# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:31:03 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: N-[(R)-hydroxy(methyl)phosphoryl]-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[P@](O)(=O)N[C@@H](CC(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
 AS9  AS9  'N-[(R)-hydroxy(methyl)phosphoryl]-L-aspartic acid'  L-peptide  20  13  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AS9
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
 AS9  CAA   C  CH3    0  -0.933  -48.8345  20.0341  -21.4426
 AS9  PAM   P  P      0   1.201  -48.6705  20.1408  -19.6177
 AS9  OAG   O  O      0  -0.825  -48.6719  18.7483  -19.0243
 AS9  OAD   O  OP    -1  -0.822  -47.4891  21.0463  -19.3262
 AS9  N     N  NH1    0  -0.793  -50.1770  20.8585  -19.2359
 AS9  CA    C  CH1    0  -0.154  -50.7752  20.7241  -17.9164
 AS9  C     C  C      0   0.396  -52.2262  21.2538  -17.9464
 AS9  OXT   O  OC    -1  -0.614  -53.0787  20.6111  -17.3007
 AS9  O     O  O      0  -0.615  -52.4228  22.3075  -18.5895
 AS9  CB    C  CH2    0  -0.544  -49.9979  21.4566  -16.8040
 AS9  CG    C  C      0   0.388  -50.5933  21.2229  -15.4062
 AS9  OD2   O  O      0  -0.626  -50.4759  20.0655  -14.9455
 AS9  OD1   O  OC    -1  -0.622  -51.1449  22.1896  -14.8389
 AS9  HAA1  H  HCH3   0   0.223  -49.6649  19.3927  -21.7387
 AS9  HAA2  H  HCH3   0   0.224  -48.9952  21.0178  -21.8877
 AS9  HAA3  H  HCH3   0   0.225  -47.9206  19.6242  -21.8767
 AS9  H     H  HNH1   0   0.329  -50.2744  21.8111  -19.5664
 AS9  HA    H  HCH1   0   0.185  -50.7937  19.6620  -17.6668
 AS9  HB2   H  HCH2   0   0.202  -48.9654  21.0947  -16.8189
 AS9  HB3   H  HCH2   0   0.175  -49.9678  22.5233  -17.0470

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
 AS9  CAA  PAM   single  1.835  0.020  1.835
 AS9  CAA  HAA1  single  0.970  0.020  1.090
 AS9  CAA  HAA2  single  0.970  0.020  1.090
 AS9  CAA  HAA3  single  0.970  0.020  1.090
 AS9  PAM  OAG   deloc   1.514  0.020  1.514
 AS9  PAM  N     single  1.712  0.020  1.712
 AS9  PAM  OAD   deloc   1.517  0.020  1.517
 AS9  N    CA    single  1.458  0.019  1.458
 AS9  N    H     single  0.860  0.020  0.860
 AS9  CA   C     single  1.525  0.021  1.525
 AS9  CA   CB    single  1.521  0.033  1.521
 AS9  CA   HA    single  0.970  0.020  0.970
 AS9  C    O     deloc   1.231  0.020  1.231
 AS9  C    OXT   deloc   1.248  0.020  1.248
 AS9  CB   CG    single  1.537  0.020  1.537
 AS9  CB   HB2   single  0.970  0.020  1.090
 AS9  CB   HB3   single  0.970  0.020  1.090
 AS9  CG   OD2   deloc   1.251  0.020  1.251
 AS9  CG   OD1   deloc   1.249  0.020  1.249

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
 AS9  HAA3  CAA  HAA2  107.43  3.000
 AS9  HAA3  CAA  HAA1  107.98  3.000
 AS9  HAA2  CAA  HAA1  107.90  3.000
 AS9  HAA3  CAA  PAM   110.02  3.000
 AS9  HAA2  CAA  PAM   111.48  3.000
 AS9  HAA1  CAA  PAM   111.86  3.000
 AS9  N     PAM  OAD   113.10  3.000
 AS9  OAD   PAM  OAG   118.33  3.000
 AS9  N     PAM  OAG   107.30  3.000
 AS9  OAD   PAM  CAA   107.19  3.000
 AS9  N     PAM  CAA    99.64  3.000
 AS9  OAG   PAM  CAA   109.65  3.000
 AS9  H     N    CA    114.00  3.000
 AS9  H     N    PAM   113.96  3.000
 AS9  CA    N    PAM   121.69  3.000
 AS9  HA    CA   CB    109.00  3.000
 AS9  HA    CA   C     110.00  3.000
 AS9  CB    CA   C     110.50  1.500
 AS9  HA    CA   N     110.00  3.000
 AS9  CB    CA   N     110.40  1.500
 AS9  C     CA   N     111.00  2.800
 AS9  O     C    OXT   126.37  3.000
 AS9  OXT   C    CA    120.80  1.700
 AS9  O     C    CA    120.80  1.700
 AS9  HB3   CB   HB2   107.06  3.000
 AS9  HB3   CB   CG    111.14  3.000
 AS9  HB2   CB   CG    109.12  3.000
 AS9  HB3   CB   CA    108.46  3.000
 AS9  HB2   CB   CA    107.98  3.000
 AS9  CG    CB   CA    112.86  3.000
 AS9  OD1   CG   OD2   126.16  3.000
 AS9  OD1   CG   CB    117.80  3.000
 AS9  OD2   CG   CB    116.05  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
 AS9  Var_01  CA    N    PAM  CAA  156.90  30.0  3
 AS9  Var_02  OD2   CG   CB   CA    68.97  30.0  3
 AS9  Var_03  HAA1  CAA  PAM  OAG   50.10  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
 AS9  chir_02  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
 AS9  plan-1  CA   0.020
 AS9  plan-1  C    0.020
 AS9  plan-1  OXT  0.020
 AS9  plan-1  O    0.020
 AS9  plan-2  CB   0.020
 AS9  plan-2  CG   0.020
 AS9  plan-2  OD2  0.020
 AS9  plan-2  OD1  0.020

