# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:30:27 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  31  16  .  2022-03-23  2022-03-23
;
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  -0.782  -2.1173   1.6543  -0.8766
 SUJ  CA    C  CH1    0  -0.198  -1.8239   0.2553  -1.1151
 SUJ  C1    C  C      0   0.557  -3.1011  -0.4856  -1.5015
 SUJ  O1    O  O      0  -0.493  -4.0470   0.1103  -1.9935
 SUJ  CB    C  CH2    0  -0.467  -1.0549  -0.4518  -0.0062
 SUJ  CG    C  CH2    0  -0.475  -0.8720  -1.9098  -0.3788
 SUJ  CD    C  CH1    0   0.189  -2.2197  -2.5866  -0.5063
 SUJ  OD    O  OH1    0  -0.702  -2.7574  -2.7702   0.7825
 SUJ  N2    N  NT     0  -0.498  -3.1297  -1.8312  -1.3472
 SUJ  C2    C  CH1    0  -0.265  -4.2583  -2.5537  -1.9161
 SUJ  C3    C  CH1    0   0.071  -5.5931  -2.3459  -1.1621
 SUJ  C4    C  CH3    0  -0.685  -6.4404  -3.6032  -1.1968
 SUJ  O3    O  OH1    0  -0.683  -5.3740  -2.0324   0.2152
 SUJ  C     C  C      0   0.435  -4.3666  -2.3115  -3.4500
 SUJ  O     O  O      0  -0.601  -3.2979  -2.1292  -4.0547
 SUJ  OXT   O  OC    -1  -0.596  -5.5074  -2.3865  -3.9438
 SUJ  HN1   H  HNH2   0   0.349  -1.2474   2.1322  -0.6762
 SUJ  HN2   H  HNH2   0   0.338  -2.6797   1.7485  -0.0386
 SUJ  HA    H  HCH1   0   0.260  -1.2021   0.2055  -2.0203
 SUJ  HBC1  H  HCH2   0   0.227  -1.5963  -0.3666   0.9403
 SUJ  HBC2  H  HCH2   0   0.245  -0.0899   0.0400   0.1340
 SUJ  HGC1  H  HCH2   0   0.234  -0.3376  -1.9913  -1.3295
 SUJ  HGC2  H  HCH2   0   0.251  -0.2784  -2.4471   0.3627
 SUJ  H0    H  HCH1   0   0.224  -2.0853  -3.5605  -0.9936
 SUJ  HD    H  HOH1   0   0.445  -3.7202  -2.6306   0.7278
 SUJ  H2    H  HCH1   0   0.250  -3.9945  -3.6142  -1.8136
 SUJ  H3    H  HCH1   0   0.225  -6.1440  -1.5281  -1.6288
 SUJ  H4C1  H  HCH3   0   0.218  -5.9451  -4.4223  -0.6697
 SUJ  H4C2  H  HCH3   0   0.236  -6.6070  -3.9143  -2.2253
 SUJ  H4C3  H  HCH3   0   0.229  -7.4121  -3.4355  -0.7299
 SUJ  HB    H  HOH1   0   0.462  -5.2926  -1.0776   0.3027

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  1.449  0.020  1.449
 SUJ  N   HN1   single  0.890  0.020  1.040
 SUJ  N   HN2   single  0.890  0.020  1.040
 SUJ  CA  C1    single  1.526  0.020  1.526
 SUJ  CA  CB    single  1.524  0.020  1.524
 SUJ  CA  HA    single  0.970  0.020  1.090
 SUJ  C1  O1    double  1.221  0.020  1.221
 SUJ  C1  N2    single  1.355  0.020  1.355
 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  1.409  0.020  1.409
 SUJ  CD  N2    single  1.451  0.020  1.451
 SUJ  CD  H0    single  0.970  0.020  1.090
 SUJ  OD  HD    single  0.850  0.020  0.980
 SUJ  N2  C2    single  1.456  0.020  1.456
 SUJ  C2  C3    single  1.547  0.020  1.547
 SUJ  C2  C     single  1.557  0.020  1.557
 SUJ  C2  H2    single  0.970  0.020  1.090
 SUJ  C3  C4    single  1.517  0.020  1.517
 SUJ  C3  O3    single  1.429  0.020  1.429
 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     deloc   1.241  0.020  1.241
 SUJ  C   OXT   deloc   1.245  0.020  1.245

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   105.62  3.000
 SUJ  HN2   N   CA    109.76  3.000
 SUJ  HN1   N   CA    108.32  3.000
 SUJ  HA    CA  CB    107.02  3.000
 SUJ  HA    CA  C1    104.05  3.000
 SUJ  CB    CA  C1    112.42  3.000
 SUJ  HA    CA  N     107.09  3.000
 SUJ  CB    CA  N     115.50  3.000
 SUJ  C1    CA  N     109.93  3.000
 SUJ  N2    C1  O1    120.93  3.000
 SUJ  N2    C1  CA    118.10  3.000
 SUJ  O1    C1  CA    120.88  3.000
 SUJ  HBC2  CB  HBC1  106.93  3.000
 SUJ  HBC2  CB  CG    110.98  3.000
 SUJ  HBC1  CB  CG    110.33  3.000
 SUJ  HBC2  CB  CA    109.29  3.000
 SUJ  HBC1  CB  CA    110.11  3.000
 SUJ  CG    CB  CA    109.17  3.000
 SUJ  HGC2  CG  HGC1  106.75  3.000
 SUJ  HGC2  CG  CD    108.75  3.000
 SUJ  HGC1  CG  CD    109.18  3.000
 SUJ  HGC2  CG  CB    111.85  3.000
 SUJ  HGC1  CG  CB    110.14  3.000
 SUJ  CD    CG  CB    110.09  3.000
 SUJ  H0    CD  N2    106.35  3.000
 SUJ  H0    CD  OD    109.72  3.000
 SUJ  N2    CD  OD    111.02  3.000
 SUJ  H0    CD  CG    108.98  3.000
 SUJ  N2    CD  CG    111.99  3.000
 SUJ  OD    CD  CG    108.73  3.000
 SUJ  HD    OD  CD    107.88  3.000
 SUJ  C2    N2  CD    117.02  3.000
 SUJ  C2    N2  C1    117.70  3.000
 SUJ  CD    N2  C1    124.74  3.000
 SUJ  H2    C2  C     105.01  3.000
 SUJ  H2    C2  C3    106.95  3.000
 SUJ  C     C2  C3    113.54  3.000
 SUJ  H2    C2  N2    104.87  3.000
 SUJ  C     C2  N2    111.21  3.000
 SUJ  C3    C2  N2    114.32  3.000
 SUJ  H3    C3  O3    108.98  3.000
 SUJ  H3    C3  C4    109.24  3.000
 SUJ  O3    C3  C4    106.83  3.000
 SUJ  H3    C3  C2    109.14  3.000
 SUJ  O3    C3  C2    111.52  3.000
 SUJ  C4    C3  C2    111.07  3.000
 SUJ  H4C3  C4  H4C2  108.20  3.000
 SUJ  H4C3  C4  H4C1  108.21  3.000
 SUJ  H4C2  C4  H4C1  108.13  3.000
 SUJ  H4C3  C4  C3    111.12  3.000
 SUJ  H4C2  C4  C3    110.15  3.000
 SUJ  H4C1  C4  C3    110.92  3.000
 SUJ  HB    O3  C3    108.55  3.000
 SUJ  OXT   C   O     127.17  3.000
 SUJ  OXT   C   C2    116.43  3.000
 SUJ  O     C   C2    116.30  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_04  C2  N2  C1  O1    0.00   0.0  0
 SUJ  Var_01    CD  CG  CB  CA  -62.03  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

