# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 16:49:17 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: ~{N}-[(2~{S})-1-[[(2~{S})-2,3-dimethylbutyl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N[P](O)(=O)CNC(=O)OCc1ccccc1)C(=O)NC[C@@H](C)C(C)C
#
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
 7AF  7AF  '~{N}-[(2~{S})-1-[[(2~{S})-2,3-dimethylbutyl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid'  ligand  66  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7AF
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
 7AF  C1   C  CR16  0  -0.286   -7.0298  -0.3480  -1.5613
 7AF  C2   C  CR16  0  -0.242   -8.3024   0.1417  -1.8181
 7AF  C3   C  CR16  0  -0.261   -9.3376  -0.1119  -0.9265
 7AF  C9   C  C     0   0.763   -3.4017  -0.7440   0.8006
 7AF  C12  C  CH2   0  -0.567   -1.4564   0.4082   1.7058
 7AF  C20  C  CH3   0  -0.663    3.6533   1.9858  -2.6462
 7AF  C21  C  CH3   0  -0.645    4.0994   4.1983  -1.5553
 7AF  C22  C  C     0   0.562    3.3684   0.4686   0.6776
 7AF  P13  P  P     0   1.311   -0.5009   1.0331   0.2821
 7AF  C6   C  CR6   0   0.075   -6.7778  -1.0956  -0.4138
 7AF  C4   C  CR16  0  -0.242   -9.0953  -0.8576   0.2194
 7AF  C5   C  CR16  0  -0.293   -7.8197  -1.3447   0.4737
 7AF  N16  N  NH1   0  -0.783    1.0570   1.0732   0.8482
 7AF  C17  C  CH1   0  -0.204    2.2042   1.1373  -0.0488
 7AF  C18  C  CH2   0  -0.402    2.5679   2.5735  -0.4316
 7AF  N24  N  NH1   0  -0.636    3.9292  -0.5732   0.0521
 7AF  O14  O  OH1   0  -0.751   -1.0766   2.5278   0.0328
 7AF  N11  N  NH1   0  -0.656   -2.8565   0.3415   1.3876
 7AF  O10  O  O     0  -0.512   -2.8236  -1.7902   0.5983
 7AF  O8   O  O2    0  -0.479   -4.6819  -0.5195   0.4921
 7AF  C25  C  CH2   0  -0.263    5.0226  -1.3587   0.5855
 7AF  C26  C  CH1   0  -0.235    6.1900  -1.5160  -0.3955
 7AF  C27  C  CH3   0  -0.679    6.6784  -0.1498  -0.8679
 7AF  C28  C  CH1   0  -0.214    7.3196  -2.3428   0.2500
 7AF  C30  C  CH3   0  -0.670    6.8459  -3.7170   0.7253
 7AF  C29  C  CH3   0  -0.661    8.5013  -2.5295  -0.7009
 7AF  H1   H  HCR6  0   0.255   -6.2268  -0.1516  -2.2623
 7AF  H2   H  HCR6  0   0.258   -8.4880   0.7188  -2.7147
 7AF  H3   H  HCR6  0   0.259  -10.3313   0.2674  -1.1272
 7AF  H4   H  HCH2  0   0.249   -5.4253  -2.4610   0.5400
 7AF  H5   H  HCH2  0   0.249   -4.8920  -1.8969  -1.0485
 7AF  H6   H  HCH2  0   0.296   -1.0794  -0.5777   1.9748
 7AF  H7   H  HCH2  0   0.303   -1.3122   1.0549   2.5731
 7AF  H8   H  HCH1  0   0.226    4.6643   2.2950  -0.7863
 7AF  H9   H  HCH3  0   0.233    4.5351   2.1276  -3.2728
 7AF  H10  H  HCH3  0   0.219    3.5256   0.9101  -2.5171
 7AF  H11  H  HCH3  0   0.224    2.7877   2.3567  -3.2003
 7AF  H12  H  HCH3  0   0.215    3.2722   4.6821  -2.0800
 7AF  H13  H  HCH3  0   0.226    4.2525   4.7299  -0.6147
 7AF  H14  H  HCH3  0   0.227    4.9968   4.3277  -2.1623
 7AF  H15  H  HCR6  0   0.258   -9.8992  -1.0622   0.9145
 7AF  H16  H  HCR6  0   0.255   -7.6349  -1.9294   1.3671
 7AF  H17  H  HNH1  0   0.399    1.2184   1.5070   1.7493
 7AF  H18  H  HCH1  0   0.266    1.9377   0.5732  -0.9444
 7AF  H19  H  HCH2  0   0.231    2.7069   3.1487   0.4888
 7AF  H20  H  HCH2  0   0.232    1.7055   3.0126  -0.9435
 7AF  H21  H  HNH1  0   0.400    3.5156  -0.8890  -0.8112
 7AF  H22  H  HOH1  0   0.483   -0.9429   3.1496   0.7592
 7AF  H23  H  HNH1  0   0.410   -3.4084   1.1794   1.4776
 7AF  H24  H  HCH2  0   0.242    5.3706  -0.8715   1.4968
 7AF  H25  H  HCH2  0   0.254    4.6319  -2.3362   0.8726
 7AF  H26  H  HCH1  0   0.215    5.8298  -2.0768  -1.2695
 7AF  H27  H  HCH3  0   0.239    7.4577  -0.2354  -1.6229
 7AF  H28  H  HCH3  0   0.242    5.8705   0.4273  -1.3161
 7AF  H29  H  HCH3  0   0.216    7.0796   0.4334  -0.0350
 7AF  H30  H  HCH1  0   0.212    7.6739  -1.7836   1.1259
 7AF  H31  H  HCH3  0   0.230    7.6896  -4.3027   1.0933
 7AF  H32  H  HCH3  0   0.232    6.1208  -3.6637   1.5365
 7AF  H33  H  HCH3  0   0.216    6.3896  -4.2772  -0.0948
 7AF  H34  H  HCH3  0   0.231    8.9755  -1.5881  -0.9754
 7AF  H35  H  HCH3  0   0.228    9.2677  -3.1542  -0.2392
 7AF  H36  H  HCH3  0   0.214    8.1852  -3.0258  -1.6222
 7AF  C7   C  CH2   0  -0.239   -5.3955  -1.5973  -0.1272
 7AF  O23  O  O     0  -0.498    3.7345   0.8969   1.7644
 7AF  C19  C  CH1   0  -0.262    3.8048   2.7206  -1.3180
 7AF  O15  O  O     0  -0.714   -0.6547   0.2640  -0.9800

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
 7AF  C2   C1   aromatic  1.388  0.020  1.388
 7AF  C2   C3   aromatic  1.390  0.020  1.390
 7AF  C1   C6   aromatic  1.393  0.020  1.393
 7AF  C3   C4   aromatic  1.388  0.020  1.388
 7AF  C6   C7   single    1.498  0.020  1.498
 7AF  C6   C5   aromatic  1.391  0.020  1.391
 7AF  C4   C5   aromatic  1.389  0.020  1.389
 7AF  C7   O8   single    1.433  0.020  1.433
 7AF  O8   C9   single    1.336  0.020  1.336
 7AF  C9   O10  double    1.212  0.020  1.212
 7AF  C9   N11  single    1.349  0.020  1.349
 7AF  N11  C12  single    1.437  0.020  1.437
 7AF  C12  P13  single    1.825  0.020  1.825
 7AF  O15  P13  double    1.486  0.020  1.486
 7AF  O14  P13  single    1.621  0.020  1.621
 7AF  P13  N16  single    1.658  0.020  1.658
 7AF  C29  C28  single    1.528  0.020  1.528
 7AF  C25  N24  single    1.448  0.020  1.448
 7AF  C25  C26  single    1.533  0.020  1.533
 7AF  N16  C17  single    1.458  0.020  1.458
 7AF  N24  C22  single    1.338  0.020  1.338
 7AF  O23  C22  double    1.224  0.020  1.224
 7AF  C22  C17  single    1.526  0.020  1.526
 7AF  C30  C28  single    1.529  0.020  1.529
 7AF  C17  C18  single    1.530  0.020  1.530
 7AF  C28  C26  single    1.542  0.020  1.542
 7AF  C26  C27  single    1.526  0.020  1.526
 7AF  C18  C19  single    1.529  0.020  1.529
 7AF  C20  C19  single    1.525  0.020  1.525
 7AF  C19  C21  single    1.525  0.020  1.525
 7AF  C1   H1   single    0.930  0.020  1.080
 7AF  C2   H2   single    0.930  0.020  1.080
 7AF  C3   H3   single    0.930  0.020  1.080
 7AF  C7   H4   single    0.970  0.020  1.090
 7AF  C7   H5   single    0.970  0.020  1.090
 7AF  C12  H6   single    0.970  0.020  1.090
 7AF  C12  H7   single    0.970  0.020  1.090
 7AF  C19  H8   single    0.970  0.020  1.090
 7AF  C20  H9   single    0.970  0.020  1.090
 7AF  C20  H10  single    0.970  0.020  1.090
 7AF  C20  H11  single    0.970  0.020  1.090
 7AF  C21  H12  single    0.970  0.020  1.090
 7AF  C21  H13  single    0.970  0.020  1.090
 7AF  C21  H14  single    0.970  0.020  1.090
 7AF  C4   H15  single    0.930  0.020  1.080
 7AF  C5   H16  single    0.930  0.020  1.080
 7AF  N16  H17  single    0.890  0.020  1.040
 7AF  C17  H18  single    0.970  0.020  1.090
 7AF  C18  H19  single    0.970  0.020  1.090
 7AF  C18  H20  single    0.970  0.020  1.090
 7AF  N24  H21  single    0.860  0.020  1.020
 7AF  O14  H22  single    0.850  0.020  0.980
 7AF  N11  H23  single    0.860  0.020  1.020
 7AF  C25  H24  single    0.970  0.020  1.090
 7AF  C25  H25  single    0.970  0.020  1.090
 7AF  C26  H26  single    0.970  0.020  1.090
 7AF  C27  H27  single    0.970  0.020  1.090
 7AF  C27  H28  single    0.970  0.020  1.090
 7AF  C27  H29  single    0.970  0.020  1.090
 7AF  C28  H30  single    0.970  0.020  1.090
 7AF  C30  H31  single    0.970  0.020  1.090
 7AF  C30  H32  single    0.970  0.020  1.090
 7AF  C30  H33  single    0.970  0.020  1.090
 7AF  C29  H34  single    0.970  0.020  1.090
 7AF  C29  H35  single    0.970  0.020  1.090
 7AF  C29  H36  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
 7AF  H1   C1   C6   119.74  3.000
 7AF  H1   C1   C2   119.73  3.000
 7AF  C6   C1   C2   120.53  3.000
 7AF  H2   C2   C3   120.07  3.000
 7AF  H2   C2   C1   119.92  3.000
 7AF  C3   C2   C1   120.01  3.000
 7AF  H3   C3   C4   120.09  3.000
 7AF  H3   C3   C2   120.07  3.000
 7AF  C4   C3   C2   119.83  3.000
 7AF  O8   C9   O10  124.30  3.000
 7AF  O10  C9   N11  125.05  3.000
 7AF  O8   C9   N11  110.65  3.000
 7AF  H7   C12  H6   107.12  3.000
 7AF  H7   C12  N11  109.39  3.000
 7AF  H6   C12  N11  110.47  3.000
 7AF  H7   C12  P13  110.35  3.000
 7AF  H6   C12  P13  108.75  3.000
 7AF  N11  C12  P13  110.69  3.000
 7AF  H11  C20  H10  107.57  3.000
 7AF  H11  C20  H9   107.76  3.000
 7AF  H10  C20  H9   106.91  3.000
 7AF  H11  C20  C19  110.90  3.000
 7AF  H10  C20  C19  112.55  3.000
 7AF  H9   C20  C19  110.93  3.000
 7AF  H14  C21  H13  107.84  3.000
 7AF  H14  C21  H12  107.64  3.000
 7AF  H13  C21  H12  107.72  3.000
 7AF  H14  C21  C19  111.12  3.000
 7AF  H13  C21  C19  111.40  3.000
 7AF  H12  C21  C19  110.94  3.000
 7AF  N24  C22  O23  124.19  3.000
 7AF  O23  C22  C17  119.82  3.000
 7AF  N24  C22  C17  115.99  3.000
 7AF  O14  P13  N16  111.34  3.000
 7AF  N16  P13  O15  113.56  3.000
 7AF  O14  P13  O15  108.05  3.000
 7AF  N16  P13  C12  103.53  3.000
 7AF  O14  P13  C12  104.47  3.000
 7AF  O15  P13  C12  115.54  3.000
 7AF  C5   C6   C7   120.60  3.000
 7AF  C5   C6   C1   119.09  3.000
 7AF  C7   C6   C1   120.29  3.000
 7AF  H15  C4   C5   119.89  3.000
 7AF  H15  C4   C3   120.12  3.000
 7AF  C5   C4   C3   119.99  3.000
 7AF  H16  C5   C4   119.79  3.000
 7AF  H16  C5   C6   119.66  3.000
 7AF  C4   C5   C6   120.55  3.000
 7AF  H17  N16  C17  113.78  3.000
 7AF  H17  N16  P13  117.63  3.000
 7AF  C17  N16  P13  122.03  3.000
 7AF  H18  C17  C18  109.74  3.000
 7AF  H18  C17  N16  106.86  3.000
 7AF  C18  C17  N16  112.48  3.000
 7AF  H18  C17  C22  110.50  3.000
 7AF  C18  C17  C22  110.42  3.000
 7AF  N16  C17  C22  106.75  3.000
 7AF  H20  C18  H19  106.41  3.000
 7AF  H20  C18  C17  107.83  3.000
 7AF  H19  C18  C17  108.25  3.000
 7AF  H20  C18  C19  109.13  3.000
 7AF  H19  C18  C19  109.53  3.000
 7AF  C17  C18  C19  115.32  3.000
 7AF  H21  N24  C25  117.09  3.000
 7AF  H21  N24  C22  118.18  3.000
 7AF  C25  N24  C22  124.51  3.000
 7AF  H22  O14  P13  115.40  3.000
 7AF  H23  N11  C12  118.38  3.000
 7AF  H23  N11  C9   119.12  3.000
 7AF  C12  N11  C9   121.82  3.000
 7AF  C9   O8   C7   116.78  3.000
 7AF  H25  C25  H24  107.14  3.000
 7AF  H25  C25  C26  110.44  3.000
 7AF  H24  C25  C26  109.74  3.000
 7AF  H25  C25  N24  108.21  3.000
 7AF  H24  C25  N24  107.84  3.000
 7AF  C26  C25  N24  113.26  3.000
 7AF  H26  C26  C28  107.42  3.000
 7AF  H26  C26  C27  108.39  3.000
 7AF  C28  C26  C27  112.04  3.000
 7AF  H26  C26  C25  108.16  3.000
 7AF  C27  C26  C25  110.49  3.000
 7AF  C28  C26  C25  110.19  3.000
 7AF  H29  C27  H28  107.65  3.000
 7AF  H29  C27  H27  107.92  3.000
 7AF  H28  C27  H27  106.70  3.000
 7AF  H29  C27  C26  111.05  3.000
 7AF  H28  C27  C26  111.36  3.000
 7AF  H27  C27  C26  111.93  3.000
 7AF  H30  C28  C29  108.00  3.000
 7AF  H30  C28  C30  108.04  3.000
 7AF  C29  C28  C30  108.85  3.000
 7AF  H30  C28  C26  107.30  3.000
 7AF  C30  C28  C26  112.65  3.000
 7AF  C29  C28  C26  111.82  3.000
 7AF  H33  C30  H32  107.81  3.000
 7AF  H33  C30  H31  107.50  3.000
 7AF  H32  C30  H31  106.85  3.000
 7AF  H33  C30  C28  110.90  3.000
 7AF  H32  C30  C28  113.19  3.000
 7AF  H31  C30  C28  110.35  3.000
 7AF  H36  C29  H35  107.45  3.000
 7AF  H36  C29  H34  107.81  3.000
 7AF  H35  C29  H34  107.20  3.000
 7AF  H36  C29  C28  110.87  3.000
 7AF  H35  C29  C28  110.47  3.000
 7AF  H34  C29  C28  112.82  3.000
 7AF  H5   C7   H4   108.13  3.000
 7AF  H5   C7   O8   109.96  3.000
 7AF  H4   C7   O8   110.15  3.000
 7AF  H5   C7   C6   110.85  3.000
 7AF  H4   C7   C6   110.89  3.000
 7AF  O8   C7   C6   106.87  3.000
 7AF  H8   C19  C18  108.40  3.000
 7AF  H8   C19  C21  107.46  3.000
 7AF  C18  C19  C21  109.86  3.000
 7AF  H8   C19  C20  108.24  3.000
 7AF  C21  C19  C20  110.51  3.000
 7AF  C18  C19  C20  112.22  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
 7AF  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 7AF  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 7AF  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 7AF  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 7AF  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 7AF  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 7AF  CONST_07  C7   C6   C1   C2    180.00   0.0  0
 7AF  CONST_08  C4   C5   C6   C7    180.00   0.0  0
 7AF  CONST_09  H3   C3   C2   C1    180.00   0.0  0
 7AF  CONST_10  H16  C5   C6   C1    180.00   0.0  0
 7AF  CONST_11  H15  C4   C3   C2    180.00   0.0  0
 7AF  CONST_12  H1   C1   C2   C3    180.00   0.0  0
 7AF  CONST_13  H2   C2   C1   C6    180.00   0.0  0
 7AF  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 7AF  CONST_15  C25  N24  C22  O23     0.00   0.0  0
 7AF  CONST_16  H21  N24  C22  C17     0.00   0.0  0
 7AF  Var_01    O8   C7   C6   C1     82.78  30.0  2
 7AF  Var_02    C6   C7   O8   C9   -178.21  30.0  1
 7AF  Var_03    O10  C9   O8   C7     -0.50  30.0  3
 7AF  Var_04    P13  C12  N11  C9     87.22  30.0  3
 7AF  Var_05    O8   C9   N11  C12  -174.11  30.0  2
 7AF  Var_06    C17  N16  P13  C12   161.83  30.0  3
 7AF  Var_07    C17  C18  C19  C20    59.91  30.0  2
 7AF  Var_08    C26  C25  N24  C22  -128.80  30.0  2
 7AF  Var_09    N11  C12  P13  O15   -56.56  30.0  1
 7AF  Var_10    H12  C21  C19  C20    62.40  30.0  3
 7AF  Var_11    H9   C20  C19  C21    55.42  30.0  3
 7AF  Var_12    H34  C29  C28  C26    62.57  30.0  3
 7AF  Var_13    H31  C30  C28  C26   174.97  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
 7AF  chir_02  C17  N16  C22  C18  positiv
 7AF  chir_03  C26  C25  C28  C27  positiv
 7AF  chir_04  P13  O15  O14  N16  both

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
 7AF  plan-1  C1   0.020
 7AF  plan-1  C2   0.020
 7AF  plan-1  C3   0.020
 7AF  plan-1  C6   0.020
 7AF  plan-1  C4   0.020
 7AF  plan-1  C5   0.020
 7AF  plan-1  H1   0.020
 7AF  plan-1  H2   0.020
 7AF  plan-1  H3   0.020
 7AF  plan-1  H15  0.020
 7AF  plan-1  H16  0.020
 7AF  plan-1  C7   0.020
 7AF  plan-2  C22  0.020
 7AF  plan-2  C17  0.020
 7AF  plan-2  N24  0.020
 7AF  plan-2  C25  0.020
 7AF  plan-2  H21  0.020
 7AF  plan-2  O23  0.020
 7AF  plan-3  C9   0.020
 7AF  plan-3  N11  0.020
 7AF  plan-3  O10  0.020
 7AF  plan-3  O8   0.020

