# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 18:21:55 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (2R,3R)-2,3-dihydroxy-4-oxo-4-(propylamino)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCNC(=O)[C@H](O)[C@@H](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
 PT3  PT3  '(2R,3R)-2,3-dihydroxy-4-oxo-4-(propylamino)butanoic acid'  ligand  26  13  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PT3
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
 PT3  O1    O  OH1   0  -0.589   1.4047   1.1624  -2.8954
 PT3  O11   O  O     0  -0.425   0.5830  -0.7342  -3.7488
 PT3  C1    C  C     0   0.512   0.8326  -0.0281  -2.8079
 PT3  C2    C  CH1   0  -0.090   0.5210  -0.3913  -1.3632
 PT3  O2    O  OH1   0  -0.647   0.1039  -1.7153  -1.2556
 PT3  C3    C  CH1   0  -0.111  -0.5269   0.5911  -0.8064
 PT3  O3    O  OH1   0  -0.666  -1.6623   0.5872  -1.6186
 PT3  C4    C  C     0   0.524  -0.9104   0.1649   0.6118
 PT3  O41   O  O     0  -0.491  -2.0191  -0.3098   0.8225
 PT3  N4    N  NH1   0  -0.635   0.0221   0.3334   1.5459
 PT3  C41   C  CH2   0  -0.236  -0.1734  -0.0237   2.9391
 PT3  C42   C  CH2   0  -0.477   1.1021   0.2018   3.7342
 PT3  C43   C  CH3   0  -0.665   0.9108  -0.1401   5.2039
 PT3  HO1   H  HOH1  0   0.489   1.5702   1.3924  -3.8224
 PT3  H21   H  HCH1  0   0.294   1.4451  -0.2954  -0.7845
 PT3  HO2   H  HOH1  0   0.449  -0.6677  -1.8487  -1.8182
 PT3  H31   H  HCH1  0   0.275  -0.0951   1.5978  -0.7717
 PT3  HO3   H  HOH1  0   0.452  -2.3604   0.1320  -1.1228
 PT3  H41N  H  HNH1  0   0.408   0.8757   0.8099   1.2979
 PT3  H411  H  HCH2  0   0.239  -0.4732  -1.0721   3.0074
 PT3  H412  H  HCH2  0   0.235  -0.9873   0.5701   3.3654
 PT3  H421  H  HCH2  0   0.233   1.4108   1.2466   3.6370
 PT3  H422  H  HCH2  0   0.235   1.9073  -0.4052   3.3120
 PT3  H431  H  HCH3  0   0.237   1.8267   0.0322   5.7682
 PT3  H432  H  HCH3  0   0.225   0.1255   0.4708   5.6516
 PT3  H433  H  HCH3  0   0.225   0.6317  -1.1867   5.3347

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
 PT3  O1   C1    single  1.324  0.020  1.324
 PT3  O1   HO1   single  0.850  0.020  0.980
 PT3  O11  C1    double  1.203  0.020  1.203
 PT3  C1   C2    single  1.522  0.020  1.522
 PT3  C2   O2    single  1.392  0.020  1.392
 PT3  C2   C3    single  1.541  0.020  1.541
 PT3  C2   H21   single  0.970  0.020  1.090
 PT3  O2   HO2   single  0.850  0.020  0.980
 PT3  C3   O3    single  1.396  0.020  1.396
 PT3  C3   C4    single  1.530  0.020  1.530
 PT3  C3   H31   single  0.970  0.020  1.090
 PT3  O3   HO3   single  0.850  0.020  0.980
 PT3  C4   O41   double  1.224  0.020  1.224
 PT3  C4   N4    single  1.331  0.020  1.331
 PT3  N4   C41   single  1.451  0.020  1.451
 PT3  N4   H41N  single  0.860  0.020  1.020
 PT3  C41  C42   single  1.520  0.020  1.520
 PT3  C41  H411  single  0.970  0.020  1.090
 PT3  C41  H412  single  0.970  0.020  1.090
 PT3  C42  C43   single  1.521  0.020  1.521
 PT3  C42  H421  single  0.970  0.020  1.090
 PT3  C42  H422  single  0.970  0.020  1.090
 PT3  C43  H431  single  0.970  0.020  1.090
 PT3  C43  H432  single  0.970  0.020  1.090
 PT3  C43  H433  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
 PT3  HO1   O1   C1    110.51  3.000
 PT3  C2    C1   O11   124.06  3.000
 PT3  C2    C1   O1    111.46  3.000
 PT3  O11   C1   O1    124.48  3.000
 PT3  H21   C2   C3    109.11  3.000
 PT3  H21   C2   O2    107.18  3.000
 PT3  C3    C2   O2    112.01  3.000
 PT3  H21   C2   C1    107.94  3.000
 PT3  C3    C2   C1    109.28  3.000
 PT3  O2    C2   C1    111.20  3.000
 PT3  HO2   O2   C2    109.04  3.000
 PT3  H31   C3   C4    108.99  3.000
 PT3  H31   C3   O3    109.97  3.000
 PT3  C4    C3   O3    109.55  3.000
 PT3  H31   C3   C2    109.22  3.000
 PT3  C4    C3   C2    109.14  3.000
 PT3  O3    C3   C2    109.94  3.000
 PT3  HO3   O3   C3    106.82  3.000
 PT3  N4    C4   O41   124.25  3.000
 PT3  N4    C4   C3    116.10  3.000
 PT3  O41   C4   C3    119.65  3.000
 PT3  H41N  N4   C41   117.80  3.000
 PT3  H41N  N4   C4    118.71  3.000
 PT3  C41   N4   C4    123.25  3.000
 PT3  H412  C41  H411  107.00  3.000
 PT3  H412  C41  C42   109.87  3.000
 PT3  H411  C41  C42   109.87  3.000
 PT3  H412  C41  N4    109.92  3.000
 PT3  H411  C41  N4    109.46  3.000
 PT3  C42   C41  N4    110.65  3.000
 PT3  H422  C42  H421  106.75  3.000
 PT3  H422  C42  C43   109.94  3.000
 PT3  H421  C42  C43   109.64  3.000
 PT3  H422  C42  C41   109.49  3.000
 PT3  H421  C42  C41   109.40  3.000
 PT3  C43   C42  C41   111.51  3.000
 PT3  H433  C43  H432  107.69  3.000
 PT3  H433  C43  H431  107.74  3.000
 PT3  H432  C43  H431  107.70  3.000
 PT3  H433  C43  C42   111.33  3.000
 PT3  H432  C43  C42   111.17  3.000
 PT3  H431  C43  C42   111.05  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
 PT3  CONST_01  C41   N4   C4   C3    180.00   0.0  0
 PT3  CONST_02  C41   N4   C4   O41     0.00   0.0  0
 PT3  CONST_03  H41N  N4   C4   C3      0.00   0.0  0
 PT3  CONST_04  HO1   O1   C1   O11     0.00   0.0  0
 PT3  Var_01    C42   C41  N4   C4    176.20  30.0  3
 PT3  Var_02    C43   C42  C41  N4    178.86  30.0  3
 PT3  Var_03    H431  C43  C42  C41  -179.52  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
 PT3  chir_01  C2  C1  O2  C3  positiv
 PT3  chir_02  C3  O3  C2  C4  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
 PT3  plan-1  C3    0.020
 PT3  plan-1  C4    0.020
 PT3  plan-1  O41   0.020
 PT3  plan-1  N4    0.020
 PT3  plan-1  C41   0.020
 PT3  plan-1  H41N  0.020
 PT3  plan-2  O1    0.020
 PT3  plan-2  O11   0.020
 PT3  plan-2  C1    0.020
 PT3  plan-2  C2    0.020
 PT3  plan-2  HO1   0.020

