# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 00:08:28 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (3S)-3-amino-6-carbamimidamidohexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=N)CC(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
 HMR  HMR  '(3S)-3-amino-6-carbamimidamidohexanoic acid'  L-peptide  28  13  .  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_HMR
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
 HMR  N     N  NH2    0  -0.791   1.1189  -1.0610   1.9293
 HMR  CA    C  CH1    0  -0.089   0.1569   0.0192   1.7359
 HMR  CB    C  CH2    0  -0.412  -0.5952  -0.0377   0.4010
 HMR  CG    C  CH2    0  -0.466   0.3095   0.0218  -0.8232
 HMR  CD    C  CH2    0  -0.224  -0.4847   0.0182  -2.1204
 HMR  NE    N  NH1    0  -0.648   0.4036   0.0923  -3.2580
 HMR  CZ    C  C      0   0.552  -0.0729  -0.0595  -4.5308
 HMR  NH1   N  N      0  -0.721  -1.2733  -0.4663  -4.7332
 HMR  NH2   N  NH2    0  -0.840   0.8691   0.1671  -5.5124
 HMR  O     O  O      0  -0.622   0.6367   1.2224   4.3459
 HMR  CH2   C  CH2    0  -0.545  -0.8198   0.0245   2.9050
 HMR  OXT   O  OC    -1  -0.626  -0.4559  -0.5190   5.1988
 HMR  H     H  HNH2   0   0.341   1.8211  -1.0380   1.2005
 HMR  H2    H  HNH2   0   0.328   0.6457  -1.9526   1.8271
 HMR  HA    H  HCH1   0   0.207   0.7212   0.9570   1.7668
 HMR  HB2   H  HCH2   0   0.206  -1.1980  -0.9541   0.3666
 HMR  HB3   H  HCH2   0   0.210  -1.3046   0.7961   0.3588
 HMR  HG2   H  HCH2   0   0.219   0.9284   0.9254  -0.7716
 HMR  HG3   H  HCH2   0   0.217   0.9972  -0.8287  -0.8325
 HMR  HD2   H  HCH2   0   0.225  -1.0676  -0.9016  -2.1912
 HMR  HD3   H  HCH2   0   0.206  -1.2079   0.8443  -2.1170
 HMR  HE    H  HNH1   0   0.377   1.1863   0.7175  -3.1451
 HMR  HH1   H  H      0   0.313  -1.4422  -0.5914  -5.7247
 HMR  HH21  H  HNH2   0   0.384   0.4967   0.3817  -6.4230
 HMR  HH22  H  HNH2   0   0.381   1.6511   0.7575  -5.2762
 HMR  HC1   H  HCH2   0   0.218  -1.5521   0.8245   2.7448
 HMR  HC2   H  HCH2   0   0.193  -1.3864  -0.9131   2.9077
 HMR  C     C  C      0   0.408  -0.1468   0.2532   4.2674

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
 HMR  N    CA    single  1.458  0.019  1.458
 HMR  N    H     single  0.860  0.020  0.860
 HMR  N    H2    single  0.890  0.020  1.040
 HMR  CA   CB    single  1.530  0.020  1.530
 HMR  CA   CH2   single  1.523  0.020  1.523
 HMR  CA   HA    single  0.970  0.020  0.970
 HMR  CB   CG    single  1.523  0.020  1.523
 HMR  CB   HB2   single  0.970  0.020  1.090
 HMR  CB   HB3   single  0.970  0.020  1.090
 HMR  CG   CD    single  1.521  0.020  1.521
 HMR  CG   HG2   single  0.970  0.020  1.090
 HMR  CG   HG3   single  0.970  0.020  1.090
 HMR  CD   NE    single  1.445  0.020  1.445
 HMR  CD   HD2   single  0.970  0.020  1.090
 HMR  CD   HD3   single  0.970  0.020  1.090
 HMR  NE   CZ    single  1.368  0.020  1.368
 HMR  NE   HE    single  0.890  0.020  1.040
 HMR  CZ   NH1   double  1.284  0.020  1.284
 HMR  CZ   NH2   single  1.379  0.020  1.379
 HMR  NH1  HH1   single  0.890  0.020  1.040
 HMR  NH2  HH21  single  0.890  0.020  1.040
 HMR  NH2  HH22  single  0.890  0.020  1.040
 HMR  C    O     deloc   1.231  0.020  1.231
 HMR  C    CH2   single  1.537  0.020  1.537
 HMR  C    OXT   deloc   1.249  0.020  1.249
 HMR  CH2  HC1   single  0.970  0.020  1.090
 HMR  CH2  HC2   single  0.970  0.020  1.090

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
 HMR  H2    N    H     105.72  3.000
 HMR  H2    N    CA    109.25  3.000
 HMR  H     N    CA    114.00  3.000
 HMR  HA    CA   CH2   107.80  3.000
 HMR  HA    CA   CB    109.00  3.000
 HMR  CH2   CA   CB    110.72  3.000
 HMR  HA    CA   N     110.00  3.000
 HMR  CH2   CA   N     108.88  3.000
 HMR  CB    CA   N     110.50  1.700
 HMR  HB3   CB   HB2   106.19  3.000
 HMR  HB3   CB   CG    108.90  3.000
 HMR  HB2   CB   CG    109.49  3.000
 HMR  HB3   CB   CA    108.84  3.000
 HMR  HB2   CB   CA    109.13  3.000
 HMR  CG    CB   CA    114.00  3.000
 HMR  HG3   CG   HG2   106.64  3.000
 HMR  HG3   CG   CD    108.61  3.000
 HMR  HG2   CG   CD    109.68  3.000
 HMR  HG3   CG   CB    110.48  3.000
 HMR  HG2   CG   CB    109.25  3.000
 HMR  CD    CG   CB    112.03  3.000
 HMR  HD3   CD   HD2   106.41  3.000
 HMR  HD3   CD   NE    111.63  3.000
 HMR  HD2   CD   NE    108.69  3.000
 HMR  HD3   CD   CG    109.85  3.000
 HMR  HD2   CD   CG    109.65  3.000
 HMR  NE    CD   CG    110.50  3.000
 HMR  HE    NE   CZ    116.33  3.000
 HMR  HE    NE   CD    114.89  3.000
 HMR  CZ    NE   CD    120.85  3.000
 HMR  NH2   CZ   NH1   125.35  3.000
 HMR  NH2   CZ   NE    113.97  3.000
 HMR  NH1   CZ   NE    120.52  3.000
 HMR  HH1   NH1  CZ    110.44  3.000
 HMR  HH22  NH2  HH21  111.97  3.000
 HMR  HH22  NH2  CZ    117.34  3.000
 HMR  HH21  NH2  CZ    115.21  3.000
 HMR  HC2   CH2  HC1   106.23  3.000
 HMR  HC2   CH2  C     110.59  3.000
 HMR  HC1   CH2  C     108.27  3.000
 HMR  HC2   CH2  CA    109.30  3.000
 HMR  HC1   CH2  CA    108.58  3.000
 HMR  C     CH2  CA    113.59  3.000
 HMR  OXT   C    CH2   117.44  3.000
 HMR  OXT   C    O     126.04  3.000
 HMR  CH2   C    O     116.49  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
 HMR  CONST_01  NH1  CZ   NE   CD     0.00   0.0  0
 HMR  CONST_02  NH2  CZ   NE   CD   180.00   0.0  0
 HMR  CONST_03  HH1  NH1  CZ   NE   180.00   0.0  0
 HMR  Var_01    CD   CG   CB   CA  -177.72  30.0  3
 HMR  Var_02    O    C    CH2  CA    49.77  30.0  2
 HMR  Var_03    NE   CD   CG   CB   179.28  30.0  3
 HMR  Var_04    CZ   NE   CD   CG   172.03  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
 HMR  chir_01  CA  N  CB  CH2  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
 HMR  plan-1  CD    0.020
 HMR  plan-1  NE    0.020
 HMR  plan-1  CZ    0.020
 HMR  plan-1  NH1   0.020
 HMR  plan-1  NH2   0.020
 HMR  plan-1  HE    0.020
 HMR  plan-1  HH1   0.020
 HMR  plan-1  HH21  0.020
 HMR  plan-1  HH22  0.020
 HMR  plan-2  O     0.020
 HMR  plan-2  CH2   0.020
 HMR  plan-2  OXT   0.020
 HMR  plan-2  C     0.020

