# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 00:08:21 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  26  16  .  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_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   1.365   0.6543   0.6209  -2.5119
 PAL  O1P   O  O     0  -0.703   0.8883   1.8369  -1.6976
 PAL  O2P   O  OH1   0  -0.738   1.4998   0.4901  -3.8669
 PAL  O3P   O  OH1   0  -0.734  -0.8955   0.5167  -2.9047
 PAL  C1P   C  CH2   0  -0.872   1.0943  -0.9366  -1.7035
 PAL  C1    C  C     0   0.551   0.2450  -1.2238  -0.4829
 PAL  O1    O  O     0  -0.473  -0.4421  -2.2262  -0.3870
 PAL  N2    N  NH1   0  -0.628   0.3169  -0.3107   0.5003
 PAL  C2    C  CH1   0  -0.157  -0.4658  -0.4719   1.6963
 PAL  C4    C  C     0   0.538  -1.9642  -0.4891   1.4203
 PAL  O2    O  O     0  -0.439  -2.7472  -1.0782   2.1214
 PAL  O3    O  OH1   0  -0.571  -2.3001   0.2518   0.3821
 PAL  C3    C  CH2   0  -0.634  -0.1643   0.6518   2.6806
 PAL  C5    C  C     0   0.562   1.2252   0.5586   3.2609
 PAL  O4    O  O     0  -0.429   1.9500  -0.3969   3.1615
 PAL  O5    O  OH1   0  -0.590   1.5405   1.6603   3.9262
 PAL  HOP2  H  HOH1  0   0.500   1.5509   1.3053  -4.3860
 PAL  HOP3  H  HOH1  0   0.493  -1.1352  -0.2073  -3.4978
 PAL  H1P1  H  HCH2  0   0.329   2.1461  -0.8657  -1.4132
 PAL  H1P2  H  HCH2  0   0.322   0.9971  -1.7645  -2.4056
 PAL  HN2   H  HNH1  0   0.407   0.8069   0.5569   0.3372
 PAL  H2    H  HCH1  0   0.303  -0.2272  -1.4281   2.1667
 PAL  HO3   H  HOH1  0   0.485  -3.2598   0.2270   0.2498
 PAL  H31   H  HCH2  0   0.324  -0.8668   0.6056   3.5180
 PAL  H32   H  HCH2  0   0.302  -0.3117   1.6324   2.2198
 PAL  HO5   H  HOH1  0   0.487   2.4207   1.5715   4.3225

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   double  1.482  0.020  1.482
 PAL  P    O2P   single  1.602  0.020  1.602
 PAL  P    O3P   single  1.602  0.020  1.602
 PAL  P    C1P   single  1.809  0.020  1.809
 PAL  O2P  HOP2  single  0.850  0.020  0.980
 PAL  O3P  HOP3  single  0.850  0.020  0.980
 PAL  C1P  C1    single  1.514  0.020  1.514
 PAL  C1P  H1P1  single  0.970  0.020  1.090
 PAL  C1P  H1P2  single  0.970  0.020  1.090
 PAL  C1   O1    double  1.219  0.020  1.219
 PAL  C1   N2    single  1.344  0.020  1.344
 PAL  N2   C2    single  1.438  0.020  1.438
 PAL  N2   HN2   single  0.860  0.020  1.020
 PAL  C2   C4    single  1.524  0.020  1.524
 PAL  C2   C3    single  1.524  0.020  1.524
 PAL  C2   H2    single  0.970  0.020  1.090
 PAL  C4   O2    double  1.205  0.020  1.205
 PAL  C4   O3    single  1.319  0.020  1.319
 PAL  O3   HO3   single  0.850  0.020  0.980
 PAL  C3   C5    single  1.509  0.020  1.509
 PAL  C3   H31   single  0.970  0.020  1.090
 PAL  C3   H32   single  0.970  0.020  1.090
 PAL  C5   O4    double  1.203  0.020  1.203
 PAL  C5   O5    single  1.325  0.020  1.325
 PAL  O5   HO5   single  0.850  0.020  0.980

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   106.79  3.000
 PAL  C1P   P    O2P   100.33  3.000
 PAL  O3P   P    O2P   107.32  3.000
 PAL  C1P   P    O1P   114.99  3.000
 PAL  O3P   P    O1P   109.93  3.000
 PAL  O2P   P    O1P   116.63  3.000
 PAL  HOP2  O2P  P     114.38  3.000
 PAL  HOP3  O3P  P     116.06  3.000
 PAL  H1P2  C1P  H1P1  107.82  3.000
 PAL  H1P2  C1P  C1    108.97  3.000
 PAL  H1P1  C1P  C1    109.74  3.000
 PAL  H1P2  C1P  P     110.15  3.000
 PAL  H1P1  C1P  P     107.27  3.000
 PAL  C1    C1P  P     112.77  3.000
 PAL  N2    C1   O1    122.09  3.000
 PAL  N2    C1   C1P   115.52  3.000
 PAL  O1    C1   C1P   122.38  3.000
 PAL  HN2   N2   C2    119.65  3.000
 PAL  HN2   N2   C1    119.45  3.000
 PAL  C2    N2   C1    120.21  3.000
 PAL  H2    C2   C3    108.92  3.000
 PAL  H2    C2   C4    106.44  3.000
 PAL  C3    C2   C4    108.66  3.000
 PAL  H2    C2   N2    109.72  3.000
 PAL  C3    C2   N2    110.29  3.000
 PAL  C4    C2   N2    112.69  3.000
 PAL  O3    C4   O2    124.56  3.000
 PAL  O3    C4   C2    112.75  3.000
 PAL  O2    C4   C2    122.63  3.000
 PAL  HO3   O3   C4    110.20  3.000
 PAL  H32   C3   H31   105.90  3.000
 PAL  H32   C3   C5    109.98  3.000
 PAL  H31   C3   C5    107.12  3.000
 PAL  H32   C3   C2    111.25  3.000
 PAL  H31   C3   C2    109.65  3.000
 PAL  C5    C3   C2    112.65  3.000
 PAL  O5    C5   O4    123.94  3.000
 PAL  O5    C5   C3    111.16  3.000
 PAL  O4    C5   C3    124.89  3.000
 PAL  HO5   O5   C5    110.19  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  CONST_03  HN2  N2   C1   C1P    0.00   0.0  0
 PAL  CONST_04  HO3  O3   C4   C2   180.00   0.0  0
 PAL  CONST_05  HO5  O5   C5   C3   180.00   0.0  0
 PAL  Var_01    O1   C1   C1P  P    120.80  30.0  3
 PAL  Var_02    C1   C1P  P    O1P   64.32  30.0  3
 PAL  Var_03    O4   C5   C3   C2   -12.20  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-2  HO3  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
 PAL  plan-3  HO5  0.020

