# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 08:41:30 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (2S,3R)-2-[(3S,6R)-3-amino-6-hydroxy-2-oxopiperidin-1-yl]-3-hydroxybutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H](N1[C@H](O)CC[C@H](N)C1=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
 SUJ  SUJ  '(2S,3R)-2-[(3S,6R)-3-amino-6-hydroxy-2-oxopiperidin-1-yl]-3-hydroxybutanoic acid'  ligand  32  16  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SUJ
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
 SUJ  N     N  NH2   0  -0.780  -2.0356   1.5210  -1.0246
 SUJ  CA    C  CH1   0  -0.206  -1.7724   0.1105  -1.2207
 SUJ  C1    C  C     0   0.581  -3.0645  -0.6085  -1.5920
 SUJ  O1    O  O     0  -0.483  -3.9493  -0.0446  -2.2150
 SUJ  CB    C  CH2   0  -0.466  -1.0065  -0.5765  -0.0966
 SUJ  CG    C  CH2   0  -0.481  -0.9179  -2.0655  -0.3686
 SUJ  CD    C  CH1   0   0.186  -2.3042  -2.6711  -0.3989
 SUJ  OD    O  OH1   0  -0.689  -2.8146  -2.6884   0.9068
 SUJ  N2    N  NT    0  -0.517  -3.1758  -1.9321  -1.3043
 SUJ  C2    C  CH1   0  -0.253  -4.3439  -2.6220  -1.8196
 SUJ  C3    C  CH1   0   0.066  -5.6782  -2.2955  -1.0988
 SUJ  C4    C  CH3   0  -0.686  -6.6249  -3.4798  -1.1508
 SUJ  O3    O  OH1   0  -0.675  -5.4360  -2.0017   0.2687
 SUJ  C     C  C     0   0.565  -4.4648  -2.4473  -3.3270
 SUJ  O     O  O     0  -0.433  -5.5097  -2.3542  -3.9188
 SUJ  OXT   O  OH1   0  -0.585  -3.2853  -2.4980  -3.9255
 SUJ  HN1   H  HNH2  0   0.354  -1.1496   2.0043  -0.9484
 SUJ  HN2   H  HNH2  0   0.342  -2.5001   1.6618  -0.1347
 SUJ  HA    H  HCH1  0   0.272  -1.1620   0.0220  -2.1302
 SUJ  HBC1  H  HCH2  0   0.232  -1.5030  -0.3919   0.8600
 SUJ  HBC2  H  HCH2  0   0.251  -0.0101  -0.1367  -0.0256
 SUJ  HGC1  H  HCH2  0   0.241  -0.4289  -2.2504  -1.3285
 SUJ  HGC2  H  HCH2  0   0.259  -0.3278  -2.5798   0.3914
 SUJ  H0    H  HCH1  0   0.236  -2.2460  -3.6906  -0.7999
 SUJ  HD    H  HOH1  0   0.449  -3.7830  -2.6113   0.8590
 SUJ  H2    H  HCH1  0   0.306  -4.1464  -3.6917  -1.6734
 SUJ  H3    H  HCH1  0   0.245  -6.1473  -1.4342  -1.5773
 SUJ  H4C1  H  HCH3  0   0.231  -6.2092  -4.3346  -0.6130
 SUJ  H4C2  H  HCH3  0   0.241  -6.8152  -3.7887  -2.1767
 SUJ  H4C3  H  HCH3  0   0.244  -7.5821  -3.2228  -0.6973
 SUJ  HB    H  HOH1  0   0.469  -5.3545  -1.0488   0.3769
 SUJ  HXT   H  HOH1  0   0.484  -3.4025  -2.4176  -4.8840

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
 SUJ  N    CA    single  1.448  0.020  1.448
 SUJ  N    HN1   single  0.890  0.020  1.040
 SUJ  N    HN2   single  0.890  0.020  1.040
 SUJ  CA   C1    single  1.525  0.020  1.525
 SUJ  CA   CB    single  1.524  0.020  1.524
 SUJ  CA   HA    single  0.970  0.020  1.090
 SUJ  C1   O1    double  1.220  0.020  1.220
 SUJ  C1   N2    single  1.359  0.020  1.359
 SUJ  CB   CG    single  1.516  0.020  1.516
 SUJ  CB   HBC1  single  0.970  0.020  1.090
 SUJ  CB   HBC2  single  0.970  0.020  1.090
 SUJ  CG   CD    single  1.513  0.020  1.513
 SUJ  CG   HGC1  single  0.970  0.020  1.090
 SUJ  CG   HGC2  single  0.970  0.020  1.090
 SUJ  CD   OD    single  1.402  0.020  1.402
 SUJ  CD   N2    single  1.458  0.020  1.458
 SUJ  CD   H0    single  0.970  0.020  1.090
 SUJ  OD   HD    single  0.850  0.020  0.980
 SUJ  N2   C2    single  1.451  0.020  1.451
 SUJ  C2   C3    single  1.551  0.020  1.551
 SUJ  C2   C     single  1.522  0.020  1.522
 SUJ  C2   H2    single  0.970  0.020  1.090
 SUJ  C3   C4    single  1.517  0.020  1.517
 SUJ  C3   O3    single  1.419  0.020  1.419
 SUJ  C3   H3    single  0.970  0.020  1.090
 SUJ  C4   H4C1  single  0.970  0.020  1.090
 SUJ  C4   H4C2  single  0.970  0.020  1.090
 SUJ  C4   H4C3  single  0.970  0.020  1.090
 SUJ  O3   HB    single  0.850  0.020  0.980
 SUJ  C    O     double  1.204  0.020  1.204
 SUJ  C    OXT   single  1.324  0.020  1.324
 SUJ  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
 SUJ  HN2   N    HN1   105.58  3.000
 SUJ  HN2   N    CA    109.72  3.000
 SUJ  HN1   N    CA    108.43  3.000
 SUJ  HA    CA   CB    107.16  3.000
 SUJ  HA    CA   C1    103.37  3.000
 SUJ  CB    CA   C1    113.14  3.000
 SUJ  HA    CA   N     106.95  3.000
 SUJ  CB    CA   N     115.51  3.000
 SUJ  C1    CA   N     109.77  3.000
 SUJ  N2    C1   O1    119.92  3.000
 SUJ  N2    C1   CA    118.50  3.000
 SUJ  O1    C1   CA    121.39  3.000
 SUJ  HBC2  CB   HBC1  106.82  3.000
 SUJ  HBC2  CB   CG    110.73  3.000
 SUJ  HBC1  CB   CG    110.45  3.000
 SUJ  HBC2  CB   CA    108.97  3.000
 SUJ  HBC1  CB   CA    109.94  3.000
 SUJ  CG    CB   CA    109.87  3.000
 SUJ  HGC2  CG   HGC1  106.86  3.000
 SUJ  HGC2  CG   CD    108.71  3.000
 SUJ  HGC1  CG   CD    108.94  3.000
 SUJ  HGC2  CG   CB    111.69  3.000
 SUJ  HGC1  CG   CB    110.48  3.000
 SUJ  CD    CG   CB    110.06  3.000
 SUJ  H0    CD   N2    106.01  3.000
 SUJ  H0    CD   OD    110.38  3.000
 SUJ  N2    CD   OD    111.53  3.000
 SUJ  H0    CD   CG    109.31  3.000
 SUJ  N2    CD   CG    110.94  3.000
 SUJ  OD    CD   CG    108.66  3.000
 SUJ  HD    OD   CD    108.41  3.000
 SUJ  C2    N2   CD    117.44  3.000
 SUJ  C2    N2   C1    116.98  3.000
 SUJ  CD    N2   C1    125.18  3.000
 SUJ  H2    C2   C     104.96  3.000
 SUJ  H2    C2   C3    107.33  3.000
 SUJ  C     C2   C3    111.58  3.000
 SUJ  H2    C2   N2    105.73  3.000
 SUJ  C     C2   N2    111.16  3.000
 SUJ  C3    C2   N2    115.29  3.000
 SUJ  H3    C3   O3    109.41  3.000
 SUJ  H3    C3   C4    109.44  3.000
 SUJ  O3    C3   C4    107.53  3.000
 SUJ  H3    C3   C2    109.39  3.000
 SUJ  O3    C3   C2    110.15  3.000
 SUJ  C4    C3   C2    110.89  3.000
 SUJ  H4C3  C4   H4C2  107.80  3.000
 SUJ  H4C3  C4   H4C1  108.30  3.000
 SUJ  H4C2  C4   H4C1  107.98  3.000
 SUJ  H4C3  C4   C3    110.47  3.000
 SUJ  H4C2  C4   C3    111.28  3.000
 SUJ  H4C1  C4   C3    110.89  3.000
 SUJ  HB    O3   C3    109.13  3.000
 SUJ  OXT   C    O     123.64  3.000
 SUJ  OXT   C    C2    111.87  3.000
 SUJ  O     C    C2    124.35  3.000
 SUJ  HXT   OXT  C     109.66  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
 SUJ  CONST_02  C2   N2   C1  CA  180.00   0.0  0
 SUJ  CONST_03  CD   N2   C1  O1  180.00   0.0  0
 SUJ  CONST_04  C2   N2   C1  O1    0.00   0.0  0
 SUJ  CONST_05  HXT  OXT  C   C2  180.00   0.0  0
 SUJ  Var_01    CD   CG   CB  CA  -62.25  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
 SUJ  chir_01  CA  N   C1  CB  positiv
 SUJ  chir_02  CD  OD  N2  CG  negativ
 SUJ  chir_03  C2  N2  C   C3  positiv
 SUJ  chir_04  C3  O3  C2  C4  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
 SUJ  plan-1  CA   0.020
 SUJ  plan-1  C1   0.020
 SUJ  plan-1  O1   0.020
 SUJ  plan-1  CD   0.020
 SUJ  plan-1  N2   0.020
 SUJ  plan-1  C2   0.020
 SUJ  plan-2  C2   0.020
 SUJ  plan-2  C    0.020
 SUJ  plan-2  O    0.020
 SUJ  plan-2  OXT  0.020
 SUJ  plan-2  HXT  0.020

