# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:31:42 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  27  12  .  2022-03-10  2022-11-17
;
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   0.528  -1.4984   1.3233   0.3379
 3PX  N     N  NH1   0  -0.590  -2.2860  -0.9788   0.0482
 3PX  O     O  O     0  -0.441  -2.2481   1.7533  -0.5044
 3PX  CA    C  CH1   0  -0.227  -1.2224  -0.1408   0.5534
 3PX  CB    C  CH1   0   0.061   0.0497  -0.5939  -0.1988
 3PX  CD    C  CH2   0  -0.311  -1.6839  -2.3058  -0.1224
 3PX  CG    C  CH2   0  -0.501  -0.1622  -2.1126  -0.3075
 3PX  OB1   O  O2    0  -0.492   1.1994  -0.2022   0.4884
 3PX  CB2   C  CH1   0   0.034   2.3749  -0.0884  -0.3030
 3PX  CB3   C  CH3   0  -0.669   2.4010   1.2318  -1.0605
 3PX  CB4   C  CH3   0  -0.675   3.5592  -0.2171   0.6363
 3PX  OXT   O  OH1   0  -0.581  -0.7860   2.0890   1.1481
 3PX  HA    H  HCH1  0   0.274  -1.0727  -0.3310   1.6228
 3PX  HB    H  HCH1  0   0.220   0.0196  -0.1550  -1.2062
 3PX  HD    H  HCH2  0   0.230  -1.8799  -2.9136   0.7632
 3PX  HDA   H  HCH2  0   0.243  -2.1521  -2.8108  -0.9661
 3PX  HG    H  HCH2  0   0.248   0.1904  -2.5054  -1.2611
 3PX  HGA   H  HCH2  0   0.243   0.3984  -2.6124   0.4845
 3PX  HB2   H  HCH1  0   0.207   2.4159  -0.9152  -1.0257
 3PX  HB3   H  HCH3  0   0.229   3.3167   1.3100  -1.6480
 3PX  HB3A  H  HCH3  0   0.230   1.5643   1.3289  -1.7542
 3PX  HB3B  H  HCH3  0   0.224   2.3681   2.0748  -0.3682
 3PX  HB4   H  HCH3  0   0.234   3.5428  -1.1711   1.1645
 3PX  HB4A  H  HCH3  0   0.227   4.4929  -0.1610   0.0768
 3PX  HB4B  H  HCH3  0   0.224   3.5632   0.5863   1.3755
 3PX  HXT   H  HOH1  0   0.483  -0.9406   3.0244   0.9459
 3PX  HN    H  HNH1  0   0.349  -2.5745  -0.6269  -0.8570

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     double  1.231  0.020  1.231
 3PX  C    OXT   single  1.323  0.020  1.323
 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  1.537  0.020  1.537
 3PX  CB   HB    single  0.970  0.020  1.090
 3PX  CD   CG    single  1.545  0.020  1.545
 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  1.395  0.020  1.395
 3PX  CB2  OB1   single  1.422  0.020  1.422
 3PX  CB2  CB4   single  1.517  0.020  1.517
 3PX  CB2  HB2   single  0.970  0.020  1.090
 3PX  CB3  CB2   single  1.522  0.020  1.522
 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
 3PX  OXT  HXT   single  0.850  0.020  0.980

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    112.12  3.000
 3PX  CA    C    O     119.00  3.000
 3PX  OXT   C    O     123.76  3.000
 3PX  HN    N    CD    109.09  3.000
 3PX  HN    N    CA    108.69  3.000
 3PX  CD    N    CA    105.25  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   111.21  3.000
 3PX  OB1   CB   CG    115.19  3.000
 3PX  HB    CB   CG    109.02  3.000
 3PX  OB1   CB   CA    110.86  3.000
 3PX  HB    CB   CA    107.84  3.000
 3PX  CG    CB   CA    102.16  3.000
 3PX  HDA   CD   HD    107.04  3.000
 3PX  HDA   CD   CG    112.86  3.000
 3PX  HD    CD   CG    110.10  3.000
 3PX  HDA   CD   N     109.46  3.000
 3PX  HD    CD   N     109.60  3.000
 3PX  CG    CD   N     103.20  1.500
 3PX  HGA   CG   HG    107.68  3.000
 3PX  HGA   CG   CD    111.20  3.000
 3PX  HG    CG   CD    112.23  3.000
 3PX  HGA   CG   CB    109.29  3.000
 3PX  HG    CG   CB    111.92  3.000
 3PX  CD    CG   CB    104.52  3.000
 3PX  CB2   OB1  CB    115.44  3.000
 3PX  HB2   CB2  CB4   108.31  3.000
 3PX  HB2   CB2  CB3   108.94  3.000
 3PX  CB4   CB2  CB3   111.61  3.000
 3PX  CB3   CB2  OB1   111.14  3.000
 3PX  HB2   CB2  OB1   109.67  3.000
 3PX  CB4   CB2  OB1   107.10  3.000
 3PX  HB3B  CB3  HB3A  108.14  3.000
 3PX  HB3B  CB3  HB3   108.16  3.000
 3PX  HB3A  CB3  HB3   107.16  3.000
 3PX  HB3B  CB3  CB2   110.71  3.000
 3PX  HB3A  CB3  CB2   112.36  3.000
 3PX  HB3   CB3  CB2   110.16  3.000
 3PX  HB4B  CB4  HB4A  107.86  3.000
 3PX  HB4B  CB4  HB4   108.41  3.000
 3PX  HB4A  CB4  HB4   107.85  3.000
 3PX  HB4B  CB4  CB2   111.08  3.000
 3PX  HB4A  CB4  CB2   110.27  3.000
 3PX  HB4   CB4  CB2   111.25  3.000
 3PX  HXT   OXT  C     110.17  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  CONST_01  HXT  OXT  C    CA    180.00   0.0  0
 3PX  Var_01    CB   CG   CD   N       1.18  30.0  1
 3PX  Var_02    CG   CD   N    CA    -24.56  30.0  1
 3PX  Var_03    CB4  CB2  OB1  CB   -157.59  30.0  1
 3PX  Var_04    HB4  CB4  CB2  OB1    59.01  30.0  3
 3PX  Var_05    HB3  CB3  CB2  OB1   179.01  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
 3PX  plan-1  HXT  0.020

