# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 14:11:23 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2S,3R,4S,5S)-2-(acetylamino)-5-carboxy-3,4-dihydroxypiperidinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[NH2+]C[C@@H]([C@H](O)[C@@H]1O)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
 3XR  3XR  (2S,3R,4S,5S)-2-(acetylamino)-5-carboxy-3,4-dihydroxypiperidinium  ligand  29  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3XR
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
 3XR  CAA  C  CH3    0  -0.775  -4.7762  -0.5129  -0.3684
 3XR  CAJ  C  C      0   0.543  -3.3899  -0.6426   0.1937
 3XR  OAB  O  O      0  -0.487  -3.1339  -1.3046   1.1877
 3XR  NAH  N  NH1    0  -0.661  -2.4145   0.0142  -0.4801
 3XR  CAO  C  CH1    0   0.101  -1.0708   0.0452  -0.0134
 3XR  NAI  N  NT2    1  -0.677  -0.4409  -1.3082  -0.1847
 3XR  CAG  C  CH2    0  -0.302   0.9912  -1.3829   0.2404
 3XR  CAN  C  CH1    0  -0.458   1.8092  -0.3525  -0.5104
 3XR  CAK  C  C      0   0.464   3.3019  -0.3954  -0.0969
 3XR  OAD  O  O      0  -0.600   4.0259   0.4812  -0.5976
 3XR  OAC  O  OC    -1  -0.588   3.6397  -1.3077   0.6784
 3XR  CAL  C  CH1    0   0.000   1.2240   1.0391  -0.3257
 3XR  OAE  O  OH1    0  -0.664   1.3399   1.3825   1.0332
 3XR  CAM  C  CH1    0  -0.012  -0.2374   1.0716  -0.7766
 3XR  OAF  O  OH1    0  -0.658  -0.8402   2.3136  -0.5243
 3XR  H1   H  HCH3   0   0.278  -5.1396  -1.4969  -0.6636
 3XR  H2   H  HCH3   0   0.278  -5.4421  -0.1397   0.4092
 3XR  H3   H  HCH3   0   0.259  -4.8356   0.1522  -1.2269
 3XR  H4   H  HNH1   0   0.423  -2.6435   0.5203  -1.3216
 3XR  H5   H  HCH1   0   0.316  -1.0367   0.2458   1.0590
 3XR  H6   H  HNT2   0   0.473  -0.9847  -1.9815   0.3597
 3XR  H8   H  HCH2   0   0.292   1.0110  -1.2324   1.3172
 3XR  H9   H  HCH2   0   0.302   1.3161  -2.3974   0.0289
 3XR  H10  H  HCH1   0   0.274   1.7652  -0.5852  -1.5823
 3XR  H12  H  HCH1   0   0.245   1.7838   1.7362  -0.9628
 3XR  H13  H  HOH1   0   0.452   0.9425   2.2505   1.1634
 3XR  H14  H  HCH1   0   0.252  -0.2700   0.8191  -1.8473
 3XR  H15  H  HOH1   0   0.469  -0.5151   2.9502  -1.1697
 3XR  H7   H  HNT2   0   0.460  -0.5298  -1.6071  -1.1584

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
 3XR  OAD  CAK  deloc   1.242  0.020  1.242
 3XR  OAC  CAK  deloc   1.244  0.020  1.244
 3XR  CAK  CAN  single  1.549  0.020  1.549
 3XR  OAE  CAL  single  1.406  0.020  1.406
 3XR  CAL  CAN  single  1.521  0.020  1.521
 3XR  CAL  CAM  single  1.530  0.020  1.530
 3XR  CAN  CAG  single  1.515  0.020  1.515
 3XR  CAG  NAI  single  1.496  0.020  1.496
 3XR  CAM  OAF  single  1.403  0.020  1.403
 3XR  CAM  CAO  single  1.527  0.020  1.527
 3XR  CAO  NAI  single  1.503  0.020  1.503
 3XR  CAO  NAH  single  1.423  0.020  1.423
 3XR  NAH  CAJ  single  1.355  0.020  1.355
 3XR  OAB  CAJ  double  1.221  0.020  1.221
 3XR  CAJ  CAA  single  1.502  0.020  1.502
 3XR  CAA  H1   single  0.970  0.020  1.090
 3XR  CAA  H2   single  0.970  0.020  1.090
 3XR  CAA  H3   single  0.970  0.020  1.090
 3XR  NAH  H4   single  0.860  0.020  1.020
 3XR  CAO  H5   single  0.970  0.020  1.090
 3XR  NAI  H6   single  0.890  0.020  1.040
 3XR  CAG  H8   single  0.970  0.020  1.090
 3XR  CAG  H9   single  0.970  0.020  1.090
 3XR  CAN  H10  single  0.970  0.020  1.090
 3XR  CAL  H12  single  0.970  0.020  1.090
 3XR  OAE  H13  single  0.850  0.020  0.980
 3XR  CAM  H14  single  0.970  0.020  1.090
 3XR  OAF  H15  single  0.850  0.020  0.980
 3XR  NAI  H7   single  0.890  0.020  1.040

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
 3XR  H3   CAA  H2   108.69  3.000
 3XR  H3   CAA  H1   108.67  3.000
 3XR  H2   CAA  H1   107.38  3.000
 3XR  H3   CAA  CAJ  113.50  3.000
 3XR  H2   CAA  CAJ  109.07  3.000
 3XR  H1   CAA  CAJ  109.35  3.000
 3XR  NAH  CAJ  OAB  121.09  3.000
 3XR  OAB  CAJ  CAA  123.02  3.000
 3XR  NAH  CAJ  CAA  115.88  3.000
 3XR  H4   NAH  CAO  118.51  3.000
 3XR  H4   NAH  CAJ  119.65  3.000
 3XR  CAO  NAH  CAJ  121.82  3.000
 3XR  H5   CAO  CAM  110.52  3.000
 3XR  H5   CAO  NAI  105.33  3.000
 3XR  CAM  CAO  NAI  108.65  3.000
 3XR  H5   CAO  NAH  110.84  3.000
 3XR  NAI  CAO  NAH  109.81  3.000
 3XR  CAM  CAO  NAH  111.48  3.000
 3XR  H7   NAI  H6   105.57  3.000
 3XR  H7   NAI  CAG  109.83  3.000
 3XR  H6   NAI  CAG  108.97  3.000
 3XR  H7   NAI  CAO  109.60  3.000
 3XR  H6   NAI  CAO  108.03  3.000
 3XR  CAG  NAI  CAO  114.45  3.000
 3XR  H9   CAG  H8   108.46  3.000
 3XR  H9   CAG  CAN  112.17  3.000
 3XR  H8   CAG  CAN  112.76  3.000
 3XR  H9   CAG  NAI  106.13  3.000
 3XR  H8   CAG  NAI  106.97  3.000
 3XR  CAN  CAG  NAI  110.01  3.000
 3XR  H10  CAN  CAL  107.28  3.000
 3XR  H10  CAN  CAK  107.05  3.000
 3XR  CAL  CAN  CAK  111.32  3.000
 3XR  H10  CAN  CAG  108.55  3.000
 3XR  CAL  CAN  CAG  110.76  3.000
 3XR  CAK  CAN  CAG  111.66  3.000
 3XR  OAC  CAK  OAD  127.62  3.000
 3XR  OAC  CAK  CAN  116.63  3.000
 3XR  OAD  CAK  CAN  115.75  3.000
 3XR  H12  CAL  CAM  107.61  3.000
 3XR  H12  CAL  OAE  111.33  3.000
 3XR  CAM  CAL  OAE  111.00  3.000
 3XR  H12  CAL  CAN  108.32  3.000
 3XR  CAM  CAL  CAN  110.56  3.000
 3XR  OAE  CAL  CAN  108.00  3.000
 3XR  H13  OAE  CAL  108.45  3.000
 3XR  H14  CAM  OAF  111.42  3.000
 3XR  H14  CAM  CAL  108.07  3.000
 3XR  OAF  CAM  CAL  112.09  3.000
 3XR  H14  CAM  CAO  108.42  3.000
 3XR  OAF  CAM  CAO  105.70  3.000
 3XR  CAL  CAM  CAO  111.09  3.000
 3XR  H15  OAF  CAM  108.64  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
 3XR  CONST_01  CAO  NAH  CAJ  CAA  180.00   0.0  0
 3XR  CONST_02  CAO  NAH  CAJ  OAB    0.00   0.0  0
 3XR  CONST_03  H4   NAH  CAJ  CAA    0.00   0.0  0
 3XR  Var_01    CAN  CAG  NAI  CAO  -56.55  30.0  1
 3XR  Var_02    H1   CAA  CAJ  OAB  -61.32  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
 3XR  chir_01  CAO  CAM  NAI  NAH  positiv
 3XR  chir_02  CAN  CAK  CAL  CAG  positiv
 3XR  chir_03  CAL  OAE  CAN  CAM  negativ
 3XR  chir_04  CAM  OAF  CAL  CAO  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
 3XR  plan-1  CAA  0.020
 3XR  plan-1  CAJ  0.020
 3XR  plan-1  OAB  0.020
 3XR  plan-1  NAH  0.020
 3XR  plan-1  CAO  0.020
 3XR  plan-1  H4   0.020
 3XR  plan-2  CAN  0.020
 3XR  plan-2  CAK  0.020
 3XR  plan-2  OAD  0.020
 3XR  plan-2  OAC  0.020

