# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:39:39 2020
#   Inital geometry file: a 37 line input string
#   Ligand name: (1S,2S)-1-amino-1,2-dihydroxypropan-1-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@@](N)(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
 PY0  PY0  (1S,2S)-1-amino-1,2-dihydroxypropan-1-olate  ligand  15  7  .  2021-08-20  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PY0
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
 PY0  C3    C  CH3    0  -0.670   1.5628   1.2505   0.2620
 PY0  C2    C  CH1    0  -0.025   0.9040  -0.1124   0.4270
 PY0  O3    O  OH1    0  -0.725   1.6165  -1.0892  -0.2961
 PY0  C1    C  CT     0   0.504  -0.5595  -0.1885  -0.1634
 PY0  O1    O  OH1    0  -0.710  -1.1953   1.1088  -0.0885
 PY0  O2    O  OC    -1  -0.752  -0.4971  -0.5679  -1.4209
 PY0  N     N  NH2    0  -0.845  -1.2984  -1.1536   0.6683
 PY0  H31C  H  HCH3   0   0.203   1.5054   1.5914  -0.7741
 PY0  H32C  H  HCH3   0   0.199   1.1041   2.0146   0.8908
 PY0  H33C  H  HCH3   0   0.209   2.6183   1.1971   0.5385
 PY0  H2    H  HCH1   0   0.165   0.9049  -0.3725   1.4960
 PY0  H3    H  HOH1   0   0.405   0.9839  -1.1532  -1.0701
 PY0  H1    H  HOH1   0   0.412  -1.2336   1.3837   0.8339
 PY0  HN1   H  HNH2   0   0.313  -1.3995  -0.8226   1.6228
 PY0  HN2   H  HNH2   0   0.316  -2.2405  -1.2473   0.3024

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
 PY0  C3  C2    single  1.523  0.020  1.523
 PY0  C2  O3    single  1.409  0.020  1.409
 PY0  C2  C1    single  1.580  0.020  1.580
 PY0  C1  O1    single  1.447  0.020  1.447
 PY0  C1  O2    single  1.315  0.020  1.315
 PY0  C1  N     single  1.473  0.020  1.473
 PY0  C3  H31C  single  0.970  0.020  1.090
 PY0  C3  H32C  single  0.970  0.020  1.090
 PY0  C3  H33C  single  0.970  0.020  1.090
 PY0  C2  H2    single  0.970  0.020  1.090
 PY0  O3  H3    single  0.850  0.020  0.980
 PY0  O1  H1    single  0.850  0.020  0.980
 PY0  N   HN1   single  0.890  0.020  1.040
 PY0  N   HN2   single  0.890  0.020  1.040

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
 PY0  H33C  C3  H32C  107.13  3.000
 PY0  H33C  C3  H31C  107.83  3.000
 PY0  H32C  C3  H31C  107.83  3.000
 PY0  H33C  C3  C2    110.30  3.000
 PY0  H32C  C3  C2    112.49  3.000
 PY0  H31C  C3  C2    111.06  3.000
 PY0  H2    C2  C1    110.64  3.000
 PY0  H2    C2  O3    109.53  3.000
 PY0  C1    C2  O3    104.08  3.000
 PY0  H2    C2  C3    108.45  3.000
 PY0  C1    C2  C3    113.79  3.000
 PY0  O3    C2  C3    110.25  3.000
 PY0  H3    O3  C2     96.98  3.000
 PY0  N     C1  O2    112.01  3.000
 PY0  N     C1  O1    109.75  3.000
 PY0  O2    C1  O1    109.22  3.000
 PY0  N     C1  C2    106.57  3.000
 PY0  O2    C1  C2    109.10  3.000
 PY0  O1    C1  C2    110.16  3.000
 PY0  H1    O1  C1    108.84  3.000
 PY0  HN2   N   HN1   106.05  3.000
 PY0  HN2   N   C1    108.82  3.000
 PY0  HN1   N   C1    111.55  3.000

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
 PY0  chir_01  C2  C3  O3  C1  positiv
 PY0  chir_02  C1  O2  N   C2  negativ

