# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 03:17:16 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  58  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  -0.569  -0.0755  -1.1981   1.2552
 8KK  C11  C  C      0   0.747   1.4189   0.6596   0.7088
 8KK  C12  C  CH2    0  -0.234   3.0292   2.2228  -0.0265
 8KK  C13  C  CR6    0   0.077   4.4751   2.2147  -0.4214
 8KK  C14  C  CR16   0  -0.292   4.8447   2.0446  -1.7523
 8KK  C15  C  CR16   0  -0.242   6.1846   2.0123  -2.1148
 8KK  C16  C  CR16   0  -0.262   7.1698   2.1479  -1.1453
 8KK  O01  O  OP    -1  -0.797   0.2165  -3.1901  -0.5268
 8KK  P01  P  P      0   1.244  -0.7199  -2.0394  -0.2570
 8KK  N01  N  NH1    0  -0.780  -2.2412  -2.6231   0.2238
 8KK  C01  C  CH1    0  -0.219  -3.4957  -1.9891  -0.1303
 8KK  C02  C  CH2    0  -0.412  -4.6516  -2.9778  -0.0546
 8KK  C03  C  CH1    0  -0.216  -4.4407  -4.2488  -0.8796
 8KK  C04  C  CH3    0  -0.652  -5.6774  -5.1373  -0.7881
 8KK  C05  C  CH3    0  -0.669  -4.0985  -3.9458  -2.3346
 8KK  C06  C  C      0   0.568  -3.7459  -0.7458   0.7335
 8KK  N02  N  NH1    0  -0.661  -3.0795   0.3409   0.3112
 8KK  C07  C  CH2    0  -0.250  -3.0280   1.5860   1.0446
 8KK  C08  C  CH2    0  -0.465  -2.6451   2.7316   0.1218
 8KK  C09  C  CH2    0  -0.273  -2.5625   4.0561   0.8629
 8KK  N03  N  NH2    0  -0.800  -2.1775   5.1301  -0.0415
 8KK  O02  O  O      0  -0.512  -4.4684  -0.7516   1.7238
 8KK  O03  O  O      0  -0.800  -0.9672  -0.9985  -1.3316
 8KK  N04  N  NH1    0  -0.648   1.2361  -0.6372   1.0118
 8KK  O04  O  O2     0  -0.485   2.6748   0.8725   0.2824
 8KK  C17  C  CR16   0  -0.243   6.8098   2.3167   0.1858
 8KK  C18  C  CR16   0  -0.290   5.4692   2.3484   0.5440
 8KK  O05  O  O      0  -0.507   0.5938   1.5426   0.8285
 8KK  H1   H  HCH2   0   0.262  -0.7416  -0.4000   1.5760
 8KK  H2   H  HCH2   0   0.246  -0.0121  -1.9120   2.0805
 8KK  H3   H  HCH2   0   0.243   2.8720   2.8659   0.8420
 8KK  H4   H  HCH2   0   0.243   2.4067   2.5997  -0.8411
 8KK  H5   H  HCR6   0   0.255   4.0797   1.9429  -2.5130
 8KK  H6   H  HCR6   0   0.258   6.4586   1.8838  -3.1540
 8KK  H7   H  HCR6   0   0.258   8.2150   2.1254  -1.4254
 8KK  H9   H  HNH1   0   0.364  -2.2819  -3.2075   1.0471
 8KK  H10  H  HCH1   0   0.252  -3.4054  -1.6468  -1.1629
 8KK  H11  H  HCH2   0   0.222  -4.8344  -3.2522   0.9888
 8KK  H12  H  HCH2   0   0.219  -5.5611  -2.4749  -0.4018
 8KK  H13  H  HCH1   0   0.214  -3.5989  -4.7974  -0.4462
 8KK  H14  H  HCH3   0   0.210  -6.5460  -4.6497  -1.2371
 8KK  H15  H  HCH3   0   0.223  -5.5239  -6.0837  -1.3102
 8KK  H16  H  HCH3   0   0.221  -5.9291  -5.3689   0.2488
 8KK  H17  H  HCH3   0   0.210  -4.8658  -3.3207  -2.7994
 8KK  H18  H  HCH3   0   0.232  -3.1432  -3.4263  -2.4238
 8KK  H19  H  HCH3   0   0.224  -4.0263  -4.8658  -2.9174
 8KK  H20  H  HNH1   0   0.397  -2.3820   0.1958  -0.4151
 8KK  H21  H  HCH2   0   0.229  -4.0052   1.7721   1.4924
 8KK  H22  H  HCH2   0   0.221  -2.3050   1.5231   1.8663
 8KK  H23  H  HCH2   0   0.232  -1.6761   2.5205  -0.3370
 8KK  H24  H  HCH2   0   0.220  -3.3803   2.8052  -0.6862
 8KK  H25  H  HCH2   0   0.188  -3.5167   4.2391   1.3789
 8KK  H26  H  HCH2   0   0.214  -1.8012   3.9790   1.6440
 8KK  H27  H  HNH2   0   0.337  -2.9166   5.2763  -0.7188
 8KK  H28  H  HNH2   0   0.345  -2.1127   5.9971   0.4765
 8KK  H30  H  HNH1   0   0.391   1.9672  -1.2854   0.7631
 8KK  H31  H  HCR6   0   0.258   7.5735   2.4262   0.9447
 8KK  H32  H  HCR6   0   0.254   5.1940   2.4851   1.5833

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    1.499  0.020  1.499
 8KK  C13  C14  aromatic  1.392  0.020  1.392
 8KK  C12  O04  single    1.430  0.020  1.430
 8KK  C15  C14  aromatic  1.388  0.020  1.388
 8KK  O04  C11  single    1.343  0.020  1.343
 8KK  O05  C11  double    1.214  0.020  1.214
 8KK  C11  N04  single    1.344  0.020  1.344
 8KK  N04  C10  single    1.447  0.020  1.447
 8KK  C10  P01  single    1.847  0.020  1.847
 8KK  O03  P01  deloc     1.516  0.020  1.516
 8KK  O01  P01  deloc     1.508  0.020  1.508
 8KK  P01  N01  single    1.699  0.020  1.699
 8KK  N01  C01  single    1.450  0.020  1.450
 8KK  C07  N02  single    1.446  0.020  1.446
 8KK  C07  C08  single    1.520  0.020  1.520
 8KK  N02  C06  single    1.343  0.020  1.343
 8KK  C06  O02  double    1.226  0.020  1.226
 8KK  C06  C01  single    1.534  0.020  1.534
 8KK  C01  C02  single    1.523  0.020  1.523
 8KK  C08  C09  single    1.520  0.020  1.520
 8KK  C02  C03  single    1.530  0.020  1.530
 8KK  C09  N03  single    1.456  0.020  1.456
 8KK  C05  C03  single    1.525  0.020  1.525
 8KK  C03  C04  single    1.526  0.020  1.526
 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  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    0.890  0.020  1.040
 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   106.98  3.000
 8KK  H2   C10  N04  109.12  3.000
 8KK  H1   C10  N04  108.67  3.000
 8KK  H2   C10  P01  109.93  3.000
 8KK  H1   C10  P01  111.23  3.000
 8KK  N04  C10  P01  110.80  3.000
 8KK  O05  C11  O04  123.45  3.000
 8KK  O05  C11  N04  125.94  3.000
 8KK  O04  C11  N04  110.58  3.000
 8KK  H4   C12  H3   107.93  3.000
 8KK  H4   C12  O04  110.23  3.000
 8KK  H3   C12  O04  110.40  3.000
 8KK  H4   C12  C13  110.80  3.000
 8KK  H3   C12  C13  110.58  3.000
 8KK  O04  C12  C13  106.91  3.000
 8KK  C18  C13  C14  119.03  3.000
 8KK  C14  C13  C12  120.58  3.000
 8KK  C18  C13  C12  120.38  3.000
 8KK  H5   C14  C15  119.73  3.000
 8KK  H5   C14  C13  119.68  3.000
 8KK  C15  C14  C13  120.59  3.000
 8KK  H6   C15  C16  120.15  3.000
 8KK  H6   C15  C14  119.85  3.000
 8KK  C16  C15  C14  120.00  3.000
 8KK  H7   C16  C17  120.05  3.000
 8KK  H7   C16  C15  120.15  3.000
 8KK  C17  C16  C15  119.80  3.000
 8KK  O03  P01  N01  106.88  3.000
 8KK  N01  P01  O01  110.15  3.000
 8KK  O03  P01  O01  119.89  3.000
 8KK  N01  P01  C10  103.73  3.000
 8KK  O01  P01  C10  106.11  3.000
 8KK  O03  P01  C10  108.94  3.000
 8KK  H9   N01  C01  114.65  3.000
 8KK  H9   N01  P01  117.74  3.000
 8KK  C01  N01  P01  123.76  3.000
 8KK  H10  C01  C06  106.98  3.000
 8KK  H10  C01  C02  108.26  3.000
 8KK  C06  C01  C02  111.98  3.000
 8KK  H10  C01  N01  107.25  3.000
 8KK  C02  C01  N01  111.15  3.000
 8KK  C06  C01  N01  110.97  3.000
 8KK  H12  C02  H11  106.17  3.000
 8KK  H12  C02  C03  108.95  3.000
 8KK  H11  C02  C03  109.20  3.000
 8KK  H12  C02  C01  108.44  3.000
 8KK  H11  C02  C01  109.70  3.000
 8KK  C03  C02  C01  114.08  3.000
 8KK  H13  C03  C05  107.74  3.000
 8KK  H13  C03  C04  107.93  3.000
 8KK  C05  C03  C04  110.78  3.000
 8KK  H13  C03  C02  108.00  3.000
 8KK  C04  C03  C02  109.87  3.000
 8KK  C05  C03  C02  112.35  3.000
 8KK  H16  C04  H15  107.62  3.000
 8KK  H16  C04  H14  107.56  3.000
 8KK  H15  C04  H14  107.58  3.000
 8KK  H16  C04  C03  111.55  3.000
 8KK  H15  C04  C03  111.24  3.000
 8KK  H14  C04  C03  111.09  3.000
 8KK  H19  C05  H18  107.44  3.000
 8KK  H19  C05  H17  107.54  3.000
 8KK  H18  C05  H17  107.91  3.000
 8KK  H19  C05  C03  110.91  3.000
 8KK  H18  C05  C03  111.66  3.000
 8KK  H17  C05  C03  111.20  3.000
 8KK  O02  C06  N02  123.39  3.000
 8KK  O02  C06  C01  123.17  3.000
 8KK  N02  C06  C01  113.44  3.000
 8KK  H20  N02  C07  117.41  3.000
 8KK  H20  N02  C06  116.70  3.000
 8KK  C07  N02  C06  123.71  3.000
 8KK  H22  C07  H21  107.03  3.000
 8KK  H22  C07  C08  109.40  3.000
 8KK  H21  C07  C08  110.26  3.000
 8KK  H22  C07  N02  110.75  3.000
 8KK  H21  C07  N02  108.85  3.000
 8KK  C08  C07  N02  110.49  3.000
 8KK  H24  C08  H23  107.38  3.000
 8KK  H24  C08  C09  109.74  3.000
 8KK  H23  C08  C09  108.95  3.000
 8KK  H24  C08  C07  109.24  3.000
 8KK  H23  C08  C07  109.43  3.000
 8KK  C09  C08  C07  111.99  3.000
 8KK  H26  C09  H25  106.30  3.000
 8KK  H26  C09  N03  108.16  3.000
 8KK  H25  C09  N03  113.45  3.000
 8KK  H26  C09  C08  108.95  3.000
 8KK  H25  C09  C08  109.05  3.000
 8KK  N03  C09  C08  110.75  3.000
 8KK  H28  N03  H27  105.39  3.000
 8KK  H28  N03  C09  109.32  3.000
 8KK  H27  N03  C09  109.20  3.000
 8KK  H30  N04  C11  117.78  3.000
 8KK  H30  N04  C10  116.71  3.000
 8KK  C11  N04  C10  122.35  3.000
 8KK  C12  O04  C11  116.74  3.000
 8KK  H31  C17  C18  119.89  3.000
 8KK  H31  C17  C16  120.09  3.000
 8KK  C18  C17  C16  120.02  3.000
 8KK  H32  C18  C17  119.70  3.000
 8KK  H32  C18  C13  119.72  3.000
 8KK  C17  C18  C13  120.57  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    90.62  30.0  2
 8KK  Var_02    C13  C12  O04  C11   177.77  30.0  2
 8KK  Var_03    O04  C11  N04  C10  -168.18  30.0  2
 8KK  Var_04    C01  N01  P01  C10   102.22  30.0  3
 8KK  Var_05    P01  C10  N04  C11    98.18  30.0  3
 8KK  Var_06    N04  C10  P01  O01    63.86  30.0  1
 8KK  Var_07    C05  C03  C02  C01   -53.53  30.0  3
 8KK  Var_08    C08  C07  N02  C06  -159.85  30.0  1
 8KK  Var_09    C09  C08  C07  N02  -179.23  30.0  3
 8KK  Var_10    N03  C09  C08  C07   179.26  30.0  3
 8KK  Var_11    H17  C05  C03  C02   -56.17  30.0  3
 8KK  Var_12    H14  C04  C03  C02    64.26  30.0  3
 8KK  Var_13    H27  N03  C09  C08    66.20  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

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

