# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 15:42:00 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 3-(4-hydroxy-1,2,5-thiadiazol-3-yl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1nsnc1O)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
 R2P  R2P  3-(4-hydroxy-1,2,5-thiadiazol-3-yl)-D-alanine  D-peptide  18  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 OK
;

data_comp_R2P
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
 R2P  ND1   N  N      0  -0.530  -1.9181   3.5071  15.9503
 R2P  N     N  NH2    0  -0.756  -1.5399   1.2098  13.8404
 R2P  CA    C  CH1    0  -0.165  -0.9103   0.9269  15.1189
 R2P  C     C  C      0   0.427  -0.1846  -0.4497  15.1405
 R2P  OD2   O  OH1    0  -0.512   1.4008   4.7296  16.1342
 R2P  CD2   C  CR5    0   0.371   0.0812   4.5776  16.1437
 R2P  NE2   N  N      0  -0.570  -0.6820   5.5938  16.4003
 R2P  SE1   S  S2     0   0.552  -2.2391   5.0737  16.3281
 R2P  CG    C  CR5    0   0.079  -0.6301   3.3434  15.8806
 R2P  CB    C  CH2    0  -0.492   0.0364   2.0348  15.6045
 R2P  O     O  O      0  -0.526  -0.3799  -1.2249  14.1897
 R2P  OXT   O  OC    -1  -0.756   0.5194  -0.6641  16.1498
 R2P  HA    H  HCH1   0   0.157  -1.7256   0.8468  15.8490
 R2P  HOD2  H  HOH1   0   0.508   1.8519   3.8960  15.9522
 R2P  HB    H  HCH2   0   0.284   0.5505   1.7126  16.5131
 R2P  HBA   H  HCH2   0   0.241   0.8135   2.1881  14.8441
 R2P  H     H  HNH2   0   0.344  -2.0973   2.0506  13.9315
 R2P  H2    H  HNH2   0   0.344  -0.8319   1.4169  13.1455

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
 R2P  ND1  SE1   aromatic  1.643  0.020  1.643
 R2P  ND1  CG    aromatic  1.300  0.020  1.300
 R2P  N    CA    single    1.458  0.019  1.458
 R2P  CA   C     single    1.525  0.021  1.525
 R2P  CA   CB    single    1.521  0.033  1.521
 R2P  C    O     deloc     1.231  0.020  1.231
 R2P  C    OXT   deloc     1.249  0.020  1.249
 R2P  OD2  CD2   single    1.328  0.020  1.328
 R2P  CD2  NE2   aromatic  1.297  0.020  1.297
 R2P  CD2  CG    aromatic  1.449  0.020  1.449
 R2P  NE2  SE1   aromatic  1.643  0.020  1.643
 R2P  CG   CB    single    1.494  0.020  1.494
 R2P  N    H     single    0.860  0.020  0.860
 R2P  N    H2    single    0.890  0.020  1.040
 R2P  CA   HA    single    0.970  0.020  0.970
 R2P  OD2  HOD2  single    0.850  0.020  0.980
 R2P  CB   HB    single    0.970  0.020  1.090
 R2P  CB   HBA   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
 R2P  CG    ND1  SE1  109.02  3.000
 R2P  H2    N    H    106.05  3.000
 R2P  H2    N    CA   109.91  3.000
 R2P  H     N    CA   114.00  3.000
 R2P  HA    CA   CB   109.00  3.000
 R2P  HA    CA   C    110.00  3.000
 R2P  CB    CA   C    110.50  1.500
 R2P  HA    CA   N    110.00  3.000
 R2P  CB    CA   N    110.40  1.500
 R2P  C     CA   N    111.00  2.800
 R2P  OXT   C    O    126.87  3.000
 R2P  OXT   C    CA   120.80  1.700
 R2P  O     C    CA   120.80  1.700
 R2P  HOD2  OD2  CD2  111.53  3.000
 R2P  CG    CD2  NE2  114.50  3.000
 R2P  CG    CD2  OD2  125.73  3.000
 R2P  NE2   CD2  OD2  119.77  3.000
 R2P  SE1   NE2  CD2  107.52  3.000
 R2P  NE2   SE1  ND1   97.28  3.000
 R2P  CB    CG   CD2  124.10  3.000
 R2P  CB    CG   ND1  124.19  3.000
 R2P  CD2   CG   ND1  111.68  3.000
 R2P  HBA   CB   HB   106.50  3.000
 R2P  HBA   CB   CG   108.75  3.000
 R2P  HB    CB   CG   108.33  3.000
 R2P  HBA   CB   CA   108.54  3.000
 R2P  HB    CB   CA   109.89  3.000
 R2P  CG    CB   CA   114.53  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
 R2P  CONST_01  CD2  NE2  SE1  ND1    0.00   0.0  0
 R2P  CONST_02  NE2  CD2  CG   ND1    0.00   0.0  0
 R2P  CONST_03  SE1  ND1  CG   CD2    0.00   0.0  0
 R2P  CONST_04  CG   ND1  SE1  NE2    0.00   0.0  0
 R2P  CONST_05  CG   CD2  NE2  SE1    0.00   0.0  0
 R2P  CONST_06  OD2  CD2  CG   ND1  180.00   0.0  0
 R2P  CONST_07  SE1  NE2  CD2  OD2  180.00   0.0  0
 R2P  CONST_08  CB   CG   CD2  NE2  180.00   0.0  0
 R2P  CONST_09  CB   CG   ND1  SE1  180.00   0.0  0
 R2P  Var_01    CA   CB   CG   ND1   11.99  30.0  2

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
 R2P  chir_01  CA  N  C  CB  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
 R2P  plan-1  ND1  0.020
 R2P  plan-1  OD2  0.020
 R2P  plan-1  CD2  0.020
 R2P  plan-1  NE2  0.020
 R2P  plan-1  SE1  0.020
 R2P  plan-1  CG   0.020
 R2P  plan-1  CB   0.020
 R2P  plan-2  CA   0.020
 R2P  plan-2  C    0.020
 R2P  plan-2  O    0.020
 R2P  plan-2  OXT  0.020

