# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 22:38:37 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  51  28  .  2021-08-14  2022-11-17
;
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   0.603   2.7597  -0.2303   0.5556
 MY1  N2    N  NT    0  -0.351   3.6179   0.7993   0.3367
 MY1  O3    O  O     0  -0.479   2.9412  -1.0293   1.4579
 MY1  N4    N  NH2   0  -0.646   3.5273   1.6617  -0.7477
 MY1  C5    C  CH2   0  -0.417   4.8354   0.8867   1.0916
 MY1  C6    C  C     0   0.538   5.9267   0.0304   0.4857
 MY1  O7    O  OH1   0  -0.591   7.0544   0.1357   1.1731
 MY1  O8    O  O     0  -0.433   5.7886  -0.6534  -0.4942
 MY1  C9    C  CH2   0  -0.640   1.5466  -0.2778  -0.3481
 MY1  C10   C  CH1   0  -0.063   0.6697  -1.4995  -0.0786
 MY1  O11   O  OH1   0  -0.661   1.3135  -2.6785  -0.4572
 MY1  C12   C  C     0   0.536  -0.6396  -1.3716  -0.8736
 MY1  N13   N  NT    0  -0.452  -1.5740  -0.4840  -0.4813
 MY1  O14   O  O     0  -0.497  -0.7723  -2.0786  -1.8651
 MY1  C15   C  CH2   0  -0.376  -1.5053   0.3072   0.7281
 MY1  C16   C  CH2   0  -0.425  -2.8218  -0.3614  -1.2305
 MY1  C17   C  CR6   0   0.134  -3.9653  -1.0673  -0.5488
 MY1  C18   C  CR16  0  -0.303  -4.9880  -0.3379   0.0482
 MY1  C19   C  CR16  0  -0.243  -6.0381  -0.9831   0.6913
 MY1  C20   C  CR16  0  -0.265  -6.0723  -2.3687   0.7436
 MY1  C21   C  CR16  0  -0.241  -5.0544  -3.1063   0.1488
 MY1  C22   C  CR16  0  -0.296  -4.0091  -2.4598  -0.4932
 MY1  C23   C  CR6   0   0.082  -1.3414   1.7925   0.4947
 MY1  C24   C  CR16  0  -0.291  -1.6239   2.6622   1.5459
 MY1  C25   C  CR16  0  -0.243  -1.4489   4.0300   1.4019
 MY1  C26   C  CR16  0  -0.266  -0.9942   4.5520   0.1967
 MY1  C27   C  CR16  0  -0.239  -0.7199   3.6945  -0.8582
 MY1  C28   C  CR16  0  -0.302  -0.8935   2.3229  -0.7107
 MY1  H4N1  H  HNH2  0   0.374   3.5537   1.1539  -1.6227
 MY1  H4N2  H  HNH2  0   0.377   2.6744   2.2040  -0.7047
 MY1  H5C1  H  HCH2  0   0.306   5.1621   1.9270   1.1120
 MY1  H5C2  H  HCH2  0   0.298   4.6762   0.5841   2.1274
 MY1  H7    H  HOH1  0   0.485   7.7433  -0.4193   0.7776
 MY1  H9C1  H  HCH2  0   0.287   0.9860   0.6517  -0.2179
 MY1  H9C2  H  HCH2  0   0.290   1.8490  -0.2877  -1.3995
 MY1  H10   H  HCH1  0   0.258   0.4510  -1.5702   0.9903
 MY1  H11   H  HOH1  0   0.443   0.9770  -2.9071  -1.3361
 MY1  H151  H  HCH2  0   0.287  -2.4178   0.1370   1.3074
 MY1  H152  H  HCH2  0   0.289  -0.7008  -0.0487   1.3697
 MY1  H161  H  HCH2  0   0.277  -3.0537   0.7000  -1.3369
 MY1  H162  H  HCH2  0   0.288  -2.6670  -0.7526  -2.2335
 MY1  H18   H  HCR6  0   0.254  -4.9671   0.7453   0.0083
 MY1  H19   H  HCR6  0   0.257  -6.8272  -0.4023   1.1511
 MY1  H20   H  HCR6  0   0.257  -6.8890  -2.8742   1.2423
 MY1  H21   H  HCR6  0   0.256  -5.0787  -4.1880   0.1821
 MY1  H22   H  HCR6  0   0.254  -3.2246  -3.0415  -0.9615
 MY1  H24   H  HCR6  0   0.254  -1.9844   2.2642   2.4875
 MY1  H25   H  HCR6  0   0.257  -1.6727   4.6902   2.2299
 MY1  H26   H  HCR6  0   0.257  -0.8602   5.6196   0.0808
 MY1  H27   H  HCR6  0   0.257  -0.3706   4.0888  -1.8034
 MY1  H28   H  HCR6  0   0.266  -0.6844   1.6731  -1.5522

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    1.358  0.020  1.358
 MY1  C1   O3    double    1.219  0.020  1.219
 MY1  C1   C9    single    1.513  0.020  1.513
 MY1  N2   N4    single    1.389  0.020  1.389
 MY1  N2   C5    single    1.435  0.020  1.435
 MY1  N4   H4N1  single    0.890  0.020  1.040
 MY1  N4   H4N2  single    0.890  0.020  1.040
 MY1  C5   C6    single    1.514  0.020  1.514
 MY1  C5   H5C1  single    0.970  0.020  1.090
 MY1  C5   H5C2  single    0.970  0.020  1.090
 MY1  C6   O7    single    1.325  0.020  1.325
 MY1  C6   O8    double    1.203  0.020  1.203
 MY1  O7   H7    single    0.850  0.020  0.980
 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    1.537  0.020  1.537
 MY1  C10  H10   single    0.970  0.020  1.090
 MY1  O11  H11   single    0.850  0.020  0.980
 MY1  C12  N13   single    1.347  0.020  1.347
 MY1  C12  O14   double    1.225  0.020  1.225
 MY1  N13  C15   single    1.447  0.020  1.447
 MY1  N13  C16   single    1.461  0.020  1.461
 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    122.74  3.000
 MY1  C9    C1   N2    115.73  3.000
 MY1  O3    C1   N2    121.47  3.000
 MY1  C5    N2   N4    115.36  3.000
 MY1  C5    N2   C1    119.84  3.000
 MY1  N4    N2   C1    123.74  3.000
 MY1  H4N2  N4   H4N1  109.12  3.000
 MY1  H4N2  N4   N2    110.78  3.000
 MY1  H4N1  N4   N2    111.22  3.000
 MY1  H5C2  C5   H5C1  106.89  3.000
 MY1  H5C2  C5   C6    109.17  3.000
 MY1  H5C1  C5   C6    109.34  3.000
 MY1  H5C2  C5   N2    111.03  3.000
 MY1  H5C1  C5   N2    108.79  3.000
 MY1  C6    C5   N2    111.50  3.000
 MY1  O8    C6   O7    124.44  3.000
 MY1  O8    C6   C5    124.40  3.000
 MY1  O7    C6   C5    111.16  3.000
 MY1  H7    O7   C6    110.36  3.000
 MY1  H9C2  C9   H9C1  105.30  3.000
 MY1  H9C2  C9   C10   108.72  3.000
 MY1  H9C1  C9   C10   111.37  3.000
 MY1  H9C2  C9   C1    110.65  3.000
 MY1  H9C1  C9   C1    108.25  3.000
 MY1  C10   C9   C1    112.32  3.000
 MY1  H10   C10  C12   109.92  3.000
 MY1  H10   C10  O11   107.62  3.000
 MY1  C12   C10  O11   108.84  3.000
 MY1  H10   C10  C9    109.82  3.000
 MY1  C12   C10  C9    109.34  3.000
 MY1  O11   C10  C9    111.27  3.000
 MY1  H11   O11  C10   106.58  3.000
 MY1  O14   C12  N13   122.74  3.000
 MY1  O14   C12  C10   117.57  3.000
 MY1  N13   C12  C10   119.67  3.000
 MY1  C16   N13  C15   115.05  3.000
 MY1  C16   N13  C12   119.90  3.000
 MY1  C15   N13  C12   124.80  3.000
 MY1  H152  C15  H151  104.68  3.000
 MY1  H152  C15  C23   109.38  3.000
 MY1  H151  C15  C23   108.96  3.000
 MY1  H152  C15  N13   110.42  3.000
 MY1  H151  C15  N13   108.53  3.000
 MY1  C23   C15  N13   114.41  3.000
 MY1  H162  C16  H161  106.87  3.000
 MY1  H162  C16  C17   110.89  3.000
 MY1  H161  C16  C17   109.78  3.000
 MY1  H162  C16  N13   108.74  3.000
 MY1  H161  C16  N13   108.25  3.000
 MY1  C17   C16  N13   112.14  3.000
 MY1  C22   C17  C18   118.92  3.000
 MY1  C22   C17  C16   120.65  3.000
 MY1  C18   C17  C16   120.43  3.000
 MY1  H18   C18  C19   119.69  3.000
 MY1  H18   C18  C17   119.61  3.000
 MY1  C19   C18  C17   120.70  3.000
 MY1  H19   C19  C20   120.14  3.000
 MY1  H19   C19  C18   119.88  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   119.72  3.000
 MY1  H21   C21  C22   119.80  3.000
 MY1  H21   C21  C20   120.03  3.000
 MY1  C22   C21  C20   120.17  3.000
 MY1  H22   C22  C21   119.72  3.000
 MY1  H22   C22  C17   119.76  3.000
 MY1  C21   C22  C17   120.52  3.000
 MY1  C28   C23  C24   118.75  3.000
 MY1  C28   C23  C15   122.90  3.000
 MY1  C24   C23  C15   118.34  3.000
 MY1  H24   C24  C25   119.63  3.000
 MY1  H24   C24  C23   119.58  3.000
 MY1  C25   C24  C23   120.79  3.000
 MY1  H25   C25  C26   120.12  3.000
 MY1  H25   C25  C24   119.75  3.000
 MY1  C26   C25  C24   120.12  3.000
 MY1  H26   C26  C27   120.27  3.000
 MY1  H26   C26  C25   120.26  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   119.02  3.000
 MY1  H28   C28  C23   120.43  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  CONST_35  H7    O7   C6   C5   180.00   0.0  0
 MY1  Var_01    C24   C23  C15  N13  162.94  30.0  2
 MY1  Var_02    C18   C17  C16  N13  109.09  30.0  2
 MY1  Var_03    C23   C15  N13  C12  112.91  30.0  3
 MY1  Var_04    C17   C16  N13  C12  101.61  30.0  3
 MY1  Var_05    C6    C5   N2   C1    83.52  30.0  3
 MY1  Var_06    C10   C9   C1   N2   177.35  30.0  3
 MY1  Var_07    O7    C6   C5   N2   178.82  30.0  3
 MY1  Var_08    H4N1  N4   N2   C1   -56.70  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
 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
 MY1  plan-5  H7   0.020

