# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 04:08:53 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: {1-[(3S)-4-(benzyloxy)-3-hydroxy-4-oxobutanoyl]hydrazino}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NN(CC(O)=O)C(=O)C[C@H](O)C(=O)OCc1ccccc1
#
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
 MY2  MY2  '{1-[(3S)-4-(benzyloxy)-3-hydroxy-4-oxobutanoyl]hydrazino}acetic acid'  ligand  37  21  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MY2
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
 MY2  C2    C  CH2   0  -0.639  -0.7974  -0.3363   0.3080
 MY2  C3    C  CH1   0  -0.064  -0.2542  -1.6175  -0.3231
 MY2  C4    C  C     0   0.563   1.0965  -1.9557   0.2952
 MY2  O5    O  O     0  -0.442   1.2930  -2.9096   1.0031
 MY2  O6    O  O2    0  -0.449   2.0153  -1.0645  -0.0352
 MY2  C7    C  C     0   0.601  -2.0128   0.1814  -0.4344
 MY2  O8    O  O     0  -0.481  -2.3295  -0.2285  -1.5380
 MY2  N9    N  NT    0  -0.353  -2.7027   1.1829   0.1690
 MY2  C10   C  CH2   0  -0.417  -3.8863   1.7036  -0.4542
 MY2  C12   C  CR16  0  -0.285   3.9718   1.1984   0.7917
 MY2  C13   C  CR16  0  -0.242   4.6811   2.3216   0.3925
 MY2  C14   C  CR16  0  -0.260   5.5487   2.2471  -0.6906
 MY2  C15   C  CR16  0  -0.242   5.7031   1.0469  -1.3710
 MY2  C16   C  CR16  0  -0.293   4.9899  -0.0755  -0.9703
 MY2  C17   C  CR6   0   0.077   4.1210  -0.0091   0.1139
 MY2  C18   C  C     0   0.539  -5.1010   0.8558  -0.1440
 MY2  C9    C  CH2   0  -0.253   3.3306  -1.2088   0.5336
 MY2  O19   O  O     0  -0.434  -5.0859  -0.1310   0.5433
 MY2  N16   N  NH2   0  -0.648  -2.4604   1.6272   1.4615
 MY2  O20   O  OH1   0  -0.591  -6.1864   1.3477  -0.7239
 MY2  O57   O  OH1   0  -0.646  -1.1368  -2.6902  -0.2083
 MY2  H2C1  H  HCH2  0   0.300  -0.0371   0.4506   0.2998
 MY2  H2C2  H  HCH2  0   0.280  -1.0255  -0.5196   1.3613
 MY2  H3    H  HCH1  0   0.281  -0.0970  -1.4507  -1.3920
 MY2  H101  H  HCH2  0   0.308  -4.0545   2.7181  -0.0914
 MY2  H102  H  HCH2  0   0.297  -3.7629   1.7706  -1.5360
 MY2  H13   H  HCR6  0   0.259   4.5604   3.2544   0.9280
 MY2  H14   H  HCR6  0   0.260   6.1071   3.1214  -0.9993
 MY2  H15   H  HCR6  0   0.260   6.3791   0.9840  -2.2137
 MY2  H16   H  HCR6  0   0.256   5.1139  -1.0116  -1.5021
 MY2  H9C1  H  HCH2  0   0.257   3.2538  -1.2702   1.6206
 MY2  H9C2  H  HCH2  0   0.259   3.7871  -2.1310   0.1700
 MY2  H161  H  HNH2  0   0.374  -2.5838   0.8816   2.1347
 MY2  H162  H  HNH2  0   0.381  -1.5235   1.9989   1.5435
 MY2  H20   H  HOH1  0   0.485  -6.9568   0.7975  -0.5169
 MY2  H57   H  HOH1  0   0.448  -1.2181  -2.9358   0.7202
 MY2  H12   H  HCR6  0   0.256   3.3008   1.2596   1.6405

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
 MY2  C2   C3    single    1.528  0.020  1.528
 MY2  C2   C7    single    1.515  0.020  1.515
 MY2  C2   H2C1  single    0.970  0.020  1.090
 MY2  C2   H2C2  single    0.970  0.020  1.090
 MY2  C3   C4    single    1.524  0.020  1.524
 MY2  C3   O57   single    1.394  0.020  1.394
 MY2  C3   H3    single    0.970  0.020  1.090
 MY2  C4   O5    double    1.204  0.020  1.204
 MY2  C4   O6    single    1.322  0.020  1.322
 MY2  O6   C9    single    1.440  0.020  1.440
 MY2  C7   O8    double    1.219  0.020  1.219
 MY2  C7   N9    single    1.358  0.020  1.358
 MY2  N9   C10   single    1.435  0.020  1.435
 MY2  N9   N16   single    1.388  0.020  1.388
 MY2  C10  C18   single    1.513  0.020  1.513
 MY2  C10  H101  single    0.970  0.020  1.090
 MY2  C10  H102  single    0.970  0.020  1.090
 MY2  C12  C13   aromatic  1.387  0.020  1.387
 MY2  C12  C17   aromatic  1.393  0.020  1.393
 MY2  C12  H12   single    0.930  0.020  1.080
 MY2  C13  C14   aromatic  1.390  0.020  1.390
 MY2  C13  H13   single    0.930  0.020  1.080
 MY2  C14  C15   aromatic  1.388  0.020  1.388
 MY2  C14  H14   single    0.930  0.020  1.080
 MY2  C15  C16   aromatic  1.389  0.020  1.389
 MY2  C15  H15   single    0.930  0.020  1.080
 MY2  C16  C17   aromatic  1.391  0.020  1.391
 MY2  C16  H16   single    0.930  0.020  1.080
 MY2  C17  C9    single    1.497  0.020  1.497
 MY2  C18  O19   double    1.203  0.020  1.203
 MY2  C18  O20   single    1.325  0.020  1.325
 MY2  C9   H9C1  single    0.970  0.020  1.090
 MY2  C9   H9C2  single    0.970  0.020  1.090
 MY2  N16  H161  single    0.890  0.020  1.040
 MY2  N16  H162  single    0.890  0.020  1.040
 MY2  O20  H20   single    0.850  0.020  0.980
 MY2  O57  H57   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
 MY2  H2C2  C2   H2C1  105.83  3.000
 MY2  H2C2  C2   C7    111.22  3.000
 MY2  H2C1  C2   C7    107.93  3.000
 MY2  H2C2  C2   C3    109.36  3.000
 MY2  H2C1  C2   C3    110.66  3.000
 MY2  C7    C2   C3    111.67  3.000
 MY2  H3    C3   O57   106.80  3.000
 MY2  H3    C3   C4    107.65  3.000
 MY2  O57   C3   C4    110.92  3.000
 MY2  H3    C3   C2    109.09  3.000
 MY2  O57   C3   C2    112.72  3.000
 MY2  C4    C3   C2    109.50  3.000
 MY2  O6    C4   O5    124.59  3.000
 MY2  O6    C4   C3    111.41  3.000
 MY2  O5    C4   C3    124.00  3.000
 MY2  C9    O6   C4    117.94  3.000
 MY2  N9    C7   O8    121.22  3.000
 MY2  N9    C7   C2    116.23  3.000
 MY2  O8    C7   C2    122.48  3.000
 MY2  N16   N9   C10   115.60  3.000
 MY2  N16   N9   C7    124.15  3.000
 MY2  C10   N9   C7    119.58  3.000
 MY2  H102  C10  H101  106.87  3.000
 MY2  H102  C10  C18   109.18  3.000
 MY2  H101  C10  C18   109.22  3.000
 MY2  H102  C10  N9    111.07  3.000
 MY2  H101  C10  N9    108.67  3.000
 MY2  C18   C10  N9    111.69  3.000
 MY2  H12   C12  C17   119.76  3.000
 MY2  H12   C12  C13   119.76  3.000
 MY2  C17   C12  C13   120.48  3.000
 MY2  H13   C13  C14   120.09  3.000
 MY2  H13   C13  C12   119.90  3.000
 MY2  C14   C13  C12   120.01  3.000
 MY2  H14   C14  C15   120.08  3.000
 MY2  H14   C14  C13   120.07  3.000
 MY2  C15   C14  C13   119.85  3.000
 MY2  H15   C15  C16   119.90  3.000
 MY2  H15   C15  C14   120.09  3.000
 MY2  C16   C15  C14   120.01  3.000
 MY2  H16   C16  C17   119.68  3.000
 MY2  H16   C16  C15   119.85  3.000
 MY2  C17   C16  C15   120.47  3.000
 MY2  C9    C17  C16   120.68  3.000
 MY2  C9    C17  C12   120.12  3.000
 MY2  C16   C17  C12   119.19  3.000
 MY2  O20   C18  O19   124.39  3.000
 MY2  O20   C18  C10   111.08  3.000
 MY2  O19   C18  C10   124.53  3.000
 MY2  H9C2  C9   H9C1  108.28  3.000
 MY2  H9C2  C9   C17   111.29  3.000
 MY2  H9C1  C9   C17   111.19  3.000
 MY2  H9C2  C9   O6    109.58  3.000
 MY2  H9C1  C9   O6    109.55  3.000
 MY2  C17   C9   O6    106.94  3.000
 MY2  H162  N16  H161  109.26  3.000
 MY2  H162  N16  N9    110.78  3.000
 MY2  H161  N16  N9    111.24  3.000
 MY2  H20   O20  C18   110.30  3.000
 MY2  H57   O57  C3    109.20  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
 MY2  CONST_01  C15   C14  C13  C12     0.00   0.0  0
 MY2  CONST_02  C15   C16  C17  C12     0.00   0.0  0
 MY2  CONST_03  C16   C17  C12  C13     0.00   0.0  0
 MY2  CONST_04  C16   C15  C14  C13     0.00   0.0  0
 MY2  CONST_05  C17   C12  C13  C14     0.00   0.0  0
 MY2  CONST_06  C17   C16  C15  C14     0.00   0.0  0
 MY2  CONST_07  C9    C17  C12  C13   180.00   0.0  0
 MY2  CONST_08  C9    C17  C16  C15   180.00   0.0  0
 MY2  CONST_09  H14   C14  C13  C12   180.00   0.0  0
 MY2  CONST_10  H16   C16  C17  C12   180.00   0.0  0
 MY2  CONST_11  H15   C15  C14  C13   180.00   0.0  0
 MY2  CONST_12  H12   C12  C13  C14   180.00   0.0  0
 MY2  CONST_13  H13   C13  C14  C15   180.00   0.0  0
 MY2  CONST_14  C10   N9   C7   C2    180.00   0.0  0
 MY2  CONST_15  N16   N9   C7   C2      0.00   0.0  0
 MY2  CONST_16  C10   N9   C7   O8      0.00   0.0  0
 MY2  CONST_17  N16   N9   C7   O8    180.00   0.0  0
 MY2  CONST_18  H20   O20  C18  C10   180.00   0.0  0
 MY2  Var_01    C12   C17  C9   O6     80.35  30.0  3
 MY2  Var_02    C17   C9   O6   C4   -174.34  30.0  3
 MY2  Var_03    O8    C7   C2   C3    -13.69  30.0  3
 MY2  Var_04    C18   C10  N9   C7     83.12  30.0  3
 MY2  Var_05    O19   C18  C10  N9      0.27  30.0  3
 MY2  Var_06    H161  N16  N9   C7    -59.70  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
 MY2  chir_01  C3  C2  C4  O57  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
 MY2  plan-1  C12  0.020
 MY2  plan-1  C13  0.020
 MY2  plan-1  C14  0.020
 MY2  plan-1  C15  0.020
 MY2  plan-1  C16  0.020
 MY2  plan-1  C17  0.020
 MY2  plan-1  C9   0.020
 MY2  plan-1  H13  0.020
 MY2  plan-1  H14  0.020
 MY2  plan-1  H15  0.020
 MY2  plan-1  H16  0.020
 MY2  plan-1  H12  0.020
 MY2  plan-2  C2   0.020
 MY2  plan-2  C7   0.020
 MY2  plan-2  O8   0.020
 MY2  plan-2  N9   0.020
 MY2  plan-2  C10  0.020
 MY2  plan-2  N16  0.020
 MY2  plan-3  C10  0.020
 MY2  plan-3  C18  0.020
 MY2  plan-3  O19  0.020
 MY2  plan-3  O20  0.020
 MY2  plan-3  H20  0.020
 MY2  plan-4  C3   0.020
 MY2  plan-4  C4   0.020
 MY2  plan-4  O5   0.020
 MY2  plan-4  O6   0.020

