# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 03:49:49 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  36  19  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.175  -3.1225   0.4070   0.2780
 PA9  CB    C  CH2   0  -0.477  -2.0766   1.0585  -0.6325
 PA9  CG    C  CH2   0  -0.429  -0.7352   0.3364  -0.5945
 PA9  CD    C  CH2   0  -0.286   0.2707   1.0024  -1.5272
 PA9  C     C  C     0   0.544  -4.3703   1.2763   0.3431
 PA9  O     O  O     0  -0.433  -5.3805   1.0715  -0.2771
 PA9  OXT   O  OH1   0  -0.591  -4.1897   2.3161   1.1452
 PA9  C1    C  C     0   0.534  -4.1935  -1.7578   0.5401
 PA9  O1    O  O     0  -0.503  -4.5686  -1.4738   1.6693
 PA9  P     P  P     0   1.371   4.3369  -0.6353   0.9093
 PA9  O1P   O  O     0  -0.704   4.8186   0.3785   1.8721
 PA9  O2P   O  OH1   0  -0.744   5.4075  -1.7560   0.4858
 PA9  O3P   O  OH1   0  -0.748   3.0667  -1.4054   1.5251
 PA9  N1    N  NH1   0  -0.629  -3.4512  -0.9089  -0.1948
 PA9  C2    C  CH3   0  -0.777  -4.5112  -3.0804  -0.1051
 PA9  N2    N  NH1   0  -0.626   1.5725   0.3732  -1.4894
 PA9  C3    C  C     0   0.547   2.5316   0.7329  -0.6277
 PA9  O2    O  O     0  -0.485   2.4092   1.6388   0.1830
 PA9  C4    C  CH2   0  -0.871   3.8177  -0.0611  -0.7266
 PA9  HA    H  HCH1  0   0.286  -2.7064   0.3387   1.2875
 PA9  HB    H  HCH2  0   0.249  -2.4614   1.0977  -1.6568
 PA9  HBA   H  HCH2  0   0.265  -1.9336   2.0934  -0.3152
 PA9  HG    H  HCH2  0   0.238  -0.3471   0.3459   0.4275
 PA9  HGA   H  HCH2  0   0.236  -0.8505  -0.7115  -0.8820
 PA9  HD    H  HCH2  0   0.255  -0.0871   0.9602  -2.5566
 PA9  HDA   H  HCH2  0   0.246   0.3839   2.0561  -1.2708
 PA9  HOXT  H  HOH1  0   0.485  -4.9764   2.8821   1.1437
 PA9  HO2P  H  HOH1  0   0.495   5.9782  -2.0419   1.2128
 PA9  HO3P  H  HOH1  0   0.491   2.7270  -2.1450   1.0047
 PA9  HN1   H  HNH1  0   0.406  -3.2482  -1.1370  -1.1547
 PA9  H2    H  HCH3  0   0.269  -4.0662  -3.8838   0.4824
 PA9  H2A   H  HCH3  0   0.267  -5.5898  -3.2348  -0.1016
 PA9  H2B   H  HCH3  0   0.251  -4.1523  -3.1655  -1.1289
 PA9  HN2   H  HNH1  0   0.407   1.7329  -0.4058  -2.1065
 PA9  H4    H  HCH2  0   0.328   4.6032   0.5916  -1.1163
 PA9  H4A   H  HCH2  0   0.309   3.7417  -0.9111  -1.4067

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  1.522  0.020  1.522
 PA9  CA   N1    single  1.436  0.020  1.436
 PA9  CA   CB    single  1.532  0.020  1.532
 PA9  CA   HA    single  0.970  0.020  1.090
 PA9  CG   CB    single  1.524  0.020  1.524
 PA9  CB   HB    single  0.970  0.020  1.090
 PA9  CB   HBA   single  0.970  0.020  1.090
 PA9  CG   CD    single  1.525  0.020  1.525
 PA9  CG   HG    single  0.970  0.020  1.090
 PA9  CG   HGA   single  0.970  0.020  1.090
 PA9  CD   N2    single  1.446  0.020  1.446
 PA9  CD   HD    single  0.970  0.020  1.090
 PA9  CD   HDA   single  0.970  0.020  1.090
 PA9  O    C     double  1.203  0.020  1.203
 PA9  OXT  C     single  1.326  0.020  1.326
 PA9  OXT  HOXT  single  0.850  0.020  0.980
 PA9  O1   C1    double  1.223  0.020  1.223
 PA9  C1   C2    single  1.506  0.020  1.506
 PA9  C1   N1    single  1.346  0.020  1.346
 PA9  O1P  P     double  1.479  0.020  1.479
 PA9  C4   P     single  1.810  0.020  1.810
 PA9  P    O2P   single  1.607  0.020  1.607
 PA9  P    O3P   single  1.608  0.020  1.608
 PA9  O2P  HO2P  single  0.850  0.020  0.980
 PA9  O3P  HO3P  single  0.850  0.020  0.980
 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  1.339  0.020  1.339
 PA9  N2   HN2   single  0.860  0.020  1.020
 PA9  O2   C3    double  1.222  0.020  1.222
 PA9  C3   C4    single  1.515  0.020  1.515
 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   109.49  3.000
 PA9  HA    CA   C    107.94  3.000
 PA9  N1    CA   C    110.47  3.000
 PA9  HA    CA   CB   108.37  3.000
 PA9  N1    CA   CB   110.50  3.000
 PA9  C     CA   CB   110.01  3.000
 PA9  HBA   CB   HB   106.50  3.000
 PA9  HBA   CB   CG   109.06  3.000
 PA9  HB    CB   CG   110.47  3.000
 PA9  HBA   CB   CA   108.65  3.000
 PA9  HB    CB   CA   109.34  3.000
 PA9  CG    CB   CA   112.62  3.000
 PA9  HGA   CG   HG   106.96  3.000
 PA9  HGA   CG   CD   109.11  3.000
 PA9  HG    CG   CD   109.50  3.000
 PA9  HGA   CG   CB   110.79  3.000
 PA9  HG    CG   CB   109.37  3.000
 PA9  CD    CG   CB   111.01  3.000
 PA9  HDA   CD   HD   107.06  3.000
 PA9  HDA   CD   N2   108.71  3.000
 PA9  HD    CD   N2   107.65  3.000
 PA9  HDA   CD   CG   110.29  3.000
 PA9  HD    CD   CG   110.12  3.000
 PA9  N2    CD   CG   112.82  3.000
 PA9  OXT   C    O    124.05  3.000
 PA9  OXT   C    CA   111.23  3.000
 PA9  O     C    CA   124.69  3.000
 PA9  HOXT  OXT  C    110.27  3.000
 PA9  C2    C1   N1   115.88  3.000
 PA9  N1    C1   O1   121.79  3.000
 PA9  C2    C1   O1   122.33  3.000
 PA9  C4    P    O3P  105.75  3.000
 PA9  O3P   P    O2P  107.05  3.000
 PA9  C4    P    O2P  100.03  3.000
 PA9  O3P   P    O1P  109.66  3.000
 PA9  O2P   P    O1P  115.64  3.000
 PA9  C4    P    O1P  117.67  3.000
 PA9  HO2P  O2P  P    113.65  3.000
 PA9  HO3P  O3P  P    115.99  3.000
 PA9  HN1   N1   C1   119.25  3.000
 PA9  HN1   N1   CA   118.36  3.000
 PA9  C1    N1   CA   121.61  3.000
 PA9  H2B   C2   H2A  108.56  3.000
 PA9  H2B   C2   H2   108.34  3.000
 PA9  H2A   C2   H2   107.33  3.000
 PA9  H2B   C2   C1   113.72  3.000
 PA9  H2A   C2   C1   109.39  3.000
 PA9  H2    C2   C1   109.29  3.000
 PA9  HN2   N2   C3   119.23  3.000
 PA9  HN2   N2   CD   117.65  3.000
 PA9  C3    N2   CD   123.01  3.000
 PA9  C4    C3   O2   121.13  3.000
 PA9  C4    C3   N2   115.18  3.000
 PA9  O2    C3   N2   123.68  3.000
 PA9  H4A   C4   H4   107.03  3.000
 PA9  H4A   C4   C3   112.95  3.000
 PA9  H4    C4   C3   108.69  3.000
 PA9  H4A   C4   P    109.64  3.000
 PA9  H4    C4   P    107.79  3.000
 PA9  C3    C4   P    110.54  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
 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  CONST_07  HOXT  OXT  C   CA    180.00   0.0  0
 PA9  Var_01    CD    CG   CB  CA    179.19  30.0  1
 PA9  Var_02    N2    CD   CG  CB    178.14  30.0  3
 PA9  Var_03    C3    N2   CD  CG    -88.89  30.0  3
 PA9  Var_04    N2    C3   C4  P    -130.72  30.0  2
 PA9  Var_05    C3    C4   P   O1P   -69.66  30.0  2
 PA9  Var_06    H2    C2   C1  O1    -61.72  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
 PA9  plan-3  HOXT  0.020

