# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:49:13 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: N~6~-carbamimidoyl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(N)=N)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
 HRG  HRG  N~6~-carbamimidoyl-L-lysine  L-peptide  28  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_HRG
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
 HRG  N     N  NH2    0  -0.806  -1.6967   6.0664  63.0345
 HRG  CA    C  CH1    0  -0.215  -2.6558   5.8109  64.1004
 HRG  CB    C  CH2    0  -0.412  -2.2303   6.4787  65.4083
 HRG  CG    C  CH2    0  -0.454   0.3788   6.5942  65.4307
 HRG  CG'   C  CH2    0  -0.468  -0.9070   5.9592  65.9863
 HRG  CD    C  CH2    0  -0.295   0.9646   7.7017  66.2955
 HRG  NE    N  NH1    0  -0.646   0.0783   8.8396  66.4047
 HRG  CZ    C  C      0   0.539   0.4830  10.0066  67.0004
 HRG  NH1   N  N      0  -0.721   1.6688  10.3098  67.3834
 HRG  NH2   N  NH2    0  -0.826  -0.5465  10.9061  67.1885
 HRG  C     C  C      0   0.410  -4.0855   6.2375  63.6670
 HRG  O     O  O      0  -0.606  -4.9493   6.2767  64.5651
 HRG  OXT   O  OC    -1  -0.601  -4.2663   6.4612  62.4531
 HRG  HN1A  H  HNH2   0   0.333  -2.1555   5.8820  62.1519
 HRG  HN2   H  HNH2   0   0.332  -0.9206   5.4210  63.1025
 HRG  HA    H  HCH1   0   0.189  -2.7374   4.7299  64.3189
 HRG  HB1   H  HCH2   0   0.196  -2.1839   7.5620  65.2500
 HRG  HB2   H  HCH2   0   0.216  -3.0213   6.3062  66.1384
 HRG  HG1   H  HCH2   0   0.232   1.1548   5.8303  65.3432
 HRG  HG2   H  HCH2   0   0.233   0.2102   6.9748  64.4223
 HRG  HG'1  H  HCH2   0   0.227  -0.9156   6.0871  67.0743
 HRG  HG'2  H  HCH2   0   0.227  -0.8717   4.8763  65.8329
 HRG  HD1   H  HCH2   0   0.217   1.2187   7.2937  67.2835
 HRG  HD2   H  HCH2   0   0.234   1.9011   8.0336  65.8410
 HRG  HNE   H  HNH1   0   0.391  -0.8991   8.6212  66.5216
 HRG  HN1   H  H      0   0.326   2.3032   9.5259  67.2975
 HRG  HN21  H  HNH2   0   0.373  -0.2264  11.8347  67.4128
 HRG  HN22  H  HNH2   0   0.376  -1.2603  10.9158  66.4759

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
 HRG  N    CA    single  1.458  0.019  1.458
 HRG  N    HN1A  single  0.890  0.020  1.040
 HRG  N    HN2   single  0.890  0.020  1.040
 HRG  CA   CB    single  1.530  0.020  1.530
 HRG  CA   C     single  1.525  0.021  1.525
 HRG  CA   HA    single  0.970  0.020  0.970
 HRG  CB   CG'   single  1.535  0.020  1.535
 HRG  CB   HB1   single  0.970  0.020  1.090
 HRG  CB   HB2   single  0.970  0.020  1.090
 HRG  CG   CG'   single  1.538  0.020  1.538
 HRG  CG   CD    single  1.522  0.020  1.522
 HRG  CG   HG1   single  0.970  0.020  1.090
 HRG  CG   HG2   single  0.970  0.020  1.090
 HRG  CG'  HG'1  single  0.970  0.020  1.090
 HRG  CG'  HG'2  single  0.970  0.020  1.090
 HRG  CD   NE    single  1.447  0.020  1.447
 HRG  CD   HD1   single  0.970  0.020  1.090
 HRG  CD   HD2   single  0.970  0.020  1.090
 HRG  NE   CZ    single  1.371  0.020  1.371
 HRG  NE   HNE   single  0.890  0.020  1.040
 HRG  CZ   NH1   double  1.282  0.020  1.282
 HRG  CZ   NH2   single  1.380  0.020  1.380
 HRG  NH1  HN1   single  0.890  0.020  1.040
 HRG  NH2  HN21  single  0.890  0.020  1.040
 HRG  NH2  HN22  single  0.890  0.020  1.040
 HRG  C    O     deloc   1.231  0.020  1.231
 HRG  C    OXT   deloc   1.248  0.020  1.248

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
 HRG  HN2   N    HN1A  106.87  3.000
 HRG  HN2   N    CA    110.12  3.000
 HRG  HN1A  N    CA    107.93  3.000
 HRG  HA    CA   C     109.00  3.000
 HRG  HA    CA   CB    109.00  3.000
 HRG  C     CA   CB    110.10  1.900
 HRG  HA    CA   N     110.00  3.000
 HRG  C     CA   N     111.00  2.800
 HRG  CB    CA   N     110.50  1.700
 HRG  HB2   CB   HB1   106.49  3.000
 HRG  HB2   CB   CG'   108.66  3.000
 HRG  HB1   CB   CG'   110.64  3.000
 HRG  HB2   CB   CA    107.57  3.000
 HRG  HB1   CB   CA    108.66  3.000
 HRG  CG'   CB   CA    114.47  3.000
 HRG  HG2   CG   HG1   106.24  3.000
 HRG  HG2   CG   CD    109.31  3.000
 HRG  HG1   CG   CD    106.31  3.000
 HRG  HG2   CG   CG'   110.41  3.000
 HRG  HG1   CG   CG'   109.52  3.000
 HRG  CD    CG   CG'   114.64  3.000
 HRG  HG'2  CG'  HG'1  104.78  3.000
 HRG  HG'2  CG'  CG    109.33  3.000
 HRG  HG'1  CG'  CG    108.49  3.000
 HRG  HG'2  CG'  CB    108.06  3.000
 HRG  HG'1  CG'  CB    109.13  3.000
 HRG  CG    CG'  CB    116.43  3.000
 HRG  HD2   CD   HD1   106.78  3.000
 HRG  HD2   CD   NE    108.52  3.000
 HRG  HD1   CD   NE    111.46  3.000
 HRG  HD2   CD   CG    108.33  3.000
 HRG  HD1   CD   CG    109.25  3.000
 HRG  NE    CD   CG    112.29  3.000
 HRG  HNE   NE   CZ    114.84  3.000
 HRG  HNE   NE   CD    115.62  3.000
 HRG  CZ    NE   CD    121.42  3.000
 HRG  NH2   CZ   NH1   119.67  3.000
 HRG  NH2   CZ   NE    113.18  3.000
 HRG  NH1   CZ   NE    127.15  3.000
 HRG  HN1   NH1  CZ    111.79  3.000
 HRG  HN22  NH2  HN21  111.91  3.000
 HRG  HN22  NH2  CZ    115.97  3.000
 HRG  HN21  NH2  CZ    113.21  3.000
 HRG  OXT   C    O     126.50  3.000
 HRG  OXT   C    CA    117.00  3.000
 HRG  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
 HRG  CONST_01  NH1   CZ   NE   CD      0.00   0.0  0
 HRG  CONST_02  NH2   CZ   NE   CD    180.00   0.0  0
 HRG  CONST_03  HN1   NH1  CZ   NE      0.00   0.0  0
 HRG  CONST_04  HN21  NH2  CZ   NE    180.00   0.0  0
 HRG  Var_01    CG    CG'  CB   CA     84.34  30.0  3
 HRG  Var_02    CD    CG   CG'  CB     98.05  30.0  1
 HRG  Var_03    CZ    NE   CD   CG   -171.88  30.0  3
 HRG  Var_04    NE    CD   CG   CG'   -63.68  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
 HRG  chir_01  CA  N  CB  C  negativ

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
 HRG  plan-1  CD    0.020
 HRG  plan-1  NE    0.020
 HRG  plan-1  CZ    0.020
 HRG  plan-1  NH1   0.020
 HRG  plan-1  NH2   0.020
 HRG  plan-1  HNE   0.020
 HRG  plan-1  HN1   0.020
 HRG  plan-1  HN21  0.020
 HRG  plan-1  HN22  0.020
 HRG  plan-2  CA    0.020
 HRG  plan-2  C     0.020
 HRG  plan-2  O     0.020
 HRG  plan-2  OXT   0.020

