# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:07:04 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  65  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  -0.274    4.7278   4.4060   1.7199
 8KN  C11  C  C     0   0.541    4.7312   0.9617  -1.9321
 8KN  C12  C  CH2   0  -0.581   -1.3453  -1.6929  -0.9610
 8KN  C13  C  C     0   0.761   -3.1660  -0.0691  -0.9458
 8KN  C14  C  CH2   0  -0.237   -5.0786   1.3023  -0.7664
 8KN  C15  C  CR6   0   0.075   -6.4949   1.1639  -0.2969
 8KN  C16  C  CR16  0  -0.282   -7.4051   0.4003  -1.0254
 8KN  C19  C  CR16  0  -0.241   -8.2294   1.6473   1.3120
 8KN  C20  C  CR16  0  -0.301   -6.9175   1.7831   0.8738
 8KN  O01  O  O     0  -0.715   -0.3261  -0.1529   1.1512
 8KN  N01  N  NH1   0  -0.781    1.0756  -2.2279   0.3003
 8KN  C01  C  CH1   0  -0.226    2.2998  -1.5236   0.5995
 8KN  C02  C  CH2   0  -0.425    3.4925  -2.4857   0.5497
 8KN  C03  C  CH1   0  -0.222    3.3379  -3.7310   1.4251
 8KN  C04  C  CH3   0  -0.652    4.6130  -4.5651   1.3495
 8KN  C05  C  CH3   0  -0.667    2.9987  -3.3837   2.8700
 8KN  C06  C  C     0   0.584    2.5315  -0.3732  -0.3797
 8KN  N02  N  NH1   0  -0.640    3.3851   0.5727   0.0484
 8KN  C07  C  CH1   0  -0.172    3.8842   1.5908  -0.8345
 8KN  O03  O  OH1   0  -0.591    4.8490   1.7743  -2.9731
 8KN  O04  O  O     0  -0.482    2.0013  -0.3331  -1.4776
 8KN  O05  O  OH1   0  -0.748   -1.1970  -2.4743   1.6367
 8KN  N04  N  NH1   0  -0.654   -2.7232  -1.3310  -0.7712
 8KN  O06  O  O2    0  -0.479   -4.4424   0.0353  -0.5648
 8KN  C17  C  CR16  0  -0.242   -8.7132   0.2582  -0.5882
 8KN  C18  C  CR16  0  -0.262   -9.1285   0.8829   0.5826
 8KN  O07  O  O     0  -0.512   -2.5128   0.8437  -1.4043
 8KN  C08  C  CH2   0  -0.476    4.7138   2.6129  -0.0512
 8KN  C09  C  CH2   0  -0.428    3.8738   3.4352   0.9183
 8KN  N03  N  NH2   0  -0.800    3.9014   5.2165   2.6024
 8KN  H1   H  HCH2  0   0.217    5.4297   3.8366   2.3355
 8KN  H2   H  HCH2  0   0.192    5.3402   4.9986   1.0249
 8KN  H3   H  HCH2  0   0.295   -0.8820  -1.0545  -1.7125
 8KN  H4   H  HCH2  0   0.299   -1.2838  -2.7187  -1.3302
 8KN  H5   H  HCH2  0   0.248   -5.0447   1.5701  -1.8248
 8KN  H6   H  HCH2  0   0.251   -4.5603   2.0810  -0.2035
 8KN  H7   H  HCR6  0   0.255   -7.0915  -0.0815  -1.9441
 8KN  H8   H  HCR6  0   0.258   -8.5460   2.1370   2.2237
 8KN  H9   H  HCR6  0   0.256   -6.2193   2.3817   1.4468
 8KN  H10  H  HNH1  0   0.402    1.1370  -2.8748  -0.4746
 8KN  H11  H  HCH1  0   0.279    2.2300  -1.1090   1.6084
 8KN  H12  H  HCH2  0   0.242    3.6634  -2.7909  -0.4883
 8KN  H13  H  HCH2  0   0.237    4.3903  -1.9432   0.8595
 8KN  H14  H  HCH1  0   0.223    2.5184  -4.3327   1.0210
 8KN  H15  H  HCH3  0   0.214    5.4623  -4.0228   1.7717
 8KN  H16  H  HCH3  0   0.227    4.5061  -5.4972   1.9069
 8KN  H17  H  HCH3  0   0.225    4.8638  -4.8222   0.3187
 8KN  H18  H  HCH3  0   0.215    3.7354  -2.6985   3.2974
 8KN  H19  H  HCH3  0   0.230    2.0164  -2.9170   2.9561
 8KN  H20  H  HCH3  0   0.231    2.9861  -4.2813   3.4900
 8KN  H21  H  HNH1  0   0.404    3.8469   0.4459   0.9356
 8KN  H22  H  HCH1  0   0.285    3.0446   2.1100  -1.3056
 8KN  H23  H  HOH1  0   0.484    5.4282   1.3803  -3.6426
 8KN  H24  H  HOH1  0   0.483   -1.0685  -3.4218   1.5034
 8KN  H25  H  HNH1  0   0.409   -3.3353  -2.0051  -0.3395
 8KN  H26  H  HCR6  0   0.258   -9.4111  -0.3381  -1.1614
 8KN  H27  H  HCR6  0   0.259  -10.1509   0.7759   0.9209
 8KN  H28  H  HCH2  0   0.244    5.5118   2.0895   0.4869
 8KN  H29  H  HCH2  0   0.261    5.2066   3.2831  -0.7583
 8KN  H30  H  HCH2  0   0.228    3.3299   2.7851   1.6083
 8KN  H31  H  HCH2  0   0.225    3.1200   3.9924   0.3515
 8KN  H32  H  HNH2  0   0.347    4.4950   5.8159   3.1614
 8KN  H33  H  HNH2  0   0.338    3.3353   5.8435   2.0437
 8KN  O02  O  O     0  -0.430    5.2556  -0.1181  -1.8562
 8KN  P01  P  P     0   1.336   -0.4021  -1.5277   0.5924

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  1.387  0.020  1.387
 8KN  C17  C18  aromatic  1.390  0.020  1.390
 8KN  C16  C15  aromatic  1.394  0.020  1.394
 8KN  C18  C19  aromatic  1.387  0.020  1.387
 8KN  C15  C14  single    1.499  0.020  1.499
 8KN  C15  C20  aromatic  1.390  0.020  1.390
 8KN  C14  O06  single    1.432  0.020  1.432
 8KN  C19  C20  aromatic  1.390  0.020  1.390
 8KN  O06  C13  single    1.336  0.020  1.336
 8KN  O07  C13  double    1.212  0.020  1.212
 8KN  C13  N04  single    1.349  0.020  1.349
 8KN  N04  C12  single    1.437  0.020  1.437
 8KN  C12  P01  single    1.825  0.020  1.825
 8KN  O01  P01  double    1.486  0.020  1.486
 8KN  O05  P01  single    1.618  0.020  1.618
 8KN  O02  C11  double    1.203  0.020  1.203
 8KN  P01  N01  single    1.661  0.020  1.661
 8KN  O03  C11  single    1.326  0.020  1.326
 8KN  C11  C07  single    1.522  0.020  1.522
 8KN  N01  C01  single    1.444  0.020  1.444
 8KN  C07  N02  single    1.437  0.020  1.437
 8KN  C07  C08  single    1.532  0.020  1.532
 8KN  N02  C06  single    1.344  0.020  1.344
 8KN  C06  O04  double    1.220  0.020  1.220
 8KN  C06  C01  single    1.528  0.020  1.528
 8KN  C01  C02  single    1.533  0.020  1.533
 8KN  C08  C09  single    1.524  0.020  1.524
 8KN  C09  C10  single    1.521  0.020  1.521
 8KN  C02  C03  single    1.530  0.020  1.530
 8KN  C10  N03  single    1.456  0.020  1.456
 8KN  C04  C03  single    1.526  0.020  1.526
 8KN  C03  C05  single    1.524  0.020  1.524
 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  O03  H23  single    0.850  0.020  0.980
 8KN  O05  H24  single    0.850  0.020  0.980
 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   106.20  3.000
 8KN  H2   C10  N03  113.53  3.000
 8KN  H1   C10  N03  108.24  3.000
 8KN  H2   C10  C09  108.88  3.000
 8KN  H1   C10  C09  108.95  3.000
 8KN  N03  C10  C09  110.86  3.000
 8KN  O03  C11  O02  124.12  3.000
 8KN  O03  C11  C07  111.24  3.000
 8KN  O02  C11  C07  124.61  3.000
 8KN  H4   C12  H3   107.06  3.000
 8KN  H4   C12  N04  109.59  3.000
 8KN  H3   C12  N04  110.56  3.000
 8KN  H4   C12  P01  110.11  3.000
 8KN  H3   C12  P01  108.32  3.000
 8KN  N04  C12  P01  111.12  3.000
 8KN  O07  C13  O06  124.30  3.000
 8KN  O07  C13  N04  125.21  3.000
 8KN  O06  C13  N04  110.48  3.000
 8KN  H6   C14  H5   108.06  3.000
 8KN  H6   C14  O06  110.34  3.000
 8KN  H5   C14  O06  109.85  3.000
 8KN  H6   C14  C15  110.68  3.000
 8KN  H5   C14  C15  110.83  3.000
 8KN  O06  C14  C15  107.10  3.000
 8KN  C20  C15  C16  119.07  3.000
 8KN  C20  C15  C14  120.66  3.000
 8KN  C16  C15  C14  120.27  3.000
 8KN  H7   C16  C17  119.65  3.000
 8KN  H7   C16  C15  119.86  3.000
 8KN  C17  C16  C15  120.49  3.000
 8KN  H8   C19  C18  120.17  3.000
 8KN  H8   C19  C20  119.84  3.000
 8KN  C18  C19  C20  119.99  3.000
 8KN  H9   C20  C19  119.70  3.000
 8KN  H9   C20  C15  119.71  3.000
 8KN  C19  C20  C15  120.59  3.000
 8KN  H10  N01  C01  114.80  3.000
 8KN  H10  N01  P01  117.29  3.000
 8KN  C01  N01  P01  120.81  3.000
 8KN  H11  C01  C06  108.39  3.000
 8KN  H11  C01  C02  108.53  3.000
 8KN  C06  C01  C02  109.49  3.000
 8KN  H11  C01  N01  108.80  3.000
 8KN  C02  C01  N01  110.29  3.000
 8KN  C06  C01  N01  111.28  3.000
 8KN  H13  C02  H12  106.17  3.000
 8KN  H13  C02  C03  108.94  3.000
 8KN  H12  C02  C03  109.34  3.000
 8KN  H13  C02  C01  108.55  3.000
 8KN  H12  C02  C01  109.09  3.000
 8KN  C03  C02  C01  114.43  3.000
 8KN  H14  C03  C05  107.99  3.000
 8KN  H14  C03  C04  107.88  3.000
 8KN  C05  C03  C04  110.95  3.000
 8KN  H14  C03  C02  108.18  3.000
 8KN  C05  C03  C02  112.30  3.000
 8KN  C04  C03  C02  109.40  3.000
 8KN  H17  C04  H16  107.68  3.000
 8KN  H17  C04  H15  107.65  3.000
 8KN  H16  C04  H15  107.62  3.000
 8KN  H17  C04  C03  111.57  3.000
 8KN  H16  C04  C03  111.09  3.000
 8KN  H15  C04  C03  111.05  3.000
 8KN  H20  C05  H19  107.25  3.000
 8KN  H20  C05  H18  107.54  3.000
 8KN  H19  C05  H18  107.93  3.000
 8KN  H20  C05  C03  110.72  3.000
 8KN  H19  C05  C03  111.88  3.000
 8KN  H18  C05  C03  111.32  3.000
 8KN  O04  C06  N02  122.65  3.000
 8KN  O04  C06  C01  122.38  3.000
 8KN  N02  C06  C01  114.95  3.000
 8KN  H21  N02  C07  118.08  3.000
 8KN  H21  N02  C06  118.86  3.000
 8KN  C07  N02  C06  121.57  3.000
 8KN  H22  C07  C08  108.61  3.000
 8KN  H22  C07  N02  109.53  3.000
 8KN  C08  C07  N02  110.28  3.000
 8KN  H22  C07  C11  108.22  3.000
 8KN  C08  C07  C11  110.06  3.000
 8KN  N02  C07  C11  110.09  3.000
 8KN  H23  O03  C11  110.27  3.000
 8KN  H24  O05  P01  114.81  3.000
 8KN  H25  N04  C13  118.81  3.000
 8KN  H25  N04  C12  118.06  3.000
 8KN  C13  N04  C12  122.23  3.000
 8KN  C14  O06  C13  116.96  3.000
 8KN  H26  C17  C18  120.06  3.000
 8KN  H26  C17  C16  119.86  3.000
 8KN  C18  C17  C16  120.08  3.000
 8KN  H27  C18  C17  120.07  3.000
 8KN  H27  C18  C19  120.15  3.000
 8KN  C17  C18  C19  119.78  3.000
 8KN  H29  C08  H28  106.42  3.000
 8KN  H29  C08  C09  109.24  3.000
 8KN  H28  C08  C09  110.29  3.000
 8KN  H29  C08  C07  108.84  3.000
 8KN  H28  C08  C07  109.08  3.000
 8KN  C09  C08  C07  112.76  3.000
 8KN  H31  C09  H30  106.66  3.000
 8KN  H31  C09  C08  108.95  3.000
 8KN  H30  C09  C08  110.80  3.000
 8KN  H31  C09  C10  109.53  3.000
 8KN  H30  C09  C10  109.04  3.000
 8KN  C08  C09  C10  111.72  3.000
 8KN  H33  N03  H32  105.42  3.000
 8KN  H33  N03  C10  109.12  3.000
 8KN  H32  N03  C10  109.38  3.000
 8KN  O05  P01  N01  107.69  3.000
 8KN  N01  P01  O01  114.24  3.000
 8KN  O05  P01  O01  108.89  3.000
 8KN  N01  P01  C12  105.78  3.000
 8KN  O05  P01  C12  104.04  3.000
 8KN  O01  P01  C12  115.49  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  CONST_17  H23  O03  C11  C07   180.00   0.0  0
 8KN  Var_01    O06  C14  C15  C16   -70.96  30.0  2
 8KN  Var_02    C15  C14  O06  C13   178.71  30.0  1
 8KN  Var_03    C07  C08  C09  C10   177.90  30.0  1
 8KN  Var_04    O06  C13  N04  C12  -173.03  30.0  1
 8KN  Var_05    C01  N01  P01  C12   128.95  30.0  3
 8KN  Var_06    P01  C12  N04  C13    90.22  30.0  3
 8KN  Var_07    N04  C12  P01  O01   -62.52  30.0  1
 8KN  Var_08    C04  C03  C02  C01  -176.92  30.0  3
 8KN  Var_09    N03  C10  C09  C08   177.84  30.0  3
 8KN  Var_10    H15  C04  C03  C02    64.38  30.0  3
 8KN  Var_11    H18  C05  C03  C02   -55.16  30.0  3
 8KN  Var_12    H32  N03  C10  C09   176.82  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
 8KN  chir_04  P01  O01  O05  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
 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  O03  0.020
 8KN  plan-3  H23  0.020
 8KN  plan-3  O02  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

