# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:17:36 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: ~{N}-[(2~{S})-1-(3-azanylpropylamino)-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)NCCCN
#
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
 8KK  8KK  '~{N}-[(2~{S})-1-(3-azanylpropylamino)-4-methyl-1-oxidanylidene-pentan-2-yl]-(phenylmethoxycarbonylaminomethyl)phosphonamidic acid'  ligand  59  28  .  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_8KK
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
 8KK  C10  C  CH2   0  -0.578   0.6519  -1.3412   1.1474
 8KK  C11  C  C     0   0.761   2.4033   0.3215   0.8071
 8KK  C12  C  CH2   0  -0.239   4.2446   1.7174   0.3301
 8KK  C13  C  CR6   0   0.075   5.6641   1.5539  -0.1206
 8KK  C14  C  CR16  0  -0.291   5.9774   1.5481  -1.4768
 8KK  C15  C  CR16  0  -0.242   7.2891   1.3767  -1.8977
 8KK  C16  C  CR16  0  -0.261   8.3018   1.2063  -0.9624
 8KK  O01  O  OH1   0  -0.749   0.5657  -2.7163  -1.1884
 8KK  P01  P  P     0   1.335  -0.2657  -1.5653  -0.4141
 8KK  N01  N  NH1   0  -0.779  -1.7500  -2.2040  -0.0201
 8KK  C01  C  CH1   0  -0.208  -2.9623  -1.4757  -0.3256
 8KK  C02  C  CH2   0  -0.428  -4.1890  -2.3593  -0.0852
 8KK  C03  C  CH1   0  -0.223  -4.1645  -3.7043  -0.8146
 8KK  C04  C  CH3   0  -0.652  -5.4609  -4.4576  -0.5338
 8KK  C05  C  CH3   0  -0.667  -3.9425  -3.5418  -2.3136
 8KK  C06  C  C     0   0.562  -3.0793  -0.2051   0.5203
 8KK  N02  N  NH1   0  -0.640  -3.8425   0.7598  -0.0040
 8KK  C07  C  CH2   0  -0.237  -4.1195   2.0031   0.6870
 8KK  C08  C  CH2   0  -0.486  -5.0074   2.9035  -0.1540
 8KK  C09  C  CH2   0  -0.272  -5.3210   4.2065   0.5662
 8KK  N03  N  NH2   0  -0.799  -6.1737   5.0534  -0.2544
 8KK  O02  O  O     0  -0.495  -2.5387  -0.1091   1.6133
 8KK  O03  O  O     0  -0.714  -0.3511  -0.3536  -1.2691
 8KK  N04  N  NH1   0  -0.655   2.0180  -0.9679   0.8990
 8KK  O04  O  O2    0  -0.479   3.6808   0.4034   0.4220
 8KK  C17  C  CR16  0  -0.243   7.9974   1.2088   0.3929
 8KK  C18  C  CR16  0  -0.289   6.6847   1.3811   0.8098
 8KK  O05  O  O     0  -0.512   1.7042   1.2796   1.0580
 8KK  H1   H  HCH2  0   0.294   0.1466  -0.5738   1.7316
 8KK  H2   H  HCH2  0   0.295   0.6228  -2.2597   1.7368
 8KK  H3   H  HCH2  0   0.248   4.2021   2.2132   1.3022
 8KK  H4   H  HCH2  0   0.248   3.6793   2.3202  -0.3837
 8KK  H5   H  HCR6  0   0.256   5.1908   1.6828  -2.2099
 8KK  H6   H  HCR6  0   0.258   7.5198   1.3784  -2.9551
 8KK  H7   H  HCR6  0   0.259   9.3257   1.0756  -1.2879
 8KK  H8   H  HOH1  0   0.484   0.4313  -3.6140  -0.8602
 8KK  H9   H  HNH1  0   0.399  -1.7986  -2.7724   0.8157
 8KK  H10  H  HCH1  0   0.272  -2.9392  -1.1911  -1.3798
 8KK  H11  H  HCH2  0   0.240  -4.2981  -2.5355   0.9908
 8KK  H12  H  HCH2  0   0.239  -5.0774  -1.8014  -0.3966
 8KK  H13  H  HCH1  0   0.222  -3.3372  -4.2964  -0.4111
 8KK  H14  H  HCH3  0   0.214  -6.3199  -3.9359  -0.9621
 8KK  H15  H  HCH3  0   0.227  -5.4339  -5.4597  -0.9643
 8KK  H16  H  HCH3  0   0.224  -5.6375  -4.5617   0.5385
 8KK  H17  H  HCH3  0   0.215  -4.6903  -2.8765  -2.7529
 8KK  H18  H  HCH3  0   0.230  -2.9563  -3.1331  -2.5380
 8KK  H19  H  HCH3  0   0.230  -4.0161  -4.5034  -2.8241
 8KK  H20  H  HNH1  0   0.401  -4.2171   0.6362  -0.9314
 8KK  H21  H  HCH2  0   0.231  -4.6052   1.7904   1.6434
 8KK  H22  H  HCH2  0   0.232  -3.1812   2.5159   0.9168
 8KK  H23  H  HCH2  0   0.234  -4.5189   3.1274  -1.1066
 8KK  H24  H  HCH2  0   0.231  -5.9422   2.3826  -0.3870
 8KK  H25  H  HCH2  0   0.194  -5.7515   3.9739   1.5508
 8KK  H26  H  HCH2  0   0.219  -4.3874   4.7418   0.7586
 8KK  H27  H  HNH2  0   0.339  -7.0815   4.6146  -0.3502
 8KK  H28  H  HNH2  0   0.348  -6.3454   5.9254   0.2293
 8KK  H30  H  HNH1  0   0.407   2.6640  -1.6887   0.6187
 8KK  H31  H  HCR6  0   0.259   8.7830   1.0802   1.1260
 8KK  H32  H  HCR6  0   0.255   6.4545   1.3881   1.8688

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
 8KK  C17  C18  aromatic  1.388  0.020  1.388
 8KK  C17  C16  aromatic  1.389  0.020  1.389
 8KK  C18  C13  aromatic  1.392  0.020  1.392
 8KK  C16  C15  aromatic  1.389  0.020  1.389
 8KK  C13  C12  single    1.498  0.020  1.498
 8KK  C13  C14  aromatic  1.392  0.020  1.392
 8KK  C12  O04  single    1.433  0.020  1.433
 8KK  C15  C14  aromatic  1.388  0.020  1.388
 8KK  O04  C11  single    1.337  0.020  1.337
 8KK  O05  C11  double    1.212  0.020  1.212
 8KK  C11  N04  single    1.349  0.020  1.349
 8KK  N04  C10  single    1.438  0.020  1.438
 8KK  C10  P01  single    1.825  0.020  1.825
 8KK  O03  P01  double    1.485  0.020  1.485
 8KK  O01  P01  single    1.617  0.020  1.617
 8KK  P01  N01  single    1.663  0.020  1.663
 8KK  N01  C01  single    1.447  0.020  1.447
 8KK  C07  N02  single    1.449  0.020  1.449
 8KK  C07  C08  single    1.519  0.020  1.519
 8KK  N02  C06  single    1.337  0.020  1.337
 8KK  C06  O02  double    1.223  0.020  1.223
 8KK  C06  C01  single    1.531  0.020  1.531
 8KK  C01  C02  single    1.531  0.020  1.531
 8KK  C08  C09  single    1.521  0.020  1.521
 8KK  C02  C03  single    1.530  0.020  1.530
 8KK  C09  N03  single    1.455  0.020  1.455
 8KK  C05  C03  single    1.524  0.020  1.524
 8KK  C03  C04  single    1.525  0.020  1.525
 8KK  C10  H1   single    0.970  0.020  1.090
 8KK  C10  H2   single    0.970  0.020  1.090
 8KK  C12  H3   single    0.970  0.020  1.090
 8KK  C12  H4   single    0.970  0.020  1.090
 8KK  C14  H5   single    0.930  0.020  1.080
 8KK  C15  H6   single    0.930  0.020  1.080
 8KK  C16  H7   single    0.930  0.020  1.080
 8KK  O01  H8   single    0.850  0.020  0.980
 8KK  N01  H9   single    0.890  0.020  1.040
 8KK  C01  H10  single    0.970  0.020  1.090
 8KK  C02  H11  single    0.970  0.020  1.090
 8KK  C02  H12  single    0.970  0.020  1.090
 8KK  C03  H13  single    0.970  0.020  1.090
 8KK  C04  H14  single    0.970  0.020  1.090
 8KK  C04  H15  single    0.970  0.020  1.090
 8KK  C04  H16  single    0.970  0.020  1.090
 8KK  C05  H17  single    0.970  0.020  1.090
 8KK  C05  H18  single    0.970  0.020  1.090
 8KK  C05  H19  single    0.970  0.020  1.090
 8KK  N02  H20  single    0.860  0.020  1.020
 8KK  C07  H21  single    0.970  0.020  1.090
 8KK  C07  H22  single    0.970  0.020  1.090
 8KK  C08  H23  single    0.970  0.020  1.090
 8KK  C08  H24  single    0.970  0.020  1.090
 8KK  C09  H25  single    0.970  0.020  1.090
 8KK  C09  H26  single    0.970  0.020  1.090
 8KK  N03  H27  single    0.890  0.020  1.040
 8KK  N03  H28  single    0.890  0.020  1.040
 8KK  N04  H30  single    0.860  0.020  1.020
 8KK  C17  H31  single    0.930  0.020  1.080
 8KK  C18  H32  single    0.930  0.020  1.080

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
 8KK  H2   C10  H1   106.91  3.000
 8KK  H2   C10  N04  109.70  3.000
 8KK  H1   C10  N04  110.53  3.000
 8KK  H2   C10  P01  110.19  3.000
 8KK  H1   C10  P01  108.20  3.000
 8KK  N04  C10  P01  111.21  3.000
 8KK  O05  C11  O04  124.22  3.000
 8KK  O05  C11  N04  125.21  3.000
 8KK  O04  C11  N04  110.56  3.000
 8KK  H4   C12  H3   108.13  3.000
 8KK  H4   C12  O04  110.15  3.000
 8KK  H3   C12  O04  110.12  3.000
 8KK  H4   C12  C13  110.74  3.000
 8KK  H3   C12  C13  110.74  3.000
 8KK  O04  C12  C13  106.98  3.000
 8KK  C18  C13  C14  119.06  3.000
 8KK  C14  C13  C12  120.45  3.000
 8KK  C18  C13  C12  120.48  3.000
 8KK  H5   C14  C15  119.74  3.000
 8KK  H5   C14  C13  119.69  3.000
 8KK  C15  C14  C13  120.57  3.000
 8KK  H6   C15  C16  120.17  3.000
 8KK  H6   C15  C14  119.83  3.000
 8KK  C16  C15  C14  120.00  3.000
 8KK  H7   C16  C17  120.06  3.000
 8KK  H7   C16  C15  120.14  3.000
 8KK  C17  C16  C15  119.80  3.000
 8KK  H8   O01  P01  115.31  3.000
 8KK  O03  P01  N01  113.47  3.000
 8KK  N01  P01  O01  107.39  3.000
 8KK  O03  P01  O01  109.54  3.000
 8KK  N01  P01  C10  107.05  3.000
 8KK  O01  P01  C10  103.80  3.000
 8KK  O03  P01  C10  114.91  3.000
 8KK  H9   N01  C01  114.64  3.000
 8KK  H9   N01  P01  117.01  3.000
 8KK  C01  N01  P01  120.30  3.000
 8KK  H10  C01  C06  108.59  3.000
 8KK  H10  C01  C02  108.60  3.000
 8KK  C06  C01  C02  109.34  3.000
 8KK  H10  C01  N01  108.49  3.000
 8KK  C02  C01  N01  110.35  3.000
 8KK  C06  C01  N01  111.41  3.000
 8KK  H12  C02  H11  106.29  3.000
 8KK  H12  C02  C03  109.00  3.000
 8KK  H11  C02  C03  109.17  3.000
 8KK  H12  C02  C01  108.15  3.000
 8KK  H11  C02  C01  109.07  3.000
 8KK  C03  C02  C01  114.82  3.000
 8KK  H13  C03  C05  108.07  3.000
 8KK  H13  C03  C04  107.90  3.000
 8KK  C05  C03  C04  110.95  3.000
 8KK  H13  C03  C02  108.17  3.000
 8KK  C04  C03  C02  109.43  3.000
 8KK  C05  C03  C02  112.17  3.000
 8KK  H16  C04  H15  107.70  3.000
 8KK  H16  C04  H14  107.66  3.000
 8KK  H15  C04  H14  107.66  3.000
 8KK  H16  C04  C03  111.43  3.000
 8KK  H15  C04  C03  111.10  3.000
 8KK  H14  C04  C03  111.11  3.000
 8KK  H19  C05  H18  107.15  3.000
 8KK  H19  C05  H17  107.59  3.000
 8KK  H18  C05  H17  107.93  3.000
 8KK  H19  C05  C03  110.87  3.000
 8KK  H18  C05  C03  111.96  3.000
 8KK  H17  C05  C03  111.13  3.000
 8KK  O02  C06  N02  123.08  3.000
 8KK  O02  C06  C01  121.68  3.000
 8KK  N02  C06  C01  115.21  3.000
 8KK  H20  N02  C07  118.23  3.000
 8KK  H20  N02  C06  118.97  3.000
 8KK  C07  N02  C06  122.77  3.000
 8KK  H22  C07  H21  106.77  3.000
 8KK  H22  C07  C08  109.87  3.000
 8KK  H21  C07  C08  109.87  3.000
 8KK  H22  C07  N02  109.79  3.000
 8KK  H21  C07  N02  109.58  3.000
 8KK  C08  C07  N02  110.88  3.000
 8KK  H24  C08  H23  107.05  3.000
 8KK  H24  C08  C09  109.40  3.000
 8KK  H23  C08  C09  109.21  3.000
 8KK  H24  C08  C07  109.56  3.000
 8KK  H23  C08  C07  110.03  3.000
 8KK  C09  C08  C07  111.48  3.000
 8KK  H26  C09  H25  106.29  3.000
 8KK  H26  C09  N03  108.34  3.000
 8KK  H25  C09  N03  113.49  3.000
 8KK  H26  C09  C08  109.06  3.000
 8KK  H25  C09  C08  108.87  3.000
 8KK  N03  C09  C08  110.63  3.000
 8KK  H28  N03  H27  105.46  3.000
 8KK  H28  N03  C09  109.35  3.000
 8KK  H27  N03  C09  109.05  3.000
 8KK  H30  N04  C11  118.79  3.000
 8KK  H30  N04  C10  118.13  3.000
 8KK  C11  N04  C10  122.10  3.000
 8KK  C12  O04  C11  116.79  3.000
 8KK  H31  C17  C18  119.86  3.000
 8KK  H31  C17  C16  120.11  3.000
 8KK  C18  C17  C16  120.03  3.000
 8KK  H32  C18  C17  119.68  3.000
 8KK  H32  C18  C13  119.78  3.000
 8KK  C17  C18  C13  120.54  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
 8KK  CONST_01  C16  C17  C18  C13     0.00   0.0  0
 8KK  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 8KK  CONST_03  C17  C18  C13  C14     0.00   0.0  0
 8KK  CONST_04  C17  C16  C15  C14     0.00   0.0  0
 8KK  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 8KK  CONST_06  C18  C13  C14  C15     0.00   0.0  0
 8KK  CONST_07  C17  C18  C13  C12   180.00   0.0  0
 8KK  CONST_08  C15  C14  C13  C12   180.00   0.0  0
 8KK  CONST_09  H31  C17  C18  C13   180.00   0.0  0
 8KK  CONST_10  H6   C15  C14  C13   180.00   0.0  0
 8KK  CONST_11  H32  C18  C13  C14   180.00   0.0  0
 8KK  CONST_12  H7   C16  C15  C14   180.00   0.0  0
 8KK  CONST_13  H5   C14  C15  C16   180.00   0.0  0
 8KK  CONST_14  C07  N02  C06  C01   180.00   0.0  0
 8KK  CONST_15  O02  C06  N02  C07     0.00   0.0  0
 8KK  CONST_16  H20  N02  C06  C01     0.00   0.0  0
 8KK  Var_01    O04  C12  C13  C14    89.95  30.0  2
 8KK  Var_02    C13  C12  O04  C11  -179.72  30.0  2
 8KK  Var_03    O04  C11  N04  C10  -172.87  30.0  2
 8KK  Var_04    C01  N01  P01  C10   118.37  30.0  3
 8KK  Var_05    P01  C10  N04  C11    90.76  30.0  3
 8KK  Var_06    N04  C10  P01  O01    58.52  30.0  1
 8KK  Var_07    C05  C03  C02  C01   -54.25  30.0  3
 8KK  Var_08    C08  C07  N02  C06   179.80  30.0  1
 8KK  Var_09    C09  C08  C07  N02   179.30  30.0  3
 8KK  Var_10    N03  C09  C08  C07  -179.91  30.0  3
 8KK  Var_11    H17  C05  C03  C02   -55.41  30.0  3
 8KK  Var_12    H14  C04  C03  C02    65.47  30.0  3
 8KK  Var_13    H27  N03  C09  C08    66.97  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
 8KK  chir_02  C01  N01  C06  C02  positiv
 8KK  chir_03  P01  O03  O01  N01  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
 8KK  plan-1  C12  0.020
 8KK  plan-1  C13  0.020
 8KK  plan-1  C14  0.020
 8KK  plan-1  C15  0.020
 8KK  plan-1  C16  0.020
 8KK  plan-1  C17  0.020
 8KK  plan-1  C18  0.020
 8KK  plan-1  H5   0.020
 8KK  plan-1  H6   0.020
 8KK  plan-1  H7   0.020
 8KK  plan-1  H31  0.020
 8KK  plan-1  H32  0.020
 8KK  plan-2  C01  0.020
 8KK  plan-2  C06  0.020
 8KK  plan-2  N02  0.020
 8KK  plan-2  C07  0.020
 8KK  plan-2  O02  0.020
 8KK  plan-2  H20  0.020
 8KK  plan-3  C11  0.020
 8KK  plan-3  N04  0.020
 8KK  plan-3  O04  0.020
 8KK  plan-3  O05  0.020

