# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:07:05 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 3-phosphono-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](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
 APO  APO  '3-phosphono-D-alanine    '  D-peptide  18  10  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_APO
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
 APO  C1    C  CH1   0  -0.209   0.1718   0.4381  -1.0996
 APO  N2    N  NH2   0  -0.769   1.5725   0.6827  -0.8845
 APO  C3    C  C     0   0.530  -0.1610  -0.0949  -2.4900
 APO  O4    O  O     0  -0.432   0.6596  -0.4581  -3.2933
 APO  O5    O  OH1   0  -0.591  -1.4683  -0.1135  -2.7138
 APO  C6    C  CH2   0  -0.773  -0.3718  -0.5343  -0.0487
 APO  P7    P  P     0   1.387  -0.0497   0.0558   1.6305
 APO  O8    O  OH1   0  -0.750  -1.0312  -0.9289   2.4472
 APO  O9    O  OH1   0  -0.744   1.4389  -0.3517   2.0764
 APO  O10   O  O     0  -0.717  -0.2623   1.5055   1.8542
 APO  HC1   H  HCH1  0   0.289  -0.3611   1.3867  -0.9856
 APO  HN21  H  HNH2  0   0.348   2.1155  -0.1526  -1.0640
 APO  HN22  H  HNH2  0   0.361   1.9110   1.3909  -1.5226
 APO  HO5   H  HOH1  0   0.484  -1.6552  -0.4708  -3.5953
 APO  HC61  H  HCH2  0   0.308  -1.4527  -0.6426  -0.1510
 APO  HC62  H  HCH2  0   0.298   0.0581  -1.5318  -0.1785
 APO  HO8   H  HOH1  0   0.491  -1.0385  -0.7741   3.4018
 APO  HO9   H  HOH1  0   0.488   1.6506  -1.2915   2.0098

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
 APO  C1  N2    single  1.438  0.020  1.438
 APO  C1  C3    single  1.526  0.020  1.526
 APO  C1  C6    single  1.531  0.020  1.531
 APO  C1  HC1   single  0.970  0.020  1.090
 APO  N2  HN21  single  0.890  0.020  1.040
 APO  N2  HN22  single  0.890  0.020  1.040
 APO  C3  O4    double  1.204  0.020  1.204
 APO  C3  O5    single  1.327  0.020  1.327
 APO  O5  HO5   single  0.850  0.020  0.980
 APO  C6  P7    single  1.809  0.020  1.809
 APO  C6  HC61  single  0.970  0.020  1.090
 APO  C6  HC62  single  0.970  0.020  1.090
 APO  P7  O8    single  1.612  0.020  1.612
 APO  P7  O9    single  1.607  0.020  1.607
 APO  P7  O10   double  1.482  0.020  1.482
 APO  O8  HO8   single  0.850  0.020  0.980
 APO  O9  HO9   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
 APO  HC1   C1  C6    107.83  3.000
 APO  HC1   C1  C3    106.95  3.000
 APO  C6    C1  C3    109.04  3.000
 APO  HC1   C1  N2    108.14  3.000
 APO  C6    C1  N2    110.55  3.000
 APO  C3    C1  N2    114.09  3.000
 APO  HN22  N2  HN21  106.64  3.000
 APO  HN22  N2  C1    110.53  3.000
 APO  HN21  N2  C1    110.82  3.000
 APO  O5    C3  O4    123.69  3.000
 APO  O5    C3  C1    111.94  3.000
 APO  O4    C3  C1    124.37  3.000
 APO  HO5   O5  C3    110.40  3.000
 APO  HC62  C6  HC61  106.72  3.000
 APO  HC62  C6  P7    109.74  3.000
 APO  HC61  C6  P7    107.21  3.000
 APO  HC62  C6  C1    110.98  3.000
 APO  HC61  C6  C1    110.50  3.000
 APO  P7    C6  C1    111.51  3.000
 APO  O10   P7  O9    109.82  3.000
 APO  O10   P7  O8    115.69  3.000
 APO  O9    P7  O8    105.58  3.000
 APO  O10   P7  C6    115.70  3.000
 APO  O9    P7  C6    109.87  3.000
 APO  O8    P7  C6     99.36  3.000
 APO  HO8   O8  P7    114.00  3.000
 APO  HO9   O9  P7    115.52  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
 APO  CONST_01  HO5  O5  C3  C1  180.00   0.0  0
 APO  Var_01    O8   P7  C6  C1  166.27  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
 APO  chir_01  C1  N2  C3  C6  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
 APO  plan-1  C1   0.020
 APO  plan-1  C3   0.020
 APO  plan-1  O4   0.020
 APO  plan-1  O5   0.020
 APO  plan-1  HO5  0.020

