# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 12:22:32 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: N~2~-acetyl-N~5~-(phosphonoacetyl)-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](CCCNC(=O)C[P](O)(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
 PA9  PA9  N~2~-acetyl-N~5~-(phosphonoacetyl)-L-ornithine  ligand  33  19  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PA9
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
 PA9  CA   C  CH1    0  -0.193  -3.2756   0.4326   0.3397
 PA9  CB   C  CH2    0  -0.456  -2.0904   1.0984  -0.3575
 PA9  CG   C  CH2    0  -0.457  -0.7945   0.3051  -0.2547
 PA9  CD   C  CH2    0  -0.232   0.3684   1.0226  -0.9222
 PA9  C    C  C      0   0.412  -4.5232   1.3578   0.3221
 PA9  O    O  O      0  -0.595  -5.5350   0.9584  -0.2771
 PA9  OXT  O  OC    -1  -0.617  -4.3785   2.4417   0.9227
 PA9  C1   C  C      0   0.520  -4.2223  -1.8251   0.3560
 PA9  O1   O  O      0  -0.524  -4.5775  -1.7569   1.5282
 PA9  P    P  P      0   1.176   4.0166  -0.9235   0.6577
 PA9  O1P  O  O      0  -0.886   4.3043   0.3426   1.4622
 PA9  O2P  O  OP    -1  -0.886   5.1417  -1.9561   0.6521
 PA9  O3P  O  OP    -1  -0.879   2.6230  -1.5358   0.9461
 PA9  N1   N  NH1    0  -0.609  -3.5268  -0.8581  -0.2551
 PA9  C2   C  CH3    0  -0.779  -4.5130  -3.0469  -0.4822
 PA9  N2   N  NH1    0  -0.659   1.5684   0.2282  -0.8292
 PA9  C3   C  C      0   0.501   2.7332   0.6025  -1.3794
 PA9  O2   O  O      0  -0.543   2.8514   1.6294  -2.0509
 PA9  C4   C  CH2    0  -0.852   3.8668  -0.3582  -1.1277
 PA9  HA   H  HCH1   0   0.234  -3.0024   0.2708   1.3868
 PA9  HB   H  HCH2   0   0.220  -2.3361   1.2689  -1.4127
 PA9  HBA  H  HCH2   0   0.237  -1.9512   2.0850   0.0875
 PA9  HG   H  HCH2   0   0.221  -0.5584   0.1309   0.8006
 PA9  HGA  H  HCH2   0   0.224  -0.9163  -0.6816  -0.7109
 PA9  HD   H  HCH2   0   0.213   0.1265   1.2113  -1.9728
 PA9  HDA  H  HCH2   0   0.209   0.5077   2.0073  -0.4589
 PA9  HN1  H  HNH1   0   0.387  -3.3712  -0.9473  -1.2465
 PA9  H2   H  HCH3   0   0.261  -4.0471  -3.9204  -0.0257
 PA9  H2A  H  HCH3   0   0.259  -5.5879  -3.2265  -0.5008
 PA9  H2B  H  HCH3   0   0.243  -4.1601  -2.9682  -1.5090
 PA9  HN2  H  HNH1   0   0.400   1.6526  -0.5201  -0.1208
 PA9  H4   H  HCH2   0   0.219   4.7983   0.0974  -1.4699
 PA9  H4A  H  HCH2   0   0.231   3.7043  -1.2460  -1.7487

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
 PA9  C    CA   single  1.553  0.020  1.553
 PA9  CA   N1   single  1.443  0.020  1.443
 PA9  CA   CB   single  1.528  0.020  1.528
 PA9  CA   HA   single  0.970  0.020  1.090
 PA9  CG   CB   single  1.523  0.020  1.523
 PA9  CB   HB   single  0.970  0.020  1.090
 PA9  CB   HBA  single  0.970  0.020  1.090
 PA9  CG   CD   single  1.521  0.020  1.521
 PA9  CG   HG   single  0.970  0.020  1.090
 PA9  CG   HGA  single  0.970  0.020  1.090
 PA9  CD   N2   single  1.442  0.020  1.442
 PA9  CD   HD   single  0.970  0.020  1.090
 PA9  CD   HDA  single  0.970  0.020  1.090
 PA9  O    C    deloc   1.242  0.020  1.242
 PA9  OXT  C    deloc   1.248  0.020  1.248
 PA9  O1   C1   double  1.227  0.020  1.227
 PA9  C1   C2   single  1.510  0.020  1.510
 PA9  C1   N1   single  1.339  0.020  1.339
 PA9  O1P  P    deloc   1.527  0.020  1.527
 PA9  C4   P    single  1.879  0.020  1.879
 PA9  P    O2P  deloc   1.527  0.020  1.527
 PA9  P    O3P  deloc   1.549  0.020  1.549
 PA9  N1   HN1  single  0.860  0.020  1.020
 PA9  C2   H2   single  0.970  0.020  1.090
 PA9  C2   H2A  single  0.970  0.020  1.090
 PA9  C2   H2B  single  0.970  0.020  1.090
 PA9  N2   C3   single  1.342  0.020  1.342
 PA9  N2   HN2  single  0.860  0.020  1.020
 PA9  O2   C3   double  1.233  0.020  1.233
 PA9  C3   C4   single  1.507  0.020  1.507
 PA9  C4   H4   single  0.970  0.020  1.090
 PA9  C4   H4A  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
 PA9  HA   CA  N1   107.80  3.000
 PA9  HA   CA  C    107.43  3.000
 PA9  N1   CA  C    112.84  3.000
 PA9  HA   CA  CB   107.90  3.000
 PA9  N1   CA  CB   109.68  3.000
 PA9  C    CA  CB   111.00  3.000
 PA9  HBA  CB  HB   106.29  3.000
 PA9  HBA  CB  CG   109.57  3.000
 PA9  HB   CB  CG   109.66  3.000
 PA9  HBA  CB  CA   107.87  3.000
 PA9  HB   CB  CA   109.45  3.000
 PA9  CG   CB  CA   113.72  3.000
 PA9  HGA  CG  HG   106.40  3.000
 PA9  HGA  CG  CD   109.13  3.000
 PA9  HG   CG  CD   109.46  3.000
 PA9  HGA  CG  CB   110.31  3.000
 PA9  HG   CG  CB   109.35  3.000
 PA9  CD   CG  CB   112.04  3.000
 PA9  HDA  CD  HD   106.19  3.000
 PA9  HDA  CD  N2   111.20  3.000
 PA9  HD   CD  N2   109.92  3.000
 PA9  HDA  CD  CG   109.58  3.000
 PA9  HD   CD  CG   109.49  3.000
 PA9  N2   CD  CG   110.37  3.000
 PA9  OXT  C   O    127.31  3.000
 PA9  OXT  C   CA   114.76  3.000
 PA9  O    C   CA   117.92  3.000
 PA9  C2   C1  N1   115.54  3.000
 PA9  N1   C1  O1   123.13  3.000
 PA9  C2   C1  O1   121.31  3.000
 PA9  C4   P   O3P  102.95  3.000
 PA9  O3P  P   O2P  113.34  3.000
 PA9  C4   P   O2P  104.99  3.000
 PA9  O3P  P   O1P  113.52  3.000
 PA9  O2P  P   O1P  115.06  3.000
 PA9  C4   P   O1P  105.43  3.000
 PA9  HN1  N1  C1   117.74  3.000
 PA9  HN1  N1  CA   117.25  3.000
 PA9  C1   N1  CA   123.25  3.000
 PA9  H2B  C2  H2A  108.39  3.000
 PA9  H2B  C2  H2   108.32  3.000
 PA9  H2A  C2  H2   107.25  3.000
 PA9  H2B  C2  C1   113.75  3.000
 PA9  H2A  C2  C1   109.43  3.000
 PA9  H2   C2  C1   109.49  3.000
 PA9  HN2  N2  C3   114.35  3.000
 PA9  HN2  N2  CD   120.71  3.000
 PA9  C3   N2  CD   122.84  3.000
 PA9  C4   C3  O2   123.36  3.000
 PA9  C4   C3  N2   114.00  3.000
 PA9  O2   C3  N2   122.63  3.000
 PA9  H4A  C4  H4   106.68  3.000
 PA9  H4A  C4  C3   108.07  3.000
 PA9  H4   C4  C3   108.86  3.000
 PA9  H4A  C4  P    107.86  3.000
 PA9  H4   C4  P    110.82  3.000
 PA9  C3   C4  P    114.24  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
 PA9  CONST_01  O1   C1  N1  CA      0.00   0.0  0
 PA9  CONST_02  C2   C1  N1  CA    180.00   0.0  0
 PA9  CONST_03  O2   C3  N2  CD      0.00   0.0  0
 PA9  CONST_04  C4   C3  N2  CD    180.00   0.0  0
 PA9  CONST_05  HN1  N1  C1  O1    180.00   0.0  0
 PA9  CONST_06  HN2  N2  C3  O2    180.00   0.0  0
 PA9  Var_01    CD   CG  CB  CA   -178.17  30.0  1
 PA9  Var_02    N2   CD  CG  CB   -178.76  30.0  3
 PA9  Var_03    C3   N2  CD  CG    177.48  30.0  3
 PA9  Var_04    N2   C3  C4  P     -46.68  30.0  1
 PA9  Var_05    C3   C4  P   O1P   -62.35  30.0  3
 PA9  Var_06    H2   C2  C1  O1    -59.79  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
 PA9  chir_01  CA  C  N1  CB  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
 PA9  plan-1  CA   0.020
 PA9  plan-1  C1   0.020
 PA9  plan-1  O1   0.020
 PA9  plan-1  N1   0.020
 PA9  plan-1  C2   0.020
 PA9  plan-1  HN1  0.020
 PA9  plan-2  CD   0.020
 PA9  plan-2  N2   0.020
 PA9  plan-2  C3   0.020
 PA9  plan-2  O2   0.020
 PA9  plan-2  C4   0.020
 PA9  plan-2  HN2  0.020
 PA9  plan-3  CA   0.020
 PA9  plan-3  C    0.020
 PA9  plan-3  O    0.020
 PA9  plan-3  OXT  0.020

