# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:36:54 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: amino{[(2R,4S)-4-amino-2,5-dihydroxy-5-oxopentyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[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
 ARO  ARO  amino{[(2R,4S)-4-amino-2,5-dihydroxy-5-oxopentyl]amino}methaniminium  L-peptide  27  13  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_ARO
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
 ARO  N     N  NH2    0  -0.809  38.5159  70.5487  46.3706
 ARO  CA    C  CH1    0  -0.200  39.4026  71.6901  46.2153
 ARO  C     C  C      0   0.399  39.1379  72.4160  44.8697
 ARO  O     O  O      0  -0.612  39.5590  73.5876  44.7921
 ARO  CB    C  CH2    0  -0.456  40.9066  71.3669  46.3032
 ARO  CG    C  CH1    0   0.044  41.4243  71.0705  47.7024
 ARO  OH    O  OH1    0  -0.665  40.8188  69.9003  48.2112
 ARO  CD    C  CH2    0  -0.339  42.9457  70.9031  47.6655
 ARO  NE    N  NH1    0  -0.632  43.5267  70.5967  48.9600
 ARO  CZ    C  C      0   0.818  43.9525  71.4817  49.8552
 ARO  NH1   N  NH2    0  -0.809  43.8222  72.7852  49.6478
 ARO  NH2   N  NC2    1  -0.817  44.5286  71.0550  50.9734
 ARO  OXT   O  OC    -1  -0.598  38.5650  71.7663  43.9731
 ARO  H     H  HNH2   0   0.334  38.8911  69.9177  47.0651
 ARO  H2    H  HNH2   0   0.321  38.4944  70.0496  45.4900
 ARO  HA    H  HCH1   0   0.195  39.1850  72.4120  47.0131
 ARO  HB2   H  HCH2   0   0.220  41.1423  70.5308  45.6336
 ARO  HB3   H  HCH2   0   0.229  41.4725  72.2278  45.9383
 ARO  HG    H  HCH1   0   0.213  41.1782  71.9319  48.3408
 ARO  HH    H  HOH1   0   0.453  40.9145  69.8915  49.1684
 ARO  HD2   H  HCH2   0   0.282  43.2024  70.0754  47.0035
 ARO  HD3   H  HCH2   0   0.261  43.4215  71.7905  47.2435
 ARO  HE    H  HNH1   0   0.428  43.6061  69.6214  49.2030
 ARO  HH11  H  HNH2   0   0.435  44.1753  73.4501  50.3163
 ARO  HH12  H  HNH2   0   0.442  43.2855  73.1595  48.8846
 ARO  HH21  H  HNC2   0   0.432  44.7591  70.0847  51.1089
 ARO  HH22  H  HNC2   0   0.432  44.8488  71.7023  51.6740

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
 ARO  N    CA    single  1.458  0.019  1.458
 ARO  N    H     single  0.860  0.020  0.860
 ARO  N    H2    single  0.890  0.020  1.040
 ARO  CA   C     single  1.525  0.021  1.525
 ARO  CA   CB    single  1.530  0.020  1.530
 ARO  CA   HA    single  0.970  0.020  0.970
 ARO  C    O     deloc   1.231  0.020  1.231
 ARO  C    OXT   deloc   1.247  0.020  1.247
 ARO  CB   CG    single  1.521  0.020  1.521
 ARO  CB   HB2   single  0.970  0.020  1.090
 ARO  CB   HB3   single  0.970  0.020  1.090
 ARO  CG   OH    single  1.412  0.020  1.412
 ARO  CG   CD    single  1.531  0.020  1.531
 ARO  CG   HG    single  0.970  0.020  1.090
 ARO  OH   HH    single  0.850  0.020  0.980
 ARO  CD   NE    single  1.452  0.020  1.452
 ARO  CD   HD2   single  0.970  0.020  1.090
 ARO  CD   HD3   single  0.970  0.020  1.090
 ARO  NE   CZ    single  1.329  0.020  1.329
 ARO  NE   HE    single  0.860  0.020  1.020
 ARO  CZ   NH1   single  1.326  0.020  1.326
 ARO  CZ   NH2   double  1.328  0.020  1.328
 ARO  NH1  HH11  single  0.860  0.020  1.020
 ARO  NH1  HH12  single  0.860  0.020  1.020
 ARO  NH2  HH21  single  0.860  0.020  1.020
 ARO  NH2  HH22  single  0.860  0.020  1.020

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
 ARO  H2    N    H     107.33  3.000
 ARO  H2    N    CA    107.88  3.000
 ARO  H     N    CA    114.00  3.000
 ARO  HA    CA   CB    109.00  3.000
 ARO  HA    CA   C     109.00  3.000
 ARO  CB    CA   C     110.10  1.900
 ARO  HA    CA   N     110.00  3.000
 ARO  CB    CA   N     110.50  1.700
 ARO  C     CA   N     111.00  2.800
 ARO  OXT   C    O     126.86  3.000
 ARO  OXT   C    CA    117.27  3.000
 ARO  O     C    CA    120.80  1.700
 ARO  HB3   CB   HB2   106.58  3.000
 ARO  HB3   CB   CG    106.52  3.000
 ARO  HB2   CB   CG    109.87  3.000
 ARO  HB3   CB   CA    108.73  3.000
 ARO  HB2   CB   CA    109.56  3.000
 ARO  CG    CB   CA    115.19  3.000
 ARO  HG    CG   CD    108.78  3.000
 ARO  HG    CG   OH    110.11  3.000
 ARO  CD    CG   OH    110.13  3.000
 ARO  HG    CG   CB    107.76  3.000
 ARO  CD    CG   CB    109.72  3.000
 ARO  OH    CG   CB    110.30  3.000
 ARO  HH    OH   CG    108.87  3.000
 ARO  HD3   CD   HD2   106.24  3.000
 ARO  HD3   CD   NE    109.98  3.000
 ARO  HD2   CD   NE    106.67  3.000
 ARO  HD3   CD   CG    110.70  3.000
 ARO  HD2   CD   CG    109.36  3.000
 ARO  NE    CD   CG    113.54  3.000
 ARO  HE    NE   CZ    117.17  3.000
 ARO  HE    NE   CD    116.78  3.000
 ARO  CZ    NE   CD    126.05  3.000
 ARO  NH2   CZ   NH1   119.34  3.000
 ARO  NH2   CZ   NE    119.48  3.000
 ARO  NH1   CZ   NE    121.18  3.000
 ARO  HH12  NH1  HH11  116.46  3.000
 ARO  HH12  NH1  CZ    122.48  3.000
 ARO  HH11  NH1  CZ    120.71  3.000
 ARO  HH22  NH2  HH21  116.97  3.000
 ARO  HH22  NH2  CZ    121.17  3.000
 ARO  HH21  NH2  CZ    121.49  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
 ARO  CONST_01  NH1   CZ   NE  CD     0.00   0.0  0
 ARO  CONST_02  NH2   CZ   NE  CD   180.00   0.0  0
 ARO  CONST_03  HH11  NH1  CZ  NE   180.00   0.0  0
 ARO  CONST_04  HH12  NH1  CZ  NE     0.00   0.0  0
 ARO  CONST_05  HH21  NH2  CZ  NE     0.00   0.0  0
 ARO  CONST_06  HH22  NH2  CZ  NE   180.00   0.0  0
 ARO  CONST_07  HE    NE   CZ  NH1  180.00   0.0  0
 ARO  Var_01    CZ    NE   CD  CG   -89.56  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
 ARO  chir_01  CA  N   C   CB  positiv
 ARO  chir_02  CG  OH  CB  CD  positiv

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
 ARO  plan-1  CD    0.020
 ARO  plan-1  NE    0.020
 ARO  plan-1  CZ    0.020
 ARO  plan-1  NH1   0.020
 ARO  plan-1  NH2   0.020
 ARO  plan-1  HE    0.020
 ARO  plan-1  HH11  0.020
 ARO  plan-1  HH12  0.020
 ARO  plan-1  HH21  0.020
 ARO  plan-1  HH22  0.020
 ARO  plan-2  CA    0.020
 ARO  plan-2  C     0.020
 ARO  plan-2  O     0.020
 ARO  plan-2  OXT   0.020

