# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:14:06 2022
#   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  30  16  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

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  -0.793  53.3083  22.1164  -3.7762
 POK  CA   C  CH1    0  -0.188  52.4870  21.0462  -4.3402
 POK  C    C  C      0   0.384  52.7366  19.6576  -3.7045
 POK  O    O  O      0  -0.612  53.9337  19.3470  -3.5213
 POK  CB   C  CH2    0  -0.418  52.7451  20.9871  -5.8471
 POK  CG   C  CH2    0  -0.442  51.8868  19.9856  -6.6081
 POK  CD   C  CH2    0  -0.323  52.1312  20.0743  -8.1131
 POK  NE   N  NH1    0  -0.658  51.4016  19.1108  -8.9115
 POK  CZ   C  C      0   0.590  50.0405  19.1305  -9.1276
 POK  NH1  N  N      0  -0.741  49.3672  18.1233  -9.5636
 POK  NH2  N  NH1    0  -0.635  49.4339  20.3452  -8.9599
 POK  CAA  C  CH2    0  -0.430  47.9967  20.4347  -8.9171
 POK  CMA  C  C      0   0.394  47.3125  19.9021  -7.6363
 POK  OMA  O  OC    -1  -0.598  48.0316  19.6323  -6.6570
 POK  OMB  O  O      0  -0.619  46.0690  19.8273  -7.7059
 POK  H1   H  HNH2   0   0.332  53.0686  22.2305  -2.7977
 POK  H2   H  HNH2   0   0.321  54.2674  21.7856  -3.7669
 POK  H4   H  HCH1   0   0.194  51.4374  21.3191  -4.1878
 POK  O1   O  OC    -1  -0.612  51.7358  18.9565  -3.4506
 POK  H6   H  HCH2   0   0.203  53.8042  20.7586  -6.0138
 POK  H7   H  HCH2   0   0.211  52.5809  21.9890  -6.2579
 POK  H8   H  HCH2   0   0.213  50.8288  20.1583  -6.3917
 POK  H9   H  HCH2   0   0.222  52.1045  18.9653  -6.2823
 POK  H10  H  HCH2   0   0.248  53.1918  19.9111  -8.3149
 POK  H11  H  HCH2   0   0.229  51.9247  21.0852  -8.4763
 POK  H12  H  HNH1   0   0.376  51.7874  18.1803  -8.8824
 POK  H13  H  H      0   0.304  49.9752  17.3240  -9.7013
 POK  H14  H  HNH1   0   0.384  49.8962  20.9904  -8.3423
 POK  H15  H  HCH2   0   0.228  47.5784  19.9265  -9.7854
 POK  H16  H  HCH2   0   0.235  47.7314  21.4906  -9.0269

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  1.547  0.020  1.547
 POK  CAA  NH2  single  1.441  0.020  1.441
 POK  OMB  CMA  deloc   1.248  0.020  1.248
 POK  NH1  CZ   double  1.287  0.020  1.287
 POK  CMA  OMA  deloc   1.245  0.020  1.245
 POK  NH2  CZ   single  1.368  0.020  1.368
 POK  CZ   NE   single  1.378  0.020  1.378
 POK  NE   CD   single  1.448  0.020  1.448
 POK  CD   CG   single  1.527  0.020  1.527
 POK  CG   CB   single  1.523  0.020  1.523
 POK  CB   CA   single  1.530  0.020  1.530
 POK  O    C    deloc   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   deloc   1.248  0.020  1.248
 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

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   104.56  3.000
 POK  H2   N    CA   107.21  3.000
 POK  H1   N    CA   108.78  3.000
 POK  H4   CA   CB   107.96  3.000
 POK  H4   CA   C    108.73  3.000
 POK  CB   CA   C    110.10  1.900
 POK  H4   CA   N    107.59  3.000
 POK  C    CA   N    111.00  2.800
 POK  CB   CA   N    110.50  1.700
 POK  O1   C    O    126.76  3.000
 POK  O1   C    CA   117.27  3.000
 POK  O    C    CA   120.80  1.700
 POK  H7   CB   H6   106.17  3.000
 POK  H7   CB   CG   109.25  3.000
 POK  H6   CB   CG   109.36  3.000
 POK  H7   CB   CA   107.99  3.000
 POK  H6   CB   CA   108.71  3.000
 POK  CG   CB   CA   115.00  3.000
 POK  H9   CG   H8   106.33  3.000
 POK  H9   CG   CD   108.42  3.000
 POK  H8   CG   CD   109.91  3.000
 POK  H9   CG   CB   110.65  3.000
 POK  H8   CG   CB   110.03  3.000
 POK  CD   CG   CB   111.35  3.000
 POK  H11  CD   H10  105.07  3.000
 POK  H11  CD   NE   109.68  3.000
 POK  H10  CD   NE   106.74  3.000
 POK  H11  CD   CG   110.52  3.000
 POK  H10  CD   CG   109.20  3.000
 POK  NE   CD   CG   115.08  3.000
 POK  H12  NE   CZ   113.31  3.000
 POK  H12  NE   CD   113.93  3.000
 POK  CZ   NE   CD   125.05  3.000
 POK  NH2  CZ   NH1  120.28  3.000
 POK  NH2  CZ   NE   115.55  3.000
 POK  NH1  CZ   NE   123.94  3.000
 POK  H13  NH1  CZ   110.44  3.000
 POK  H14  NH2  CAA  113.61  3.000
 POK  H14  NH2  CZ   116.17  3.000
 POK  CAA  NH2  CZ   120.07  3.000
 POK  H16  CAA  H15  106.08  3.000
 POK  H16  CAA  CMA  107.94  3.000
 POK  H15  CAA  CMA  109.24  3.000
 POK  H16  CAA  NH2  107.38  3.000
 POK  H15  CAA  NH2  109.29  3.000
 POK  CMA  CAA  NH2  116.39  3.000
 POK  OMB  CMA  OMA  127.35  3.000
 POK  OMA  CMA  CAA  118.08  3.000
 POK  OMB  CMA  CAA  114.54  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
 POK  CONST_03  CAA  NH2  CZ   NE    180.00   0.0  0
 POK  CONST_05  H13  NH1  CZ   NE      0.00   0.0  0
 POK  Var_01    CD   CG   CB   CA    175.43  30.0  1
 POK  Var_02    NE   CD   CG   CB    177.17  30.0  1
 POK  Var_03    CZ   NE   CD   CG     70.61  30.0  1
 POK  Var_04    CMA  CAA  NH2  CZ     72.68  30.0  1
 POK  Var_05    OMB  CMA  CAA  NH2  -170.76  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-3  CAA  0.020
 POK  plan-3  CMA  0.020
 POK  plan-3  OMA  0.020
 POK  plan-3  OMB  0.020

