# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:35:32 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: amino{[(4S)-4-amino-5,5-dihydroxypentyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(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
 AR7  AR7  amino{[(4S)-4-amino-5,5-dihydroxypentyl]amino}methaniminium  peptide  29  12  .  2016-04-22  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AR7
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
 AR7  N     N  NH2   0  -0.813  62.0075  17.7734  60.5077
 AR7  CA    C  CH1   0  -0.138  61.1650  17.0855  61.4758
 AR7  C     C  CH1   0   0.289  62.0340  16.0961  62.2501
 AR7  O     O  OH1   0  -0.670  63.0729  16.8171  62.8531
 AR7  CB    C  CH2   0  -0.411  60.0327  16.3558  60.7564
 AR7  CG    C  CH2   0  -0.489  59.1146  17.2833  59.9687
 AR7  CD    C  CH2   0  -0.268  57.9287  16.5198  59.4020
 AR7  NE    N  NH1   0  -0.635  57.0731  17.4130  58.6379
 AR7  CZ    C  C     0   0.824  55.9032  17.0716  58.1142
 AR7  NH1   N  NC2   1  -0.815  55.4627  15.8236  58.2118
 AR7  NH2   N  NH2   0  -0.821  55.1574  17.9839  57.5011
 AR7  OXT   O  OH1   0  -0.664  61.2301  15.4581  63.1969
 AR7  H     H  HNH2  0   0.349  61.4826  18.5174  60.0673
 AR7  H2    H  HNH2  0   0.345  62.7695  18.2311  60.9910
 AR7  HA    H  HCH1  0   0.204  60.7115  17.7726  62.2112
 AR7  HF    H  HCH1  0   0.184  62.4498  15.3642  61.5412
 AR7  H1    H  HOH1  0   0.455  63.8037  16.2215  63.0476
 AR7  HB1   H  HCH2  0   0.219  60.4632  15.6106  60.0791
 AR7  HB2   H  HCH2  0   0.234  59.4376  15.8111  61.4910
 AR7  HG1   H  HCH2  0   0.243  58.7490  18.0874  60.6149
 AR7  HG2   H  HCH2  0   0.241  59.6565  17.7526  59.1430
 AR7  HD1   H  HCH2  0   0.255  58.2873  15.7046  58.7660
 AR7  HD2   H  HCH2  0   0.257  57.3562  16.0759  60.2211
 AR7  HNE   H  HNH1  0   0.427  57.3871  18.3628  58.5065
 AR7  HN11  H  HNC2  0   0.434  54.5837  15.5534  57.8025
 AR7  HN21  H  HNH2  0   0.431  54.2879  17.7369  57.0595
 AR7  HN22  H  HNH2  0   0.431  55.4395  18.9485  57.4537
 AR7  HXT   H  HOH1  0   0.456  61.6508  14.6376  63.4720
 AR7  HN12  H  HNC2  0   0.444  56.0393  15.0821  58.5715

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
 AR7  N    CA    single  1.458  0.019  1.458
 AR7  N    H     single  0.860  0.020  0.860
 AR7  N    H2    single  0.890  0.020  1.040
 AR7  CA   C     single  1.525  0.021  1.525
 AR7  CA   CB    single  1.530  0.020  1.530
 AR7  CA   HA    single  0.970  0.020  0.970
 AR7  C    O     single  1.231  0.020  1.231
 AR7  C    OXT   single  1.396  0.020  1.396
 AR7  C    HF    single  0.970  0.020  1.090
 AR7  O    H1    single  0.850  0.020  0.980
 AR7  CB   CG    single  1.524  0.020  1.524
 AR7  CB   HB1   single  0.970  0.020  1.090
 AR7  CB   HB2   single  0.970  0.020  1.090
 AR7  CG   CD    single  1.520  0.020  1.520
 AR7  CG   HG1   single  0.970  0.020  1.090
 AR7  CG   HG2   single  0.970  0.020  1.090
 AR7  CD   NE    single  1.454  0.020  1.454
 AR7  CD   HD1   single  0.970  0.020  1.090
 AR7  CD   HD2   single  0.970  0.020  1.090
 AR7  NE   CZ    single  1.326  0.020  1.326
 AR7  NE   HNE   single  0.860  0.020  1.020
 AR7  CZ   NH1   double  1.327  0.020  1.327
 AR7  CZ   NH2   single  1.328  0.020  1.328
 AR7  NH1  HN11  single  0.860  0.020  1.020
 AR7  NH2  HN21  single  0.860  0.020  1.020
 AR7  NH2  HN22  single  0.860  0.020  1.020
 AR7  OXT  HXT   single  0.850  0.020  0.980
 AR7  NH1  HN12  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
 AR7  H2    N    H     105.43  3.000
 AR7  H2    N    CA    109.39  3.000
 AR7  H     N    CA    114.00  3.000
 AR7  HA    CA   CB    109.00  3.000
 AR7  HA    CA   C     109.00  3.000
 AR7  CB    CA   C     110.10  1.900
 AR7  HA    CA   N     110.00  3.000
 AR7  CB    CA   N     110.50  1.700
 AR7  C     CA   N     111.00  2.800
 AR7  HF    C    OXT   110.52  3.000
 AR7  HF    C    O     109.83  3.000
 AR7  OXT   C    O     111.73  3.000
 AR7  HF    C    CA    108.61  3.000
 AR7  OXT   C    CA    108.19  3.000
 AR7  O     C    CA    120.80  1.700
 AR7  H1    O    C     109.36  3.000
 AR7  HB2   CB   HB1   106.92  3.000
 AR7  HB2   CB   CG    108.85  3.000
 AR7  HB1   CB   CG    109.34  3.000
 AR7  HB2   CB   CA    109.01  3.000
 AR7  HB1   CB   CA    108.97  3.000
 AR7  CG    CB   CA    113.54  3.000
 AR7  HG2   CG   HG1   107.22  3.000
 AR7  HG2   CG   CD    108.70  3.000
 AR7  HG1   CG   CD    109.18  3.000
 AR7  HG2   CG   CB    110.66  3.000
 AR7  HG1   CG   CB    110.07  3.000
 AR7  CD    CG   CB    110.91  3.000
 AR7  HD2   CD   HD1   107.73  3.000
 AR7  HD2   CD   NE    109.57  3.000
 AR7  HD1   CD   NE    110.19  3.000
 AR7  HD2   CD   CG    109.45  3.000
 AR7  HD1   CD   CG    109.58  3.000
 AR7  NE    CD   CG    110.27  3.000
 AR7  HNE   NE   CZ    117.74  3.000
 AR7  HNE   NE   CD    117.62  3.000
 AR7  CZ    NE   CD    124.64  3.000
 AR7  NH2   CZ   NH1   119.57  3.000
 AR7  NH2   CZ   NE    120.04  3.000
 AR7  NH1   CZ   NE    120.38  3.000
 AR7  HN12  NH1  HN11  116.63  3.000
 AR7  HN12  NH1  CZ    121.96  3.000
 AR7  HN11  NH1  CZ    120.82  3.000
 AR7  HN22  NH2  HN21  117.19  3.000
 AR7  HN22  NH2  CZ    121.52  3.000
 AR7  HN21  NH2  CZ    121.28  3.000
 AR7  HXT   OXT  C     109.37  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
 AR7  CONST_01  NH1   CZ   NE  CD      0.00   0.0  0
 AR7  CONST_02  NH2   CZ   NE  CD    180.00   0.0  0
 AR7  CONST_03  HN11  NH1  CZ  NE    180.00   0.0  0
 AR7  CONST_04  HN12  NH1  CZ  NE      0.00   0.0  0
 AR7  CONST_05  HN21  NH2  CZ  NE    180.00   0.0  0
 AR7  CONST_06  HN22  NH2  CZ  NE      0.00   0.0  0
 AR7  CONST_07  HNE   NE   CZ  NH1   180.00   0.0  0
 AR7  Var_01    CD    CG   CB  CA   -173.91  30.0  3
 AR7  Var_02    NE    CD   CG  CB   -179.18  30.0  3
 AR7  Var_03    CZ    NE   CD  CG   -174.06  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
 AR7  chir_01  CA  N  C  CB  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
 AR7  plan-1  CD    0.020
 AR7  plan-1  NE    0.020
 AR7  plan-1  CZ    0.020
 AR7  plan-1  NH1   0.020
 AR7  plan-1  NH2   0.020
 AR7  plan-1  HNE   0.020
 AR7  plan-1  HN11  0.020
 AR7  plan-1  HN21  0.020
 AR7  plan-1  HN22  0.020
 AR7  plan-1  HN12  0.020

