# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 06:28:03 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  62  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  -0.287   2.6599  -3.6299  -0.6239
 6NN  C2   C  CR16   0  -0.242   2.8872  -4.7012   0.2272
 6NN  C3   C  CR16   0  -0.263   4.0468  -4.7469   0.9917
 6NN  C9   C  C      0   0.758   1.7290   0.3502  -1.5689
 6NN  C12  C  CH2    0  -0.564  -0.0529   1.9772  -1.2361
 6NN  C20  C  CH3    0  -0.653  -6.3734   4.7963   0.5957
 6NN  C21  C  CH3    0  -0.667  -4.5758   4.2874   2.2704
 6NN  C22  C  C      0   0.563  -3.3772   0.8855  -0.3575
 6NN  C27  C  CH3    0  -0.694  -0.2840  -1.7131   1.3164
 6NN  P13  P  P      0   1.241  -0.7519   2.9703   0.1766
 6NN  C6   C  CR6    0   0.085   3.5837  -2.5924  -0.7211
 6NN  C4   C  CR16   0  -0.243   4.9751  -3.7186   0.8990
 6NN  C5   C  CR16   0  -0.292   4.7419  -2.6462   0.0471
 6NN  N16  N  NH1    0  -0.779  -2.3980   3.1482  -0.1913
 6NN  C17  C  CH1    0  -0.219  -3.4350   2.2664   0.3139
 6NN  C18  C  CH2    0  -0.415  -4.8097   2.9009   0.1532
 6NN  C25  C  CH2    0  -0.240  -2.1247  -1.2323  -0.3517
 6NN  C26  C  CH1    0  -0.255  -1.5992  -2.1964   0.7117
 6NN  C28  C  CH2    0  -0.414  -1.4557  -3.5873   0.0893
 6NN  C29  C  CH3    0  -0.671  -1.0276  -4.6749   1.0645
 6NN  O14  O  OP    -1  -0.786  -0.0906   4.3205   0.1644
 6NN  N11  N  NH1    0  -0.664   0.9918   1.1091  -0.7427
 6NN  O10  O  O      0  -0.524   1.7216   0.4269  -2.7818
 6NN  O8   O  O2     0  -0.483   2.4909  -0.5099  -0.8771
 6NN  H1   H  HCR6   0   0.253   1.7591  -3.6058  -1.2263
 6NN  H2   H  HCR6   0   0.256   2.1632  -5.5032   0.2897
 6NN  H3   H  HCR6   0   0.258   4.2285  -5.5842   1.6530
 6NN  H4   H  HCH2   0   0.245   4.2325  -0.9277  -1.9174
 6NN  H5   H  HCH2   0   0.249   2.7896  -1.7472  -2.5219
 6NN  H6   H  HCH2   0   0.241  -0.8427   1.3938  -1.7196
 6NN  H7   H  HCH2   0   0.251   0.3433   2.6595  -1.9899
 6NN  H8   H  HCH1   0   0.215  -4.2715   4.9677   0.2735
 6NN  H9   H  HCH3   0   0.224  -6.4833   5.8156   0.9700
 6NN  H10  H  HCH3   0   0.221  -6.6539   4.8004  -0.4596
 6NN  H11  H  HCH3   0   0.211  -7.0950   4.1704   1.1269
 6NN  H12  H  HCH3   0   0.211  -5.1749   3.5646   2.8305
 6NN  H13  H  HCH3   0   0.231  -3.5237   4.0449   2.4252
 6NN  H14  H  HCH3   0   0.224  -4.7510   5.2707   2.7110
 6NN  H16  H  HCH3   0   0.225   0.5093  -1.7091   0.5661
 6NN  H17  H  HCH3   0   0.228  -0.3528  -0.7043   1.7279
 6NN  H18  H  HCR6   0   0.258   5.8824  -3.7509   1.4882
 6NN  H19  H  HCR6   0   0.256   5.4699  -1.8467  -0.0234
 6NN  H20  H  HNH1   0   0.368  -2.6219   3.5817  -1.0769
 6NN  H21  H  HCH1   0   0.253  -3.2466   2.1174   1.3790
 6NN  H22  H  HCH2   0   0.222  -5.5537   2.2277   0.5929
 6NN  H23  H  HCH2   0   0.224  -5.0547   2.9740  -0.9108
 6NN  H25  H  HCH2   0   0.240  -3.0127  -1.6567  -0.8218
 6NN  H26  H  HCH2   0   0.215  -1.3702  -1.1207  -1.1426
 6NN  H27  H  HCH1   0   0.221  -2.3523  -2.2550   1.5070
 6NN  H28  H  HCH2   0   0.223  -2.4138  -3.8708  -0.3568
 6NN  H29  H  HCH2   0   0.213  -0.7403  -3.5373  -0.7393
 6NN  H30  H  HCH3   0   0.230  -1.0243  -5.6508   0.5777
 6NN  H31  H  HCH3   0   0.223  -0.0239  -4.5065   1.4558
 6NN  H32  H  HCH3   0   0.219  -1.7095  -4.7323   1.9153
 6NN  H34  H  HNH1   0   0.394   0.9740   0.8865   0.2419
 6NN  C7   C  CH2    0  -0.244   3.3063  -1.4236  -1.6177
 6NN  O23  O  O      0  -0.507  -4.0714   0.5849  -1.3212
 6NN  C19  C  CH1    0  -0.217  -4.9501   4.2836   0.7923
 6NN  O15  O  O      0  -0.798  -0.6673   2.0860   1.4103
 6NN  N24  N  NH1    0  -0.668  -2.4796   0.0555   0.2018
 6NN  H15  H  HCH3   0   0.239   0.0419  -2.3545   2.1350
 6NN  H24  H  HNH1   0   0.406  -1.8365   0.4857   0.8596

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  1.389  0.020  1.389
 6NN  C4   C3   aromatic  1.388  0.020  1.388
 6NN  C5   C6   aromatic  1.391  0.020  1.391
 6NN  C3   C2   aromatic  1.390  0.020  1.390
 6NN  C6   C7   single    1.499  0.020  1.499
 6NN  C6   C1   aromatic  1.393  0.020  1.393
 6NN  C2   C1   aromatic  1.387  0.020  1.387
 6NN  C7   O8   single    1.431  0.020  1.431
 6NN  O8   C9   single    1.341  0.020  1.341
 6NN  C9   O10  double    1.215  0.020  1.215
 6NN  C9   N11  single    1.342  0.020  1.342
 6NN  N11  C12  single    1.445  0.020  1.445
 6NN  C12  P13  single    1.863  0.020  1.863
 6NN  O15  P13  deloc     1.520  0.020  1.520
 6NN  O14  P13  deloc     1.503  0.020  1.503
 6NN  P13  N16  single    1.696  0.020  1.696
 6NN  C25  N24  single    1.446  0.020  1.446
 6NN  C25  C26  single    1.529  0.020  1.529
 6NN  N16  C17  single    1.452  0.020  1.452
 6NN  N24  C22  single    1.344  0.020  1.344
 6NN  C22  O23  double    1.225  0.020  1.225
 6NN  C22  C17  single    1.537  0.020  1.537
 6NN  C28  C29  single    1.522  0.020  1.522
 6NN  C28  C26  single    1.531  0.020  1.531
 6NN  C17  C18  single    1.523  0.020  1.523
 6NN  C26  C27  single    1.526  0.020  1.526
 6NN  C18  C19  single    1.530  0.020  1.530
 6NN  C20  C19  single    1.526  0.020  1.526
 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    0.890  0.020  1.040
 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  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   119.73  3.000
 6NN  H1   C1   C2   119.64  3.000
 6NN  C6   C1   C2   120.63  3.000
 6NN  H2   C2   C3   120.14  3.000
 6NN  H2   C2   C1   119.88  3.000
 6NN  C3   C2   C1   119.98  3.000
 6NN  H3   C3   C4   120.10  3.000
 6NN  H3   C3   C2   120.11  3.000
 6NN  C4   C3   C2   119.79  3.000
 6NN  O8   C9   O10  123.97  3.000
 6NN  O10  C9   N11  125.11  3.000
 6NN  O8   C9   N11  110.92  3.000
 6NN  H7   C12  H6   106.86  3.000
 6NN  H7   C12  N11  110.42  3.000
 6NN  H6   C12  N11  110.63  3.000
 6NN  H7   C12  P13  109.07  3.000
 6NN  H6   C12  P13  110.39  3.000
 6NN  N11  C12  P13  109.43  3.000
 6NN  H11  C20  H10  107.60  3.000
 6NN  H11  C20  H9   107.55  3.000
 6NN  H10  C20  H9   107.58  3.000
 6NN  H11  C20  C19  111.15  3.000
 6NN  H10  C20  C19  111.44  3.000
 6NN  H9   C20  C19  111.32  3.000
 6NN  H14  C21  H13  107.32  3.000
 6NN  H14  C21  H12  107.51  3.000
 6NN  H13  C21  H12  108.00  3.000
 6NN  H14  C21  C19  110.73  3.000
 6NN  H13  C21  C19  111.95  3.000
 6NN  H12  C21  C19  111.13  3.000
 6NN  N24  C22  O23  123.65  3.000
 6NN  O23  C22  C17  122.88  3.000
 6NN  N24  C22  C17  113.46  3.000
 6NN  H17  C27  H16  107.54  3.000
 6NN  H17  C27  H15  106.24  3.000
 6NN  H16  C27  H15  107.51  3.000
 6NN  H17  C27  C26  112.82  3.000
 6NN  H16  C27  C26  110.79  3.000
 6NN  H15  C27  C26  111.65  3.000
 6NN  O14  P13  N16  109.32  3.000
 6NN  N16  P13  O15  106.92  3.000
 6NN  O14  P13  O15  120.30  3.000
 6NN  N16  P13  C12  104.81  3.000
 6NN  O14  P13  C12  107.91  3.000
 6NN  O15  P13  C12  106.52  3.000
 6NN  C5   C6   C7   120.97  3.000
 6NN  C7   C6   C1   119.99  3.000
 6NN  C5   C6   C1   119.01  3.000
 6NN  H18  C4   C5   119.84  3.000
 6NN  H18  C4   C3   120.13  3.000
 6NN  C5   C4   C3   120.03  3.000
 6NN  H19  C5   C4   119.78  3.000
 6NN  H19  C5   C6   119.67  3.000
 6NN  C4   C5   C6   120.55  3.000
 6NN  H20  N16  C17  114.02  3.000
 6NN  H20  N16  P13  116.73  3.000
 6NN  C17  N16  P13  123.64  3.000
 6NN  H21  C17  C18  108.40  3.000
 6NN  H21  C17  N16  107.40  3.000
 6NN  C18  C17  N16  110.79  3.000
 6NN  H21  C17  C22  107.28  3.000
 6NN  C18  C17  C22  111.25  3.000
 6NN  N16  C17  C22  111.52  3.000
 6NN  H23  C18  H22  106.21  3.000
 6NN  H23  C18  C17  109.43  3.000
 6NN  H22  C18  C17  108.35  3.000
 6NN  H23  C18  C19  108.98  3.000
 6NN  H22  C18  C19  108.99  3.000
 6NN  C17  C18  C19  114.55  3.000
 6NN  H26  C25  H25  106.76  3.000
 6NN  H26  C25  C26  109.19  3.000
 6NN  H25  C25  C26  109.53  3.000
 6NN  H26  C25  N24  110.71  3.000
 6NN  H25  C25  N24  108.17  3.000
 6NN  C26  C25  N24  112.32  3.000
 6NN  H27  C26  C28  108.10  3.000
 6NN  H27  C26  C25  107.58  3.000
 6NN  C28  C26  C25  108.82  3.000
 6NN  H27  C26  C27  108.74  3.000
 6NN  C28  C26  C27  111.60  3.000
 6NN  C25  C26  C27  111.85  3.000
 6NN  H29  C28  H28  105.97  3.000
 6NN  H29  C28  C29  109.48  3.000
 6NN  H28  C28  C29  108.81  3.000
 6NN  H29  C28  C26  109.10  3.000
 6NN  H28  C28  C26  108.61  3.000
 6NN  C29  C28  C26  114.53  3.000
 6NN  H32  C29  H31  107.66  3.000
 6NN  H32  C29  H30  107.62  3.000
 6NN  H31  C29  H30  107.19  3.000
 6NN  H32  C29  C28  111.17  3.000
 6NN  H31  C29  C28  112.24  3.000
 6NN  H30  C29  C28  110.75  3.000
 6NN  H34  N11  C12  116.91  3.000
 6NN  H34  N11  C9   119.03  3.000
 6NN  C12  N11  C9   121.77  3.000
 6NN  C9   O8   C7   117.78  3.000
 6NN  H5   C7   H4   107.99  3.000
 6NN  H5   C7   O8   110.40  3.000
 6NN  H4   C7   O8   109.58  3.000
 6NN  H5   C7   C6   110.62  3.000
 6NN  H4   C7   C6   111.17  3.000
 6NN  O8   C7   C6   107.08  3.000
 6NN  H8   C19  C18  108.07  3.000
 6NN  H8   C19  C21  107.81  3.000
 6NN  C18  C19  C21  112.63  3.000
 6NN  H8   C19  C20  107.90  3.000
 6NN  C21  C19  C20  110.68  3.000
 6NN  C18  C19  C20  109.61  3.000
 6NN  H24  N24  C25  118.02  3.000
 6NN  H24  N24  C22  115.51  3.000
 6NN  C25  N24  C22  123.67  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     84.09  30.0  2
 6NN  Var_02    C6   C7   O8   C9   -156.71  30.0  1
 6NN  Var_03    O10  C9   O8   C7     -2.38  30.0  3
 6NN  Var_04    P13  C12  N11  C9   -175.26  30.0  3
 6NN  Var_05    O8   C9   N11  C12  -170.83  30.0  1
 6NN  Var_06    C17  N16  P13  C12    94.74  30.0  3
 6NN  Var_07    C17  C18  C19  C20  -178.58  30.0  2
 6NN  Var_08    C26  C25  N24  C22  -155.01  30.0  1
 6NN  Var_09    N11  C12  P13  O15   -32.65  30.0  1
 6NN  Var_10    H12  C21  C19  C20    66.32  30.0  3
 6NN  Var_11    H9   C20  C19  C21    59.79  30.0  3
 6NN  Var_12    H30  C29  C28  C26   175.33  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

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  C25  0.020
 6NN  plan-2  O23  0.020
 6NN  plan-2  N24  0.020
 6NN  plan-2  H24  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

