# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 14:39:56 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  25  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  OC    -1  -0.594   1.4076   1.0598  -2.9149
 PT3  O11   O  O      0  -0.602   0.4945  -0.8365  -3.6761
 PT3  C1    C  C      0   0.407   0.8142  -0.0202  -2.7844
 PT3  C2    C  CH1    0  -0.118   0.4127  -0.4424  -1.3523
 PT3  O2    O  OH1    0  -0.692  -0.2218  -1.6923  -1.3850
 PT3  C3    C  CH1    0  -0.100  -0.5190   0.6085  -0.7391
 PT3  O3    O  OH1    0  -0.660  -1.6543   0.8198  -1.5275
 PT3  C4    C  C      0   0.509  -0.9184   0.1800   0.6726
 PT3  O41   O  O      0  -0.497  -2.0183  -0.3002   0.9095
 PT3  N4    N  NH1    0  -0.638   0.0273   0.3368   1.6069
 PT3  C41   C  CH2    0  -0.230  -0.1564  -0.0491   2.9915
 PT3  C42   C  CH2    0  -0.476   1.1076   0.2061   3.7961
 PT3  C43   C  CH3    0  -0.665   0.9232  -0.1660   5.2595
 PT3  H21   H  HCH1   0   0.217   1.3277  -0.4891  -0.7445
 PT3  HO2   H  HOH1   0   0.433  -0.2319  -1.8946  -2.3400
 PT3  H31   H  HCH1   0   0.261   0.0239   1.5568  -0.6921
 PT3  HO3   H  HOH1   0   0.439  -2.1918   0.0203  -1.4879
 PT3  H41N  H  HNH1   0   0.401   0.8900   0.7921   1.3534
 PT3  H411  H  HCH2   0   0.231  -0.4218  -1.1084   3.0481
 PT3  H412  H  HCH2   0   0.228  -0.9902   0.5091   3.4283
 PT3  H421  H  HCH2   0   0.231   1.3819   1.2620   3.7169
 PT3  H422  H  HCH2   0   0.233   1.9351  -0.3663   3.3681
 PT3  H431  H  HCH3   0   0.236   1.8322   0.0216   5.8302
 PT3  H432  H  HCH3   0   0.223   0.1198   0.4149   5.7153
 PT3  H433  H  HCH3   0   0.223   0.6726  -1.2221   5.3718

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    deloc   1.239  0.020  1.239
 PT3  O11  C1    deloc   1.250  0.020  1.250
 PT3  C1   C2    single  1.546  0.020  1.546
 PT3  C2   O2    single  1.402  0.020  1.402
 PT3  C2   C3    single  1.532  0.020  1.532
 PT3  C2   H21   single  0.970  0.020  1.090
 PT3  O2   HO2   single  0.850  0.020  0.980
 PT3  C3   O3    single  1.398  0.020  1.398
 PT3  C3   C4    single  1.528  0.020  1.528
 PT3  C3   H31   single  0.970  0.020  1.090
 PT3  O3   HO3   single  0.850  0.020  0.980
 PT3  C4   O41   double  1.223  0.020  1.223
 PT3  C4   N4    single  1.339  0.020  1.339
 PT3  N4   C41   single  1.449  0.020  1.449
 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  C2    C1   O11   114.58  3.000
 PT3  C2    C1   O1    117.38  3.000
 PT3  O11   C1   O1    128.04  3.000
 PT3  H21   C2   C3    108.29  3.000
 PT3  H21   C2   O2    110.58  3.000
 PT3  C3    C2   O2    110.22  3.000
 PT3  H21   C2   C1    107.91  3.000
 PT3  C3    C2   C1    109.96  3.000
 PT3  O2    C2   C1    109.84  3.000
 PT3  HO2   O2   C2    102.25  3.000
 PT3  H31   C3   C4    109.46  3.000
 PT3  H31   C3   O3    107.23  3.000
 PT3  C4    C3   O3    110.55  3.000
 PT3  H31   C3   C2    108.06  3.000
 PT3  C4    C3   C2    109.65  3.000
 PT3  O3    C3   C2    111.81  3.000
 PT3  HO3   O3   C3    107.70  3.000
 PT3  N4    C4   O41   123.09  3.000
 PT3  N4    C4   C3    115.29  3.000
 PT3  O41   C4   C3    121.59  3.000
 PT3  H41N  N4   C41   117.98  3.000
 PT3  H41N  N4   C4    118.82  3.000
 PT3  C41   N4   C4    123.10  3.000
 PT3  H412  C41  H411  106.77  3.000
 PT3  H412  C41  C42   109.68  3.000
 PT3  H411  C41  C42   109.70  3.000
 PT3  H412  C41  N4    110.01  3.000
 PT3  H411  C41  N4    109.77  3.000
 PT3  C42   C41  N4    110.83  3.000
 PT3  H422  C42  H421  106.69  3.000
 PT3  H422  C42  C43   109.89  3.000
 PT3  H421  C42  C43   109.65  3.000
 PT3  H422  C42  C41   109.53  3.000
 PT3  H421  C42  C41   109.41  3.000
 PT3  C43   C42  C41   111.55  3.000
 PT3  H433  C43  H432  107.65  3.000
 PT3  H433  C43  H431  107.72  3.000
 PT3  H432  C43  H431  107.68  3.000
 PT3  H433  C43  C42   111.32  3.000
 PT3  H432  C43  C42   111.15  3.000
 PT3  H431  C43  C42   111.14  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  Var_01    C42   C41  N4   C4    177.97  30.0  3
 PT3  Var_02    C43   C42  C41  N4    178.79  30.0  3
 PT3  Var_03    H431  C43  C42  C41  -179.87  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

