# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 15:22:37 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: N-[(1R)-1-phosphonoethyl]-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C(=O)N[C@@H](C)[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
 AFS  AFS  N-[(1R)-1-phosphonoethyl]-L-alaninamide  ligand  23  12  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AFS
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
 AFS  O1   O  O      0  -0.631  -1.7792   0.9686  -1.3945
 AFS  N1   N  NH2    0  -0.819  -4.1082   0.2607  -0.0014
 AFS  CA1  C  CH1    0  -0.157  -2.8081  -0.1770   0.4633
 AFS  C1   C  C      0   0.474  -1.6901   0.5964  -0.2292
 AFS  CB1  C  CH3    0  -0.675  -2.6099  -1.6533   0.1264
 AFS  N2   N  NH1    0  -0.544  -0.6066   0.7613   0.5359
 AFS  CA2  C  CH1    0  -0.378   0.7413   0.9968   0.0449
 AFS  CB2  C  CH3    0  -0.655   1.3047   2.2970   0.5974
 AFS  P    P  P      0   1.140   1.7546  -0.5076   0.5301
 AFS  O21  O  OP    -1  -0.881   3.1845  -0.1881   0.0821
 AFS  O22  O  OP    -1  -0.840   1.5672  -0.5721   2.0555
 AFS  O23  O  O      0  -0.864   1.1033  -1.6770  -0.2171
 AFS  H4   H  HCH1   0   0.240  -2.6836  -0.0597   1.5508
 AFS  H5   H  HCH3   0   0.259  -2.8003  -1.8235  -0.9340
 AFS  H6   H  HCH3   0   0.216  -1.5880  -1.9695   0.3418
 AFS  H7   H  HCH3   0   0.209  -3.2977  -2.2761   0.7009
 AFS  H8   H  HNH1   0   0.378  -0.6255   0.3358   1.4529
 AFS  H9   H  HCH1   0   0.216   0.6887   1.0651  -1.0435
 AFS  H10  H  HCH3   0   0.196   0.7021   3.1626   0.3103
 AFS  H11  H  HCH3   0   0.214   1.3521   2.2641   1.6877
 AFS  H12  H  HCH3   0   0.202   2.3188   2.4529   0.2302
 AFS  H1   H  HNH2   0   0.355  -4.8207  -0.2982   0.4515
 AFS  H2   H  HNH2   0   0.346  -4.2798   1.2142   0.2927

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
 AFS  CB1  CA1  single  1.527  0.020  1.527
 AFS  CA1  N1   single  1.448  0.020  1.448
 AFS  CA1  C1   single  1.526  0.020  1.526
 AFS  O23  P    deloc   1.533  0.020  1.533
 AFS  N2   C1   single  1.337  0.020  1.337
 AFS  N2   CA2  single  1.454  0.020  1.454
 AFS  C1   O1   double  1.226  0.020  1.226
 AFS  P    O22  deloc   1.538  0.020  1.538
 AFS  P    CA2  single  1.878  0.020  1.878
 AFS  P    O21  deloc   1.532  0.020  1.532
 AFS  CA2  CB2  single  1.521  0.020  1.521
 AFS  N1   H1   single  0.890  0.020  1.040
 AFS  N1   H2   single  0.890  0.020  1.040
 AFS  CA1  H4   single  0.970  0.020  1.090
 AFS  CB1  H5   single  0.970  0.020  1.090
 AFS  CB1  H6   single  0.970  0.020  1.090
 AFS  CB1  H7   single  0.970  0.020  1.090
 AFS  N2   H8   single  0.890  0.020  1.040
 AFS  CA2  H9   single  0.970  0.020  1.090
 AFS  CB2  H10  single  0.970  0.020  1.090
 AFS  CB2  H11  single  0.970  0.020  1.090
 AFS  CB2  H12  single  0.970  0.020  1.090

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
 AFS  H2   N1   H1   105.71  3.000
 AFS  H2   N1   CA1  110.09  3.000
 AFS  H1   N1   CA1  108.75  3.000
 AFS  H4   CA1  CB1  107.83  3.000
 AFS  H4   CA1  C1   108.15  3.000
 AFS  CB1  CA1  C1   107.15  3.000
 AFS  H4   CA1  N1   112.72  3.000
 AFS  C1   CA1  N1   111.04  3.000
 AFS  CB1  CA1  N1   109.74  3.000
 AFS  N2   C1   CA1  113.37  3.000
 AFS  N2   C1   O1   124.42  3.000
 AFS  CA1  C1   O1   122.13  3.000
 AFS  H7   CB1  H6   108.71  3.000
 AFS  H7   CB1  H5   108.22  3.000
 AFS  H6   CB1  H5   108.07  3.000
 AFS  H7   CB1  CA1  110.72  3.000
 AFS  H6   CB1  CA1  110.99  3.000
 AFS  H5   CB1  CA1  110.04  3.000
 AFS  H8   N2   CA2  113.08  3.000
 AFS  H8   N2   C1   116.87  3.000
 AFS  CA2  N2   C1   125.32  3.000
 AFS  H9   CA2  P    109.50  3.000
 AFS  H9   CA2  CB2  109.05  3.000
 AFS  P    CA2  CB2  113.03  3.000
 AFS  H9   CA2  N2   107.59  3.000
 AFS  CB2  CA2  N2   111.05  3.000
 AFS  P    CA2  N2   106.46  3.000
 AFS  H12  CB2  H11  107.48  3.000
 AFS  H12  CB2  H10  108.14  3.000
 AFS  H11  CB2  H10  108.07  3.000
 AFS  H12  CB2  CA2  110.16  3.000
 AFS  H11  CB2  CA2  110.67  3.000
 AFS  H10  CB2  CA2  112.17  3.000
 AFS  O23  P    O22  113.55  3.000
 AFS  O22  P    O21  114.35  3.000
 AFS  O23  P    O21  114.40  3.000
 AFS  O21  P    CA2  105.13  3.000
 AFS  O22  P    CA2  102.95  3.000
 AFS  O23  P    CA2  104.83  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
 AFS  CONST_03  H8  N2  C1  O1  180.00  0.0  0

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
 AFS  chir_01  CA1  CB1  N1  C1   positiv
 AFS  chir_02  CA2  P    N2  CB2  negativ

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
 AFS  plan-1  O1   0.020
 AFS  plan-1  CA1  0.020
 AFS  plan-1  C1   0.020
 AFS  plan-1  N2   0.020
 AFS  plan-1  CA2  0.020
 AFS  plan-1  H8   0.020

