# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 09:53:01 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: {1-[(3S)-4-{[(2S)-1-(benzylamino)-1-oxopropan-2-yl]amino}-3-hydroxy-4-oxobutanoyl]hydrazinyl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@@H](O)CC(=O)N(N)CC(O)=O)C(=O)NCc1ccccc1
#
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
 MY5  MY5  '{1-[(3S)-4-{[(2S)-1-(benzylamino)-1-oxopropan-2-yl]amino}-3-hydroxy-4-oxobutanoyl]hydrazinyl}acetic acid'  ligand  47  26  .  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_MY5
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
 MY5  N1    N  NT     0  -0.334   4.3085  -1.5260   0.0013
 MY5  N2    N  NH2    0  -0.653   3.8469  -2.1165   1.1740
 MY5  C3    C  CH2    0  -0.435   5.6283  -1.9502  -0.3988
 MY5  C4    C  C      0   0.587   3.7909  -0.3789  -0.4947
 MY5  O5    O  O      0  -0.501   4.2949   0.1956  -1.4493
 MY5  C6    C  C      0   0.404   6.7559  -1.2512   0.3927
 MY5  O7    O  O      0  -0.596   6.4177  -0.4091   1.2418
 MY5  O8    O  OC    -1  -0.623   7.9106  -1.6133   0.0932
 MY5  C9    C  CH2    0  -0.624   2.4957   0.1053   0.1316
 MY5  C10   C  CH1    0  -0.062   2.1260   1.5131  -0.3297
 MY5  C11   C  C      0   0.515   0.7141   1.8243   0.1647
 MY5  O12   O  O      0  -0.496   0.5425   2.3750   1.2440
 MY5  N13   N  NH1    0  -0.632  -0.2766   1.4101  -0.6312
 MY5  C14   C  CH1    0  -0.198  -1.6754   1.5706  -0.3117
 MY5  C15   C  CH3    0  -0.650  -2.1901   2.9673  -0.6654
 MY5  C16   C  C      0   0.560  -2.4597   0.5282  -1.1012
 MY5  O17   O  O      0  -0.495  -2.0695   0.1210  -2.1870
 MY5  N18   N  NH1    0  -0.632  -3.6138   0.1474  -0.5473
 MY5  C19   C  CH2    0  -0.319  -4.5326  -0.7602  -1.2151
 MY5  C20   C  C1     0  -0.263  -8.0725  -1.2053   1.1759
 MY5  C21   C  C1     0  -0.241  -7.9673  -0.1541   0.2737
 MY5  C22   C  C1     0  -0.284  -6.8257  -0.0167  -0.5037
 MY5  C23   C  C      0   0.047  -5.7785  -0.9277  -0.3915
 MY5  C24   C  C1     0  -0.288  -5.8909  -1.9762   0.5169
 MY5  C25   C  C1     0  -0.241  -7.0318  -2.1166   1.2961
 MY5  O28   O  OH1    0  -0.656   3.0241   2.4752   0.1427
 MY5  H2N1  H  HNH2   0   0.362   3.9743  -1.4889   1.9591
 MY5  H2N2  H  HNH2   0   0.373   2.8671  -2.3510   1.0916
 MY5  H3C1  H  HCH2   0   0.248   5.6914  -3.0294  -0.2491
 MY5  H3C2  H  HCH2   0   0.247   5.7676  -1.7729  -1.4657
 MY5  H9C1  H  HCH2   0   0.285   1.7018  -0.6016  -0.1341
 MY5  H9C2  H  HCH2   0   0.269   2.5533   0.0898   1.2231
 MY5  H10   H  HCH1   0   0.257   2.1499   1.5564  -1.4215
 MY5  H13   H  HNH1   0   0.403  -0.0577   1.0389  -1.5445
 MY5  H14   H  HCH1   0   0.280  -1.8096   1.3978   0.7583
 MY5  H151  H  HCH3   0   0.241  -3.2454   3.0706  -0.4141
 MY5  H152  H  HCH3   0   0.253  -1.6378   3.7228  -0.1092
 MY5  H153  H  HCH3   0   0.237  -2.0690   3.1640  -1.7308
 MY5  H18   H  HNH1   0   0.410  -3.8562   0.4848   0.3707
 MY5  H191  H  HCH2   0   0.260  -4.7822  -0.3627  -2.2012
 MY5  H192  H  HCH2   0   0.259  -4.0505  -1.7279  -1.3714
 MY5  H22   H  H      0   0.255  -6.7517   0.8016  -1.2102
 MY5  H24   H  H      0   0.255  -5.0834  -2.6921   0.6139
 MY5  H25   H  H      0   0.258  -7.1081  -2.9396   1.9947
 MY5  H28   H  HOH1   0   0.441   2.7877   2.6718   1.0579
 MY5  H20   H  H      0   0.258  -8.9639  -1.3158   1.7796
 MY5  H21   H  H      0   0.258  -8.7774   0.5562   0.1708

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
 MY5  N1   N2    single    1.392  0.020  1.392
 MY5  N1   C3    single    1.443  0.020  1.443
 MY5  N1   C4    single    1.353  0.020  1.353
 MY5  N2   H2N1  single    0.890  0.020  1.040
 MY5  N2   H2N2  single    0.890  0.020  1.040
 MY5  C3   C6    single    1.545  0.020  1.545
 MY5  C3   H3C1  single    0.970  0.020  1.090
 MY5  C3   H3C2  single    0.970  0.020  1.090
 MY5  C4   O5    double    1.223  0.020  1.223
 MY5  C4   C9    single    1.518  0.020  1.518
 MY5  C6   O7    deloc     1.243  0.020  1.243
 MY5  C6   O8    deloc     1.247  0.020  1.247
 MY5  C9   C10   single    1.527  0.020  1.527
 MY5  C9   H9C1  single    0.970  0.020  1.090
 MY5  C9   H9C2  single    0.970  0.020  1.090
 MY5  C10  C11   single    1.528  0.020  1.528
 MY5  C10  O28   single    1.398  0.020  1.398
 MY5  C10  H10   single    0.970  0.020  1.090
 MY5  C11  O12   double    1.224  0.020  1.224
 MY5  C11  N13   single    1.337  0.020  1.337
 MY5  N13  C14   single    1.444  0.020  1.444
 MY5  N13  H13   single    0.860  0.020  1.020
 MY5  C14  C15   single    1.530  0.020  1.530
 MY5  C14  C16   single    1.525  0.020  1.525
 MY5  C14  H14   single    0.970  0.020  1.090
 MY5  C15  H151  single    0.970  0.020  1.090
 MY5  C15  H152  single    0.970  0.020  1.090
 MY5  C15  H153  single    0.970  0.020  1.090
 MY5  C16  O17   double    1.223  0.020  1.223
 MY5  C16  N18   single    1.335  0.020  1.335
 MY5  N18  C19   single    1.454  0.020  1.454
 MY5  N18  H18   single    0.860  0.020  1.020
 MY5  C19  C23   single    1.503  0.020  1.503
 MY5  C19  H191  single    0.970  0.020  1.090
 MY5  C19  H192  single    0.970  0.020  1.090
 MY5  C20  C21   aromatic  1.389  0.020  1.389
 MY5  C20  C25   aromatic  1.389  0.020  1.389
 MY5  C20  H20   single    0.930  0.020  1.080
 MY5  C21  C22   aromatic  1.388  0.020  1.388
 MY5  C21  H21   single    0.930  0.020  1.080
 MY5  C22  C23   aromatic  1.393  0.020  1.393
 MY5  C22  H22   single    0.930  0.020  1.080
 MY5  C23  C24   aromatic  1.392  0.020  1.392
 MY5  C24  C25   aromatic  1.389  0.020  1.389
 MY5  C24  H24   single    0.930  0.020  1.080
 MY5  C25  H25   single    0.930  0.020  1.080
 MY5  O28  H28   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
 MY5  C4    N1   C3    119.84  3.000
 MY5  C4    N1   N2    122.81  3.000
 MY5  C3    N1   N2    114.35  3.000
 MY5  H2N2  N2   H2N1  109.19  3.000
 MY5  H2N2  N2   N1    110.56  3.000
 MY5  H2N1  N2   N1    110.39  3.000
 MY5  H3C2  C3   H3C1  106.72  3.000
 MY5  H3C2  C3   C6    109.54  3.000
 MY5  H3C1  C3   C6    109.57  3.000
 MY5  H3C2  C3   N1    109.90  3.000
 MY5  H3C1  C3   N1    107.79  3.000
 MY5  C6    C3   N1    113.11  3.000
 MY5  C9    C4   O5    121.60  3.000
 MY5  C9    C4   N1    116.46  3.000
 MY5  O5    C4   N1    121.80  3.000
 MY5  O8    C6   O7    127.80  3.000
 MY5  O8    C6   C3    114.93  3.000
 MY5  O7    C6   C3    117.26  3.000
 MY5  H9C2  C9   H9C1  105.73  3.000
 MY5  H9C2  C9   C10   109.11  3.000
 MY5  H9C1  C9   C10   110.25  3.000
 MY5  H9C2  C9   C4    111.26  3.000
 MY5  H9C1  C9   C4    108.21  3.000
 MY5  C10   C9   C4    112.09  3.000
 MY5  H10   C10  O28   107.23  3.000
 MY5  H10   C10  C11   109.60  3.000
 MY5  O28   C10  C11   110.12  3.000
 MY5  H10   C10  C9    109.46  3.000
 MY5  O28   C10  C9    112.13  3.000
 MY5  C11   C10  C9    108.28  3.000
 MY5  N13   C11  O12   124.10  3.000
 MY5  N13   C11  C10   115.41  3.000
 MY5  O12   C11  C10   120.44  3.000
 MY5  H13   N13  C14   116.81  3.000
 MY5  H13   N13  C11   119.46  3.000
 MY5  C14   N13  C11   123.50  3.000
 MY5  H14   C14  C16   109.63  3.000
 MY5  H14   C14  C15   109.24  3.000
 MY5  C16   C14  C15   109.35  3.000
 MY5  H14   C14  N13   108.56  3.000
 MY5  C16   C14  N13   107.93  3.000
 MY5  C15   C14  N13   112.10  3.000
 MY5  H153  C15  H152  108.53  3.000
 MY5  H153  C15  H151  108.41  3.000
 MY5  H152  C15  H151  107.92  3.000
 MY5  H153  C15  C14   110.68  3.000
 MY5  H152  C15  C14   110.16  3.000
 MY5  H151  C15  C14   111.04  3.000
 MY5  N18   C16  O17   123.28  3.000
 MY5  N18   C16  C14   115.13  3.000
 MY5  O17   C16  C14   121.53  3.000
 MY5  H18   N18  C19   118.39  3.000
 MY5  H18   N18  C16   119.36  3.000
 MY5  C19   N18  C16   122.25  3.000
 MY5  H192  C19  H191  107.10  3.000
 MY5  H192  C19  C23   110.22  3.000
 MY5  H191  C19  C23   110.24  3.000
 MY5  H192  C19  N18   109.86  3.000
 MY5  H191  C19  N18   109.38  3.000
 MY5  C23   C19  N18   109.99  3.000
 MY5  H20   C20  C25   120.14  3.000
 MY5  H20   C20  C21   120.12  3.000
 MY5  C25   C20  C21   119.74  3.000
 MY5  H21   C21  C22   119.83  3.000
 MY5  H21   C21  C20   120.11  3.000
 MY5  C22   C21  C20   120.06  3.000
 MY5  H22   C22  C23   119.68  3.000
 MY5  H22   C22  C21   119.74  3.000
 MY5  C23   C22  C21   120.58  3.000
 MY5  C24   C23  C22   118.99  3.000
 MY5  C24   C23  C19   120.57  3.000
 MY5  C22   C23  C19   120.42  3.000
 MY5  H24   C24  C25   119.68  3.000
 MY5  H24   C24  C23   119.73  3.000
 MY5  C25   C24  C23   120.58  3.000
 MY5  H25   C25  C24   119.80  3.000
 MY5  H25   C25  C20   120.14  3.000
 MY5  C24   C25  C20   120.05  3.000
 MY5  H28   O28  C10   107.64  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
 MY5  CONST_01  C23   C22  C21  C20     0.00   0.0  0
 MY5  CONST_02  C23   C24  C25  C20     0.00   0.0  0
 MY5  CONST_03  C24   C25  C20  C21     0.00   0.0  0
 MY5  CONST_04  C24   C23  C22  C21     0.00   0.0  0
 MY5  CONST_05  C25   C20  C21  C22     0.00   0.0  0
 MY5  CONST_06  C25   C24  C23  C22     0.00   0.0  0
 MY5  CONST_07  C21   C22  C23  C19   180.00   0.0  0
 MY5  CONST_08  C25   C24  C23  C19   180.00   0.0  0
 MY5  CONST_09  H22   C22  C21  C20   180.00   0.0  0
 MY5  CONST_10  H24   C24  C25  C20   180.00   0.0  0
 MY5  CONST_11  H25   C25  C20  C21   180.00   0.0  0
 MY5  CONST_12  H20   C20  C21  C22   180.00   0.0  0
 MY5  CONST_13  H21   C21  C22  C23   180.00   0.0  0
 MY5  CONST_14  O5    C4   N1   N2    180.00   0.0  0
 MY5  CONST_15  C9    C4   N1   N2      0.00   0.0  0
 MY5  CONST_16  O5    C4   N1   C3      0.00   0.0  0
 MY5  CONST_17  C9    C4   N1   C3    180.00   0.0  0
 MY5  CONST_18  C14   N13  C11  C10   180.00   0.0  0
 MY5  CONST_19  C14   N13  C11  O12     0.00   0.0  0
 MY5  CONST_20  C19   N18  C16  C14   180.00   0.0  0
 MY5  CONST_21  C19   N18  C16  O17     0.00   0.0  0
 MY5  CONST_22  H13   N13  C11  C10     0.00   0.0  0
 MY5  CONST_23  H18   N18  C16  C14     0.00   0.0  0
 MY5  Var_01    C22   C23  C19  N18    85.10  30.0  2
 MY5  Var_02    C23   C19  N18  C16  -176.19  30.0  3
 MY5  Var_03    O7    C6   C3   N1     -1.29  30.0  3
 MY5  Var_04    C10   C9   C4   N1    170.34  30.0  3
 MY5  Var_05    C6    C3   N1   N2    -79.03  30.0  3
 MY5  Var_06    H2N1  N2   N1   C3     99.33  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
 MY5  chir_01  C10  C9   C11  O28  negativ
 MY5  chir_02  C14  N13  C15  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
 MY5  plan-1  C19  0.020
 MY5  plan-1  C20  0.020
 MY5  plan-1  C21  0.020
 MY5  plan-1  C22  0.020
 MY5  plan-1  C23  0.020
 MY5  plan-1  C24  0.020
 MY5  plan-1  C25  0.020
 MY5  plan-1  H22  0.020
 MY5  plan-1  H24  0.020
 MY5  plan-1  H25  0.020
 MY5  plan-1  H20  0.020
 MY5  plan-1  H21  0.020
 MY5  plan-2  N1   0.020
 MY5  plan-2  N2   0.020
 MY5  plan-2  C3   0.020
 MY5  plan-2  C4   0.020
 MY5  plan-2  O5   0.020
 MY5  plan-2  C9   0.020
 MY5  plan-3  C10  0.020
 MY5  plan-3  C11  0.020
 MY5  plan-3  O12  0.020
 MY5  plan-3  N13  0.020
 MY5  plan-3  C14  0.020
 MY5  plan-3  H13  0.020
 MY5  plan-4  C14  0.020
 MY5  plan-4  C16  0.020
 MY5  plan-4  O17  0.020
 MY5  plan-4  N18  0.020
 MY5  plan-4  C19  0.020
 MY5  plan-4  H18  0.020
 MY5  plan-5  C3   0.020
 MY5  plan-5  C6   0.020
 MY5  plan-5  O7   0.020
 MY5  plan-5  O8   0.020

