# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:07:58 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: amino{[(4S)-4-amino-5-oxopentyl]amino}methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=[NH2+])C=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
 RGL  RGL  amino{[(4S)-4-amino-5-oxopentyl]amino}methaniminium  L-peptide  26  11  .  2019-03-22  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RGL
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
 RGL  N     N  NH2   0  -0.801  -2.3091  22.1370  74.8442
 RGL  CA    C  CH1   0  -0.189  -1.5731  22.1739  76.0873
 RGL  C     C  C1    0   0.177  -0.1205  22.4787  75.8495
 RGL  O     O  O     0  -0.369   0.3618  22.7634  74.7833
 RGL  CB    C  CH2   0  -0.431  -1.6737  20.8449  76.8422
 RGL  CG    C  CH2   0  -0.440  -3.0917  20.5200  77.2946
 RGL  CD    C  CH2   0  -0.322  -3.1201  19.2260  78.1004
 RGL  NE    N  NH1   0  -0.624  -4.4518  18.8361  78.5259
 RGL  CZ    C  C     0   0.819  -5.0960  19.3124  79.5849
 RGL  NH1   N  NH2   0  -0.811  -4.5198  20.1825  80.4031
 RGL  NH2   N  NC2   1  -0.819  -6.3383  18.9101  79.8298
 RGL  HX    H  H     0   0.192   0.4966  22.4409  76.7669
 RGL  HN1   H  HNH2  0   0.356  -3.3022  22.1231  75.0353
 RGL  HN2   H  HNH2  0   0.351  -2.1442  22.9840  74.3151
 RGL  HA    H  HCH1  0   0.243  -1.9048  22.9643  76.7871
 RGL  HB1   H  HCH2  0   0.240  -1.2941  20.0417  76.2035
 RGL  HB2   H  HCH2  0   0.238  -1.0221  20.8872  77.7206
 RGL  HG1   H  HCH2  0   0.237  -3.4841  21.3487  77.8917
 RGL  HG2   H  HCH2  0   0.242  -3.7553  20.4053  76.4344
 RGL  HD1   H  HCH2  0   0.284  -2.7376  18.4041  77.4962
 RGL  HD2   H  HCH2  0   0.260  -2.4597  19.2883  78.9690
 RGL  HE    H  HNH1  0   0.427  -4.9644  18.2189  77.9147
 RGL  HH11  H  HNH2  0   0.435  -4.9972  20.5131  81.2249
 RGL  HH12  H  HNH2  0   0.442  -3.5986  20.5506  80.2402
 RGL  HH21  H  HNC2  0   0.431  -6.7722  18.1917  79.2752
 RGL  HH22  H  HNC2  0   0.432  -6.8334  19.2150  80.6517

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
 RGL  N    CA    single  1.458  0.019  1.458
 RGL  CA   C     single  1.525  0.021  1.525
 RGL  CA   CB    single  1.530  0.020  1.530
 RGL  C    O     double  1.231  0.020  1.231
 RGL  C    HX    single  0.930  0.020  1.080
 RGL  CB   CG    single  1.524  0.020  1.524
 RGL  CG   CD    single  1.525  0.020  1.525
 RGL  CD   NE    single  1.451  0.020  1.451
 RGL  NE   CZ    single  1.328  0.020  1.328
 RGL  CZ   NH1   single  1.326  0.020  1.326
 RGL  CZ   NH2   double  1.329  0.020  1.329
 RGL  N    HN1   single  0.890  0.020  1.040
 RGL  N    HN2   single  0.890  0.020  1.040
 RGL  CA   HA    single  0.970  0.020  0.970
 RGL  CB   HB1   single  0.970  0.020  1.090
 RGL  CB   HB2   single  0.970  0.020  1.090
 RGL  CG   HG1   single  0.970  0.020  1.090
 RGL  CG   HG2   single  0.970  0.020  1.090
 RGL  CD   HD1   single  0.970  0.020  1.090
 RGL  CD   HD2   single  0.970  0.020  1.090
 RGL  NE   HE    single  0.860  0.020  1.020
 RGL  NH1  HH11  single  0.860  0.020  1.020
 RGL  NH1  HH12  single  0.860  0.020  1.020
 RGL  NH2  HH21  single  0.860  0.020  1.020
 RGL  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
 RGL  HN2   N    HN1   105.68  3.000
 RGL  HN2   N    CA    110.20  3.000
 RGL  HN1   N    CA    109.75  3.000
 RGL  HA    CA   CB    109.00  3.000
 RGL  HA    CA   C     109.00  3.000
 RGL  CB    CA   C     110.10  1.900
 RGL  HA    CA   N     110.00  3.000
 RGL  CB    CA   N     110.50  1.700
 RGL  C     CA   N     111.00  2.800
 RGL  HX    C    O     121.26  3.000
 RGL  HX    C    CA    113.64  3.000
 RGL  O     C    CA    120.80  1.700
 RGL  HB2   CB   HB1   106.88  3.000
 RGL  HB2   CB   CG    108.90  3.000
 RGL  HB1   CB   CG    109.86  3.000
 RGL  HB2   CB   CA    108.84  3.000
 RGL  HB1   CB   CA    109.06  3.000
 RGL  CG    CB   CA    113.11  3.000
 RGL  HG2   CG   HG1   106.94  3.000
 RGL  HG2   CG   CD    108.40  3.000
 RGL  HG1   CG   CD    110.35  3.000
 RGL  HG2   CG   CB    110.72  3.000
 RGL  HG1   CG   CB    109.53  3.000
 RGL  CD    CG   CB    110.81  3.000
 RGL  HD2   CD   HD1   105.76  3.000
 RGL  HD2   CD   NE    109.68  3.000
 RGL  HD1   CD   NE    106.38  3.000
 RGL  HD2   CD   CG    111.13  3.000
 RGL  HD1   CD   CG    109.92  3.000
 RGL  NE    CD   CG    113.58  3.000
 RGL  HE    NE   CZ    117.14  3.000
 RGL  HE    NE   CD    116.94  3.000
 RGL  CZ    NE   CD    125.63  3.000
 RGL  NH2   CZ   NH1   119.42  3.000
 RGL  NH2   CZ   NE    119.47  3.000
 RGL  NH1   CZ   NE    121.11  3.000
 RGL  HH12  NH1  HH11  116.53  3.000
 RGL  HH12  NH1  CZ    122.57  3.000
 RGL  HH11  NH1  CZ    120.89  3.000
 RGL  HH22  NH2  HH21  117.02  3.000
 RGL  HH22  NH2  CZ    121.24  3.000
 RGL  HH21  NH2  CZ    121.19  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
 RGL  CONST_01  NH1   CZ   NE  CD      0.00   0.0  0
 RGL  CONST_02  NH2   CZ   NE  CD    180.00   0.0  0
 RGL  CONST_03  HH11  NH1  CZ  NE    180.00   0.0  0
 RGL  CONST_04  HH12  NH1  CZ  NE      0.00   0.0  0
 RGL  CONST_05  HH21  NH2  CZ  NE      0.00   0.0  0
 RGL  CONST_06  HH22  NH2  CZ  NE    180.00   0.0  0
 RGL  CONST_07  HE    NE   CZ  NH1   180.00   0.0  0
 RGL  Var_01    CD    CG   CB  CA   -177.08  30.0  3
 RGL  Var_02    NE    CD   CG  CB   -178.12  30.0  3
 RGL  Var_03    CZ    NE   CD  CG    -81.74  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
 RGL  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
 RGL  plan-1  CD    0.020
 RGL  plan-1  NE    0.020
 RGL  plan-1  CZ    0.020
 RGL  plan-1  NH1   0.020
 RGL  plan-1  NH2   0.020
 RGL  plan-1  HE    0.020
 RGL  plan-1  HH11  0.020
 RGL  plan-1  HH12  0.020
 RGL  plan-1  HH21  0.020
 RGL  plan-1  HH22  0.020
 RGL  plan-2  CA    0.020
 RGL  plan-2  C     0.020
 RGL  plan-2  O     0.020
 RGL  plan-2  HX    0.020

