# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 17:51:51 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: {1-[(3S)-4-(dibenzylamino)-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)N(Cc1ccccc1)Cc2ccccc2
#
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
 MY1  MY1  '{1-[(3S)-4-(dibenzylamino)-3-hydroxy-4-oxobutanoyl]hydrazino}acetic acid'  ligand  50  28  .  2021-08-14  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MY1
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
 MY1  C1    C  C      0   0.594   2.7101  -0.1610   0.6804
 MY1  N2    N  NT     0  -0.334   3.5397   0.8905   0.4946
 MY1  O3    O  O      0  -0.497   2.8533  -0.9460   1.6062
 MY1  N4    N  NH2    0  -0.648   3.4807   1.6999  -0.6360
 MY1  C5    C  CH2    0  -0.435   4.7937   0.9532   1.2055
 MY1  C6    C  C      0   0.404   5.9085   0.1152   0.5413
 MY1  O7    O  OC    -1  -0.623   7.0210   0.1856   1.0989
 MY1  O8    O  O      0  -0.597   5.6035  -0.5412  -0.4691
 MY1  C9    C  CH2    0  -0.641   1.5383  -0.2588  -0.2786
 MY1  C10   C  CH1    0  -0.062   0.6681  -1.4859  -0.0129
 MY1  O11   O  OH1    0  -0.661   1.3311  -2.6659  -0.3559
 MY1  C12   C  C      0   0.532  -0.6246  -1.3840  -0.8363
 MY1  N13   N  NT     0  -0.453  -1.5759  -0.4997  -0.4749
 MY1  O14   O  O      0  -0.498  -0.7330  -2.1063  -1.8196
 MY1  C15   C  CH2    0  -0.374  -1.5387   0.3108   0.7229
 MY1  C16   C  CH2    0  -0.424  -2.8106  -0.4017  -1.2478
 MY1  C17   C  CR6    0   0.133  -3.9632  -1.0967  -0.5698
 MY1  C18   C  CR16   0  -0.304  -5.0127  -0.3601  -0.0311
 MY1  C19   C  CR16   0  -0.242  -6.0719  -0.9955   0.6068
 MY1  C20   C  CR16   0  -0.265  -6.0884  -2.3784   0.7125
 MY1  C21   C  CR16   0  -0.240  -5.0436  -3.1231   0.1762
 MY1  C22   C  CR16   0  -0.296  -3.9893  -2.4864  -0.4607
 MY1  C23   C  CR6    0   0.081  -1.3857   1.7944   0.4724
 MY1  C24   C  CR16   0  -0.289  -1.6830   2.6731   1.5121
 MY1  C25   C  CR16   0  -0.242  -1.5171   4.0404   1.3553
 MY1  C26   C  CR16   0  -0.264  -1.0568   4.5534   0.1483
 MY1  C27   C  CR16   0  -0.243  -0.7681   3.6869  -0.8954
 MY1  C28   C  CR16   0  -0.306  -0.9319   2.3155  -0.7347
 MY1  H4N1  H  HNH2   0   0.364   3.6058   1.1489  -1.4767
 MY1  H4N2  H  HNH2   0   0.364   2.5911   2.1786  -0.6842
 MY1  H5C1  H  HCH2   0   0.249   5.0990   1.9997   1.2523
 MY1  H5C2  H  HCH2   0   0.248   4.6534   0.6205   2.2343
 MY1  H9C1  H  HCH2   0   0.276   0.9545   0.6624  -0.2045
 MY1  H9C2  H  HCH2   0   0.285   1.8887  -0.2952  -1.3145
 MY1  H10   H  HCH1   0   0.255   0.4260  -1.5436   1.0516
 MY1  H11   H  HOH1   0   0.442   1.0261  -2.9089  -1.2420
 MY1  H151  H  HCH2   0   0.286  -2.4604   0.1395   1.2873
 MY1  H152  H  HCH2   0   0.289  -0.7429  -0.0253   1.3860
 MY1  H161  H  HCH2   0   0.276  -3.0463   0.6553  -1.3861
 MY1  H162  H  HCH2   0   0.288  -2.6371  -0.8173  -2.2378
 MY1  H18   H  HCR6   0   0.254  -5.0058   0.7209  -0.1124
 MY1  H19   H  HCR6   0   0.257  -6.8816  -0.4093   1.0218
 MY1  H20   H  HCR6   0   0.257  -6.9120  -2.8762   1.2075
 MY1  H21   H  HCR6   0   0.257  -5.0535  -4.2029   0.2514
 MY1  H22   H  HCR6   0   0.253  -3.1841  -3.0743  -0.8842
 MY1  H24   H  HCR6   0   0.254  -2.0472   2.2824   2.4553
 MY1  H25   H  HCR6   0   0.258  -1.7512   4.7072   2.1751
 MY1  H26   H  HCR6   0   0.257  -0.9294   5.6205   0.0223
 MY1  H27   H  HCR6   0   0.258  -0.4143   4.0740  -1.8420
 MY1  H28   H  HCR6   0   0.267  -0.7096   1.6585  -1.5674

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
 MY1  C1   N2    single    1.352  0.020  1.352
 MY1  C1   O3    double    1.222  0.020  1.222
 MY1  C1   C9    single    1.517  0.020  1.517
 MY1  N2   N4    single    1.392  0.020  1.392
 MY1  N2   C5    single    1.443  0.020  1.443
 MY1  N4   H4N1  single    0.890  0.020  1.040
 MY1  N4   H4N2  single    0.890  0.020  1.040
 MY1  C5   C6    single    1.545  0.020  1.545
 MY1  C5   H5C1  single    0.970  0.020  1.090
 MY1  C5   H5C2  single    0.970  0.020  1.090
 MY1  C6   O7    deloc     1.247  0.020  1.247
 MY1  C6   O8    deloc     1.243  0.020  1.243
 MY1  C9   C10   single    1.528  0.020  1.528
 MY1  C9   H9C1  single    0.970  0.020  1.090
 MY1  C9   H9C2  single    0.970  0.020  1.090
 MY1  C10  O11   single    1.396  0.020  1.396
 MY1  C10  C12   single    1.536  0.020  1.536
 MY1  C10  H10   single    0.970  0.020  1.090
 MY1  O11  H11   single    0.850  0.020  0.980
 MY1  C12  N13   single    1.348  0.020  1.348
 MY1  C12  O14   double    1.225  0.020  1.225
 MY1  N13  C15   single    1.447  0.020  1.447
 MY1  N13  C16   single    1.460  0.020  1.460
 MY1  C15  C23   single    1.512  0.020  1.512
 MY1  C15  H151  single    0.970  0.020  1.090
 MY1  C15  H152  single    0.970  0.020  1.090
 MY1  C16  C17   single    1.507  0.020  1.507
 MY1  C16  H161  single    0.970  0.020  1.090
 MY1  C16  H162  single    0.970  0.020  1.090
 MY1  C17  C18   aromatic  1.391  0.020  1.391
 MY1  C17  C22   aromatic  1.394  0.020  1.394
 MY1  C18  C19   aromatic  1.390  0.020  1.390
 MY1  C18  H18   single    0.930  0.020  1.080
 MY1  C19  C20   aromatic  1.387  0.020  1.387
 MY1  C19  H19   single    0.930  0.020  1.080
 MY1  C20  C21   aromatic  1.391  0.020  1.391
 MY1  C20  H20   single    0.930  0.020  1.080
 MY1  C21  C22   aromatic  1.387  0.020  1.387
 MY1  C21  H21   single    0.930  0.020  1.080
 MY1  C22  H22   single    0.930  0.020  1.080
 MY1  C23  C24   aromatic  1.393  0.020  1.393
 MY1  C23  C28   aromatic  1.391  0.020  1.391
 MY1  C24  C25   aromatic  1.386  0.020  1.386
 MY1  C24  H24   single    0.930  0.020  1.080
 MY1  C25  C26   aromatic  1.390  0.020  1.390
 MY1  C25  H25   single    0.930  0.020  1.080
 MY1  C26  C27   aromatic  1.387  0.020  1.387
 MY1  C26  H26   single    0.930  0.020  1.080
 MY1  C27  C28   aromatic  1.390  0.020  1.390
 MY1  C27  H27   single    0.930  0.020  1.080
 MY1  C28  H28   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
 MY1  C9    C1   O3    121.86  3.000
 MY1  C9    C1   N2    115.92  3.000
 MY1  O3    C1   N2    122.12  3.000
 MY1  C5    N2   N4    114.32  3.000
 MY1  C5    N2   C1    119.96  3.000
 MY1  N4    N2   C1    122.54  3.000
 MY1  H4N2  N4   H4N1  109.06  3.000
 MY1  H4N2  N4   N2    110.56  3.000
 MY1  H4N1  N4   N2    110.65  3.000
 MY1  H5C2  C5   H5C1  106.75  3.000
 MY1  H5C2  C5   C6    109.45  3.000
 MY1  H5C1  C5   C6    109.69  3.000
 MY1  H5C2  C5   N2    109.86  3.000
 MY1  H5C1  C5   N2    107.82  3.000
 MY1  C6    C5   N2    113.06  3.000
 MY1  O8    C6   O7    127.77  3.000
 MY1  O8    C6   C5    117.32  3.000
 MY1  O7    C6   C5    114.90  3.000
 MY1  H9C2  C9   H9C1  105.26  3.000
 MY1  H9C2  C9   C10   108.69  3.000
 MY1  H9C1  C9   C10   111.15  3.000
 MY1  H9C2  C9   C1    110.68  3.000
 MY1  H9C1  C9   C1    108.38  3.000
 MY1  C10   C9   C1    112.44  3.000
 MY1  H10   C10  C12   109.82  3.000
 MY1  H10   C10  O11   107.44  3.000
 MY1  C12   C10  O11   108.90  3.000
 MY1  H10   C10  C9    109.75  3.000
 MY1  C12   C10  C9    109.44  3.000
 MY1  O11   C10  C9    111.45  3.000
 MY1  H11   O11  C10   106.70  3.000
 MY1  O14   C12  N13   122.65  3.000
 MY1  O14   C12  C10   117.75  3.000
 MY1  N13   C12  C10   119.58  3.000
 MY1  C16   N13  C15   114.99  3.000
 MY1  C16   N13  C12   119.92  3.000
 MY1  C15   N13  C12   124.84  3.000
 MY1  H152  C15  H151  104.66  3.000
 MY1  H152  C15  C23   109.24  3.000
 MY1  H151  C15  C23   108.92  3.000
 MY1  H152  C15  N13   110.49  3.000
 MY1  H151  C15  N13   108.52  3.000
 MY1  C23   C15  N13   114.52  3.000
 MY1  H162  C16  H161  106.80  3.000
 MY1  H162  C16  C17   110.81  3.000
 MY1  H161  C16  C17   109.78  3.000
 MY1  H162  C16  N13   108.74  3.000
 MY1  H161  C16  N13   108.34  3.000
 MY1  C17   C16  N13   112.19  3.000
 MY1  C22   C17  C18   118.91  3.000
 MY1  C22   C17  C16   120.61  3.000
 MY1  C18   C17  C16   120.47  3.000
 MY1  H18   C18  C19   119.67  3.000
 MY1  H18   C18  C17   119.62  3.000
 MY1  C19   C18  C17   120.71  3.000
 MY1  H19   C19  C20   120.12  3.000
 MY1  H19   C19  C18   119.89  3.000
 MY1  C20   C19  C18   119.98  3.000
 MY1  H20   C20  C21   120.12  3.000
 MY1  H20   C20  C19   120.17  3.000
 MY1  C21   C20  C19   119.71  3.000
 MY1  H21   C21  C22   119.79  3.000
 MY1  H21   C21  C20   120.04  3.000
 MY1  C22   C21  C20   120.16  3.000
 MY1  H22   C22  C21   119.71  3.000
 MY1  H22   C22  C17   119.76  3.000
 MY1  C21   C22  C17   120.52  3.000
 MY1  C28   C23  C24   118.74  3.000
 MY1  C28   C23  C15   122.98  3.000
 MY1  C24   C23  C15   118.26  3.000
 MY1  H24   C24  C25   119.61  3.000
 MY1  H24   C24  C23   119.58  3.000
 MY1  C25   C24  C23   120.80  3.000
 MY1  H25   C25  C26   120.14  3.000
 MY1  H25   C25  C24   119.74  3.000
 MY1  C26   C25  C24   120.12  3.000
 MY1  H26   C26  C27   120.27  3.000
 MY1  H26   C26  C25   120.27  3.000
 MY1  C27   C26  C25   119.47  3.000
 MY1  H27   C27  C28   119.50  3.000
 MY1  H27   C27  C26   120.19  3.000
 MY1  C28   C27  C26   120.31  3.000
 MY1  H28   C28  C27   119.01  3.000
 MY1  H28   C28  C23   120.44  3.000
 MY1  C27   C28  C23   120.55  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
 MY1  CONST_01  C20   C19  C18  C17    0.00   0.0  0
 MY1  CONST_02  C20   C21  C22  C17    0.00   0.0  0
 MY1  CONST_03  C21   C22  C17  C18    0.00   0.0  0
 MY1  CONST_04  C21   C20  C19  C18    0.00   0.0  0
 MY1  CONST_05  C22   C17  C18  C19    0.00   0.0  0
 MY1  CONST_06  C22   C21  C20  C19    0.00   0.0  0
 MY1  CONST_07  C26   C25  C24  C23    0.00   0.0  0
 MY1  CONST_08  C26   C27  C28  C23    0.00   0.0  0
 MY1  CONST_09  C27   C28  C23  C24    0.00   0.0  0
 MY1  CONST_10  C27   C26  C25  C24    0.00   0.0  0
 MY1  CONST_11  C28   C23  C24  C25    0.00   0.0  0
 MY1  CONST_12  C28   C27  C26  C25    0.00   0.0  0
 MY1  CONST_13  C25   C24  C23  C15  180.00   0.0  0
 MY1  CONST_14  C27   C28  C23  C15  180.00   0.0  0
 MY1  CONST_15  C19   C18  C17  C16  180.00   0.0  0
 MY1  CONST_16  C21   C22  C17  C16  180.00   0.0  0
 MY1  CONST_17  H19   C19  C18  C17  180.00   0.0  0
 MY1  CONST_18  H21   C21  C22  C17  180.00   0.0  0
 MY1  CONST_19  H22   C22  C17  C18  180.00   0.0  0
 MY1  CONST_20  H20   C20  C19  C18  180.00   0.0  0
 MY1  CONST_21  H18   C18  C19  C20  180.00   0.0  0
 MY1  CONST_22  H25   C25  C24  C23  180.00   0.0  0
 MY1  CONST_23  H27   C27  C28  C23  180.00   0.0  0
 MY1  CONST_24  H28   C28  C23  C24  180.00   0.0  0
 MY1  CONST_25  H26   C26  C25  C24  180.00   0.0  0
 MY1  CONST_26  H24   C24  C25  C26  180.00   0.0  0
 MY1  CONST_27  N4    N2   C1   O3   180.00   0.0  0
 MY1  CONST_28  C5    N2   C1   O3     0.00   0.0  0
 MY1  CONST_29  C9    C1   N2   N4     0.00   0.0  0
 MY1  CONST_30  C9    C1   N2   C5   180.00   0.0  0
 MY1  CONST_31  C15   N13  C12  C10    0.00   0.0  0
 MY1  CONST_32  C16   N13  C12  C10  180.00   0.0  0
 MY1  CONST_33  C15   N13  C12  O14  180.00   0.0  0
 MY1  CONST_34  C16   N13  C12  O14    0.00   0.0  0
 MY1  Var_01    C24   C23  C15  N13  163.68  30.0  2
 MY1  Var_02    C18   C17  C16  N13  110.32  30.0  2
 MY1  Var_03    C23   C15  N13  C12  112.90  30.0  3
 MY1  Var_04    C17   C16  N13  C12  102.18  30.0  3
 MY1  Var_05    C6    C5   N2   C1    81.65  30.0  3
 MY1  Var_06    C10   C9   C1   N2   179.03  30.0  3
 MY1  Var_07    O7    C6   C5   N2   177.39  30.0  3
 MY1  Var_08    H4N1  N4   N2   C1   -57.58  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
 MY1  chir_01  C10  C9  O11  C12  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
 MY1  plan-1  C16  0.020
 MY1  plan-1  C17  0.020
 MY1  plan-1  C18  0.020
 MY1  plan-1  C19  0.020
 MY1  plan-1  C20  0.020
 MY1  plan-1  C21  0.020
 MY1  plan-1  C22  0.020
 MY1  plan-1  H18  0.020
 MY1  plan-1  H19  0.020
 MY1  plan-1  H20  0.020
 MY1  plan-1  H21  0.020
 MY1  plan-1  H22  0.020
 MY1  plan-2  C15  0.020
 MY1  plan-2  C23  0.020
 MY1  plan-2  C24  0.020
 MY1  plan-2  C25  0.020
 MY1  plan-2  C26  0.020
 MY1  plan-2  C27  0.020
 MY1  plan-2  C28  0.020
 MY1  plan-2  H24  0.020
 MY1  plan-2  H25  0.020
 MY1  plan-2  H26  0.020
 MY1  plan-2  H27  0.020
 MY1  plan-2  H28  0.020
 MY1  plan-3  C1   0.020
 MY1  plan-3  N2   0.020
 MY1  plan-3  O3   0.020
 MY1  plan-3  N4   0.020
 MY1  plan-3  C5   0.020
 MY1  plan-3  C9   0.020
 MY1  plan-4  C10  0.020
 MY1  plan-4  C12  0.020
 MY1  plan-4  N13  0.020
 MY1  plan-4  O14  0.020
 MY1  plan-4  C15  0.020
 MY1  plan-4  C16  0.020
 MY1  plan-5  C5   0.020
 MY1  plan-5  C6   0.020
 MY1  plan-5  O7   0.020
 MY1  plan-5  O8   0.020

