# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:16:16 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2R)-2-amino-3-(propyldisulfanyl)propanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCSSC[C@H](N)C=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
 PR3  PR3  (2R)-2-amino-3-(propyldisulfanyl)propanal  L-peptide  23  10  .  2019-03-22  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PR3
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
 PR3  N    N  NH2   0  -0.766  12.6973  21.0138  16.4445
 PR3  CA   C  CH1   0  -0.225  13.9293  21.3957  15.8048
 PR3  C    C  C1    0   0.163  14.9572  22.0708  16.6898
 PR3  O    O  O     0  -0.356  14.8026  22.2983  17.8614
 PR3  CB   C  CH2   0  -0.557  13.6842  22.2437  14.5568
 PR3  SG   S  S2    0  -0.070  12.9377  23.8529  15.0161
 PR3  SD   S  S2    0  -0.044  11.7920  24.3387  13.3891
 PR3  CE   C  CH2   0  -0.553  10.1334  23.7474  13.8660
 PR3  CZ   C  CH2   0  -0.433   9.9898  22.2400  13.9656
 PR3  CH   C  CH3   0  -0.661  10.2108  21.5072  12.6523
 PR3  H    H  HNH2  0   0.360  12.8822  20.3760  17.2082
 PR3  H2   H  HNH2  0   0.349  12.2410  21.8222  16.8489
 PR3  HA   H  HCH1  0   0.296  14.4315  20.4906  15.4352
 PR3  HC   H  H     0   0.191  15.8981  22.3369  16.1716
 PR3  HB2  H  HCH2  0   0.290  14.6187  22.4244  14.0258
 PR3  HB3  H  HCH2  0   0.307  13.0022  21.7177  13.8925
 PR3  HE2  H  HCH2  0   0.283   9.8597  24.2359  14.8012
 PR3  HE3  H  HCH2  0   0.276   9.4827  24.1513  13.0848
 PR3  HZ2  H  HCH2  0   0.231  10.6652  21.8569  14.7350
 PR3  HZ3  H  HCH2  0   0.241   8.9787  22.0387  14.3310
 PR3  HH1  H  HCH3  0   0.232  10.0639  20.4346  12.7772
 PR3  HH2  H  HCH3  0   0.223   9.5137  21.8517  11.8866
 PR3  HH3  H  HCH3  0   0.222  11.2208  21.6588  12.2695

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
 PR3  N   CA   single  1.458  0.019  1.458
 PR3  N   H    single  0.860  0.020  0.860
 PR3  N   H2   single  0.890  0.020  1.040
 PR3  CA  C    single  1.525  0.021  1.525
 PR3  CA  CB   single  1.530  0.020  1.530
 PR3  CA  HA   single  0.970  0.020  0.970
 PR3  C   O    double  1.231  0.020  1.231
 PR3  C   HC   single  0.930  0.020  1.080
 PR3  CB  SG   single  1.832  0.020  1.832
 PR3  CB  HB2  single  0.970  0.020  1.090
 PR3  CB  HB3  single  0.970  0.020  1.090
 PR3  SG  SD   single  2.048  0.020  2.048
 PR3  SD  CE   single  1.824  0.020  1.824
 PR3  CE  CZ   single  1.517  0.020  1.517
 PR3  CE  HE2  single  0.970  0.020  1.090
 PR3  CE  HE3  single  0.970  0.020  1.090
 PR3  CZ  CH   single  1.520  0.020  1.520
 PR3  CZ  HZ2  single  0.970  0.020  1.090
 PR3  CZ  HZ3  single  0.970  0.020  1.090
 PR3  CH  HH1  single  0.970  0.020  1.090
 PR3  CH  HH2  single  0.970  0.020  1.090
 PR3  CH  HH3  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
 PR3  H2   N   H    106.50  3.000
 PR3  H2   N   CA   110.57  3.000
 PR3  H    N   CA   114.00  3.000
 PR3  HA   CA  CB   109.00  3.000
 PR3  HA   CA  C    109.00  3.000
 PR3  CB   CA  C    110.10  1.900
 PR3  HA   CA  N    110.00  3.000
 PR3  CB   CA  N    110.50  1.700
 PR3  C    CA  N    111.00  2.800
 PR3  HC   C   O    121.31  3.000
 PR3  HC   C   CA   114.23  3.000
 PR3  O    C   CA   120.80  1.700
 PR3  HB3  CB  HB2  108.67  3.000
 PR3  HB3  CB  SG   108.80  3.000
 PR3  HB2  CB  SG   109.01  3.000
 PR3  HB3  CB  CA   109.33  3.000
 PR3  HB2  CB  CA   110.63  3.000
 PR3  SG   CB  CA   110.35  3.000
 PR3  SD   SG  CB   103.71  3.000
 PR3  CE   SD  SG   102.94  3.000
 PR3  HE3  CE  HE2  107.33  3.000
 PR3  HE3  CE  CZ   110.93  3.000
 PR3  HE2  CE  CZ   111.41  3.000
 PR3  HE3  CE  SD   103.56  3.000
 PR3  HE2  CE  SD   107.90  3.000
 PR3  CZ   CE  SD   115.16  3.000
 PR3  HZ3  CZ  HZ2  105.76  3.000
 PR3  HZ3  CZ  CH   109.53  3.000
 PR3  HZ2  CZ  CH   110.44  3.000
 PR3  HZ3  CZ  CE   106.99  3.000
 PR3  HZ2  CZ  CE   109.63  3.000
 PR3  CH   CZ  CE   114.11  3.000
 PR3  HH3  CH  HH2  107.54  3.000
 PR3  HH3  CH  HH1  107.57  3.000
 PR3  HH2  CH  HH1  107.76  3.000
 PR3  HH3  CH  CZ   111.77  3.000
 PR3  HH2  CH  CZ   111.17  3.000
 PR3  HH1  CH  CZ   110.85  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
 PR3  Var_01  CZ   CE  SD  SG   -68.03  30.0  3
 PR3  Var_02  CH   CZ  CE  SD   -62.97  30.0  3
 PR3  Var_03  HB2  CB  SG  SD    88.50  30.0  1
 PR3  Var_04  HH1  CH  CZ  CE  -178.18  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
 PR3  chir_01  CA  N  C  CB  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
 PR3  plan-1  CA  0.020
 PR3  plan-1  C   0.020
 PR3  plan-1  O   0.020
 PR3  plan-1  HC  0.020

