# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 23:59:13 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: [(1R)-1-amino-3-methylbutyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)[P](O)(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
 PLU  PLU  '[(1R)-1-amino-3-methylbutyl]phosphonic acid'  ligand  22  10  .  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_PLU
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
 PLU  CA    C  CH1    0  -0.360  -0.4788   0.3491   0.0492
 PLU  CB    C  CH2    0  -0.396   0.2786  -0.3607   1.1730
 PLU  CG    C  CH1    0  -0.237  -0.1374  -0.0157   2.6058
 PLU  CD1   C  CH3    0  -0.646   0.6461  -0.8684   3.5997
 PLU  CD2   C  CH3    0  -0.653   0.0498   1.4665   2.9135
 PLU  N     N  NH2    0  -0.808  -1.9222   0.1035   0.0657
 PLU  P     P  P      0   1.174   0.2010  -0.1397  -1.6243
 PLU  O1    O  O      0  -0.915  -0.2263  -1.6099  -1.7848
 PLU  O2    O  OP    -1  -0.912  -0.4502   0.8023  -2.6452
 PLU  O3    O  OP    -1  -0.912   1.7219   0.0506  -1.5103
 PLU  HA    H  HCH1   0   0.172  -0.3258   1.4313   0.1603
 PLU  HB1   H  HCH2   0   0.187   1.3463  -0.1461   1.0629
 PLU  HB2   H  HCH2   0   0.189   0.1721  -1.4425   1.0253
 PLU  HG    H  HCH1   0   0.193  -1.1999  -0.2600   2.7338
 PLU  HD11  H  HCH3   0   0.218   0.3625  -0.6504   4.6314
 PLU  HD12  H  HCH3   0   0.218   0.4792  -1.9339   3.4287
 PLU  HD13  H  HCH3   0   0.207   1.7200  -0.6854   3.5069
 PLU  HD21  H  HCH3   0   0.207   1.0917   1.7634   2.7630
 PLU  HD22  H  HCH3   0   0.223  -0.5660   2.0999   2.2739
 PLU  HD23  H  HCH3   0   0.218  -0.2125   1.6935   3.9485
 PLU  HN1   H  HNH2   0   0.313  -2.0670  -0.8649  -0.1971
 PLU  HN2   H  HNH2   0   0.321  -2.2837   0.1889   1.0093

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
 PLU  CA   CB    single  1.530  0.020  1.530
 PLU  CA   N     single  1.464  0.020  1.464
 PLU  CA   P     single  1.871  0.020  1.871
 PLU  CA   HA    single  0.970  0.020  1.090
 PLU  CB   CG    single  1.531  0.020  1.531
 PLU  CB   HB1   single  0.970  0.020  1.090
 PLU  CB   HB2   single  0.970  0.020  1.090
 PLU  CG   CD1   single  1.526  0.020  1.526
 PLU  CG   CD2   single  1.525  0.020  1.525
 PLU  CG   HG    single  0.970  0.020  1.090
 PLU  CD1  HD11  single  0.970  0.020  1.090
 PLU  CD1  HD12  single  0.970  0.020  1.090
 PLU  CD1  HD13  single  0.970  0.020  1.090
 PLU  CD2  HD21  single  0.970  0.020  1.090
 PLU  CD2  HD22  single  0.970  0.020  1.090
 PLU  CD2  HD23  single  0.970  0.020  1.090
 PLU  N    HN1   single  0.890  0.020  1.040
 PLU  N    HN2   single  0.890  0.020  1.040
 PLU  P    O1    deloc   1.539  0.020  1.539
 PLU  P    O2    deloc   1.534  0.020  1.534
 PLU  P    O3    deloc   1.537  0.020  1.537

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
 PLU  HA    CA   P     107.29  3.000
 PLU  HA    CA   N     107.54  3.000
 PLU  P     CA   N     108.93  3.000
 PLU  HA    CA   CB    108.29  3.000
 PLU  P     CA   CB    110.85  3.000
 PLU  N     CA   CB    113.70  3.000
 PLU  HB2   CB   HB1   105.93  3.000
 PLU  HB2   CB   CG    108.77  3.000
 PLU  HB1   CB   CG    108.35  3.000
 PLU  HB2   CB   CA    108.10  3.000
 PLU  HB1   CB   CA    108.55  3.000
 PLU  CG    CB   CA    116.63  3.000
 PLU  HG    CG   CD2   108.16  3.000
 PLU  HG    CG   CD1   107.26  3.000
 PLU  CD2   CG   CD1   110.40  3.000
 PLU  HG    CG   CB    108.78  3.000
 PLU  CD2   CG   CB    111.98  3.000
 PLU  CD1   CG   CB    110.12  3.000
 PLU  HD13  CD1  HD12  107.47  3.000
 PLU  HD13  CD1  HD11  107.57  3.000
 PLU  HD12  CD1  HD11  107.64  3.000
 PLU  HD13  CD1  CG    110.82  3.000
 PLU  HD12  CD1  CG    111.39  3.000
 PLU  HD11  CD1  CG    111.74  3.000
 PLU  HD23  CD2  HD22  107.43  3.000
 PLU  HD23  CD2  HD21  107.63  3.000
 PLU  HD22  CD2  HD21  107.43  3.000
 PLU  HD23  CD2  CG    111.34  3.000
 PLU  HD22  CD2  CG    112.13  3.000
 PLU  HD21  CD2  CG    110.67  3.000
 PLU  HN2   N    HN1   105.70  3.000
 PLU  HN2   N    CA    110.35  3.000
 PLU  HN1   N    CA    107.34  3.000
 PLU  O3    P    O2    113.16  3.000
 PLU  O3    P    O1    113.62  3.000
 PLU  O2    P    O1    113.53  3.000
 PLU  O3    P    CA    105.12  3.000
 PLU  O2    P    CA    106.29  3.000
 PLU  O1    P    CA    104.00  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
 PLU  Var_01  CD1   CG   CB  CA   176.38  30.0  3
 PLU  Var_02  HD11  CD1  CG  CB  -179.44  30.0  3
 PLU  Var_03  HD21  CD2  CG  CB   -58.10  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
 PLU  chir_01  CA  CB  N  P  positiv

