# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:58:00 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (2S,3R)-2-amino-5-carbamimidamido-3-hydroxypentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H](O)CCNC(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
 4D4  4D4  '(2S,3R)-2-amino-5-carbamimidamido-3-hydroxypentanoic acid (non-preferred name)'  L-peptide  26  13  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_4D4
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
 4D4  C    C  C      0   0.389  -68.5442  127.4914  158.2006
 4D4  O    O  O      0  -0.597  -69.4670  127.3966  157.3697
 4D4  CA   C  CH1    0  -0.238  -67.3964  126.4451  158.1235
 4D4  N    N  NH2    0  -0.791  -67.6003  125.3536  157.1830
 4D4  CB   C  CH1    0   0.057  -66.0751  127.1648  157.8499
 4D4  OB   O  OH1    0  -0.681  -66.2048  127.8198  156.5980
 4D4  CG   C  CH2    0  -0.474  -64.8801  126.2164  157.8754
 4D4  CD   C  CH2    0  -0.263  -63.5468  126.9397  157.7641
 4D4  NE   N  NH1    0  -0.653  -62.4562  125.9954  157.8100
 4D4  CZ   C  C      0   0.551  -61.1522  126.3912  157.7902
 4D4  NH2  N  N      0  -0.732  -60.7200  127.5794  157.5614
 4D4  NH1  N  NH2    0  -0.828  -60.2470  125.3642  157.9710
 4D4  O1   O  OC    -1  -0.617  -68.4366  128.3457  159.1054
 4D4  H1   H  HCH1   0   0.220  -67.2965  126.0022  159.1210
 4D4  H2   H  HNH2   0   0.335  -68.3792  124.7942  157.5066
 4D4  H3   H  HNH2   0   0.324  -67.9222  125.7469  156.3067
 4D4  H5   H  HCH1   0   0.198  -65.9402  127.9016  158.6523
 4D4  H6   H  HOH1   0   0.447  -65.5101  128.4781  156.5124
 4D4  H7   H  HCH2   0   0.231  -64.9753  125.4834  157.0719
 4D4  H8   H  HCH2   0   0.222  -64.9023  125.6613  158.8190
 4D4  H9   H  HCH2   0   0.220  -63.4595  127.6789  158.5711
 4D4  H10  H  HCH2   0   0.218  -63.5032  127.4954  156.8211
 4D4  H11  H  HNH1   0   0.387  -62.6697  125.0632  158.1255
 4D4  H12  H  H      0   0.325  -61.4771  128.2228  157.3679
 4D4  H14  H  HNH2   0   0.376  -60.5238  124.6226  158.5957
 4D4  H15  H  HNH2   0   0.373  -59.3168  125.6938  158.1734

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
 4D4  OB   CB   single  1.419  0.020  1.419
 4D4  N    CA   single  1.458  0.019  1.458
 4D4  NH2  CZ   double  1.285  0.020  1.285
 4D4  O    C    deloc   1.231  0.020  1.231
 4D4  CZ   NH1  single  1.381  0.020  1.381
 4D4  CZ   NE   single  1.363  0.020  1.363
 4D4  CD   NE   single  1.443  0.020  1.443
 4D4  CD   CG   single  1.521  0.020  1.521
 4D4  CA   CB   single  1.530  0.020  1.530
 4D4  CA   C    single  1.525  0.021  1.525
 4D4  CB   CG   single  1.526  0.020  1.526
 4D4  C    O1   deloc   1.249  0.020  1.249
 4D4  CA   H1   single  0.970  0.020  1.090
 4D4  N    H2   single  0.890  0.020  1.040
 4D4  N    H3   single  0.890  0.020  1.040
 4D4  CB   H5   single  0.970  0.020  1.090
 4D4  OB   H6   single  0.850  0.020  0.980
 4D4  CG   H7   single  0.970  0.020  1.090
 4D4  CG   H8   single  0.970  0.020  1.090
 4D4  CD   H9   single  0.970  0.020  1.090
 4D4  CD   H10  single  0.970  0.020  1.090
 4D4  NE   H11  single  0.860  0.020  1.020
 4D4  NH2  H12  single  0.890  0.020  1.040
 4D4  NH1  H14  single  0.890  0.020  1.040
 4D4  NH1  H15  single  0.890  0.020  1.040

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
 4D4  O1   C    CA   115.63  3.000
 4D4  O1   C    O    126.82  3.000
 4D4  CA   C    O    120.80  1.700
 4D4  H1   CA   CB   105.91  3.000
 4D4  H1   CA   N    107.33  3.000
 4D4  CB   CA   N    110.50  1.700
 4D4  H1   CA   C    107.10  3.000
 4D4  CB   CA   C    110.10  1.900
 4D4  N    CA   C    111.00  2.800
 4D4  H3   N    H2   104.28  3.000
 4D4  H3   N    CA   108.20  3.000
 4D4  H2   N    CA   108.40  3.000
 4D4  H5   CB   CG   107.98  3.000
 4D4  H5   CB   OB   110.26  3.000
 4D4  CG   CB   OB   111.92  3.000
 4D4  H5   CB   CA   106.94  3.000
 4D4  CG   CB   CA   112.41  3.000
 4D4  OB   CB   CA   107.22  3.000
 4D4  H6   OB   CB   109.20  3.000
 4D4  H8   CG   H7   106.99  3.000
 4D4  H8   CG   CD   108.78  3.000
 4D4  H7   CG   CD   109.99  3.000
 4D4  H8   CG   CB   108.27  3.000
 4D4  H7   CG   CB   109.67  3.000
 4D4  CD   CG   CB   112.94  3.000
 4D4  H10  CD   H9   106.74  3.000
 4D4  H10  CD   NE   109.22  3.000
 4D4  H9   CD   NE   110.92  3.000
 4D4  H10  CD   CG   109.83  3.000
 4D4  H9   CD   CG   109.64  3.000
 4D4  NE   CD   CG   110.42  3.000
 4D4  H11  NE   CZ   118.44  3.000
 4D4  H11  NE   CD   117.09  3.000
 4D4  CZ   NE   CD   122.18  3.000
 4D4  NH1  CZ   NH2  119.37  3.000
 4D4  NH1  CZ   NE   114.16  3.000
 4D4  NH2  CZ   NE   126.37  3.000
 4D4  H12  NH2  CZ   111.73  3.000
 4D4  H15  NH1  H14  111.69  3.000
 4D4  H15  NH1  CZ   112.85  3.000
 4D4  H14  NH1  CZ   116.62  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
 4D4  CONST_01  NH2  CZ   NE  CD      0.00   0.0  0
 4D4  CONST_02  NH1  CZ   NE  CD    180.00   0.0  0
 4D4  CONST_03  H12  NH2  CZ  NE      0.00   0.0  0
 4D4  CONST_05  H15  NH1  CZ  NE    180.00   0.0  0
 4D4  CONST_06  H11  NE   CZ  NH2   180.00   0.0  0
 4D4  Var_01    NE   CD   CG  CB    179.31  30.0  1
 4D4  Var_02    CZ   NE   CD  CG   -176.96  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
 4D4  chir_01  CA  N   CB  C   negativ
 4D4  chir_02  CB  OB  CA  CG  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
 4D4  plan-1  CD   0.020
 4D4  plan-1  NE   0.020
 4D4  plan-1  CZ   0.020
 4D4  plan-1  NH2  0.020
 4D4  plan-1  NH1  0.020
 4D4  plan-1  H11  0.020
 4D4  plan-1  H12  0.020
 4D4  plan-1  H14  0.020
 4D4  plan-1  H15  0.020
 4D4  plan-2  C    0.020
 4D4  plan-2  O    0.020
 4D4  plan-2  CA   0.020
 4D4  plan-2  O1   0.020

