# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:06:16 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: (2~{S})-2-azanyl-5-[[~{N}-(2-hydroxy-2-oxoethyl)carbamimidoyl]amino]pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(=N)NCC(O)=O)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
 POK  POK  '(2~{S})-2-azanyl-5-[[~{N}-(2-hydroxy-2-oxoethyl)carbamimidoyl]amino]pentanoic acid'  L-peptide  32  16  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_POK
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
 POK  N    N  NH2   0  -0.779  53.3687  22.0122  -3.8034
 POK  CA   C  CH1   0  -0.193  52.5687  20.9561  -4.3887
 POK  C    C  C     0   0.521  52.9011  19.5816  -3.8246
 POK  O    O  O     0  -0.446  54.0263  19.1971  -3.6182
 POK  CB   C  CH2   0  -0.436  52.7719  20.9446  -5.9072
 POK  CG   C  CH2   0  -0.450  51.9066  19.9461  -6.6650
 POK  CD   C  CH2   0  -0.328  52.0923  20.0893  -8.1746
 POK  NE   N  NH1   0  -0.656  51.3116  19.1605  -8.9644
 POK  CZ   C  C     0   0.608  49.9494  19.2178  -9.1160
 POK  NH1  N  N     0  -0.727  49.2024  18.2427  -9.4914
 POK  NH2  N  NH1   0  -0.646  49.3725  20.4470  -8.9243
 POK  CAA  C  CH2   0  -0.400  47.9445  20.5346  -8.9342
 POK  CMA  C  C     0   0.533  47.2343  19.7068  -7.8817
 POK  OMA  O  OH1   0  -0.584  47.9589  19.5358  -6.7861
 POK  OMB  O  O     0  -0.456  46.1033  19.3052  -8.0038
 POK  H1   H  HNH2  0   0.355  53.2129  22.0604  -2.8044
 POK  H2   H  HNH2  0   0.345  54.3540  21.8140  -3.9297
 POK  H4   H  HCH1  0   0.261  51.5173  21.1722  -4.1828
 POK  O1   O  OH1   0  -0.588  51.8244  18.8416  -3.5930
 POK  H6   H  HCH2  0   0.232  53.8293  20.7582  -6.1234
 POK  H7   H  HCH2  0   0.246  52.5548  21.9566  -6.2589
 POK  H8   H  HCH2  0   0.228  50.8545  20.0929  -6.4023
 POK  H9   H  HCH2  0   0.235  52.1562  18.9187  -6.3865
 POK  H10  H  HCH2  0   0.262  53.1394  19.9176  -8.4291
 POK  H11  H  HCH2  0   0.238  51.8841  21.1144  -8.4929
 POK  H12  H  HNH1  0   0.384  51.6760  18.2209  -8.9739
 POK  H13  H  H     0   0.317  49.7483  17.4015  -9.6355
 POK  H14  H  HNH1  0   0.402  49.8496  21.1249  -8.3563
 POK  H15  H  HCH2  0   0.271  47.5396  20.2482  -9.9040
 POK  H16  H  HCH2  0   0.294  47.6666  21.5787  -8.7704
 POK  H17  H  HOH1  0   0.480  47.4570  19.0236  -6.1350
 POK  H3   H  HOH1  0   0.478  52.0845  17.9670  -3.2644

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
 POK  CAA  CMA  single  1.516  0.020  1.516
 POK  CAA  NH2  single  1.431  0.020  1.431
 POK  OMB  CMA  double  1.206  0.020  1.206
 POK  NH1  CZ   double  1.284  0.020  1.284
 POK  CMA  OMA  single  1.325  0.020  1.325
 POK  NH2  CZ   single  1.371  0.020  1.371
 POK  CZ   NE   single  1.372  0.020  1.372
 POK  NE   CD   single  1.448  0.020  1.448
 POK  CD   CG   single  1.528  0.020  1.528
 POK  CG   CB   single  1.523  0.020  1.523
 POK  CB   CA   single  1.530  0.020  1.530
 POK  O    C    double  1.231  0.020  1.231
 POK  CA   C    single  1.525  0.021  1.525
 POK  CA   N    single  1.458  0.019  1.458
 POK  N    H1   single  0.890  0.020  1.040
 POK  N    H2   single  0.890  0.020  1.040
 POK  CA   H4   single  0.970  0.020  1.090
 POK  C    O1   single  1.327  0.020  1.327
 POK  CB   H6   single  0.970  0.020  1.090
 POK  CB   H7   single  0.970  0.020  1.090
 POK  CG   H8   single  0.970  0.020  1.090
 POK  CG   H9   single  0.970  0.020  1.090
 POK  CD   H10  single  0.970  0.020  1.090
 POK  CD   H11  single  0.970  0.020  1.090
 POK  NE   H12  single  0.890  0.020  1.040
 POK  NH1  H13  single  0.890  0.020  1.040
 POK  NH2  H14  single  0.890  0.020  1.040
 POK  CAA  H15  single  0.970  0.020  1.090
 POK  CAA  H16  single  0.970  0.020  1.090
 POK  OMA  H17  single  0.850  0.020  0.980
 POK  O1   H3   single  0.850  0.020  0.980

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
 POK  H2   N    H1   106.38  3.000
 POK  H2   N    CA   110.14  3.000
 POK  H1   N    CA   110.39  3.000
 POK  H4   CA   CB   108.41  3.000
 POK  H4   CA   C    108.59  3.000
 POK  CB   CA   C    110.10  1.900
 POK  H4   CA   N    108.12  3.000
 POK  C    CA   N    111.00  2.800
 POK  CB   CA   N    110.50  1.700
 POK  O1   C    O    123.30  3.000
 POK  O1   C    CA   113.02  3.000
 POK  O    C    CA   120.80  1.700
 POK  H7   CB   H6   106.60  3.000
 POK  H7   CB   CG   109.51  3.000
 POK  H6   CB   CG   109.80  3.000
 POK  H7   CB   CA   106.60  3.000
 POK  H6   CB   CA   108.97  3.000
 POK  CG   CB   CA   115.00  3.000
 POK  H9   CG   H8   106.52  3.000
 POK  H9   CG   CD   108.18  3.000
 POK  H8   CG   CD   109.97  3.000
 POK  H9   CG   CB   111.07  3.000
 POK  H8   CG   CB   109.81  3.000
 POK  CD   CG   CB   111.17  3.000
 POK  H11  CD   H10  105.21  3.000
 POK  H11  CD   NE   109.87  3.000
 POK  H10  CD   NE   106.81  3.000
 POK  H11  CD   CG   110.63  3.000
 POK  H10  CD   CG   109.42  3.000
 POK  NE   CD   CG   114.42  3.000
 POK  H12  NE   CZ   113.38  3.000
 POK  H12  NE   CD   114.10  3.000
 POK  CZ   NE   CD   124.68  3.000
 POK  NH2  CZ   NH1  118.47  3.000
 POK  NH2  CZ   NE   116.08  3.000
 POK  NH1  CZ   NE   125.32  3.000
 POK  H13  NH1  CZ   111.00  3.000
 POK  H14  NH2  CAA  115.88  3.000
 POK  H14  NH2  CZ   118.94  3.000
 POK  CAA  NH2  CZ   118.28  3.000
 POK  H16  CAA  H15  106.86  3.000
 POK  H16  CAA  CMA  107.37  3.000
 POK  H15  CAA  CMA  107.48  3.000
 POK  H16  CAA  NH2  108.14  3.000
 POK  H15  CAA  NH2  111.17  3.000
 POK  CMA  CAA  NH2  115.43  3.000
 POK  OMB  CMA  OMA  123.61  3.000
 POK  OMA  CMA  CAA  112.86  3.000
 POK  OMB  CMA  CAA  123.42  3.000
 POK  H17  OMA  CMA  109.92  3.000
 POK  H3   O1   C    110.15  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
 POK  CONST_03  CAA  NH2  CZ   NE    180.00   0.0  0
 POK  CONST_04  CAA  NH2  CZ   NH1     0.00   0.0  0
 POK  CONST_05  H3   O1   C    CA    180.00   0.0  0
 POK  CONST_06  H13  NH1  CZ   NE      0.00   0.0  0
 POK  CONST_08  H12  NE   CZ   NH1     0.00   0.0  0
 POK  CONST_09  H17  OMA  CMA  CAA   180.00   0.0  0
 POK  Var_01    CD   CG   CB   CA    175.21  30.0  1
 POK  Var_02    NE   CD   CG   CB    179.32  30.0  2
 POK  Var_03    CZ   NE   CD   CG     71.07  30.0  1
 POK  Var_04    CMA  CAA  NH2  CZ     59.90  30.0  1
 POK  Var_05    OMB  CMA  CAA  NH2  -154.36  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
 POK  chir_01  CA  CB  C  N  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
 POK  plan-1  CD   0.020
 POK  plan-1  NE   0.020
 POK  plan-1  CZ   0.020
 POK  plan-1  NH1  0.020
 POK  plan-1  NH2  0.020
 POK  plan-1  CAA  0.020
 POK  plan-1  H12  0.020
 POK  plan-1  H13  0.020
 POK  plan-1  H14  0.020
 POK  plan-2  CA   0.020
 POK  plan-2  C    0.020
 POK  plan-2  O    0.020
 POK  plan-2  O1   0.020
 POK  plan-2  H3   0.020
 POK  plan-3  CAA  0.020
 POK  plan-3  CMA  0.020
 POK  plan-3  OMA  0.020
 POK  plan-3  OMB  0.020
 POK  plan-3  H17  0.020

