# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 21:26:17 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: (2~{S})-5-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]pentanoic 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)N[C@@H](CCCN)C(O)=O
#
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
 8KN  8KN  '(2~{S})-5-azanyl-2-[[(2~{S})-4-methyl-2-[[oxidanyl(phenylmethoxycarbonylaminomethyl)phosphoryl]amino]pentanoyl]amino]pentanoic acid'  ligand  63  32  .  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_8KN
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
 8KN  C10  C  CH2    0  -0.253   0.2068   3.3724   0.2491
 8KN  C11  C  C      0   0.419   5.0093   2.0098   0.7363
 8KN  C12  C  CH2    0  -0.548  -0.6997  -1.4871  -0.6507
 8KN  C13  C  C      0   0.764  -2.5825  -0.0187  -1.1842
 8KN  C14  C  CH2    0  -0.238  -4.4936   1.3926  -1.3358
 8KN  C15  C  CR6    0   0.078  -5.3119   2.0805  -0.2830
 8KN  C16  C  CR16   0  -0.306  -6.6952   2.1532  -0.3895
 8KN  C19  C  CR16   0  -0.244  -5.4316   3.3092   1.7896
 8KN  C20  C  CR16   0  -0.297  -4.6834   2.6644   0.8169
 8KN  O01  O  O      0  -0.793   0.2446  -0.9320   1.8485
 8KN  N01  N  NH1    0  -0.808   1.4736  -2.7773   0.4613
 8KN  C01  C  CH1    0  -0.158   2.7204  -2.1096   0.7449
 8KN  C02  C  CH2    0  -0.424   3.9100  -2.9674   0.3011
 8KN  C03  C  CH1    0  -0.248   4.1187  -4.2672   1.0823
 8KN  C04  C  CH3    0  -0.648   5.2842  -5.0387   0.4702
 8KN  C05  C  CH3    0  -0.660   4.3620  -4.0102   2.5658
 8KN  C06  C  C      0   0.563   2.8026  -0.7848  -0.0136
 8KN  N02  N  NH1    0  -0.610   3.3281   0.2208   0.6911
 8KN  C07  C  CH1    0  -0.216   3.6528   1.5267   0.1702
 8KN  O04  O  O      0  -0.517   2.4685  -0.6972  -1.1895
 8KN  O05  O  OP    -1  -0.810  -0.9297  -3.2307   1.3920
 8KN  N04  N  NH1    0  -0.658  -2.0406  -0.9905  -0.4415
 8KN  O06  O  O2     0  -0.488  -3.7942   0.3185  -0.7118
 8KN  C17  C  CR16   0  -0.242  -7.4465   2.8054   0.5820
 8KN  C18  C  CR16   0  -0.264  -6.8161   3.3820   1.6745
 8KN  O07  O  O      0  -0.533  -2.0656   0.4967  -2.1581
 8KN  C08  C  CH2    0  -0.407   2.5755   2.5690   0.4988
 8KN  C09  C  CH2    0  -0.458   1.1680   2.2115   0.0379
 8KN  N03  N  NH2    0  -0.798  -1.1640   2.9981  -0.0741
 8KN  H1   H  HCH2   0   0.199   0.2436   3.6838   1.2984
 8KN  H2   H  HCH2   0   0.180   0.5685   4.2324  -0.3336
 8KN  H3   H  HCH2   0   0.262  -0.0669  -0.6828  -1.0207
 8KN  H4   H  HCH2   0   0.223  -0.6821  -2.2900  -1.3958
 8KN  H5   H  HCH2   0   0.246  -5.1324   1.0015  -2.1318
 8KN  H6   H  HCH2   0   0.247  -3.7929   2.0939  -1.7917
 8KN  H7   H  HCR6   0   0.254  -7.1929   1.6963  -1.2367
 8KN  H8   H  HCR6   0   0.256  -4.9352   3.7594   2.6396
 8KN  H9   H  HCR6   0   0.259  -3.6027   2.6186   0.9071
 8KN  H10  H  HNH1   0   0.367   1.5222  -3.7838   0.5073
 8KN  H11  H  HCH1   0   0.222   2.8357  -1.8933   1.8155
 8KN  H12  H  HCH2   0   0.231   3.7969  -3.1929  -0.7638
 8KN  H13  H  HCH2   0   0.225   4.8210  -2.3661   0.3978
 8KN  H14  H  HCH1   0   0.216   3.2255  -4.8965   0.9887
 8KN  H15  H  HCH3   0   0.214   6.2048  -4.4510   0.5127
 8KN  H16  H  HCH3   0   0.226   5.4647  -5.9746   1.0013
 8KN  H17  H  HCH3   0   0.225   5.0951  -5.2822  -0.5767
 8KN  H18  H  HCH3   0   0.215   5.1966  -3.3189   2.7090
 8KN  H19  H  HCH3   0   0.230   3.4897  -3.5827   3.0614
 8KN  H20  H  HCH3   0   0.229   4.6063  -4.9375   3.0866
 8KN  H21  H  HNH1   0   0.373   3.6445   0.0406   1.6312
 8KN  H22  H  HCH1   0   0.229   3.7329   1.4448  -0.9161
 8KN  H25  H  HNH1   0   0.388  -2.5915  -1.3951   0.2997
 8KN  H26  H  HCR6   0   0.256  -8.5234   2.8562   0.4856
 8KN  H27  H  HCR6   0   0.256  -7.3978   3.8869   2.4349
 8KN  H28  H  HCH2   0   0.206   2.5647   2.7409   1.5815
 8KN  H29  H  HCH2   0   0.214   2.8840   3.5130   0.0417
 8KN  H30  H  HCH2   0   0.248   0.8023   1.3280   0.5681
 8KN  H31  H  HCH2   0   0.203   1.1835   1.9499  -1.0252
 8KN  H32  H  HNH2   0   0.340  -1.7357   3.8293  -0.1521
 8KN  H33  H  HNH2   0   0.341  -1.1885   2.5572  -0.9848
 8KN  O02  O  O      0  -0.600   5.4613   1.4100   1.7309
 8KN  O03  O  OC    -1  -0.611   5.5127   2.9923   0.1600
 8KN  P01  P  P      0   1.233  -0.0166  -2.1114   0.9456

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
 8KN  C17  C16  aromatic  1.391  0.020  1.391
 8KN  C17  C18  aromatic  1.387  0.020  1.387
 8KN  C16  C15  aromatic  1.389  0.020  1.389
 8KN  C18  C19  aromatic  1.391  0.020  1.391
 8KN  C15  C14  single    1.500  0.020  1.500
 8KN  C15  C20  aromatic  1.395  0.020  1.395
 8KN  C14  O06  single    1.426  0.020  1.426
 8KN  C19  C20  aromatic  1.386  0.020  1.386
 8KN  O06  C13  single    1.344  0.020  1.344
 8KN  O07  C13  double    1.217  0.020  1.217
 8KN  C13  N04  single    1.338  0.020  1.338
 8KN  N04  C12  single    1.445  0.020  1.445
 8KN  C12  P01  single    1.845  0.020  1.845
 8KN  O01  P01  deloc     1.508  0.020  1.508
 8KN  O05  P01  deloc     1.512  0.020  1.512
 8KN  O02  C11  deloc     1.246  0.020  1.246
 8KN  P01  N01  single    1.703  0.020  1.703
 8KN  O03  C11  deloc     1.245  0.020  1.245
 8KN  C11  C07  single    1.547  0.020  1.547
 8KN  N01  C01  single    1.443  0.020  1.443
 8KN  C07  N02  single    1.443  0.020  1.443
 8KN  C07  C08  single    1.535  0.020  1.535
 8KN  N02  C06  single    1.336  0.020  1.336
 8KN  C06  O04  double    1.226  0.020  1.226
 8KN  C06  C01  single    1.529  0.020  1.529
 8KN  C01  C02  single    1.532  0.020  1.532
 8KN  C08  C09  single    1.524  0.020  1.524
 8KN  C09  C10  single    1.522  0.020  1.522
 8KN  C02  C03  single    1.531  0.020  1.531
 8KN  C10  N03  single    1.457  0.020  1.457
 8KN  C04  C03  single    1.526  0.020  1.526
 8KN  C03  C05  single    1.525  0.020  1.525
 8KN  C10  H1   single    0.970  0.020  1.090
 8KN  C10  H2   single    0.970  0.020  1.090
 8KN  C12  H3   single    0.970  0.020  1.090
 8KN  C12  H4   single    0.970  0.020  1.090
 8KN  C14  H5   single    0.970  0.020  1.090
 8KN  C14  H6   single    0.970  0.020  1.090
 8KN  C16  H7   single    0.930  0.020  1.080
 8KN  C19  H8   single    0.930  0.020  1.080
 8KN  C20  H9   single    0.930  0.020  1.080
 8KN  N01  H10  single    0.890  0.020  1.040
 8KN  C01  H11  single    0.970  0.020  1.090
 8KN  C02  H12  single    0.970  0.020  1.090
 8KN  C02  H13  single    0.970  0.020  1.090
 8KN  C03  H14  single    0.970  0.020  1.090
 8KN  C04  H15  single    0.970  0.020  1.090
 8KN  C04  H16  single    0.970  0.020  1.090
 8KN  C04  H17  single    0.970  0.020  1.090
 8KN  C05  H18  single    0.970  0.020  1.090
 8KN  C05  H19  single    0.970  0.020  1.090
 8KN  C05  H20  single    0.970  0.020  1.090
 8KN  N02  H21  single    0.860  0.020  1.020
 8KN  C07  H22  single    0.970  0.020  1.090
 8KN  N04  H25  single    0.860  0.020  1.020
 8KN  C17  H26  single    0.930  0.020  1.080
 8KN  C18  H27  single    0.930  0.020  1.080
 8KN  C08  H28  single    0.970  0.020  1.090
 8KN  C08  H29  single    0.970  0.020  1.090
 8KN  C09  H30  single    0.970  0.020  1.090
 8KN  C09  H31  single    0.970  0.020  1.090
 8KN  N03  H32  single    0.890  0.020  1.040
 8KN  N03  H33  single    0.890  0.020  1.040

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
 8KN  H2   C10  H1   105.92  3.000
 8KN  H2   C10  N03  113.12  3.000
 8KN  H1   C10  N03  108.49  3.000
 8KN  H2   C10  C09  108.37  3.000
 8KN  H1   C10  C09  109.19  3.000
 8KN  N03  C10  C09  111.55  3.000
 8KN  O03  C11  O02  127.05  3.000
 8KN  O03  C11  C07  115.55  3.000
 8KN  O02  C11  C07  117.37  3.000
 8KN  H4   C12  H3   107.52  3.000
 8KN  H4   C12  N04  111.43  3.000
 8KN  H3   C12  N04  109.56  3.000
 8KN  H4   C12  P01  109.54  3.000
 8KN  H3   C12  P01  109.20  3.000
 8KN  N04  C12  P01  109.54  3.000
 8KN  O07  C13  O06  123.93  3.000
 8KN  O07  C13  N04  125.44  3.000
 8KN  O06  C13  N04  110.64  3.000
 8KN  H6   C14  H5   107.52  3.000
 8KN  H6   C14  O06  110.62  3.000
 8KN  H5   C14  O06  109.63  3.000
 8KN  H6   C14  C15  110.41  3.000
 8KN  H5   C14  C15  110.87  3.000
 8KN  O06  C14  C15  107.81  3.000
 8KN  C20  C15  C16  119.16  3.000
 8KN  C20  C15  C14  119.96  3.000
 8KN  C16  C15  C14  120.88  3.000
 8KN  H7   C16  C17  119.72  3.000
 8KN  H7   C16  C15  119.69  3.000
 8KN  C17  C16  C15  120.59  3.000
 8KN  H8   C19  C18  119.97  3.000
 8KN  H8   C19  C20  119.80  3.000
 8KN  C18  C19  C20  120.23  3.000
 8KN  H9   C20  C19  119.91  3.000
 8KN  H9   C20  C15  119.77  3.000
 8KN  C19  C20  C15  120.32  3.000
 8KN  H10  N01  C01  114.28  3.000
 8KN  H10  N01  P01  114.81  3.000
 8KN  C01  N01  P01  121.30  3.000
 8KN  H11  C01  C06  107.90  3.000
 8KN  H11  C01  C02  108.12  3.000
 8KN  C06  C01  C02  107.44  3.000
 8KN  H11  C01  N01  111.93  3.000
 8KN  C02  C01  N01  110.79  3.000
 8KN  C06  C01  N01  110.49  3.000
 8KN  H13  C02  H12  106.55  3.000
 8KN  H13  C02  C03  107.90  3.000
 8KN  H12  C02  C03  109.61  3.000
 8KN  H13  C02  C01  108.22  3.000
 8KN  H12  C02  C01  108.48  3.000
 8KN  C03  C02  C01  115.69  3.000
 8KN  H14  C03  C05  108.04  3.000
 8KN  H14  C03  C04  107.33  3.000
 8KN  C05  C03  C04  110.70  3.000
 8KN  H14  C03  C02  109.43  3.000
 8KN  C05  C03  C02  112.03  3.000
 8KN  C04  C03  C02  109.20  3.000
 8KN  H17  C04  H16  107.71  3.000
 8KN  H17  C04  H15  107.64  3.000
 8KN  H16  C04  H15  107.64  3.000
 8KN  H17  C04  C03  111.43  3.000
 8KN  H16  C04  C03  111.40  3.000
 8KN  H15  C04  C03  110.85  3.000
 8KN  H20  C05  H19  107.18  3.000
 8KN  H20  C05  H18  107.70  3.000
 8KN  H19  C05  H18  107.66  3.000
 8KN  H20  C05  C03  110.90  3.000
 8KN  H19  C05  C03  112.36  3.000
 8KN  H18  C05  C03  110.84  3.000
 8KN  O04  C06  N02  124.03  3.000
 8KN  O04  C06  C01  121.55  3.000
 8KN  N02  C06  C01  114.32  3.000
 8KN  H21  N02  C07  115.33  3.000
 8KN  H21  N02  C06  118.74  3.000
 8KN  C07  N02  C06  125.42  3.000
 8KN  H22  C07  C08  108.38  3.000
 8KN  H22  C07  N02  107.92  3.000
 8KN  C08  C07  N02  112.29  3.000
 8KN  H22  C07  C11  108.84  3.000
 8KN  C08  C07  C11  108.97  3.000
 8KN  N02  C07  C11  110.35  3.000
 8KN  H25  N04  C13  118.58  3.000
 8KN  H25  N04  C12  118.39  3.000
 8KN  C13  N04  C12  123.03  3.000
 8KN  C14  O06  C13  118.53  3.000
 8KN  H26  C17  C18  120.19  3.000
 8KN  H26  C17  C16  119.83  3.000
 8KN  C18  C17  C16  119.98  3.000
 8KN  H27  C18  C17  120.20  3.000
 8KN  H27  C18  C19  120.07  3.000
 8KN  C17  C18  C19  119.72  3.000
 8KN  H29  C08  H28  106.27  3.000
 8KN  H29  C08  C09  109.68  3.000
 8KN  H28  C08  C09  109.05  3.000
 8KN  H29  C08  C07  107.39  3.000
 8KN  H28  C08  C07  108.96  3.000
 8KN  C09  C08  C07  115.11  3.000
 8KN  H31  C09  H30  106.41  3.000
 8KN  H31  C09  C08  109.67  3.000
 8KN  H30  C09  C08  110.60  3.000
 8KN  H31  C09  C10  109.02  3.000
 8KN  H30  C09  C10  109.74  3.000
 8KN  C08  C09  C10  111.25  3.000
 8KN  H33  N03  H32  105.95  3.000
 8KN  H33  N03  C10  109.53  3.000
 8KN  H32  N03  C10  109.73  3.000
 8KN  O05  P01  N01  108.85  3.000
 8KN  N01  P01  O01  108.94  3.000
 8KN  O05  P01  O01  120.45  3.000
 8KN  N01  P01  C12  102.14  3.000
 8KN  O05  P01  C12  106.40  3.000
 8KN  O01  P01  C12  108.51  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
 8KN  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 8KN  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 8KN  CONST_03  C19  C18  C17  C16     0.00   0.0  0
 8KN  CONST_04  C19  C20  C15  C16     0.00   0.0  0
 8KN  CONST_05  C17  C16  C15  C20     0.00   0.0  0
 8KN  CONST_06  C17  C18  C19  C20     0.00   0.0  0
 8KN  CONST_07  C17  C16  C15  C14   180.00   0.0  0
 8KN  CONST_08  C19  C20  C15  C14   180.00   0.0  0
 8KN  CONST_09  H26  C17  C16  C15   180.00   0.0  0
 8KN  CONST_10  H8   C19  C20  C15   180.00   0.0  0
 8KN  CONST_11  H27  C18  C17  C16   180.00   0.0  0
 8KN  CONST_12  H9   C20  C15  C16   180.00   0.0  0
 8KN  CONST_13  H7   C16  C15  C20   180.00   0.0  0
 8KN  CONST_14  C07  N02  C06  C01   180.00   0.0  0
 8KN  CONST_15  O04  C06  N02  C07     0.00   0.0  0
 8KN  CONST_16  H21  N02  C06  C01     0.00   0.0  0
 8KN  Var_01    O06  C14  C15  C16  -119.67  30.0  2
 8KN  Var_02    C15  C14  O06  C13  -147.77  30.0  1
 8KN  Var_03    C07  C08  C09  C10  -172.86  30.0  1
 8KN  Var_04    O06  C13  N04  C12  -175.24  30.0  1
 8KN  Var_05    C01  N01  P01  C12   105.57  30.0  3
 8KN  Var_06    P01  C12  N04  C13   151.40  30.0  3
 8KN  Var_07    N04  C12  P01  O01   -70.32  30.0  1
 8KN  Var_08    C04  C03  C02  C01   176.76  30.0  3
 8KN  Var_09    N03  C10  C09  C08  -174.75  30.0  3
 8KN  Var_10    H15  C04  C03  C02    60.18  30.0  3
 8KN  Var_11    H18  C05  C03  C02   -54.80  30.0  3
 8KN  Var_12    H32  N03  C10  C09  -165.80  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
 8KN  chir_02  C01  N01  C06  C02  positiv
 8KN  chir_03  C07  N02  C08  C11  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
 8KN  plan-1  C14  0.020
 8KN  plan-1  C15  0.020
 8KN  plan-1  C16  0.020
 8KN  plan-1  C19  0.020
 8KN  plan-1  C20  0.020
 8KN  plan-1  C17  0.020
 8KN  plan-1  C18  0.020
 8KN  plan-1  H7   0.020
 8KN  plan-1  H8   0.020
 8KN  plan-1  H9   0.020
 8KN  plan-1  H26  0.020
 8KN  plan-1  H27  0.020
 8KN  plan-2  C01  0.020
 8KN  plan-2  C06  0.020
 8KN  plan-2  N02  0.020
 8KN  plan-2  C07  0.020
 8KN  plan-2  O04  0.020
 8KN  plan-2  H21  0.020
 8KN  plan-3  C11  0.020
 8KN  plan-3  C07  0.020
 8KN  plan-3  O02  0.020
 8KN  plan-3  O03  0.020
 8KN  plan-4  C13  0.020
 8KN  plan-4  N04  0.020
 8KN  plan-4  O06  0.020
 8KN  plan-4  O07  0.020

