# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 19:10:30 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: (1R)-1-[(2S)-pyrrolidin-2-yl]ethane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)[C@@H]1CCCN1
#
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
 TPK  TPK  (1R)-1-[(2S)-pyrrolidin-2-yl]ethane-1,2-diol  L-peptide  22  9  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_TPK
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
 TPK  C    C  CH1   0   0.028  36.7173  38.9351  82.0767
 TPK  O    O  OH1   0  -0.671  35.8546  37.8145  82.0470
 TPK  C3   C  CH2   0  -0.166  36.5670  39.5325  83.4663
 TPK  O4   O  OH1   0  -0.672  37.3554  40.6990  83.5456
 TPK  CA   C  CH1   0  -0.140  38.1685  38.5894  81.7342
 TPK  CB   C  CH2   0  -0.467  38.3118  37.8793  80.3748
 TPK  CG   C  CH2   0  -0.479  38.3079  36.3808  80.7114
 TPK  CD   C  CH2   0  -0.293  38.5642  36.3199  82.2350
 TPK  N    N  NH1   0  -0.591  38.7753  37.6879  82.7088
 TPK  H1   H  HCH1  0   0.201  36.3873  39.6885  81.3448
 TPK  HO   H  HOH1  0   0.455  35.6963  37.5695  81.1310
 TPK  H3   H  HCH2  0   0.198  35.5055  39.7549  83.6400
 TPK  H3A  H  HCH2  0   0.195  36.8711  38.7848  84.2082
 TPK  HO4  H  HOH1  0   0.453  37.3627  40.9942  84.4596
 TPK  HA   H  HCH1  0   0.242  38.7221  39.5308  81.7337
 TPK  HB2  H  HCH2  0   0.231  37.5382  38.1577  79.6551
 TPK  HB3  H  HCH2  0   0.237  39.2659  38.1619  79.9267
 TPK  HG2  H  HCH2  0   0.227  37.3559  35.9128  80.4581
 TPK  HG3  H  HCH2  0   0.232  39.0773  35.8484  80.1515
 TPK  HD2  H  HCH2  0   0.214  37.7083  35.8732  82.7427
 TPK  HD3  H  HCH2  0   0.222  39.4321  35.7074  82.4827
 TPK  H    H  HNH1  0   0.346  39.7690  37.8731  82.7312

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
 TPK  C   O    single  1.231  0.020  1.231
 TPK  C   C3   single  1.520  0.020  1.520
 TPK  C   CA   single  1.525  0.021  1.525
 TPK  C3  O4   single  1.410  0.020  1.410
 TPK  CA  CB   single  1.530  0.020  1.530
 TPK  CA  N    single  1.466  0.015  1.466
 TPK  CB  CG   single  1.536  0.020  1.536
 TPK  CG  CD   single  1.546  0.020  1.546
 TPK  CD  N    single  1.473  0.014  1.473
 TPK  C   H1   single  0.970  0.020  1.090
 TPK  O   HO   single  0.850  0.020  0.980
 TPK  C3  H3   single  0.970  0.020  1.090
 TPK  C3  H3A  single  0.970  0.020  1.090
 TPK  O4  HO4  single  0.850  0.020  0.980
 TPK  CA  HA   single  0.970  0.020  0.970
 TPK  CB  HB2  single  0.970  0.020  1.090
 TPK  CB  HB3  single  0.970  0.020  1.090
 TPK  CG  HG2  single  0.970  0.020  1.090
 TPK  CG  HG3  single  0.970  0.020  1.090
 TPK  CD  HD2  single  0.970  0.020  1.090
 TPK  CD  HD3  single  0.970  0.020  1.090
 TPK  N   H    single  0.860  0.020  1.020

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
 TPK  H1   C   CA   106.85  3.000
 TPK  H1   C   C3   108.01  3.000
 TPK  CA   C   C3   112.77  3.000
 TPK  H1   C   O    110.21  3.000
 TPK  CA   C   O    119.00  3.000
 TPK  C3   C   O    105.68  3.000
 TPK  HO   O   C    108.80  3.000
 TPK  H3A  C3  H3   107.41  3.000
 TPK  H3A  C3  O4   111.78  3.000
 TPK  H3   C3  O4   111.34  3.000
 TPK  H3A  C3  C    108.85  3.000
 TPK  H3   C3  C    108.65  3.000
 TPK  O4   C3  C    108.74  3.000
 TPK  HO4  O4  C3   108.17  3.000
 TPK  HA   CA  N    110.00  3.000
 TPK  HA   CA  CB   109.00  3.000
 TPK  N    CA  CB   103.00  1.100
 TPK  HA   CA  C    109.00  3.000
 TPK  N    CA  C    112.10  2.500
 TPK  CB   CA  C    110.10  1.900
 TPK  HB3  CB  HB2  106.41  3.000
 TPK  HB3  CB  CG   110.17  3.000
 TPK  HB2  CB  CG   113.03  3.000
 TPK  HB3  CB  CA   108.92  3.000
 TPK  HB2  CB  CA   113.45  3.000
 TPK  CG   CB  CA   104.85  3.000
 TPK  HG3  CG  HG2  106.69  3.000
 TPK  HG3  CG  CD   111.70  3.000
 TPK  HG2  CG  CD   110.89  3.000
 TPK  HG3  CG  CB   111.23  3.000
 TPK  HG2  CG  CB   111.71  3.000
 TPK  CD   CG  CB   104.71  3.000
 TPK  HD3  CD  HD2  106.78  3.000
 TPK  HD3  CD  N    109.68  3.000
 TPK  HD2  CD  N    110.21  3.000
 TPK  HD3  CD  CG   112.20  3.000
 TPK  HD2  CD  CG   110.16  3.000
 TPK  N    CD  CG   103.20  1.500
 TPK  H    N   CD   108.68  3.000
 TPK  H    N   CA   108.07  3.000
 TPK  CD   N   CA   107.53  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
 TPK  Var_01  CD  CG  CB  CA  -15.47  30.0  1
 TPK  Var_02  N   CD  CG  CB   -3.04  30.0  1

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
 TPK  chir_01  C   O  C3  CA  negativ
 TPK  chir_02  CA  N  CB  C   negativ

