# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 13:17:13 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  65  30  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   -6.9388   0.2276  -1.1177
 7AF  C2   C  CR16   0  -0.243   -8.2629   0.5945  -0.9253
 7AF  C3   C  CR16   0  -0.262   -9.1258  -0.2499  -0.2370
 7AF  C9   C  C      0   0.746   -2.9608  -0.8751   0.2461
 7AF  C12  C  CH2    0  -0.558   -0.9885  -0.0411   1.4356
 7AF  C20  C  CH3    0  -0.659    3.3260   1.7742  -2.7720
 7AF  C21  C  CH3    0  -0.645    4.0130   4.1040  -2.1407
 7AF  C22  C  C      0   0.564    3.3776   0.7854   0.7404
 7AF  P13  P  P      0   1.231   -0.5030   1.6110   0.7712
 7AF  C6   C  CR6    0   0.075   -6.4614  -0.9853  -0.6270
 7AF  C4   C  CR16   0  -0.242   -8.6586  -1.4613   0.2547
 7AF  C5   C  CR16   0  -0.296   -7.3320  -1.8244   0.0610
 7AF  N16  N  NH1    0  -0.791    1.1692   1.6315   1.1056
 7AF  C17  C  CH1    0  -0.186    2.1785   1.4611   0.0821
 7AF  C18  C  CH2    0  -0.399    2.5888   2.7853  -0.5638
 7AF  O14  O  OP    -1  -0.812   -1.1693   2.6516   1.6402
 7AF  N11  N  NH1    0  -0.649   -2.4153  -0.2522   1.3038
 7AF  O10  O  O      0  -0.525   -2.3632  -1.5429  -0.5739
 7AF  O8   O  O2     0  -0.485   -4.2921  -0.6999   0.2307
 7AF  C25  C  CH2    0  -0.270    4.7073  -1.2947   0.8424
 7AF  C26  C  CH1    0  -0.219    5.8583  -1.5455  -0.1412
 7AF  C27  C  CH3    0  -0.680    6.4061  -0.2253  -0.6735
 7AF  C28  C  CH1    0  -0.214    6.9532  -2.4009   0.5262
 7AF  C30  C  CH3    0  -0.670    6.4178  -3.7319   1.0557
 7AF  C29  C  CH3    0  -0.661    8.1188  -2.6781  -0.4216
 7AF  H1   H  HCR6   0   0.255   -6.2722   0.8867  -1.6615
 7AF  H2   H  HCR6   0   0.258   -8.6226   1.5378  -1.3153
 7AF  H3   H  HCR6   0   0.258  -10.1599   0.0332  -0.0892
 7AF  H4   H  HCH2   0   0.243   -4.8908  -2.4415  -0.7349
 7AF  H5   H  HCH2   0   0.243   -4.6575  -1.0402  -1.7866
 7AF  H6   H  HCH2   0   0.246   -0.4598  -0.8400   0.9167
 7AF  H7   H  HCH2   0   0.245   -0.7190  -0.1170   2.4914
 7AF  H8   H  HCH1   0   0.220    4.5998   2.3192  -1.1440
 7AF  H9   H  HCH3   0   0.228    4.1048   1.7730  -3.5365
 7AF  H10  H  HCH3   0   0.217    3.1989   0.7412  -2.4447
 7AF  H11  H  HCH3   0   0.219    2.3924   2.0855  -3.2469
 7AF  H12  H  HCH3   0   0.213    3.1447   4.5493  -2.6322
 7AF  H13  H  HCH3   0   0.223    4.3109   4.7708  -1.3293
 7AF  H14  H  HCH3   0   0.224    4.8278   4.0790  -2.8661
 7AF  H15  H  HCR6   0   0.258   -9.3261  -2.1242   0.7899
 7AF  H16  H  HCR6   0   0.255   -6.9737  -2.7716   0.4463
 7AF  H17  H  HNH1   0   0.359    1.4502   2.2643   1.8418
 7AF  H18  H  HCH1   0   0.241    1.7571   0.8088  -0.6860
 7AF  H19  H  HCH2   0   0.214    2.8994   3.4724   0.2302
 7AF  H20  H  HCH2   0   0.225    1.6864   3.2121  -1.0118
 7AF  H21  H  HNH1   0   0.395    3.0632  -0.8557  -0.3973
 7AF  H23  H  HNH1   0   0.391   -3.0103   0.3610   1.8388
 7AF  H24  H  HCH2   0   0.237    5.0915  -0.8197   1.7460
 7AF  H25  H  HCH2   0   0.251    4.2561  -2.2404   1.1446
 7AF  H26  H  HCH1   0   0.210    5.4616  -2.1206  -0.9895
 7AF  H27  H  HCH3   0   0.237    7.1800  -0.3793  -1.4238
 7AF  H28  H  HCH3   0   0.240    5.6224   0.3630  -1.1496
 7AF  H29  H  HCH3   0   0.214    6.8326   0.3786   0.1311
 7AF  H30  H  HCH1   0   0.210    7.3398  -1.8273   1.3790
 7AF  H31  H  HCH3   0   0.229    7.2325  -4.3356   1.4584
 7AF  H32  H  HCH3   0   0.231    5.6866  -3.6111   1.8541
 7AF  H33  H  HCH3   0   0.215    5.9456  -4.3080   0.2559
 7AF  H34  H  HCH3   0   0.230    8.6363  -1.7707  -0.7306
 7AF  H35  H  HCH3   0   0.227    8.8567  -3.3225   0.0592
 7AF  H36  H  HCH3   0   0.213    7.7753  -3.1905  -1.3242
 7AF  C7   C  CH2    0  -0.233   -5.0211  -1.3594  -0.8074
 7AF  O23  O  O      0  -0.508    4.0112   1.3577   1.6191
 7AF  C19  C  CH1    0  -0.260    3.6909   2.7065  -1.6202
 7AF  O15  O  O      0  -0.803   -0.7281   1.5952  -0.7200
 7AF  N24  N  NH1    0  -0.637    3.6540  -0.4565   0.3141

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  1.387  0.020  1.387
 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    1.499  0.020  1.499
 7AF  C6   C5   aromatic  1.391  0.020  1.391
 7AF  C4   C5   aromatic  1.389  0.020  1.389
 7AF  C7   O8   single    1.430  0.020  1.430
 7AF  O8   C9   single    1.343  0.020  1.343
 7AF  C9   O10  double    1.215  0.020  1.215
 7AF  C9   N11  single    1.343  0.020  1.343
 7AF  N11  C12  single    1.448  0.020  1.448
 7AF  C12  P13  single    1.846  0.020  1.846
 7AF  O15  P13  deloc     1.508  0.020  1.508
 7AF  O14  P13  deloc     1.511  0.020  1.511
 7AF  P13  N16  single    1.706  0.020  1.706
 7AF  C29  C28  single    1.528  0.020  1.528
 7AF  C25  N24  single    1.446  0.020  1.446
 7AF  C25  C26  single    1.535  0.020  1.535
 7AF  N16  C17  single    1.447  0.020  1.447
 7AF  N24  C22  single    1.342  0.020  1.342
 7AF  O23  C22  double    1.225  0.020  1.225
 7AF  C22  C17  single    1.526  0.020  1.526
 7AF  C30  C28  single    1.529  0.020  1.529
 7AF  C17  C18  single    1.529  0.020  1.529
 7AF  C28  C26  single    1.541  0.020  1.541
 7AF  C26  C27  single    1.525  0.020  1.525
 7AF  C18  C19  single    1.529  0.020  1.529
 7AF  C20  C19  single    1.526  0.020  1.526
 7AF  C19  C21  single    1.526  0.020  1.526
 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  N11  H23  single    0.890  0.020  1.040
 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   119.71  3.000
 7AF  H1   C1   C2   119.72  3.000
 7AF  C6   C1   C2   120.57  3.000
 7AF  H2   C2   C3   120.12  3.000
 7AF  H2   C2   C1   119.85  3.000
 7AF  C3   C2   C1   120.03  3.000
 7AF  H3   C3   C4   120.09  3.000
 7AF  H3   C3   C2   120.13  3.000
 7AF  C4   C3   C2   119.78  3.000
 7AF  O8   C9   O10  123.49  3.000
 7AF  O10  C9   N11  125.93  3.000
 7AF  O8   C9   N11  110.55  3.000
 7AF  H7   C12  H6   106.84  3.000
 7AF  H7   C12  N11  108.72  3.000
 7AF  H6   C12  N11  109.13  3.000
 7AF  H7   C12  P13  110.20  3.000
 7AF  H6   C12  P13  110.94  3.000
 7AF  N11  C12  P13  110.91  3.000
 7AF  H11  C20  H10  107.50  3.000
 7AF  H11  C20  H9   107.79  3.000
 7AF  H10  C20  H9   106.99  3.000
 7AF  H11  C20  C19  110.99  3.000
 7AF  H10  C20  C19  112.33  3.000
 7AF  H9   C20  C19  111.02  3.000
 7AF  H14  C21  H13  107.72  3.000
 7AF  H14  C21  H12  107.68  3.000
 7AF  H13  C21  H12  107.59  3.000
 7AF  H14  C21  C19  111.32  3.000
 7AF  H13  C21  C19  111.32  3.000
 7AF  H12  C21  C19  111.04  3.000
 7AF  N24  C22  O23  123.61  3.000
 7AF  O23  C22  C17  120.60  3.000
 7AF  N24  C22  C17  115.77  3.000
 7AF  O14  P13  N16  108.15  3.000
 7AF  N16  P13  O15  109.90  3.000
 7AF  O14  P13  O15  120.68  3.000
 7AF  N16  P13  C12  101.42  3.000
 7AF  O14  P13  C12  107.07  3.000
 7AF  O15  P13  C12  107.89  3.000
 7AF  C5   C6   C7   120.68  3.000
 7AF  C5   C6   C1   119.01  3.000
 7AF  C7   C6   C1   120.29  3.000
 7AF  H15  C4   C5   119.86  3.000
 7AF  H15  C4   C3   120.13  3.000
 7AF  C5   C4   C3   120.01  3.000
 7AF  H16  C5   C4   119.65  3.000
 7AF  H16  C5   C6   119.75  3.000
 7AF  C4   C5   C6   120.60  3.000
 7AF  H17  N16  C17  113.27  3.000
 7AF  H17  N16  P13  115.02  3.000
 7AF  C17  N16  P13  122.93  3.000
 7AF  H18  C17  C18  108.88  3.000
 7AF  H18  C17  N16  107.37  3.000
 7AF  C18  C17  N16  112.57  3.000
 7AF  H18  C17  C22  110.01  3.000
 7AF  C18  C17  C22  110.79  3.000
 7AF  N16  C17  C22  107.16  3.000
 7AF  H20  C18  H19  106.62  3.000
 7AF  H20  C18  C17  106.83  3.000
 7AF  H19  C18  C17  108.25  3.000
 7AF  H20  C18  C19  109.38  3.000
 7AF  H19  C18  C19  109.20  3.000
 7AF  C17  C18  C19  116.15  3.000
 7AF  H23  N11  C12  116.39  3.000
 7AF  H23  N11  C9   117.41  3.000
 7AF  C12  N11  C9   122.63  3.000
 7AF  C9   O8   C7   116.98  3.000
 7AF  H25  C25  H24  107.09  3.000
 7AF  H25  C25  C26  110.26  3.000
 7AF  H24  C25  C26  109.75  3.000
 7AF  H25  C25  N24  107.61  3.000
 7AF  H24  C25  N24  107.87  3.000
 7AF  C26  C25  N24  114.00  3.000
 7AF  H26  C26  C28  107.47  3.000
 7AF  H26  C26  C27  108.26  3.000
 7AF  C28  C26  C27  112.10  3.000
 7AF  H26  C26  C25  108.03  3.000
 7AF  C27  C26  C25  110.59  3.000
 7AF  C28  C26  C25  110.24  3.000
 7AF  H29  C27  H28  107.71  3.000
 7AF  H29  C27  H27  107.95  3.000
 7AF  H28  C27  H27  106.64  3.000
 7AF  H29  C27  C26  111.20  3.000
 7AF  H28  C27  C26  111.20  3.000
 7AF  H27  C27  C26  111.92  3.000
 7AF  H30  C28  C29  107.94  3.000
 7AF  H30  C28  C30  108.00  3.000
 7AF  C29  C28  C30  108.90  3.000
 7AF  H30  C28  C26  107.25  3.000
 7AF  C30  C28  C26  112.60  3.000
 7AF  C29  C28  C26  111.97  3.000
 7AF  H33  C30  H32  107.75  3.000
 7AF  H33  C30  H31  107.52  3.000
 7AF  H32  C30  H31  106.98  3.000
 7AF  H33  C30  C28  110.90  3.000
 7AF  H32  C30  C28  113.09  3.000
 7AF  H31  C30  C28  110.36  3.000
 7AF  H36  C29  H35  107.43  3.000
 7AF  H36  C29  H34  107.79  3.000
 7AF  H35  C29  H34  107.20  3.000
 7AF  H36  C29  C28  110.95  3.000
 7AF  H35  C29  C28  110.47  3.000
 7AF  H34  C29  C28  112.78  3.000
 7AF  H5   C7   H4   108.02  3.000
 7AF  H5   C7   O8   110.26  3.000
 7AF  H4   C7   O8   110.36  3.000
 7AF  H5   C7   C6   110.78  3.000
 7AF  H4   C7   C6   110.73  3.000
 7AF  O8   C7   C6   106.70  3.000
 7AF  H8   C19  C18  108.40  3.000
 7AF  H8   C19  C21  107.26  3.000
 7AF  C18  C19  C21  109.92  3.000
 7AF  H8   C19  C20  108.06  3.000
 7AF  C21  C19  C20  110.65  3.000
 7AF  C18  C19  C20  112.37  3.000
 7AF  H21  N24  C25  117.10  3.000
 7AF  H21  N24  C22  118.06  3.000
 7AF  C25  N24  C22  124.79  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     81.93  30.0  2
 7AF  Var_02    C6   C7   O8   C9   -178.72  30.0  1
 7AF  Var_03    O10  C9   O8   C7      0.80  30.0  3
 7AF  Var_04    P13  C12  N11  C9     93.35  30.0  3
 7AF  Var_05    O8   C9   N11  C12  -167.33  30.0  1
 7AF  Var_06    C17  N16  P13  C12   105.86  30.0  3
 7AF  Var_07    C17  C18  C19  C20    57.82  30.0  3
 7AF  Var_08    C26  C25  N24  C22  -111.69  30.0  2
 7AF  Var_09    N11  C12  P13  O15   -66.94  30.0  1
 7AF  Var_10    H12  C21  C19  C20    62.21  30.0  3
 7AF  Var_11    H9   C20  C19  C21    53.86  30.0  3
 7AF  Var_12    H34  C29  C28  C26    62.67  30.0  3
 7AF  Var_13    H31  C30  C28  C26   176.16  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

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  C25  0.020
 7AF  plan-2  H21  0.020
 7AF  plan-2  O23  0.020
 7AF  plan-2  N24  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

