# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 15:22:34 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: (2S,3R,4S)-2,5-diamino-3,4-dihydroxy-5-oxopentanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@@H](O)[C@H](O)C(N)=O)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
 R2T  R2T  '(2S,3R,4S)-2,5-diamino-3,4-dihydroxy-5-oxopentanoic acid (non-preferred name)'  L-peptide  21  12  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R2T
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
 R2T  N     N  NH2    0  -0.805  16.7532   -99.2494   1.1208
 R2T  CA    C  CH1    0  -0.246  16.3041  -100.3038   0.2263
 R2T  C     C  C      0   0.403  15.6811   -99.7723  -1.0933
 R2T  O     O  O      0  -0.606  15.1889  -100.6365  -1.8471
 R2T  CB    C  CH1    0   0.061  15.3726  -101.3158   0.9157
 R2T  CG    C  CH1    0  -0.085  13.9136  -100.8530   1.0629
 R2T  CD    C  C      0   0.447  13.1751  -101.8762   1.9251
 R2T  OE1   O  O      0  -0.494  13.0112  -103.0216   1.5231
 R2T  NE2   N  NH2    0  -0.787  12.7540  -101.4386   3.1159
 R2T  OG1   O  OH1    0  -0.657  13.8400   -99.5458   1.5738
 R2T  OB1   O  OH1    0  -0.673  15.9401  -101.6561   2.1681
 R2T  H     H  HNH2   0   0.329  17.7552   -99.2997   1.2354
 R2T  HA    H  HCH1   0   0.222  17.1696  -100.9021  -0.0919
 R2T  HB2   H  HCH1   0   0.213  15.3300  -102.1989   0.2710
 R2T  HG2   H  HCH1   0   0.242  13.4635  -100.9088   0.0655
 R2T  HE22  H  HNH2   0   0.397  12.2966  -102.0636   3.7592
 R2T  HE21  H  HNH2   0   0.400  12.9623  -100.5056   3.4275
 R2T  HOG   H  HOH1   0   0.454  12.9676   -99.1912   1.3744
 R2T  HOB   H  HOH1   0   0.447  15.7292  -102.5753   2.3535
 R2T  H2    H  HNH2   0   0.327  16.5657   -98.3711   0.6522
 R2T  OXT   O  OC    -1  -0.590  15.7487   -98.5464  -1.3048

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
 R2T  N    CA    single  1.458  0.019  1.458
 R2T  CA   C     single  1.525  0.021  1.525
 R2T  CA   CB    single  1.521  0.033  1.521
 R2T  C    O     deloc   1.231  0.020  1.231
 R2T  CB   CG    single  1.538  0.020  1.538
 R2T  CB   OB1   single  1.416  0.020  1.416
 R2T  CG   CD    single  1.528  0.020  1.528
 R2T  CG   OG1   single  1.405  0.020  1.405
 R2T  CD   OE1   double  1.225  0.020  1.225
 R2T  CD   NE2   single  1.337  0.020  1.337
 R2T  N    H     single  0.860  0.020  0.860
 R2T  CA   HA    single  0.970  0.020  0.970
 R2T  CB   HB2   single  0.970  0.020  1.090
 R2T  CG   HG2   single  0.970  0.020  1.090
 R2T  NE2  HE22  single  0.860  0.020  1.020
 R2T  NE2  HE21  single  0.860  0.020  1.020
 R2T  OG1  HOG   single  0.850  0.020  0.980
 R2T  OB1  HOB   single  0.850  0.020  0.980
 R2T  N    H2    single  0.890  0.020  1.040
 R2T  C    OXT   deloc   1.246  0.020  1.246

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
 R2T  H2    N    H     106.22  3.000
 R2T  H2    N    CA    106.68  3.000
 R2T  H     N    CA    114.00  3.000
 R2T  HA    CA   CB    109.00  3.000
 R2T  HA    CA   C     110.00  3.000
 R2T  CB    CA   C     110.50  1.500
 R2T  HA    CA   N     110.00  3.000
 R2T  CB    CA   N     110.40  1.500
 R2T  C     CA   N     111.00  2.800
 R2T  OXT   C    O     126.89  3.000
 R2T  OXT   C    CA    120.80  1.700
 R2T  O     C    CA    120.80  1.700
 R2T  HB2   CB   OB1   110.04  3.000
 R2T  HB2   CB   CG    105.21  3.000
 R2T  OB1   CB   CG    111.58  3.000
 R2T  HB2   CB   CA    106.89  3.000
 R2T  OB1   CB   CA    108.16  3.000
 R2T  CG    CB   CA    114.80  3.000
 R2T  HG2   CG   OG1   110.90  3.000
 R2T  HG2   CG   CD    106.32  3.000
 R2T  OG1   CG   CD    113.10  3.000
 R2T  HG2   CG   CB    106.70  3.000
 R2T  OG1   CG   CB    111.37  3.000
 R2T  CD    CG   CB    108.12  3.000
 R2T  NE2   CD   OE1   123.80  3.000
 R2T  NE2   CD   CG    115.83  3.000
 R2T  OE1   CD   CG    120.37  3.000
 R2T  HE21  NE2  HE22  118.17  3.000
 R2T  HE21  NE2  CD    120.97  3.000
 R2T  HE22  NE2  CD    120.61  3.000
 R2T  HOG   OG1  CG    108.35  3.000
 R2T  HOB   OB1  CB    108.20  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
 R2T  CONST_01  HE22  NE2  CD  CG  180.00  0.0  0
 R2T  CONST_02  HE21  NE2  CD  CG    0.00  0.0  0

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
 R2T  chir_01  CA  N    C   CB  positiv
 R2T  chir_02  CB  OB1  CA  CG  positiv
 R2T  chir_03  CG  OG1  CB  CD  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
 R2T  plan-1  CG    0.020
 R2T  plan-1  CD    0.020
 R2T  plan-1  OE1   0.020
 R2T  plan-1  NE2   0.020
 R2T  plan-1  HE22  0.020
 R2T  plan-1  HE21  0.020
 R2T  plan-2  CA    0.020
 R2T  plan-2  C     0.020
 R2T  plan-2  O     0.020
 R2T  plan-2  OXT   0.020

