# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 19:53:52 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (3S)-3-(propan-2-yloxy)-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)O[C@H]1CCN[C@@H]1C(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
 3PX  3PX  (3S)-3-(propan-2-yloxy)-L-proline  L-peptide  26  12  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3PX
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
 3PX  C     C  C      0   0.402  -1.5401   1.2657   0.8709
 3PX  N     N  NH1    0  -0.599  -2.2347  -1.0094   0.1344
 3PX  O     O  O      0  -0.610  -2.1693   1.7581  -0.0890
 3PX  CA    C  CH1    0  -0.231  -1.1793  -0.2239   0.7500
 3PX  CB    C  CH1    0   0.068   0.0368  -0.4516  -0.1609
 3PX  CD    C  CH2    0  -0.299  -1.5965  -2.2231  -0.3850
 3PX  CG    C  CH2    0  -0.518  -0.0843  -1.9360  -0.5247
 3PX  OB1   O  O2     0  -0.499   1.2192  -0.0777   0.4949
 3PX  CB2   C  CH1    0   0.044   2.4211  -0.2354  -0.2411
 3PX  CB3   C  CH3    0  -0.687   2.5036   0.7098  -1.4330
 3PX  CB4   C  CH3    0  -0.674   3.5614   0.0035   0.7318
 3PX  OXT   O  OC    -1  -0.607  -1.1458   1.8623   1.8896
 3PX  HA    H  HCH1   0   0.205  -0.9471  -0.6338   1.7411
 3PX  HB    H  HCH1   0   0.194  -0.1141   0.1542  -1.0663
 3PX  HD    H  HCH2   0   0.215  -1.7550  -3.0549   0.3059
 3PX  HDA   H  HCH2   0   0.228  -2.0563  -2.5087  -1.3315
 3PX  HG    H  HCH2   0   0.238   0.2894  -2.1596  -1.5247
 3PX  HGA   H  HCH2   0   0.232   0.4950  -2.5360   0.1820
 3PX  HB2   H  HCH1   0   0.203   2.4938  -1.2675  -0.6115
 3PX  HB3   H  HCH3   0   0.231   3.4599   0.5843  -1.9420
 3PX  HB3A  H  HCH3   0   0.234   1.7212   0.5234  -2.1695
 3PX  HB3B  H  HCH3   0   0.222   2.4270   1.7502  -1.1106
 3PX  HB4   H  HCH3   0   0.232   3.5188  -0.6902   1.5725
 3PX  HB4A  H  HCH3   0   0.225   4.5203  -0.1347   0.2323
 3PX  HB4B  H  HCH3   0   0.221   3.5347   1.0218   1.1258
 3PX  HN    H  HNH1   0   0.332  -2.5947  -0.4599  -0.6372

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
 3PX  C    O     deloc   1.231  0.020  1.231
 3PX  C    OXT   deloc   1.245  0.020  1.245
 3PX  N    CD    single  1.473  0.014  1.473
 3PX  N    CA    single  1.466  0.015  1.466
 3PX  N    HN    single  0.890  0.020  1.040
 3PX  CA   C     single  1.525  0.021  1.525
 3PX  CA   CB    single  1.530  0.020  1.530
 3PX  CA   HA    single  0.970  0.020  0.970
 3PX  CB   CG    single  1.533  0.020  1.533
 3PX  CB   HB    single  0.970  0.020  1.090
 3PX  CD   CG    single  1.546  0.020  1.546
 3PX  CD   HD    single  0.970  0.020  1.090
 3PX  CD   HDA   single  0.970  0.020  1.090
 3PX  CG   HG    single  0.970  0.020  1.090
 3PX  CG   HGA   single  0.970  0.020  1.090
 3PX  OB1  CB    single  1.403  0.020  1.403
 3PX  CB2  OB1   single  1.418  0.020  1.418
 3PX  CB2  CB4   single  1.518  0.020  1.518
 3PX  CB2  HB2   single  0.970  0.020  1.090
 3PX  CB3  CB2   single  1.523  0.020  1.523
 3PX  CB3  HB3   single  0.970  0.020  1.090
 3PX  CB3  HB3A  single  0.970  0.020  1.090
 3PX  CB3  HB3B  single  0.970  0.020  1.090
 3PX  CB4  HB4   single  0.970  0.020  1.090
 3PX  CB4  HB4A  single  0.970  0.020  1.090
 3PX  CB4  HB4B  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
 3PX  OXT   C    CA    117.03  3.000
 3PX  CA    C    O     119.00  3.000
 3PX  OXT   C    O     126.85  3.000
 3PX  HN    N    CD    109.49  3.000
 3PX  HN    N    CA    106.72  3.000
 3PX  CD    N    CA    106.35  3.000
 3PX  HA    CA   CB    109.00  3.000
 3PX  HA    CA   N     110.00  3.000
 3PX  CB    CA   N     103.00  1.100
 3PX  HA    CA   C     109.00  3.000
 3PX  CB    CA   C     110.10  1.900
 3PX  N     CA   C     112.10  2.500
 3PX  HB    CB   OB1   110.71  3.000
 3PX  OB1   CB   CG    115.82  3.000
 3PX  HB    CB   CG    109.09  3.000
 3PX  OB1   CB   CA    110.52  3.000
 3PX  HB    CB   CA    107.33  3.000
 3PX  CG    CB   CA    102.81  3.000
 3PX  HDA   CD   HD    106.76  3.000
 3PX  HDA   CD   CG    112.50  3.000
 3PX  HD    CD   CG    109.90  3.000
 3PX  HDA   CD   N     109.92  3.000
 3PX  HD    CD   N     110.06  3.000
 3PX  CG    CD   N     103.20  1.500
 3PX  HGA   CG   HG    107.37  3.000
 3PX  HGA   CG   CD    110.98  3.000
 3PX  HG    CG   CD    112.33  3.000
 3PX  HGA   CG   CB    109.65  3.000
 3PX  HG    CG   CB    112.90  3.000
 3PX  CD    CG   CB    103.63  3.000
 3PX  CB2   OB1  CB    116.24  3.000
 3PX  HB2   CB2  CB4   108.31  3.000
 3PX  HB2   CB2  CB3   108.38  3.000
 3PX  CB4   CB2  CB3   111.29  3.000
 3PX  CB3   CB2  OB1   112.52  3.000
 3PX  HB2   CB2  OB1   109.60  3.000
 3PX  CB4   CB2  OB1   106.65  3.000
 3PX  HB3B  CB3  HB3A  108.17  3.000
 3PX  HB3B  CB3  HB3   108.00  3.000
 3PX  HB3A  CB3  HB3   107.11  3.000
 3PX  HB3B  CB3  CB2   110.88  3.000
 3PX  HB3A  CB3  CB2   112.55  3.000
 3PX  HB3   CB3  CB2   109.95  3.000
 3PX  HB4B  CB4  HB4A  107.76  3.000
 3PX  HB4B  CB4  HB4   108.30  3.000
 3PX  HB4A  CB4  HB4   107.87  3.000
 3PX  HB4B  CB4  CB2   111.08  3.000
 3PX  HB4A  CB4  CB2   110.31  3.000
 3PX  HB4   CB4  CB2   111.38  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
 3PX  Var_01  CB   CG   CD   N      -4.65  30.0  1
 3PX  Var_02  CG   CD   N    CA    -20.06  30.0  1
 3PX  Var_03  CB4  CB2  OB1  CB   -170.73  30.0  2
 3PX  Var_04  HB4  CB4  CB2  OB1    58.45  30.0  3
 3PX  Var_05  HB3  CB3  CB2  OB1   177.53  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
 3PX  chir_01  CA  N    C   CB  positiv
 3PX  chir_02  CB  OB1  CG  CA  negativ

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
 3PX  plan-1  C    0.020
 3PX  plan-1  O    0.020
 3PX  plan-1  CA   0.020
 3PX  plan-1  OXT  0.020

