# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 16:58:40 2022
#   Inital geometry file: a 165 line input string
#   Ligand name: (2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]ethanoylamino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)CN[P](O)(=O)[C@@H](Cc1ccccc1)NC(=O)OCc2ccccc2)C(O)=O
#
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
 OZH  OZH  '(2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]ethanoylamino]pentanoic acid'  ligand  65  35  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OZH
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
 OZH  O5   O  O      0  -0.602  33.1410  40.0672  -11.5729
 OZH  O4   O  O2     0  -0.483  38.6449  39.1402   -3.1888
 OZH  C2   C  CH3    0  -0.647  29.8264  36.9679   -8.6697
 OZH  C1   C  CH1    0  -0.229  31.3348  37.1000   -8.8583
 OZH  C    C  CH3    0  -0.657  31.8743  35.9212   -9.6621
 OZH  C7   C  CH1    0  -0.368  36.3256  41.5888   -4.3935
 OZH  N    N  NH1    0  -0.604  33.6843  38.9743   -8.2220
 OZH  C6   C  CH2    0  -0.382  35.0714  38.6483   -6.2757
 OZH  C5   C  C      0   0.497  34.5321  38.1482   -7.6143
 OZH  C4   C  CH1    0  -0.224  33.1476  38.8268   -9.5535
 OZH  C3   C  CH2    0  -0.395  31.6630  38.4389   -9.5192
 OZH  O    O  O      0  -0.525  34.8929  37.0543   -8.0435
 OZH  C8   C  CH2    0  -0.518  35.3644  41.9294   -3.2422
 OZH  C9   C  CR6    0   0.139  36.0759  42.0276   -1.9236
 OZH  C11  C  CR16   0  -0.242  36.9778  40.9760    0.0631
 OZH  C10  C  CR16   0  -0.313  36.2522  40.9028   -1.1191
 OZH  C12  C  CR16   0  -0.271  37.5338  42.1828    0.4662
 OZH  C17  C  CR6    0   0.077  39.9383  37.5923   -1.9825
 OZH  C18  C  CR16   0  -0.296  40.6147  36.5515   -2.6086
 OZH  C16  C  CH2    0  -0.235  39.9242  38.9691   -2.5757
 OZH  C14  C  CR16   0  -0.305  36.6328  43.2338   -1.5030
 OZH  C13  C  CR16   0  -0.241  37.3531  43.3146   -0.3192
 OZH  C23  C  C      0   0.420  33.3081  40.1534  -10.3424
 OZH  C19  C  CR16   0  -0.240  40.6013  35.2721   -2.0664
 OZH  C20  C  CR16   0  -0.260  39.9030  35.0231   -0.8934
 OZH  C21  C  CR16   0  -0.242  39.2243  36.0585   -0.2607
 OZH  O3   O  O      0  -0.512  39.0666  41.3279   -3.5261
 OZH  C22  C  CR16   0  -0.287  39.2423  37.3345   -0.8032
 OZH  N1   N  NH1    0  -0.822  34.6041  39.9363   -5.8479
 OZH  N2   N  NH1    0  -0.649  37.0705  40.3836   -4.1041
 OZH  O6   O  OC    -1  -0.595  33.5521  41.1811   -9.6807
 OZH  P    P  P      0   1.276  35.4535  41.4034   -6.0287
 OZH  H1   H  HCH3   0   0.221  29.5690  36.0291   -8.1758
 OZH  H2   H  HCH3   0   0.220  29.4268  37.7826   -8.0629
 OZH  H3   H  HCH3   0   0.209  29.3057  36.9866   -9.6308
 OZH  H4   H  HCH1   0   0.212  31.7953  37.0814   -7.8647
 OZH  H5   H  HCH3   0   0.220  31.6193  34.9727   -9.1854
 OZH  H6   H  HCH3   0   0.206  31.4460  35.9117  -10.6675
 OZH  H7   H  HCH3   0   0.229  32.9589  35.9565   -9.7598
 OZH  H8   H  HCH1   0   0.256  37.0433  42.4044   -4.5063
 OZH  H9   H  HNH1   0   0.384  33.5599  39.8816   -7.7946
 OZH  H10  H  HCH2   0   0.252  34.8336  37.8822   -5.5319
 OZH  H11  H  HCH2   0   0.247  36.1592  38.6481   -6.3670
 OZH  H12  H  HCH1   0   0.231  33.7164  38.0494  -10.0671
 OZH  H13  H  HCH2   0   0.212  31.1182  39.2366   -9.0007
 OZH  H14  H  HCH2   0   0.212  31.2853  38.4249  -10.5459
 OZH  H15  H  HCH2   0   0.249  34.8663  42.8702   -3.4785
 OZH  H16  H  HCH2   0   0.237  34.5865  41.1616   -3.1865
 OZH  H17  H  HCR6   0   0.249  37.1059  40.0884    0.6702
 OZH  H18  H  HCR6   0   0.246  35.8122  39.9581   -1.4169
 OZH  H19  H  HCR6   0   0.249  38.0977  42.2428    1.3883
 OZH  H20  H  HCR6   0   0.254  41.1582  36.7417   -3.5266
 OZH  H21  H  HCH2   0   0.244  40.7193  39.0829   -3.3165
 OZH  H22  H  HCH2   0   0.242  40.0750  39.7231   -1.8003
 OZH  H23  H  HCR6   0   0.242  36.5040  44.1207   -2.1133
 OZH  H24  H  HCR6   0   0.249  37.7752  44.2624   -0.0093
 OZH  H25  H  HCR6   0   0.256  41.1340  34.4708   -2.5621
 OZH  H26  H  HCR6   0   0.256  39.8897  34.0272   -0.4697
 OZH  H27  H  HCR6   0   0.255  38.6825  35.8704    0.6573
 OZH  H29  H  HCR6   0   0.257  38.7158  38.1398   -0.3032
 OZH  H30  H  HNH1   0   0.373  33.7553  39.9364   -5.3040
 OZH  H31  H  HNH1   0   0.399  36.5320  39.5345   -4.0168
 OZH  O1   O  O      0  -0.791  36.5002  41.1879   -7.0909
 OZH  O2   O  OP    -1  -0.794  34.4403  42.5142   -6.1177
 OZH  C15  C  C      0   0.752  38.3161  40.3763   -3.5949

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
 OZH  O5   C23  deloc     1.245  0.020  1.245
 OZH  C23  O6   deloc     1.246  0.020  1.246
 OZH  C23  C4   single    1.552  0.020  1.552
 OZH  C4   C3   single    1.535  0.020  1.535
 OZH  C4   N    single    1.443  0.020  1.443
 OZH  C3   C1   single    1.529  0.020  1.529
 OZH  C    C1   single    1.525  0.020  1.525
 OZH  C1   C2   single    1.526  0.020  1.526
 OZH  N    C5   single    1.331  0.020  1.331
 OZH  O    C5   double    1.229  0.020  1.229
 OZH  C5   C6   single    1.527  0.020  1.527
 OZH  O1   P    deloc     1.507  0.020  1.507
 OZH  C6   N1   single    1.435  0.020  1.435
 OZH  N1   P    single    1.705  0.020  1.705
 OZH  P    O2   deloc     1.506  0.020  1.506
 OZH  P    C7   single    1.862  0.020  1.862
 OZH  C7   N2   single    1.446  0.020  1.446
 OZH  C7   C8   single    1.538  0.020  1.538
 OZH  O3   C15  double    1.214  0.020  1.214
 OZH  N2   C15  single    1.346  0.020  1.346
 OZH  C15  O4   single    1.342  0.020  1.342
 OZH  C16  O4   single    1.429  0.020  1.429
 OZH  C16  C17  single    1.499  0.020  1.499
 OZH  C8   C9   single    1.502  0.020  1.502
 OZH  C18  C17  aromatic  1.390  0.020  1.390
 OZH  C18  C19  aromatic  1.390  0.020  1.390
 OZH  C17  C22  aromatic  1.393  0.020  1.393
 OZH  C19  C20  aromatic  1.388  0.020  1.388
 OZH  C22  C21  aromatic  1.387  0.020  1.387
 OZH  C9   C14  aromatic  1.394  0.020  1.394
 OZH  C9   C10  aromatic  1.394  0.020  1.394
 OZH  C14  C13  aromatic  1.388  0.020  1.388
 OZH  C20  C21  aromatic  1.390  0.020  1.390
 OZH  C10  C11  aromatic  1.389  0.020  1.389
 OZH  C13  C12  aromatic  1.389  0.020  1.389
 OZH  C11  C12  aromatic  1.389  0.020  1.389
 OZH  C2   H1   single    0.970  0.020  1.090
 OZH  C2   H2   single    0.970  0.020  1.090
 OZH  C2   H3   single    0.970  0.020  1.090
 OZH  C1   H4   single    0.970  0.020  1.090
 OZH  C    H5   single    0.970  0.020  1.090
 OZH  C    H6   single    0.970  0.020  1.090
 OZH  C    H7   single    0.970  0.020  1.090
 OZH  C7   H8   single    0.970  0.020  1.090
 OZH  N    H9   single    0.860  0.020  1.020
 OZH  C6   H10  single    0.970  0.020  1.090
 OZH  C6   H11  single    0.970  0.020  1.090
 OZH  C4   H12  single    0.970  0.020  1.090
 OZH  C3   H13  single    0.970  0.020  1.090
 OZH  C3   H14  single    0.970  0.020  1.090
 OZH  C8   H15  single    0.970  0.020  1.090
 OZH  C8   H16  single    0.970  0.020  1.090
 OZH  C11  H17  single    0.930  0.020  1.080
 OZH  C10  H18  single    0.930  0.020  1.080
 OZH  C12  H19  single    0.930  0.020  1.080
 OZH  C18  H20  single    0.930  0.020  1.080
 OZH  C16  H21  single    0.970  0.020  1.090
 OZH  C16  H22  single    0.970  0.020  1.090
 OZH  C14  H23  single    0.930  0.020  1.080
 OZH  C13  H24  single    0.930  0.020  1.080
 OZH  C19  H25  single    0.930  0.020  1.080
 OZH  C20  H26  single    0.930  0.020  1.080
 OZH  C21  H27  single    0.930  0.020  1.080
 OZH  C22  H29  single    0.930  0.020  1.080
 OZH  N1   H30  single    0.860  0.020  1.020
 OZH  N2   H31  single    0.860  0.020  1.020

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
 OZH  C15  O4   C16  117.36  3.000
 OZH  H3   C2   H2   107.55  3.000
 OZH  H3   C2   H1   107.46  3.000
 OZH  H2   C2   H1   107.70  3.000
 OZH  H3   C2   C1   111.14  3.000
 OZH  H2   C2   C1   111.47  3.000
 OZH  H1   C2   C1   111.31  3.000
 OZH  H4   C1   C3   108.47  3.000
 OZH  H4   C1   C    108.43  3.000
 OZH  C3   C1   C    111.90  3.000
 OZH  H4   C1   C2   107.58  3.000
 OZH  C    C1   C2   110.35  3.000
 OZH  C3   C1   C2   109.97  3.000
 OZH  H7   C    H6   107.93  3.000
 OZH  H7   C    H5   107.44  3.000
 OZH  H6   C    H5   107.61  3.000
 OZH  H7   C    C1   111.98  3.000
 OZH  H6   C    C1   110.67  3.000
 OZH  H5   C    C1   111.02  3.000
 OZH  H8   C7   P    106.94  3.000
 OZH  H8   C7   N2   107.73  3.000
 OZH  P    C7   N2   109.51  3.000
 OZH  H8   C7   C8   108.82  3.000
 OZH  N2   C7   C8   110.90  3.000
 OZH  P    C7   C8   112.75  3.000
 OZH  H9   N    C4   115.85  3.000
 OZH  H9   N    C5   116.28  3.000
 OZH  C4   N    C5   126.51  3.000
 OZH  H11  C6   H10  105.86  3.000
 OZH  H11  C6   N1   110.46  3.000
 OZH  H10  C6   N1   110.79  3.000
 OZH  H11  C6   C5   106.17  3.000
 OZH  H10  C6   C5   106.85  3.000
 OZH  N1   C6   C5   116.11  3.000
 OZH  O    C5   C6   119.59  3.000
 OZH  C6   C5   N    114.96  3.000
 OZH  O    C5   N    125.45  3.000
 OZH  H12  C4   C23  108.40  3.000
 OZH  H12  C4   C3   109.54  3.000
 OZH  C23  C4   C3   109.11  3.000
 OZH  H12  C4   N    108.25  3.000
 OZH  C3   C4   N    111.41  3.000
 OZH  C23  C4   N    110.07  3.000
 OZH  H14  C3   H13  106.36  3.000
 OZH  H14  C3   C4   108.44  3.000
 OZH  H13  C3   C4   107.90  3.000
 OZH  H14  C3   C1   108.69  3.000
 OZH  H13  C3   C1   109.03  3.000
 OZH  C4   C3   C1   116.02  3.000
 OZH  H16  C8   H15  106.96  3.000
 OZH  H16  C8   C9   109.75  3.000
 OZH  H15  C8   C9   110.51  3.000
 OZH  H16  C8   C7   109.08  3.000
 OZH  H15  C8   C7   108.32  3.000
 OZH  C9   C8   C7   112.07  3.000
 OZH  C14  C9   C10  118.27  3.000
 OZH  C10  C9   C8   120.93  3.000
 OZH  C14  C9   C8   120.73  3.000
 OZH  H17  C11  C12  120.14  3.000
 OZH  H17  C11  C10  119.72  3.000
 OZH  C12  C11  C10  120.14  3.000
 OZH  H18  C10  C11  119.46  3.000
 OZH  H18  C10  C9   119.56  3.000
 OZH  C11  C10  C9   120.98  3.000
 OZH  H19  C12  C13  120.27  3.000
 OZH  H19  C12  C11  120.27  3.000
 OZH  C13  C12  C11  119.45  3.000
 OZH  C22  C17  C16  120.00  3.000
 OZH  C22  C17  C18  119.06  3.000
 OZH  C16  C17  C18  120.92  3.000
 OZH  H20  C18  C19  119.80  3.000
 OZH  H20  C18  C17  119.61  3.000
 OZH  C19  C18  C17  120.59  3.000
 OZH  H22  C16  H21  108.00  3.000
 OZH  H22  C16  C17  110.60  3.000
 OZH  H21  C16  C17  110.92  3.000
 OZH  H22  C16  O4   110.22  3.000
 OZH  H21  C16  O4   110.38  3.000
 OZH  C17  C16  O4   106.75  3.000
 OZH  H23  C14  C13  119.61  3.000
 OZH  H23  C14  C9   119.38  3.000
 OZH  C13  C14  C9   121.01  3.000
 OZH  H24  C13  C14  119.83  3.000
 OZH  H24  C13  C12  120.03  3.000
 OZH  C14  C13  C12  120.14  3.000
 OZH  O6   C23  C4   117.08  3.000
 OZH  C4   C23  O5   115.43  3.000
 OZH  O6   C23  O5   127.46  3.000
 OZH  H25  C19  C20  120.13  3.000
 OZH  H25  C19  C18  119.88  3.000
 OZH  C20  C19  C18  119.99  3.000
 OZH  H26  C20  C21  120.07  3.000
 OZH  H26  C20  C19  120.14  3.000
 OZH  C21  C20  C19  119.79  3.000
 OZH  H27  C21  C22  119.88  3.000
 OZH  H27  C21  C20  120.06  3.000
 OZH  C22  C21  C20  120.06  3.000
 OZH  H29  C22  C21  119.78  3.000
 OZH  H29  C22  C17  119.70  3.000
 OZH  C21  C22  C17  120.52  3.000
 OZH  H30  N1   P    118.46  3.000
 OZH  H30  N1   C6   115.79  3.000
 OZH  P    N1   C6   125.33  3.000
 OZH  H31  N2   C15  117.17  3.000
 OZH  H31  N2   C7   116.34  3.000
 OZH  C15  N2   C7   123.85  3.000
 OZH  N1   P    O2   107.80  3.000
 OZH  O2   P    O1   122.08  3.000
 OZH  N1   P    O1   107.33  3.000
 OZH  O2   P    C7   107.06  3.000
 OZH  N1   P    C7   103.05  3.000
 OZH  O1   P    C7   107.94  3.000
 OZH  N2   C15  O3   126.12  3.000
 OZH  N2   C15  O4   110.26  3.000
 OZH  O3   C15  O4   123.60  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
 OZH  CONST_01  C12  C13  C14  C9     0.00   0.0  0
 OZH  CONST_02  C12  C11  C10  C9     0.00   0.0  0
 OZH  CONST_03  C14  C9   C10  C11    0.00   0.0  0
 OZH  CONST_04  C14  C13  C12  C11    0.00   0.0  0
 OZH  CONST_05  C13  C14  C9   C10    0.00   0.0  0
 OZH  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 OZH  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 OZH  CONST_08  C20  C21  C22  C17    0.00   0.0  0
 OZH  CONST_09  C21  C22  C17  C18    0.00   0.0  0
 OZH  CONST_10  C21  C20  C19  C18    0.00   0.0  0
 OZH  CONST_11  C22  C17  C18  C19    0.00   0.0  0
 OZH  CONST_12  C22  C21  C20  C19    0.00   0.0  0
 OZH  CONST_13  C13  C14  C9   C8   180.00   0.0  0
 OZH  CONST_14  C11  C10  C9   C8   180.00   0.0  0
 OZH  CONST_15  C19  C18  C17  C16  180.00   0.0  0
 OZH  CONST_16  C21  C22  C17  C16  180.00   0.0  0
 OZH  CONST_17  H24  C13  C14  C9   180.00   0.0  0
 OZH  CONST_18  H17  C11  C10  C9   180.00   0.0  0
 OZH  CONST_19  H23  C14  C9   C10  180.00   0.0  0
 OZH  CONST_20  H19  C12  C11  C10  180.00   0.0  0
 OZH  CONST_21  H18  C10  C11  C12  180.00   0.0  0
 OZH  CONST_22  H25  C19  C18  C17  180.00   0.0  0
 OZH  CONST_23  H27  C21  C22  C17  180.00   0.0  0
 OZH  CONST_24  H29  C22  C17  C18  180.00   0.0  0
 OZH  CONST_25  H26  C20  C19  C18  180.00   0.0  0
 OZH  CONST_26  H20  C18  C19  C20  180.00   0.0  0
 OZH  CONST_27  C4   N    C5   C6   180.00   0.0  0
 OZH  CONST_28  O    C5   N    C4     0.00   0.0  0
 OZH  CONST_29  H9   N    C5   C6     0.00   0.0  0
 OZH  Var_01    C18  C17  C16  O4   102.94  30.0  2
 OZH  Var_02    C14  C9   C8   C7    88.27  30.0  2
 OZH  Var_03    C7   N2   C15  O4   167.81  30.0  1
 OZH  Var_04    C4   C3   C1   C2   169.71  30.0  2
 OZH  Var_05    C6   N1   P    C7   -94.91  30.0  2
 OZH  Var_06    N1   C6   C5   N     -0.22  30.0  3
 OZH  Var_07    P    N1   C6   C5   -98.65  30.0  3
 OZH  Var_08    H5   C    C1   C2   -56.36  30.0  3
 OZH  Var_09    H1   C2   C1   C     57.50  30.0  3

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
 OZH  chir_01  C7  P  N2   C8  positiv
 OZH  chir_02  C4  N  C23  C3  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
 OZH  plan-1  C8   0.020
 OZH  plan-1  C9   0.020
 OZH  plan-1  C11  0.020
 OZH  plan-1  C10  0.020
 OZH  plan-1  C12  0.020
 OZH  plan-1  C14  0.020
 OZH  plan-1  C13  0.020
 OZH  plan-1  H17  0.020
 OZH  plan-1  H18  0.020
 OZH  plan-1  H19  0.020
 OZH  plan-1  H23  0.020
 OZH  plan-1  H24  0.020
 OZH  plan-2  C17  0.020
 OZH  plan-2  C18  0.020
 OZH  plan-2  C16  0.020
 OZH  plan-2  C19  0.020
 OZH  plan-2  C20  0.020
 OZH  plan-2  C21  0.020
 OZH  plan-2  C22  0.020
 OZH  plan-2  H20  0.020
 OZH  plan-2  H25  0.020
 OZH  plan-2  H26  0.020
 OZH  plan-2  H27  0.020
 OZH  plan-2  H29  0.020
 OZH  plan-3  N    0.020
 OZH  plan-3  C6   0.020
 OZH  plan-3  C5   0.020
 OZH  plan-3  C4   0.020
 OZH  plan-3  O    0.020
 OZH  plan-3  H9   0.020
 OZH  plan-4  O5   0.020
 OZH  plan-4  C4   0.020
 OZH  plan-4  C23  0.020
 OZH  plan-4  O6   0.020
 OZH  plan-5  O4   0.020
 OZH  plan-5  O3   0.020
 OZH  plan-5  N2   0.020
 OZH  plan-5  C15  0.020

