# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 01:49:46 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 4-oxo-O-phosphono-L-homoserine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)O[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
 PHD  PHD  4-oxo-O-phosphono-L-homoserine  L-peptide  18  13  .  2016-04-26  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_PHD
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
 PHD  N    N  NH2    0  -0.794   8.1759  34.4026   0.3894
 PHD  CA   C  CH1    0  -0.188   9.3692  34.7412  -0.3704
 PHD  C    C  C      0   0.402   9.5335  36.2766  -0.4402
 PHD  O    O  O      0  -0.606   8.4885  36.9319  -0.6312
 PHD  CB   C  CH2    0  -0.547   9.3416  34.1715  -1.8063
 PHD  CG   C  C      0   0.533  10.6147  34.4471  -2.5811
 PHD  OD1  O  O2     0  -0.611  11.5985  33.6838  -2.2071
 PHD  OD2  O  O      0  -0.509  10.6615  35.3044  -3.4446
 PHD  P    P  P      0   1.218  13.2777  33.7088  -2.8990
 PHD  OP1  O  O      0  -0.866  13.8412  32.5505  -2.1019
 PHD  OP2  O  OP    -1  -0.869  13.0555  33.4483  -4.3737
 PHD  OP3  O  OP    -1  -0.870  13.7818  35.0852  -2.5184
 PHD  OXT  O  OC    -1  -0.606  10.6919  36.7244  -0.3402
 PHD  H2   H  HNH2   0   0.330   7.9657  33.4173   0.2815
 PHD  H    H  HNH2   0   0.325   7.3946  34.9077  -0.0113
 PHD  HA   H  HCH1   0   0.202  10.2342  34.3160   0.1461
 PHD  HB2  H  HCH2   0   0.233   9.1775  33.0915  -1.7452
 PHD  HB3  H  HCH2   0   0.220   8.4916  34.6065  -2.3373

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
 PHD  N    CA   single  1.458  0.019  1.458
 PHD  N    H2   single  0.890  0.020  1.040
 PHD  N    H    single  0.860  0.020  0.860
 PHD  CA   C    single  1.525  0.021  1.525
 PHD  CA   CB   single  1.530  0.020  1.530
 PHD  CA   HA   single  0.970  0.020  0.970
 PHD  C    O    deloc   1.231  0.020  1.231
 PHD  C    OXT  deloc   1.246  0.020  1.246
 PHD  CB   CG   single  1.516  0.020  1.516
 PHD  CB   HB2  single  0.970  0.020  1.090
 PHD  CB   HB3  single  0.970  0.020  1.090
 PHD  CG   OD1  single  1.300  0.020  1.300
 PHD  CG   OD2  double  1.218  0.020  1.218
 PHD  OD1  P    single  1.816  0.020  1.816
 PHD  P    OP1  deloc   1.515  0.020  1.515
 PHD  P    OP2  deloc   1.514  0.020  1.514
 PHD  P    OP3  deloc   1.514  0.020  1.514

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
 PHD  H    N    H2   106.42  3.000
 PHD  H    N    CA   114.00  3.000
 PHD  H2   N    CA   109.94  3.000
 PHD  HA   CA   CB   109.00  3.000
 PHD  HA   CA   C    109.00  3.000
 PHD  CB   CA   C    110.10  1.900
 PHD  HA   CA   N    110.00  3.000
 PHD  CB   CA   N    110.50  1.700
 PHD  C    CA   N    111.00  2.800
 PHD  OXT  C    O    127.02  3.000
 PHD  OXT  C    CA   116.88  3.000
 PHD  O    C    CA   120.80  1.700
 PHD  HB3  CB   HB2  107.67  3.000
 PHD  HB3  CB   CG   109.43  3.000
 PHD  HB2  CB   CG   109.51  3.000
 PHD  HB3  CB   CA   108.59  3.000
 PHD  HB2  CB   CA   108.34  3.000
 PHD  CG   CB   CA   113.14  3.000
 PHD  OD2  CG   OD1  126.03  3.000
 PHD  OD2  CG   CB   121.52  3.000
 PHD  OD1  CG   CB   112.45  3.000
 PHD  P    OD1  CG   125.58  3.000
 PHD  OP3  P    OP2  116.75  3.000
 PHD  OP3  P    OP1  116.04  3.000
 PHD  OP2  P    OP1  115.82  3.000
 PHD  OP3  P    OD1  102.98  3.000
 PHD  OP2  P    OD1  103.47  3.000
 PHD  OP1  P    OD1   97.64  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
 PHD  Var_01  OD1  CG  CB   CA    75.38  30.0  3
 PHD  Var_02  OP1  P   OD1  CG  -176.38  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
 PHD  chir_01  CA  N  C  CB  positiv

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
 PHD  plan-1  CA   0.020
 PHD  plan-1  C    0.020
 PHD  plan-1  O    0.020
 PHD  plan-1  OXT  0.020
 PHD  plan-2  CB   0.020
 PHD  plan-2  CG   0.020
 PHD  plan-2  OD1  0.020
 PHD  plan-2  OD2  0.020

