# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 11:15:19 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: amino{[(4R)-4-amino-4-carboxybutyl]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
 DAR  DAR  amino{[(4R)-4-amino-4-carboxybutyl]amino}methaniminium  D-peptide  26  12  .  2022-09-22  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_DAR
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
 DAR  N     N  NH2    0  -0.774  18.1372   -6.2047  31.2305
 DAR  CA    C  CH1    0  -0.203  18.9200   -6.8992  32.2388
 DAR  CB    C  CH2    0  -0.437  18.5809   -8.3967  32.2403
 DAR  CG    C  CH2    0  -0.432  18.5164   -9.0770  30.8772
 DAR  CD    C  CH2    0  -0.344  19.8283   -9.1685  30.1055
 DAR  NE    N  NH1    0  -0.618  20.3840   -7.8990  29.6642
 DAR  CZ    C  C      0   0.834  19.8410   -7.1027  28.7555
 DAR  NH1   N  NH2    0  -0.809  18.8481   -7.5233  27.9832
 DAR  NH2   N  NC2    1  -0.821  20.3569   -5.8941  28.5499
 DAR  C     C  C      0   0.389  18.7621   -6.3710  33.6859
 DAR  O     O  O      0  -0.624  19.6263   -6.7509  34.5037
 DAR  OXT   O  OC    -1  -0.608  17.7805   -5.6413  33.9298
 DAR  H     H  HNH2   0   0.333  18.4508   -5.2430  31.1800
 DAR  H2    H  HNH2   0   0.324  17.1813   -6.1410  31.5648
 DAR  HA    H  HCH1   0   0.201  19.9749   -6.7839  31.9726
 DAR  HB2   H  HCH2   0   0.223  19.2942   -8.9188  32.8826
 DAR  HB3   H  HCH2   0   0.220  17.5987   -8.5294  32.7090
 DAR  HG2   H  HCH2   0   0.239  18.1825  -10.1080  31.0243
 DAR  HG3   H  HCH2   0   0.228  17.7491   -8.5976  30.2673
 DAR  HD2   H  HCH2   0   0.276  20.5959   -9.6294  30.7257
 DAR  HD3   H  HCH2   0   0.264  19.7084   -9.8283  29.2418
 DAR  HE    H  HNH1   0   0.421  21.1648   -7.5333  30.1838
 DAR  HH11  H  HNH2   0   0.429  18.3802   -6.8885  27.3594
 DAR  HH12  H  HNH2   0   0.439  18.4077   -8.4147  28.1279
 DAR  HH21  H  HNC2   0   0.425  21.0184   -5.4999  29.1964
 DAR  HH22  H  HNC2   0   0.426  19.9243   -5.2539  27.9063

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
 DAR  N    CA    single  1.458  0.019  1.458
 DAR  N    H     single  0.860  0.020  0.860
 DAR  N    H2    single  0.890  0.020  1.040
 DAR  CA   CB    single  1.521  0.033  1.521
 DAR  CA   C     single  1.525  0.021  1.525
 DAR  CA   HA    single  0.970  0.020  0.970
 DAR  CB   CG    single  1.525  0.020  1.525
 DAR  CB   HB2   single  0.970  0.020  1.090
 DAR  CB   HB3   single  0.970  0.020  1.090
 DAR  CG   CD    single  1.525  0.020  1.525
 DAR  CG   HG2   single  0.970  0.020  1.090
 DAR  CG   HG3   single  0.970  0.020  1.090
 DAR  CD   NE    single  1.454  0.020  1.454
 DAR  CD   HD2   single  0.970  0.020  1.090
 DAR  CD   HD3   single  0.970  0.020  1.090
 DAR  NE   CZ    single  1.325  0.020  1.325
 DAR  NE   HE    single  0.860  0.020  1.020
 DAR  CZ   NH1   single  1.326  0.020  1.326
 DAR  CZ   NH2   double  1.330  0.020  1.330
 DAR  NH1  HH11  single  0.860  0.020  1.020
 DAR  NH1  HH12  single  0.860  0.020  1.020
 DAR  NH2  HH21  single  0.860  0.020  1.020
 DAR  NH2  HH22  single  0.860  0.020  1.020
 DAR  C    O     deloc   1.231  0.020  1.231
 DAR  C    OXT   deloc   1.247  0.020  1.247

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
 DAR  H2    N    H     104.40  3.000
 DAR  H2    N    CA    108.00  3.000
 DAR  H     N    CA    114.00  3.000
 DAR  HA    CA   C     110.00  3.000
 DAR  HA    CA   CB    109.00  3.000
 DAR  C     CA   CB    110.50  1.500
 DAR  HA    CA   N     110.00  3.000
 DAR  C     CA   N     111.00  2.800
 DAR  CB    CA   N     110.40  1.500
 DAR  HB3   CB   HB2   106.01  3.000
 DAR  HB3   CB   CG    106.87  3.000
 DAR  HB2   CB   CG    109.88  3.000
 DAR  HB3   CB   CA    108.44  3.000
 DAR  HB2   CB   CA    108.81  3.000
 DAR  CG    CB   CA    116.33  3.000
 DAR  HG3   CG   HG2   105.94  3.000
 DAR  HG3   CG   CD    110.40  3.000
 DAR  HG2   CG   CD    105.92  3.000
 DAR  HG3   CG   CB    109.48  3.000
 DAR  HG2   CG   CB    108.26  3.000
 DAR  CD    CG   CB    116.29  3.000
 DAR  HD3   CD   HD2   105.77  3.000
 DAR  HD3   CD   NE    109.20  3.000
 DAR  HD2   CD   NE    105.83  3.000
 DAR  HD3   CD   CG    109.98  3.000
 DAR  HD2   CD   CG    110.09  3.000
 DAR  NE    CD   CG    115.46  3.000
 DAR  HE    NE   CZ    116.99  3.000
 DAR  HE    NE   CD    117.18  3.000
 DAR  CZ    NE   CD    125.18  3.000
 DAR  NH2   CZ   NH1   119.24  3.000
 DAR  NH2   CZ   NE    119.55  3.000
 DAR  NH1   CZ   NE    121.05  3.000
 DAR  HH12  NH1  HH11  116.45  3.000
 DAR  HH12  NH1  CZ    121.71  3.000
 DAR  HH11  NH1  CZ    120.63  3.000
 DAR  HH22  NH2  HH21  116.42  3.000
 DAR  HH22  NH2  CZ    120.70  3.000
 DAR  HH21  NH2  CZ    120.80  3.000
 DAR  OXT   C    O     126.47  3.000
 DAR  OXT   C    CA    120.80  1.700
 DAR  O     C    CA    120.80  1.700

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
 DAR  CONST_01  NH1   CZ   NE  CD     0.00   0.0  0
 DAR  CONST_02  NH2   CZ   NE  CD   180.00   0.0  0
 DAR  CONST_03  HH11  NH1  CZ  NE   180.00   0.0  0
 DAR  CONST_04  HH12  NH1  CZ  NE     0.00   0.0  0
 DAR  CONST_05  HH21  NH2  CZ  NE     0.00   0.0  0
 DAR  CONST_06  HH22  NH2  CZ  NE   180.00   0.0  0
 DAR  CONST_07  HE    NE   CZ  NH1  180.00   0.0  0
 DAR  Var_01    CD    CG   CB  CA    65.87  30.0  3
 DAR  Var_02    NE    CD   CG  CB   -66.35  30.0  3
 DAR  Var_03    CZ    NE   CD  CG   -66.92  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
 DAR  chir_01  CA  N  CB  C  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
 DAR  plan-1  CD    0.020
 DAR  plan-1  NE    0.020
 DAR  plan-1  CZ    0.020
 DAR  plan-1  NH1   0.020
 DAR  plan-1  NH2   0.020
 DAR  plan-1  HE    0.020
 DAR  plan-1  HH11  0.020
 DAR  plan-1  HH12  0.020
 DAR  plan-1  HH21  0.020
 DAR  plan-1  HH22  0.020
 DAR  plan-2  CA    0.020
 DAR  plan-2  C     0.020
 DAR  plan-2  O     0.020
 DAR  plan-2  OXT   0.020

