# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:07:03 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2R)-2-methylbutyl]-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)CNC(=O)[C@H](CC(C)C)N[P](O)(=O)CNC(=O)OCc1ccccc1
#
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
 6NN  6NN  N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2R)-2-methylbutyl]-L-leucinamide  ligand  63  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6NN
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
 6NN  C1   C  CR16  0  -0.292   5.2815  -1.9205   1.7805
 6NN  C2   C  CR16  0  -0.242   6.6183  -1.8356   2.1450
 6NN  C3   C  CR16  0  -0.262   7.6102  -1.9650   1.1814
 6NN  C9   C  C     0   0.758   1.7960  -0.7023  -0.6322
 6NN  C12  C  CH2   0  -0.578   0.2414   1.0916  -1.2043
 6NN  C20  C  CH3   0  -0.653  -5.1884   5.2965   0.7854
 6NN  C21  C  CH3   0  -0.667  -3.7652   4.0478   2.4355
 6NN  C22  C  C     0   0.559  -3.5360   0.7803  -0.5825
 6NN  C27  C  CH3   0  -0.662  -2.3804  -2.4099  -0.3259
 6NN  P13  P  P     0   1.336  -0.4885   1.7709   0.3262
 6NN  C6   C  CR6   0   0.076   4.9219  -2.1377   0.4535
 6NN  C4   C  CR16  0  -0.242   7.2602  -2.1803  -0.1455
 6NN  C5   C  CR16  0  -0.289   5.9224  -2.2649  -0.5059
 6NN  N16  N  NH1   0  -0.770  -1.9028   2.5473  -0.0777
 6NN  C17  C  CH1   0  -0.224  -3.1887   1.9908   0.2879
 6NN  C18  C  CH2   0  -0.418  -4.2846   3.0519   0.1643
 6NN  N24  N  NH1   0  -0.629  -4.2933  -0.1423   0.0255
 6NN  C25  C  CH2   0  -0.266  -4.6859  -1.4014  -0.5651
 6NN  C26  C  CH1   0  -0.237  -3.8690  -2.5923  -0.0564
 6NN  C28  C  CH2   0  -0.415  -4.4251  -3.8721  -0.6843
 6NN  C29  C  CH3   0  -0.668  -3.8338  -5.1563  -0.1191
 6NN  O14  O  OH1   0  -0.747   0.5630   2.9083   0.7826
 6NN  N11  N  NH1   0  -0.655   1.5663   0.5856  -0.9641
 6NN  O10  O  O     0  -0.497   0.9739  -1.5916  -0.6638
 6NN  O8   O  O2    0  -0.480   3.0766  -0.8741  -0.2854
 6NN  H1   H  HCR6  0   0.256   4.5114  -1.8244   2.5368
 6NN  H2   H  HCR6  0   0.258   6.8851  -1.6713   3.1809
 6NN  H3   H  HCR6  0   0.259   8.6532  -1.9020   1.4638
 6NN  H4   H  HCH2  0   0.247   3.3411  -2.8713  -0.7960
 6NN  H5   H  HCH2  0   0.248   2.8676  -2.5815   0.8818
 6NN  H6   H  HCH2  0   0.296  -0.4065   0.2947  -1.5669
 6NN  H7   H  HCH2  0   0.292   0.2735   1.8578  -1.9817
 6NN  H8   H  HCH1  0   0.223  -3.1252   4.8083   0.5476
 6NN  H9   H  HCH3  0   0.227  -4.9879   6.2466   1.2834
 6NN  H10  H  HCH3  0   0.225  -5.3795   5.5093  -0.2681
 6NN  H11  H  HCH3  0   0.214  -6.1065   4.8862   1.2125
 6NN  H12  H  HCH3  0   0.215  -4.5998   3.5006   2.8812
 6NN  H13  H  HCH3  0   0.230  -2.8599   3.4578   2.5874
 6NN  H14  H  HCH3  0   0.231  -3.6437   4.9776   2.9933
 6NN  H15  H  HCH3  0   0.226  -1.7992  -3.2451   0.0655
 6NN  H16  H  HCH3  0   0.207  -2.1821  -2.3437  -1.3978
 6NN  H17  H  HCH3  0   0.238  -1.9842  -1.5063   0.1375
 6NN  H18  H  HCR6  0   0.259   8.0294  -2.2850  -0.8995
 6NN  H19  H  HCR6  0   0.255   5.6547  -2.4379  -1.5417
 6NN  H20  H  HNH1  0   0.395  -1.9079   3.0758  -0.9411
 6NN  H21  H  HCH1  0   0.271  -3.1296   1.6660   1.3283
 6NN  H22  H  HCH2  0   0.237  -5.2290   2.6084   0.4970
 6NN  H23  H  HCH2  0   0.239  -4.4200   3.3029  -0.8934
 6NN  H24  H  HNH1  0   0.397  -4.5000  -0.0143   1.0037
 6NN  H25  H  HCH2  0   0.246  -5.7450  -1.5663  -0.3534
 6NN  H26  H  HCH2  0   0.237  -4.5854  -1.3155  -1.6477
 6NN  H27  H  HCH1  0   0.213  -4.0203  -2.6627   1.0291
 6NN  H28  H  HCH2  0   0.220  -5.5105  -3.8923  -0.5413
 6NN  H29  H  HCH2  0   0.212  -4.2643  -3.8395  -1.7675
 6NN  H30  H  HCH3  0   0.229  -4.3131  -6.0319  -0.5580
 6NN  H31  H  HCH3  0   0.222  -2.7646  -5.2386  -0.3164
 6NN  H32  H  HCH3  0   0.217  -3.9740  -5.2108   0.9624
 6NN  H33  H  HOH1  0   0.486   0.6196   3.6849   0.2118
 6NN  H34  H  HNH1  0   0.405   2.3141   1.2521  -0.8562
 6NN  C7   C  CH2   0  -0.238   3.4782  -2.2054   0.0585
 6NN  O23  O  O     0  -0.495  -3.1573   0.7041  -1.7429
 6NN  C19  C  CH1   0  -0.223  -4.0201   4.3312   0.9592
 6NN  O15  O  O     0  -0.711  -0.6607   0.7754   1.4156

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
 6NN  C4   C5   aromatic  1.388  0.020  1.388
 6NN  C4   C3   aromatic  1.389  0.020  1.389
 6NN  C5   C6   aromatic  1.392  0.020  1.392
 6NN  C3   C2   aromatic  1.389  0.020  1.389
 6NN  C6   C7   single    1.498  0.020  1.498
 6NN  C6   C1   aromatic  1.392  0.020  1.392
 6NN  C2   C1   aromatic  1.388  0.020  1.388
 6NN  C7   O8   single    1.432  0.020  1.432
 6NN  O8   C9   single    1.338  0.020  1.338
 6NN  C9   O10  double    1.211  0.020  1.211
 6NN  C9   N11  single    1.350  0.020  1.350
 6NN  N11  C12  single    1.438  0.020  1.438
 6NN  C12  P13  single    1.827  0.020  1.827
 6NN  O15  P13  double    1.486  0.020  1.486
 6NN  O14  P13  single    1.615  0.020  1.615
 6NN  P13  N16  single    1.663  0.020  1.663
 6NN  C25  N24  single    1.445  0.020  1.445
 6NN  C25  C26  single    1.531  0.020  1.531
 6NN  N16  C17  single    1.448  0.020  1.448
 6NN  N24  C22  single    1.340  0.020  1.340
 6NN  C22  O23  double    1.223  0.020  1.223
 6NN  C22  C17  single    1.531  0.020  1.531
 6NN  C28  C29  single    1.523  0.020  1.523
 6NN  C28  C26  single    1.530  0.020  1.530
 6NN  C17  C18  single    1.530  0.020  1.530
 6NN  C26  C27  single    1.524  0.020  1.524
 6NN  C18  C19  single    1.529  0.020  1.529
 6NN  C20  C19  single    1.525  0.020  1.525
 6NN  C19  C21  single    1.525  0.020  1.525
 6NN  C1   H1   single    0.930  0.020  1.080
 6NN  C2   H2   single    0.930  0.020  1.080
 6NN  C3   H3   single    0.930  0.020  1.080
 6NN  C7   H4   single    0.970  0.020  1.090
 6NN  C7   H5   single    0.970  0.020  1.090
 6NN  C12  H6   single    0.970  0.020  1.090
 6NN  C12  H7   single    0.970  0.020  1.090
 6NN  C19  H8   single    0.970  0.020  1.090
 6NN  C20  H9   single    0.970  0.020  1.090
 6NN  C20  H10  single    0.970  0.020  1.090
 6NN  C20  H11  single    0.970  0.020  1.090
 6NN  C21  H12  single    0.970  0.020  1.090
 6NN  C21  H13  single    0.970  0.020  1.090
 6NN  C21  H14  single    0.970  0.020  1.090
 6NN  C27  H15  single    0.970  0.020  1.090
 6NN  C27  H16  single    0.970  0.020  1.090
 6NN  C27  H17  single    0.970  0.020  1.090
 6NN  C4   H18  single    0.930  0.020  1.080
 6NN  C5   H19  single    0.930  0.020  1.080
 6NN  N16  H20  single    0.890  0.020  1.040
 6NN  C17  H21  single    0.970  0.020  1.090
 6NN  C18  H22  single    0.970  0.020  1.090
 6NN  C18  H23  single    0.970  0.020  1.090
 6NN  N24  H24  single    0.860  0.020  1.020
 6NN  C25  H25  single    0.970  0.020  1.090
 6NN  C25  H26  single    0.970  0.020  1.090
 6NN  C26  H27  single    0.970  0.020  1.090
 6NN  C28  H28  single    0.970  0.020  1.090
 6NN  C28  H29  single    0.970  0.020  1.090
 6NN  C29  H30  single    0.970  0.020  1.090
 6NN  C29  H31  single    0.970  0.020  1.090
 6NN  C29  H32  single    0.970  0.020  1.090
 6NN  O14  H33  single    0.850  0.020  0.980
 6NN  N11  H34  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
 6NN  H1   C1   C6   119.71  3.000
 6NN  H1   C1   C2   119.71  3.000
 6NN  C6   C1   C2   120.57  3.000
 6NN  H2   C2   C3   120.14  3.000
 6NN  H2   C2   C1   119.86  3.000
 6NN  C3   C2   C1   119.99  3.000
 6NN  H3   C3   C4   120.07  3.000
 6NN  H3   C3   C2   120.12  3.000
 6NN  C4   C3   C2   119.81  3.000
 6NN  O8   C9   O10  124.19  3.000
 6NN  O10  C9   N11  125.35  3.000
 6NN  O8   C9   N11  110.44  3.000
 6NN  H7   C12  H6   107.09  3.000
 6NN  H7   C12  N11  109.79  3.000
 6NN  H6   C12  N11  110.25  3.000
 6NN  H7   C12  P13  110.32  3.000
 6NN  H6   C12  P13  108.26  3.000
 6NN  N11  C12  P13  111.04  3.000
 6NN  H11  C20  H10  107.66  3.000
 6NN  H11  C20  H9   107.63  3.000
 6NN  H10  C20  H9   107.63  3.000
 6NN  H11  C20  C19  111.19  3.000
 6NN  H10  C20  C19  111.56  3.000
 6NN  H9   C20  C19  110.99  3.000
 6NN  H14  C21  H13  107.29  3.000
 6NN  H14  C21  H12  107.65  3.000
 6NN  H13  C21  H12  107.82  3.000
 6NN  H14  C21  C19  110.81  3.000
 6NN  H13  C21  C19  111.96  3.000
 6NN  H12  C21  C19  111.11  3.000
 6NN  N24  C22  O23  124.25  3.000
 6NN  O23  C22  C17  121.23  3.000
 6NN  N24  C22  C17  114.51  3.000
 6NN  H17  C27  H16  107.51  3.000
 6NN  H17  C27  H15  106.78  3.000
 6NN  H16  C27  H15  107.58  3.000
 6NN  H17  C27  C26  112.28  3.000
 6NN  H16  C27  C26  110.99  3.000
 6NN  H15  C27  C26  111.45  3.000
 6NN  O14  P13  N16  107.07  3.000
 6NN  N16  P13  O15  113.10  3.000
 6NN  O14  P13  O15  109.89  3.000
 6NN  N16  P13  C12  108.05  3.000
 6NN  O14  P13  C12  103.80  3.000
 6NN  O15  P13  C12  114.30  3.000
 6NN  C5   C6   C7   120.44  3.000
 6NN  C7   C6   C1   120.48  3.000
 6NN  C5   C6   C1   119.06  3.000
 6NN  H18  C4   C5   119.89  3.000
 6NN  H18  C4   C3   120.09  3.000
 6NN  C5   C4   C3   120.02  3.000
 6NN  H19  C5   C4   119.73  3.000
 6NN  H19  C5   C6   119.72  3.000
 6NN  C4   C5   C6   120.54  3.000
 6NN  H20  N16  C17  114.30  3.000
 6NN  H20  N16  P13  117.07  3.000
 6NN  C17  N16  P13  120.96  3.000
 6NN  H21  C17  C18  108.78  3.000
 6NN  H21  C17  N16  107.88  3.000
 6NN  C18  C17  N16  110.43  3.000
 6NN  H21  C17  C22  108.60  3.000
 6NN  C18  C17  C22  109.87  3.000
 6NN  N16  C17  C22  111.21  3.000
 6NN  H23  C18  H22  106.23  3.000
 6NN  H23  C18  C17  108.99  3.000
 6NN  H22  C18  C17  108.19  3.000
 6NN  H23  C18  C19  109.37  3.000
 6NN  H22  C18  C19  109.27  3.000
 6NN  C17  C18  C19  114.47  3.000
 6NN  H24  N24  C25  116.85  3.000
 6NN  H24  N24  C22  117.97  3.000
 6NN  C25  N24  C22  124.62  3.000
 6NN  H26  C25  H25  107.07  3.000
 6NN  H26  C25  C26  109.99  3.000
 6NN  H25  C25  C26  109.60  3.000
 6NN  H26  C25  N24  108.18  3.000
 6NN  H25  C25  N24  108.40  3.000
 6NN  C26  C25  N24  113.39  3.000
 6NN  H27  C26  C28  107.57  3.000
 6NN  H27  C26  C25  107.74  3.000
 6NN  C28  C26  C25  108.68  3.000
 6NN  H27  C26  C27  108.49  3.000
 6NN  C28  C26  C27  112.49  3.000
 6NN  C25  C26  C27  111.68  3.000
 6NN  H29  C28  H28  105.98  3.000
 6NN  H29  C28  C29  109.58  3.000
 6NN  H28  C28  C29  108.72  3.000
 6NN  H29  C28  C26  109.11  3.000
 6NN  H28  C28  C26  108.79  3.000
 6NN  C29  C28  C26  114.33  3.000
 6NN  H32  C29  H31  107.54  3.000
 6NN  H32  C29  H30  107.58  3.000
 6NN  H31  C29  H30  107.31  3.000
 6NN  H32  C29  C28  111.10  3.000
 6NN  H31  C29  C28  112.17  3.000
 6NN  H30  C29  C28  110.93  3.000
 6NN  H33  O14  P13  115.96  3.000
 6NN  H34  N11  C12  117.96  3.000
 6NN  H34  N11  C9   118.60  3.000
 6NN  C12  N11  C9   122.24  3.000
 6NN  C9   O8   C7   116.74  3.000
 6NN  H5   C7   H4   108.05  3.000
 6NN  H5   C7   O8   110.14  3.000
 6NN  H4   C7   O8   110.10  3.000
 6NN  H5   C7   C6   110.83  3.000
 6NN  H4   C7   C6   110.79  3.000
 6NN  O8   C7   C6   106.94  3.000
 6NN  H8   C19  C18  108.09  3.000
 6NN  H8   C19  C21  107.97  3.000
 6NN  C18  C19  C21  112.14  3.000
 6NN  H8   C19  C20  107.91  3.000
 6NN  C21  C19  C20  110.86  3.000
 6NN  C18  C19  C20  109.73  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
 6NN  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 6NN  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 6NN  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 6NN  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 6NN  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 6NN  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 6NN  CONST_07  C7   C6   C1   C2    180.00   0.0  0
 6NN  CONST_08  C4   C5   C6   C7    180.00   0.0  0
 6NN  CONST_09  H19  C5   C6   C1    180.00   0.0  0
 6NN  CONST_10  H3   C3   C2   C1    180.00   0.0  0
 6NN  CONST_11  H18  C4   C3   C2    180.00   0.0  0
 6NN  CONST_12  H1   C1   C2   C3    180.00   0.0  0
 6NN  CONST_13  H2   C2   C1   C6    180.00   0.0  0
 6NN  CONST_14  C25  N24  C22  C17   180.00   0.0  0
 6NN  CONST_15  C25  N24  C22  O23     0.00   0.0  0
 6NN  CONST_16  H24  N24  C22  C17     0.00   0.0  0
 6NN  Var_01    O8   C7   C6   C1     90.59  30.0  2
 6NN  Var_02    C6   C7   O8   C9   -178.01  30.0  1
 6NN  Var_03    O10  C9   O8   C7      0.39  30.0  3
 6NN  Var_04    P13  C12  N11  C9     91.84  30.0  3
 6NN  Var_05    O8   C9   N11  C12  -171.50  30.0  1
 6NN  Var_06    C17  N16  P13  C12   108.90  30.0  3
 6NN  Var_07    C17  C18  C19  C20  -178.72  30.0  2
 6NN  Var_08    C26  C25  N24  C22   102.18  30.0  2
 6NN  Var_09    N11  C12  P13  O15   -62.02  30.0  1
 6NN  Var_10    H12  C21  C19  C20    66.35  30.0  3
 6NN  Var_11    H9   C20  C19  C21    59.84  30.0  3
 6NN  Var_12    H30  C29  C28  C26   176.36  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
 6NN  chir_02  C17  N16  C22  C18  positiv
 6NN  chir_03  C26  C25  C28  C27  negativ
 6NN  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
 6NN  plan-1  C1   0.020
 6NN  plan-1  C2   0.020
 6NN  plan-1  C3   0.020
 6NN  plan-1  C6   0.020
 6NN  plan-1  C4   0.020
 6NN  plan-1  C5   0.020
 6NN  plan-1  H1   0.020
 6NN  plan-1  H2   0.020
 6NN  plan-1  H3   0.020
 6NN  plan-1  H18  0.020
 6NN  plan-1  H19  0.020
 6NN  plan-1  C7   0.020
 6NN  plan-2  C22  0.020
 6NN  plan-2  C17  0.020
 6NN  plan-2  N24  0.020
 6NN  plan-2  C25  0.020
 6NN  plan-2  H24  0.020
 6NN  plan-2  O23  0.020
 6NN  plan-3  C9   0.020
 6NN  plan-3  N11  0.020
 6NN  plan-3  O10  0.020
 6NN  plan-3  O8   0.020

