# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 09:54:33 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: N-(phosphonoacetyl)-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](NC(=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
 PAL  PAL  'N-(phosphonoacetyl)-L-aspartic acid'  ligand  22  16  .  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_PAL
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
 PAL  P     P  P      0   1.175   0.7861   0.9169  -2.3944
 PAL  O1P   O  O      0  -0.880   1.0216   1.8345  -1.1725
 PAL  O2P   O  OP    -1  -0.898   1.8650   1.0595  -3.4719
 PAL  O3P   O  OP    -1  -0.888  -0.6447   0.9467  -2.9279
 PAL  C1P   C  CH2    0  -0.853   1.0460  -0.8085  -1.7073
 PAL  C1    C  C      0   0.510   0.2342  -1.1816  -0.4910
 PAL  O1    O  O      0  -0.559  -0.2866  -2.2938  -0.3579
 PAL  N2    N  NH1    0  -0.637   0.1870  -0.2452   0.4596
 PAL  C2    C  CH1    0  -0.141  -0.5119  -0.4536   1.7007
 PAL  C4    C  C      0   0.395  -2.0410  -0.6060   1.5425
 PAL  O2    O  O      0  -0.638  -2.6121  -1.2336   2.4633
 PAL  O3    O  OC    -1  -0.604  -2.5874  -0.0638   0.5666
 PAL  C3    C  CH2    0  -0.600  -0.2117   0.7083   2.6414
 PAL  C5    C  C      0   0.407   1.2717   0.8435   3.0308
 PAL  O4    O  O      0  -0.616   1.8889  -0.2111   3.2832
 PAL  O5    O  OC    -1  -0.625   1.7340   2.0013   3.1010
 PAL  H1P1  H  HCH2   0   0.224   2.1031  -0.8944  -1.4297
 PAL  H1P2  H  HCH2   0   0.211   0.8732  -1.5569  -2.4845
 PAL  HN2   H  HNH1   0   0.391   0.4867   0.6907   0.1622
 PAL  H2    H  HCH1   0   0.194  -0.1300  -1.3638   2.1708
 PAL  H31   H  HCH2   0   0.230  -0.7863   0.5553   3.5616
 PAL  H32   H  HCH2   0   0.203  -0.5750   1.6440   2.2055

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
 PAL  P    O1P   deloc   1.546  0.020  1.546
 PAL  P    O2P   deloc   1.532  0.020  1.532
 PAL  P    O3P   deloc   1.527  0.020  1.527
 PAL  P    C1P   single  1.875  0.020  1.875
 PAL  C1P  C1    single  1.509  0.020  1.509
 PAL  C1P  H1P1  single  0.970  0.020  1.090
 PAL  C1P  H1P2  single  0.970  0.020  1.090
 PAL  C1   O1    double  1.235  0.020  1.235
 PAL  C1   N2    single  1.335  0.020  1.335
 PAL  N2   C2    single  1.439  0.020  1.439
 PAL  N2   HN2   single  0.860  0.020  1.020
 PAL  C2   C4    single  1.545  0.020  1.545
 PAL  C2   C3    single  1.525  0.020  1.525
 PAL  C2   H2    single  0.970  0.020  1.090
 PAL  C4   O2    deloc   1.252  0.020  1.252
 PAL  C4   O3    deloc   1.243  0.020  1.243
 PAL  C3   C5    single  1.540  0.020  1.540
 PAL  C3   H31   single  0.970  0.020  1.090
 PAL  C3   H32   single  0.970  0.020  1.090
 PAL  C5   O4    deloc   1.248  0.020  1.248
 PAL  C5   O5    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
 PAL  C1P   P    O3P   106.01  3.000
 PAL  C1P   P    O2P   104.23  3.000
 PAL  O3P   P    O2P   114.35  3.000
 PAL  C1P   P    O1P   103.62  3.000
 PAL  O3P   P    O1P   114.03  3.000
 PAL  O2P   P    O1P   113.17  3.000
 PAL  H1P2  C1P  H1P1  106.19  3.000
 PAL  H1P2  C1P  C1    108.59  3.000
 PAL  H1P1  C1P  C1    107.17  3.000
 PAL  H1P2  C1P  P     110.35  3.000
 PAL  H1P1  C1P  P     107.37  3.000
 PAL  C1    C1P  P     116.63  3.000
 PAL  N2    C1   O1    122.67  3.000
 PAL  N2    C1   C1P   114.80  3.000
 PAL  O1    C1   C1P   122.43  3.000
 PAL  HN2   N2   C2    121.56  3.000
 PAL  HN2   N2   C1    115.01  3.000
 PAL  C2    N2   C1    121.97  3.000
 PAL  H2    C2   C3    107.48  3.000
 PAL  H2    C2   C4    107.92  3.000
 PAL  C3    C2   C4    109.46  3.000
 PAL  H2    C2   N2    108.76  3.000
 PAL  C3    C2   N2    109.03  3.000
 PAL  C4    C2   N2    113.99  3.000
 PAL  O3    C4   O2    126.55  3.000
 PAL  O3    C4   C2    118.20  3.000
 PAL  O2    C4   C2    115.19  3.000
 PAL  H32   C3   H31   106.25  3.000
 PAL  H32   C3   C5    110.21  3.000
 PAL  H31   C3   C5    107.76  3.000
 PAL  H32   C3   C2    109.90  3.000
 PAL  H31   C3   C2    107.97  3.000
 PAL  C5    C3   C2    114.38  3.000
 PAL  O5    C5   O4    126.10  3.000
 PAL  O5    C5   C3    116.90  3.000
 PAL  O4    C5   C3    116.97  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
 PAL  CONST_01  C2  N2   C1   C1P  180.00   0.0  0
 PAL  CONST_02  C2  N2   C1   O1     0.00   0.0  0
 PAL  Var_01    O1  C1   C1P  P    138.96  30.0  3
 PAL  Var_02    C1  C1P  P    O1P   53.75  30.0  3
 PAL  Var_03    O4  C5   C3   C2   -41.39  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
 PAL  chir_01  C2  N2  C4  C3  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
 PAL  plan-1  C1P  0.020
 PAL  plan-1  C1   0.020
 PAL  plan-1  O1   0.020
 PAL  plan-1  N2   0.020
 PAL  plan-1  C2   0.020
 PAL  plan-1  HN2  0.020
 PAL  plan-2  C2   0.020
 PAL  plan-2  C4   0.020
 PAL  plan-2  O2   0.020
 PAL  plan-2  O3   0.020
 PAL  plan-3  C3   0.020
 PAL  plan-3  C5   0.020
 PAL  plan-3  O4   0.020
 PAL  plan-3  O5   0.020

