# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:35:30 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  25  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 OK
;

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  -0.475  -1.5543   0.5729  -1.4971
 AFS  N1   N  NH2   0  -0.792  -4.0261   0.1482  -0.3513
 AFS  CA1  C  CH1   0  -0.212  -2.8376  -0.1153   0.4316
 AFS  C1   C  C     0   0.555  -1.6113   0.4327  -0.2893
 AFS  CB1  C  CH3   0  -0.656  -2.6609  -1.6229   0.6078
 AFS  N2   N  NH1   0  -0.639  -0.5832   0.7267   0.5372
 AFS  CA2  C  CH1   0  -0.365   0.7401   1.0726   0.0755
 AFS  CB2  C  CH3   0  -0.679   1.3669   2.1537   0.9453
 AFS  P    P  P     0   1.375   1.6974  -0.4828  -0.0008
 AFS  O21  O  OH1   0  -0.747   3.1234   0.0405  -0.5192
 AFS  O22  O  OH1   0  -0.752   1.9003  -0.9593   1.5250
 AFS  O23  O  O     0  -0.699   1.0594  -1.5744  -0.7707
 AFS  H2   H  HNH2  0   0.348  -4.2079   1.1434  -0.3876
 AFS  H4   H  HCH1  0   0.233  -2.8725   0.3362   1.4348
 AFS  H5   H  HCH3  0   0.233  -2.5696  -2.1182  -0.3590
 AFS  H6   H  HCH3  0   0.233  -1.7753  -1.8551   1.1983
 AFS  H7   H  HCH3  0   0.242  -3.5240  -2.0427   1.1264
 AFS  H8   H  HNH1  0   0.403  -0.7067   0.5828   1.5280
 AFS  H9   H  HCH1  0   0.302   0.6535   1.4388  -0.9494
 AFS  H10  H  HCH3  0   0.263   0.7441   3.0470   0.9177
 AFS  H11  H  HCH3  0   0.236   1.4544   1.8425   1.9872
 AFS  H12  H  HCH3  0   0.256   2.3578   2.4228   0.5848
 AFS  H13  H  HOH1  0   0.497   3.7594  -0.6589  -0.7261
 AFS  H14  H  HOH1  0   0.490   2.4865  -0.4181   2.0690
 AFS  H1   H  HNH2  0   0.350  -4.8228  -0.2609   0.1202

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  1.528  0.020  1.528
 AFS  CA1  N1   single  1.447  0.020  1.447
 AFS  CA1  C1   single  1.524  0.020  1.524
 AFS  O23  P    double  1.480  0.020  1.480
 AFS  N2   C1   single  1.351  0.020  1.351
 AFS  N2   CA2  single  1.444  0.020  1.444
 AFS  C1   O1   double  1.217  0.020  1.217
 AFS  P    O22  single  1.611  0.020  1.611
 AFS  P    CA2  single  1.828  0.020  1.828
 AFS  P    O21  single  1.605  0.020  1.605
 AFS  CA2  CB2  single  1.523  0.020  1.523
 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  0.860  0.020  1.020
 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
 AFS  O21  H13  single  0.850  0.020  0.980
 AFS  O22  H14  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
 AFS  H2   N1   H1   105.82  3.000
 AFS  H2   N1   CA1  110.23  3.000
 AFS  H1   N1   CA1  108.72  3.000
 AFS  H4   CA1  CB1  107.65  3.000
 AFS  H4   CA1  C1   108.00  3.000
 AFS  CB1  CA1  C1   108.43  3.000
 AFS  H4   CA1  N1   113.10  3.000
 AFS  C1   CA1  N1   109.83  3.000
 AFS  CB1  CA1  N1   109.69  3.000
 AFS  N2   C1   CA1  113.64  3.000
 AFS  N2   C1   O1   123.10  3.000
 AFS  CA1  C1   O1   123.25  3.000
 AFS  H7   CB1  H6   107.67  3.000
 AFS  H7   CB1  H5   108.24  3.000
 AFS  H6   CB1  H5   108.41  3.000
 AFS  H7   CB1  CA1  110.06  3.000
 AFS  H6   CB1  CA1  111.51  3.000
 AFS  H5   CB1  CA1  110.83  3.000
 AFS  H8   N2   CA2  117.42  3.000
 AFS  H8   N2   C1   118.46  3.000
 AFS  CA2  N2   C1   123.63  3.000
 AFS  H9   CA2  P    106.72  3.000
 AFS  H9   CA2  CB2  109.31  3.000
 AFS  P    CA2  CB2  114.36  3.000
 AFS  H9   CA2  N2   107.93  3.000
 AFS  CB2  CA2  N2   111.40  3.000
 AFS  P    CA2  N2   106.83  3.000
 AFS  H12  CB2  H11  108.29  3.000
 AFS  H12  CB2  H10  108.03  3.000
 AFS  H11  CB2  H10  107.70  3.000
 AFS  H12  CB2  CA2  111.18  3.000
 AFS  H11  CB2  CA2  112.09  3.000
 AFS  H10  CB2  CA2  109.41  3.000
 AFS  O23  P    O22  109.19  3.000
 AFS  O22  P    O21  106.88  3.000
 AFS  O23  P    O21  117.09  3.000
 AFS  O21  P    CA2  101.62  3.000
 AFS  O22  P    CA2  106.14  3.000
 AFS  O23  P    CA2  115.06  3.000
 AFS  H13  O21  P    114.67  3.000
 AFS  H14  O22  P    116.37  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_01  CA2  N2  C1  O1     0.00  0.0  0
 AFS  CONST_02  CA2  N2  C1  CA1  180.00  0.0  0
 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

