# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 09:01:05 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  27  12  .  2022-09-22  2023-02-16
;
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  -0.773  18.2819   -6.1312  31.3384
 DAR  CA    C  CH1   0  -0.193  19.0706   -6.8948  32.2714
 DAR  CB    C  CH2   0  -0.455  18.6428   -8.3724  32.2792
 DAR  CG    C  CH2   0  -0.438  18.4866   -9.0131  30.9056
 DAR  CD    C  CH2   0  -0.342  19.7664   -9.1734  30.0925
 DAR  NE    N  NH1   0  -0.624  20.3648   -7.9325  29.6269
 DAR  CZ    C  C     0   0.833  19.8243   -7.1118  28.7367
 DAR  NH1   N  NH2   0  -0.807  18.7696   -7.4791  28.0243
 DAR  NH2   N  NC2   1  -0.818  20.3786   -5.9230  28.5208
 DAR  C     C  C     0   0.529  19.0729   -6.4220  33.7214
 DAR  O     O  O     0  -0.454  19.8941   -6.7794  34.5316
 DAR  OXT   O  OH1   0  -0.585  18.0733   -5.6024  34.0146
 DAR  H     H  HNH2  0   0.356  18.5646   -5.1603  31.3326
 DAR  H2    H  HNH2  0   0.348  17.3000   -6.1530  31.5841
 DAR  HA    H  HCH1  0   0.259  20.1165   -6.8360  31.9597
 DAR  HB2   H  HCH2  0   0.246  19.3568   -8.9445  32.8759
 DAR  HB3   H  HCH2  0   0.248  17.6787   -8.4544  32.7916
 DAR  HG2   H  HCH2  0   0.252  18.0924  -10.0215  31.0539
 DAR  HG3   H  HCH2  0   0.239  17.7315   -8.4761  30.3302
 DAR  HD2   H  HCH2  0   0.281  20.5304   -9.6651  30.6929
 DAR  HD3   H  HCH2  0   0.268  19.5854   -9.8354  29.2414
 DAR  HE    H  HNH1  0   0.424  21.2249   -7.6401  30.0608
 DAR  HH11  H  HNH2  0   0.431  18.3480   -6.8497  27.3629
 DAR  HH12  H  HNH2  0   0.438  18.4097   -8.4174  28.0472
 DAR  HH21  H  HNC2  0   0.426  21.0505   -5.5436  29.1658
 DAR  HH22  H  HNC2  0   0.427  19.9719   -5.2772  27.8657
 DAR  HXT   H  HOH1  0   0.481  18.1151   -5.3521  34.9500

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  1.524  0.020  1.524
 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  1.326  0.020  1.326
 DAR  NE   HE    single  0.860  0.020  1.020
 DAR  CZ   NH1   single  1.325  0.020  1.325
 DAR  CZ   NH2   double  1.329  0.020  1.329
 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     double  1.231  0.020  1.231
 DAR  C    OXT   single  1.326  0.020  1.326
 DAR  OXT  HXT   single  0.850  0.020  0.980

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     107.06  3.000
 DAR  H2    N    CA    111.25  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   106.30  3.000
 DAR  HB3   CB   CG    107.47  3.000
 DAR  HB2   CB   CG    109.84  3.000
 DAR  HB3   CB   CA    108.61  3.000
 DAR  HB2   CB   CA    108.90  3.000
 DAR  CG    CB   CA    115.33  3.000
 DAR  HG3   CG   HG2   106.04  3.000
 DAR  HG3   CG   CD    110.58  3.000
 DAR  HG2   CG   CD    106.15  3.000
 DAR  HG3   CG   CB    109.85  3.000
 DAR  HG2   CG   CB    107.61  3.000
 DAR  CD    CG   CB    116.03  3.000
 DAR  HD3   CD   HD2   105.78  3.000
 DAR  HD3   CD   NE    109.61  3.000
 DAR  HD2   CD   NE    105.85  3.000
 DAR  HD3   CD   CG    109.87  3.000
 DAR  HD2   CD   CG    110.02  3.000
 DAR  NE    CD   CG    115.24  3.000
 DAR  HE    NE   CZ    117.25  3.000
 DAR  HE    NE   CD    117.48  3.000
 DAR  CZ    NE   CD    125.13  3.000
 DAR  NH2   CZ   NH1   119.51  3.000
 DAR  NH2   CZ   NE    119.51  3.000
 DAR  NH1   CZ   NE    120.93  3.000
 DAR  HH12  NH1  HH11  116.68  3.000
 DAR  HH12  NH1  CZ    122.12  3.000
 DAR  HH11  NH1  CZ    120.92  3.000
 DAR  HH22  NH2  HH21  116.46  3.000
 DAR  HH22  NH2  CZ    120.76  3.000
 DAR  HH21  NH2  CZ    120.79  3.000
 DAR  OXT   C    O     123.19  3.000
 DAR  OXT   C    CA    120.80  1.700
 DAR  O     C    CA    120.80  1.700
 DAR  HXT   OXT  C     109.91  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
 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  HXT   OXT  C   CA   180.00   0.0  0
 DAR  CONST_04  HH11  NH1  CZ  NE   180.00   0.0  0
 DAR  CONST_05  HH12  NH1  CZ  NE     0.00   0.0  0
 DAR  CONST_07  HH22  NH2  CZ  NE   180.00   0.0  0
 DAR  CONST_08  HE    NE   CZ  NH1  180.00   0.0  0
 DAR  Var_01    CD    CG   CB  CA    66.57  30.0  3
 DAR  Var_02    NE    CD   CG  CB   -68.37  30.0  3
 DAR  Var_03    CZ    NE   CD  CG   -66.53  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
 DAR  plan-2  HXT   0.020

