# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 16:43:25 2022
#   Inital geometry file: a 165 line input string
#   Ligand name: (2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{R})-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
 OZE  OZE  '(2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{R})-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_OZE
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
 OZE  C5   C  C      0   0.506   8.5717  38.9182   -3.4280
 OZE  C6   C  CH2    0  -0.392   9.9216  38.2145   -3.4463
 OZE  N1   N  NH1    0  -0.806  10.9479  38.8536   -4.2461
 OZE  C2   C  CH3    0  -0.646   9.3275  42.6946   -2.4325
 OZE  C4   C  CH1    0  -0.208   7.3333  40.9009   -4.1811
 OZE  C7   C  CH1    0  -0.349  12.4336  39.4527   -6.4938
 OZE  N2   N  NH1    0  -0.647  12.5617  39.1553   -7.9052
 OZE  C9   C  C      0   0.163  13.0869  41.8480   -6.8793
 OZE  C8   C  CH2    0  -0.533  12.0630  40.9231   -6.2860
 OZE  C10  C  C1     0  -0.303  14.3154  42.0366   -6.2474
 OZE  C11  C  C1     0  -0.238  15.2827  42.8650   -6.7979
 OZE  N    N  NH1    0  -0.615   8.5277  40.1053   -4.0245
 OZE  C    C  CH3    0  -0.649   7.2678  43.7717   -1.5093
 OZE  O    O  O      0  -0.530   7.6199  38.3880   -2.8571
 OZE  C12  C  C1     0  -0.273  15.0364  43.5241   -7.9965
 OZE  C13  C  C1     0  -0.239  13.8174  43.3454   -8.6357
 OZE  C14  C  C1     0  -0.323  12.8533  42.5129   -8.0798
 OZE  C15  C  C      0   0.743  13.6372  38.5665   -8.4515
 OZE  C16  C  CH2    0  -0.229  14.4245  37.5770  -10.4529
 OZE  C17  C  CR6    0   0.077  13.8063  37.0225  -11.7021
 OZE  C18  C  CR16   0  -0.283  12.8191  36.0416  -11.6145
 OZE  C19  C  CR16   0  -0.240  12.2437  35.5175  -12.7611
 OZE  C20  C  CR16   0  -0.262  12.6514  35.9655  -14.0130
 OZE  C21  C  CR16   0  -0.238  13.6342  36.9393  -14.1087
 OZE  C22  C  CR16   0  -0.303  14.2055  37.4673  -12.9564
 OZE  C23  C  C      0   0.416   7.4309  41.7872   -5.4468
 OZE  C3   C  CH2    0  -0.392   6.9996  41.7536   -2.9472
 OZE  O3   O  O      0  -0.515  14.6946  38.3539   -7.8933
 OZE  O4   O  O2     0  -0.484  13.3921  38.2489   -9.7324
 OZE  O5   O  OC    -1  -0.600   6.3767  42.3632   -5.7711
 OZE  O6   O  O      0  -0.590   8.5405  41.8654   -6.0108
 OZE  P    P  P      0   1.238  11.1944  38.2349   -5.8349
 OZE  H1   H  HCH2   0   0.233   9.7317  37.1733   -3.7324
 OZE  H2   H  HCH2   0   0.264  10.2556  38.1690   -2.4071
 OZE  H3   H  HNH1   0   0.370  11.8113  38.9457   -3.7273
 OZE  H4   H  HCH3   0   0.215   9.8603  43.6046   -2.1484
 OZE  H5   H  HCH3   0   0.207   9.4458  41.9752   -1.6187
 OZE  H6   H  HCH3   0   0.221   9.8264  42.2884   -3.3108
 OZE  H7   H  HCH1   0   0.232   6.4911  40.2159   -4.3238
 OZE  H8   H  HCH1   0   0.262  13.3995  39.2597   -6.0243
 OZE  H9   H  HNH1   0   0.388  11.7144  39.1925   -8.4530
 OZE  H10  H  HCH2   0   0.251  11.9671  41.1069   -5.2145
 OZE  H11  H  HCH2   0   0.248  11.0800  41.1163   -6.7207
 OZE  H12  H  H      0   0.242  14.5166  41.5308   -5.3092
 OZE  H13  H  H      0   0.248  16.2292  42.9998   -6.2896
 OZE  H14  H  HNH1   0   0.399   9.3433  40.3917   -4.5473
 OZE  H15  H  HCH3   0   0.221   7.8271  44.6894   -1.3181
 OZE  H16  H  HCH3   0   0.220   6.2275  44.0487   -1.6896
 OZE  H17  H  HCH3   0   0.210   7.2962  43.1723   -0.5957
 OZE  H18  H  HCH1   0   0.213   7.7885  43.6472   -3.5690
 OZE  H19  H  H      0   0.249  15.7885  44.1728   -8.4269
 OZE  H20  H  H      0   0.248  13.6142  43.8550   -9.5693
 OZE  H21  H  H      0   0.242  11.9033  42.3812   -8.5846
 OZE  H22  H  HCH2   0   0.244  14.8439  36.7707   -9.8474
 OZE  H23  H  HCH2   0   0.245  15.2335  38.2711  -10.6941
 OZE  H24  H  HCR6   0   0.253  12.5005  35.6825  -10.6428
 OZE  H25  H  HCR6   0   0.255  11.4788  34.7558  -12.6804
 OZE  H26  H  HCR6   0   0.256  12.2040  35.5546  -14.9088
 OZE  H27  H  HCR6   0   0.255  13.9553  37.2931  -15.0799
 OZE  H28  H  HCR6   0   0.254  14.9689  38.2321  -13.0369
 OZE  H29  H  HCH2   0   0.215   5.9600  42.0749   -3.0530
 OZE  H30  H  HCH2   0   0.212   7.0265  41.1136   -2.0592
 OZE  C1   C  CH1    0  -0.241   7.8539  42.9982   -2.6889
 OZE  O1   O  OP    -1  -0.788  11.8426  36.8711   -5.8103
 OZE  O2   O  O      0  -0.800   9.9070  38.4163   -6.6019

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
 OZE  C20  C19  aromatic  1.391  0.020  1.391
 OZE  C20  C21  aromatic  1.387  0.020  1.387
 OZE  C19  C18  aromatic  1.386  0.020  1.386
 OZE  C21  C22  aromatic  1.390  0.020  1.390
 OZE  C18  C17  aromatic  1.394  0.020  1.394
 OZE  C22  C17  aromatic  1.389  0.020  1.389
 OZE  C17  C16  single    1.500  0.020  1.500
 OZE  C16  O4   single    1.427  0.020  1.427
 OZE  O4   C15  single    1.342  0.020  1.342
 OZE  C13  C14  aromatic  1.390  0.020  1.390
 OZE  C13  C12  aromatic  1.388  0.020  1.388
 OZE  C14  C9   aromatic  1.392  0.020  1.392
 OZE  C12  C11  aromatic  1.390  0.020  1.390
 OZE  C15  N2   single    1.342  0.020  1.342
 OZE  C15  O3   double    1.214  0.020  1.214
 OZE  N2   C7   single    1.448  0.020  1.448
 OZE  C9   C8   single    1.502  0.020  1.502
 OZE  C9   C10  aromatic  1.394  0.020  1.394
 OZE  C11  C10  aromatic  1.388  0.020  1.388
 OZE  C7   C8   single    1.531  0.020  1.531
 OZE  C7   P    single    1.858  0.020  1.858
 OZE  O2   P    deloc     1.510  0.020  1.510
 OZE  O1   P    deloc     1.510  0.020  1.510
 OZE  P    N1   single    1.723  0.020  1.723
 OZE  O6   C23  deloc     1.247  0.020  1.247
 OZE  O5   C23  deloc     1.244  0.020  1.244
 OZE  C23  C4   single    1.548  0.020  1.548
 OZE  N1   C6   single    1.450  0.020  1.450
 OZE  C4   N    single    1.444  0.020  1.444
 OZE  C4   C3   single    1.536  0.020  1.536
 OZE  N    C5   single    1.329  0.020  1.329
 OZE  C5   C6   single    1.522  0.020  1.522
 OZE  C5   O    double    1.230  0.020  1.230
 OZE  C3   C1   single    1.531  0.020  1.531
 OZE  C1   C2   single    1.526  0.020  1.526
 OZE  C1   C    single    1.527  0.020  1.527
 OZE  C6   H1   single    0.970  0.020  1.090
 OZE  C6   H2   single    0.970  0.020  1.090
 OZE  N1   H3   single    0.890  0.020  1.040
 OZE  C2   H4   single    0.970  0.020  1.090
 OZE  C2   H5   single    0.970  0.020  1.090
 OZE  C2   H6   single    0.970  0.020  1.090
 OZE  C4   H7   single    0.970  0.020  1.090
 OZE  C7   H8   single    0.970  0.020  1.090
 OZE  N2   H9   single    0.860  0.020  1.020
 OZE  C8   H10  single    0.970  0.020  1.090
 OZE  C8   H11  single    0.970  0.020  1.090
 OZE  C10  H12  single    0.930  0.020  1.080
 OZE  C11  H13  single    0.930  0.020  1.080
 OZE  N    H14  single    0.860  0.020  1.020
 OZE  C    H15  single    0.970  0.020  1.090
 OZE  C    H16  single    0.970  0.020  1.090
 OZE  C    H17  single    0.970  0.020  1.090
 OZE  C1   H18  single    0.970  0.020  1.090
 OZE  C12  H19  single    0.930  0.020  1.080
 OZE  C13  H20  single    0.930  0.020  1.080
 OZE  C14  H21  single    0.930  0.020  1.080
 OZE  C16  H22  single    0.970  0.020  1.090
 OZE  C16  H23  single    0.970  0.020  1.090
 OZE  C18  H24  single    0.930  0.020  1.080
 OZE  C19  H25  single    0.930  0.020  1.080
 OZE  C20  H26  single    0.930  0.020  1.080
 OZE  C21  H27  single    0.930  0.020  1.080
 OZE  C22  H28  single    0.930  0.020  1.080
 OZE  C3   H29  single    0.970  0.020  1.090
 OZE  C3   H30  single    0.970  0.020  1.090

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
 OZE  O    C5   N    124.59  3.000
 OZE  O    C5   C6   119.50  3.000
 OZE  N    C5   C6   115.90  3.000
 OZE  H2   C6   H1   105.17  3.000
 OZE  H2   C6   N1   109.07  3.000
 OZE  H1   C6   N1   113.41  3.000
 OZE  H2   C6   C5   106.19  3.000
 OZE  H1   C6   C5   106.77  3.000
 OZE  N1   C6   C5   115.50  3.000
 OZE  H3   N1   P    112.56  3.000
 OZE  H3   N1   C6   111.19  3.000
 OZE  P    N1   C6   116.86  3.000
 OZE  H6   C2   H5   107.80  3.000
 OZE  H6   C2   H4   107.29  3.000
 OZE  H5   C2   H4   107.58  3.000
 OZE  H6   C2   C1   112.41  3.000
 OZE  H5   C2   C1   111.14  3.000
 OZE  H4   C2   C1   110.42  3.000
 OZE  H7   C4   C3   106.55  3.000
 OZE  H7   C4   C23  107.46  3.000
 OZE  C3   C4   C23  110.64  3.000
 OZE  H7   C4   N    107.80  3.000
 OZE  C3   C4   N    113.48  3.000
 OZE  C23  C4   N    110.61  3.000
 OZE  H8   C7   P    108.77  3.000
 OZE  H8   C7   C8   109.02  3.000
 OZE  P    C7   C8   114.83  3.000
 OZE  H8   C7   N2   107.74  3.000
 OZE  P    C7   N2   105.66  3.000
 OZE  C8   C7   N2   110.55  3.000
 OZE  H9   N2   C15  117.89  3.000
 OZE  H9   N2   C7   116.56  3.000
 OZE  C15  N2   C7   123.89  3.000
 OZE  C14  C9   C10  118.30  3.000
 OZE  C10  C9   C8   120.33  3.000
 OZE  C14  C9   C8   121.35  3.000
 OZE  H11  C8   H10  106.37  3.000
 OZE  H11  C8   C9   110.34  3.000
 OZE  H10  C8   C9   110.12  3.000
 OZE  H11  C8   C7   109.50  3.000
 OZE  H10  C8   C7   108.44  3.000
 OZE  C9   C8   C7   111.90  3.000
 OZE  H12  C10  C11  119.49  3.000
 OZE  H12  C10  C9   119.50  3.000
 OZE  C11  C10  C9   121.01  3.000
 OZE  H13  C11  C12  120.05  3.000
 OZE  H13  C11  C10  119.84  3.000
 OZE  C12  C11  C10  120.11  3.000
 OZE  H14  N    C4   117.10  3.000
 OZE  H14  N    C5   117.30  3.000
 OZE  C4   N    C5   124.62  3.000
 OZE  H17  C    H16  107.57  3.000
 OZE  H17  C    H15  107.53  3.000
 OZE  H16  C    H15  107.69  3.000
 OZE  H17  C    C1   110.97  3.000
 OZE  H16  C    C1   111.51  3.000
 OZE  H15  C    C1   111.38  3.000
 OZE  H19  C12  C13  120.28  3.000
 OZE  H19  C12  C11  120.26  3.000
 OZE  C13  C12  C11  119.46  3.000
 OZE  H20  C13  C14  119.78  3.000
 OZE  H20  C13  C12  120.08  3.000
 OZE  C14  C13  C12  120.14  3.000
 OZE  H21  C14  C13  119.64  3.000
 OZE  H21  C14  C9   119.39  3.000
 OZE  C13  C14  C9   120.97  3.000
 OZE  O4   C15  O3   123.80  3.000
 OZE  O3   C15  N2   125.97  3.000
 OZE  O4   C15  N2   110.23  3.000
 OZE  H23  C16  H22  107.88  3.000
 OZE  H23  C16  O4   110.36  3.000
 OZE  H22  C16  O4   110.21  3.000
 OZE  H23  C16  C17  110.85  3.000
 OZE  H22  C16  C17  110.31  3.000
 OZE  O4   C16  C17  107.24  3.000
 OZE  C22  C17  C18  119.03  3.000
 OZE  C22  C17  C16  121.00  3.000
 OZE  C18  C17  C16  119.97  3.000
 OZE  H24  C18  C19  119.64  3.000
 OZE  H24  C18  C17  119.83  3.000
 OZE  C19  C18  C17  120.53  3.000
 OZE  H25  C19  C20  120.06  3.000
 OZE  H25  C19  C18  119.86  3.000
 OZE  C20  C19  C18  120.08  3.000
 OZE  H26  C20  C21  120.16  3.000
 OZE  H26  C20  C19  120.11  3.000
 OZE  C21  C20  C19  119.74  3.000
 OZE  H27  C21  C22  119.84  3.000
 OZE  H27  C21  C20  120.11  3.000
 OZE  C22  C21  C20  120.05  3.000
 OZE  H28  C22  C21  119.74  3.000
 OZE  H28  C22  C17  119.69  3.000
 OZE  C21  C22  C17  120.57  3.000
 OZE  O6   C23  O5   127.36  3.000
 OZE  O5   C23  C4   115.12  3.000
 OZE  O6   C23  C4   117.50  3.000
 OZE  H30  C3   H29  105.88  3.000
 OZE  H30  C3   C1   108.94  3.000
 OZE  H29  C3   C1   107.93  3.000
 OZE  H30  C3   C4   108.76  3.000
 OZE  H29  C3   C4   106.97  3.000
 OZE  C1   C3   C4   117.73  3.000
 OZE  C16  O4   C15  117.46  3.000
 OZE  O2   P    O1   118.87  3.000
 OZE  O1   P    C7   108.14  3.000
 OZE  O2   P    C7   108.05  3.000
 OZE  O1   P    N1   111.76  3.000
 OZE  O2   P    N1   107.67  3.000
 OZE  C7   P    N1   100.78  3.000
 OZE  H18  C1   C3   108.22  3.000
 OZE  H18  C1   C    107.30  3.000
 OZE  C3   C1   C    109.13  3.000
 OZE  H18  C1   C2   108.09  3.000
 OZE  C    C1   C2   109.96  3.000
 OZE  C3   C1   C2   113.91  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
 OZE  CONST_01  C12  C13  C14  C9     0.00   0.0  0
 OZE  CONST_02  C12  C11  C10  C9     0.00   0.0  0
 OZE  CONST_03  C13  C14  C9   C10    0.00   0.0  0
 OZE  CONST_04  C13  C12  C11  C10    0.00   0.0  0
 OZE  CONST_05  C14  C13  C12  C11    0.00   0.0  0
 OZE  CONST_06  C14  C9   C10  C11    0.00   0.0  0
 OZE  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 OZE  CONST_08  C20  C21  C22  C17    0.00   0.0  0
 OZE  CONST_09  C21  C20  C19  C18    0.00   0.0  0
 OZE  CONST_10  C21  C22  C17  C18    0.00   0.0  0
 OZE  CONST_11  C22  C21  C20  C19    0.00   0.0  0
 OZE  CONST_12  C22  C17  C18  C19    0.00   0.0  0
 OZE  CONST_13  C13  C14  C9   C8   180.00   0.0  0
 OZE  CONST_14  C11  C10  C9   C8   180.00   0.0  0
 OZE  CONST_15  C19  C18  C17  C16  180.00   0.0  0
 OZE  CONST_16  C21  C22  C17  C16  180.00   0.0  0
 OZE  CONST_17  H20  C13  C14  C9   180.00   0.0  0
 OZE  CONST_18  H13  C11  C10  C9   180.00   0.0  0
 OZE  CONST_19  H21  C14  C9   C10  180.00   0.0  0
 OZE  CONST_20  H19  C12  C11  C10  180.00   0.0  0
 OZE  CONST_21  H12  C10  C11  C12  180.00   0.0  0
 OZE  CONST_22  H25  C19  C18  C17  180.00   0.0  0
 OZE  CONST_23  H27  C21  C22  C17  180.00   0.0  0
 OZE  CONST_24  H26  C20  C19  C18  180.00   0.0  0
 OZE  CONST_25  H28  C22  C17  C18  180.00   0.0  0
 OZE  CONST_26  H24  C18  C19  C20  180.00   0.0  0
 OZE  CONST_27  C4   N    C5   C6   180.00   0.0  0
 OZE  CONST_28  O    C5   N    C4     0.00   0.0  0
 OZE  CONST_29  H14  N    C5   C6     0.00   0.0  0
 OZE  Var_01    C14  C9   C8   C7   103.75  30.0  3
 OZE  Var_02    O4   C16  C17  C18  -64.15  30.0  2
 OZE  Var_03    C17  C16  O4   C15  165.58  30.0  1
 OZE  Var_04    P    N1   C6   C5   -97.81  30.0  2
 OZE  Var_05    C7   P    N1   C6   174.41  30.0  1
 OZE  Var_06    N    C5   C6   N1    -6.96  30.0  1
 OZE  Var_07    C4   C3   C1   C2   -62.49  30.0  2
 OZE  Var_08    O4   C15  N2   C7   171.21  30.0  1
 OZE  Var_09    H15  C    C1   C2    56.64  30.0  3
 OZE  Var_10    H4   C2   C1   C    -50.96  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
 OZE  chir_01  C4  C23  N   C3  negativ
 OZE  chir_02  C7  P    N2  C8  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
 OZE  plan-1  C9   0.020
 OZE  plan-1  C8   0.020
 OZE  plan-1  C10  0.020
 OZE  plan-1  C11  0.020
 OZE  plan-1  C12  0.020
 OZE  plan-1  C13  0.020
 OZE  plan-1  C14  0.020
 OZE  plan-1  H12  0.020
 OZE  plan-1  H13  0.020
 OZE  plan-1  H19  0.020
 OZE  plan-1  H20  0.020
 OZE  plan-1  H21  0.020
 OZE  plan-2  C16  0.020
 OZE  plan-2  C17  0.020
 OZE  plan-2  C18  0.020
 OZE  plan-2  C19  0.020
 OZE  plan-2  C20  0.020
 OZE  plan-2  C21  0.020
 OZE  plan-2  C22  0.020
 OZE  plan-2  H24  0.020
 OZE  plan-2  H25  0.020
 OZE  plan-2  H26  0.020
 OZE  plan-2  H27  0.020
 OZE  plan-2  H28  0.020
 OZE  plan-3  C5   0.020
 OZE  plan-3  C6   0.020
 OZE  plan-3  C4   0.020
 OZE  plan-3  N    0.020
 OZE  plan-3  O    0.020
 OZE  plan-3  H14  0.020
 OZE  plan-4  C4   0.020
 OZE  plan-4  C23  0.020
 OZE  plan-4  O5   0.020
 OZE  plan-4  O6   0.020
 OZE  plan-5  N2   0.020
 OZE  plan-5  C15  0.020
 OZE  plan-5  O3   0.020
 OZE  plan-5  O4   0.020

