00   0.0  0
 L59  CONST_15  C8   C5   C6   C7   180.00   0.0  0
 L59  CONST_16  C8   C5   C4   C3   180.00   0.0  0
 L59  CONST_17  C14  C15  C10  C9   180.00   0.0  0
 L59  CONST_18  C12  C11  C10  C9   180.00   0.0  0
 L59  CONST_19  H5   C4   C3   C2   180.00   0.0  0
 L59  CONST_20  H6   C6   C7   C2   180.00   0.0  0
 L59  CONST_21  H4   C3   C2   C7   180.00   0.0  0
 L59  CONST_22  H7   C7   C6   C5   180.00   0.0  0
 L59  CONST_23  H11  C14  C15  C10  180.00   0.0  0
 L59  CONST_24  H9   C12  C11  C10  180.00   0.0  0
 L59  CONST_25  H10  C13  C14  C15  180.00   0.0  0
 L59  CONST_26  H8   C11  C10  C15  180.00   0.0  0
 L59  CONST_27  H12  C15  C14  C13  180.00   0.0  0
 L59  CONST_28  C2   C1   N1   C16  180.00   0.0  0
 L59  CONST_29  H3   N1   C1   C2     0.00   0.0  0
 L59  CONST_30  O3   N2   C17  O2     0.00   0.0  0
 L59  CONST_31  C16  C17  N2   O3   180.00   0.0  0
 L59  CONST_32  O1   C1   N1   C16    0.00   0.0  0
 L59  CONST_33  H13  N2   C17  O2   180.00   0.0  0
 L59  Var_01    C3   C2   C1   N1    21.64  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
 L59  chir_01  C16  C18  C17  N1   negativ
 L59  chir_02  C18  O4   C16  C19  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
 L59  plan-1  C1   0.020
 L59  plan-1  C2   0.020
 L59  plan-1  C7   0.020
 L59  plan-1  C6   0.020
 L59  plan-1  C5   0.020
 L59  plan-1  C4   0.020
 L59  plan-1  C3   0.020
 L59  plan-1  C8   0.020
 L59  plan-1  C9   0.020
 L59  plan-1  H7   0.020
 L59  plan-1  H6   0.020
 L59  plan-1  H5   0.020
 L59  plan-1  H4   0.020
 L59  plan-2  C8   0.020
 L59  plan-2  C9   0.020
 L59  plan-2  C10  0.020
 L59  plan-2  C15  0.020
 L59  plan-2  C14  0.020
 L59  plan-2  C13  0.020
 L59  plan-2  C12  0.020
 L59  plan-2  C11  0.020
 L59  plan-2  H12  0.020
 L59  plan-2  H11  0.020
 L59  plan-2  H10  0.020
 L59  plan-2  H9   0.020
 L59  plan-2  H8   0.020
 L59  plan-3  O2   0.020
 L59  plan-3  C17  0.020
 L59  plan-3  N2   0.020
 L59  plan-3  O3   0.020
 L59  plan-3  C16  0.020
 L59  plan-3  H13  0.020
 L59  plan-4  C16  0.020
 L59  plan-4  N1   0.020
 L59  plan-4  C1   0.020
 L59  plan-4  O1   0.020
 L59  plan-4  C2   0.020
 L59  plan-4  H3   0.020

