# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:56:33 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: amino{[(2R,3R,4S)-4-amino-2,3,5-trihydroxy-5-oxopentyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H](O)[C@H](O)CNC(N)=[NH2+])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
 2OR  2OR  amino{[(2R,3R,4S)-4-amino-2,3,5-trihydroxy-5-oxopentyl]amino}methaniminium  L-peptide  28  14  .  2016-04-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2OR
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
 2OR  O    O  O      0  -0.588  39.1799   -2.3068  5.5672
 2OR  C    C  C      0   0.424  38.8595   -3.3012  6.2433
 2OR  OXT  O  OC    -1  -0.594  39.5339   -4.3359  6.4177
 2OR  CA   C  CH1    0  -0.271  37.4996   -3.2440  6.9910
 2OR  N    N  NH2    0  -0.820  36.7715   -2.0294  6.6434
 2OR  CB   C  CH1    0   0.074  36.5474   -4.4043  6.6403
 2OR  OB   O  OH1    0  -0.686  36.1504   -4.2631  5.2986
 2OR  CG   C  CH1    0   0.029  37.0416   -5.8327  6.8421
 2OR  OG   O  OH1    0  -0.678  35.9410   -6.7125  6.6264
 2OR  CD   C  CH2    0  -0.336  37.5647   -6.0537  8.2550
 2OR  NE   N  NH1    0  -0.620  38.0674   -7.3982  8.4801
 2OR  CZ   C  C      0   0.781  37.3617   -8.4250  8.9416
 2OR  NH2  N  NC2    1  -0.809  37.9948   -9.4925  9.4119
 2OR  NH1  N  NH2    0  -0.808  36.0336   -8.3677  8.9653
 2OR  H2   H  HCH1   0   0.223  37.7277   -3.2911  8.0654
 2OR  HN   H  HNH2   0   0.345  36.2256   -1.6960  7.4262
 2OR  H4   H  HNH2   0   0.349  37.4362   -1.3117  6.3888
 2OR  H6   H  HCH1   0   0.182  35.6748   -4.2917  7.3106
 2OR  H7   H  HOH1   0   0.433  36.0412   -3.3010  5.2056
 2OR  H8   H  HCH1   0   0.231  37.8427   -6.0466  6.1321
 2OR  H9   H  HOH1   0   0.463  36.1186   -7.2620  5.8591
 2OR  H10  H  HCH2   0   0.283  38.3960   -5.3795  8.4394
 2OR  H11  H  HCH2   0   0.258  36.7903   -5.8306  8.9936
 2OR  H12  H  HNH1   0   0.422  39.0621   -7.5326  8.3847
 2OR  H13  H  HNC2   0   0.430  37.4976  -10.3405  9.6275
 2OR  H14  H  HNC2   0   0.429  38.9893   -9.4872  9.5653
 2OR  H15  H  HNH2   0   0.422  35.5085   -9.1446  9.3323
 2OR  H16  H  HNH2   0   0.430  35.5784   -7.7851  8.2719

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
 2OR  OB   CB   single  1.406  0.020  1.406
 2OR  O    C    deloc   1.231  0.020  1.231
 2OR  OG   CG   single  1.425  0.020  1.425
 2OR  C    OXT  deloc   1.247  0.020  1.247
 2OR  C    CA   single  1.525  0.021  1.525
 2OR  CB   CG   single  1.525  0.020  1.525
 2OR  CB   CA   single  1.530  0.020  1.530
 2OR  CG   CD   single  1.523  0.020  1.523
 2OR  CA   N    single  1.458  0.019  1.458
 2OR  CD   NE   single  1.453  0.020  1.453
 2OR  NE   CZ   single  1.329  0.020  1.329
 2OR  CZ   NH2  double  1.327  0.020  1.327
 2OR  CZ   NH1  single  1.330  0.020  1.330
 2OR  CA   H2   single  0.970  0.020  1.090
 2OR  N    HN   single  0.890  0.020  1.040
 2OR  N    H4   single  0.890  0.020  1.040
 2OR  CB   H6   single  0.970  0.020  1.090
 2OR  OB   H7   single  0.850  0.020  0.980
 2OR  CG   H8   single  0.970  0.020  1.090
 2OR  OG   H9   single  0.850  0.020  0.980
 2OR  CD   H10  single  0.970  0.020  1.090
 2OR  CD   H11  single  0.970  0.020  1.090
 2OR  NE   H12  single  0.860  0.020  1.020
 2OR  NH2  H13  single  0.860  0.020  1.020
 2OR  NH2  H14  single  0.860  0.020  1.020
 2OR  NH1  H15  single  0.890  0.020  1.040
 2OR  NH1  H16  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
 2OR  CA   C    OXT  115.89  3.000
 2OR  CA   C    O    120.80  1.700
 2OR  OXT  C    O    126.84  3.000
 2OR  H2   CA   CB   108.56  3.000
 2OR  H2   CA   N    111.86  3.000
 2OR  CB   CA   N    110.50  1.700
 2OR  H2   CA   C    106.69  3.000
 2OR  N    CA   C    111.00  2.800
 2OR  CB   CA   C    110.10  1.900
 2OR  H4   N    HN   108.41  3.000
 2OR  H4   N    CA   108.85  3.000
 2OR  HN   N    CA   111.09  3.000
 2OR  H6   CB   CG   105.72  3.000
 2OR  H6   CB   OB   110.20  3.000
 2OR  CG   CB   OB   108.17  3.000
 2OR  H6   CB   CA   105.83  3.000
 2OR  CG   CB   CA   118.35  3.000
 2OR  OB   CB   CA   108.41  3.000
 2OR  H7   OB   CB   102.84  3.000
 2OR  H8   CG   CD   108.84  3.000
 2OR  H8   CG   OG   110.31  3.000
 2OR  CD   CG   OG   108.42  3.000
 2OR  H8   CG   CB   109.60  3.000
 2OR  CD   CG   CB   111.72  3.000
 2OR  OG   CG   CB   107.93  3.000
 2OR  H9   OG   CG   109.35  3.000
 2OR  H11  CD   H10  107.51  3.000
 2OR  H11  CD   NE   109.22  3.000
 2OR  H10  CD   NE   106.46  3.000
 2OR  H11  CD   CG   110.72  3.000
 2OR  H10  CD   CG   109.29  3.000
 2OR  NE   CD   CG   113.39  3.000
 2OR  H12  NE   CZ   116.99  3.000
 2OR  H12  NE   CD   116.74  3.000
 2OR  CZ   NE   CD   125.82  3.000
 2OR  NH1  CZ   NH2  120.32  3.000
 2OR  NH1  CZ   NE   120.23  3.000
 2OR  NH2  CZ   NE   119.43  3.000
 2OR  H14  NH2  H13  117.39  3.000
 2OR  H14  NH2  CZ   121.41  3.000
 2OR  H13  NH2  CZ   121.20  3.000
 2OR  H16  NH1  H15  117.29  3.000
 2OR  H16  NH1  CZ   117.47  3.000
 2OR  H15  NH1  CZ   119.61  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
 2OR  CONST_02  NH1  CZ   NE  CD     0.00   0.0  0
 2OR  CONST_03  H13  NH2  CZ  NE   180.00   0.0  0
 2OR  CONST_04  H14  NH2  CZ  NE     0.00   0.0  0
 2OR  CONST_05  H15  NH1  CZ  NE   180.00   0.0  0
 2OR  CONST_07  H12  NE   CZ  NH2    0.00   0.0  0
 2OR  Var_01    CZ   NE   CD  CG   -91.52  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
 2OR  chir_01  CA  C   CB  N   positiv
 2OR  chir_02  CB  OB  CA  CG  positiv
 2OR  chir_03  CG  OG  CB  CD  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
 2OR  plan-1  CD   0.020
 2OR  plan-1  NE   0.020
 2OR  plan-1  CZ   0.020
 2OR  plan-1  NH2  0.020
 2OR  plan-1  NH1  0.020
 2OR  plan-1  H12  0.020
 2OR  plan-1  H13  0.020
 2OR  plan-1  H14  0.020
 2OR  plan-1  H15  0.020
 2OR  plan-1  H16  0.020
 2OR  plan-2  O    0.020
 2OR  plan-2  C    0.020
 2OR  plan-2  OXT  0.020
 2OR  plan-2  CA   0.020

