# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 14:59:37 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (4S,5S)-5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=N[C@@H]([C@@H](O)CN1)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
 6CS  6CS  '(4S,5S)-5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  20  11  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6CS
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
 6CS  O     O  O      0  -0.614   1.8376  -1.1457   1.1017
 6CS  C     C  C      0   0.403   1.7360  -0.8544  -0.1060
 6CS  OXT   O  OC    -1  -0.619   2.5369  -1.1568  -1.0133
 6CS  CA    C  CH1    0  -0.220   0.4689  -0.0696  -0.5150
 6CS  N     N  N      0  -0.479  -0.6652  -0.9805  -0.4465
 6CS  CAI   C  C      0   0.413  -1.8132  -0.5009  -0.1510
 6CS  CAA   C  CH3    0  -0.736  -3.0031  -1.4127  -0.0788
 6CS  NAG   N  NH1    0  -0.650  -2.0785   0.8036   0.1191
 6CS  CG2   C  CH2    0  -0.280  -1.0566   1.8157   0.0199
 6CS  CB    C  CH1    0   0.008   0.2834   1.1691   0.3460
 6CS  OG1   O  OH1    0  -0.674   1.3583   2.0442   0.0905
 6CS  HA    H  HCH1   0   0.196   0.5891   0.2608  -1.5563
 6CS  HN    H  HNH1   0   0.391  -3.0307   1.0864   0.2715
 6CS  HAA1  H  HCH3   0   0.249  -2.6983  -2.4421  -0.2452
 6CS  HAA2  H  HCH3   0   0.247  -3.4916  -1.3456   0.8949
 6CS  HAA3  H  HCH3   0   0.249  -3.7455  -1.1416  -0.8316
 6CS  HG21  H  HCH2   0   0.219  -1.0180   2.2615  -0.9817
 6CS  HG22  H  HCH2   0   0.243  -1.2803   2.6183   0.7264
 6CS  HB    H  HCH1   0   0.202   0.2688   0.8539   1.3974
 6CS  HOG1  H  HOH1   0   0.449   1.3290   2.7587   0.7340

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
 6CS  O    C     deloc   1.246  0.020  1.246
 6CS  C    OXT   deloc   1.247  0.020  1.247
 6CS  C    CA    single  1.546  0.020  1.546
 6CS  CA   N     single  1.456  0.020  1.456
 6CS  CA   CB    single  1.520  0.020  1.520
 6CS  CA   HA    single  0.970  0.020  1.090
 6CS  N    CAI   double  1.279  0.020  1.279
 6CS  CAI  CAA   single  1.501  0.020  1.501
 6CS  CAI  NAG   single  1.358  0.020  1.358
 6CS  CAA  HAA1  single  0.970  0.020  1.090
 6CS  CAA  HAA2  single  0.970  0.020  1.090
 6CS  CAA  HAA3  single  0.970  0.020  1.090
 6CS  NAG  CG2   single  1.442  0.020  1.442
 6CS  NAG  HN    single  0.860  0.020  1.020
 6CS  CG2  CB    single  1.523  0.020  1.523
 6CS  CG2  HG21  single  0.970  0.020  1.090
 6CS  CG2  HG22  single  0.970  0.020  1.090
 6CS  CB   OG1   single  1.409  0.020  1.409
 6CS  CB   HB    single  0.970  0.020  1.090
 6CS  OG1  HOG1  single  0.850  0.020  0.980

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
 6CS  CA    C    OXT   117.19  3.000
 6CS  CA    C    O     116.23  3.000
 6CS  OXT   C    O     126.57  3.000
 6CS  HA    CA   CB    107.76  3.000
 6CS  HA    CA   N     108.53  3.000
 6CS  CB    CA   N     112.84  3.000
 6CS  HA    CA   C     108.29  3.000
 6CS  CB    CA   C     111.35  3.000
 6CS  N     CA   C     107.97  3.000
 6CS  CAI   N    CA    118.38  3.000
 6CS  NAG   CAI  CAA   114.77  3.000
 6CS  NAG   CAI  N     125.56  3.000
 6CS  CAA   CAI  N     119.67  3.000
 6CS  HAA3  CAA  HAA2  107.20  3.000
 6CS  HAA3  CAA  HAA1  108.69  3.000
 6CS  HAA2  CAA  HAA1  108.69  3.000
 6CS  HAA3  CAA  CAI   110.81  3.000
 6CS  HAA2  CAA  CAI   111.12  3.000
 6CS  HAA1  CAA  CAI   110.23  3.000
 6CS  HN    NAG  CG2   118.98  3.000
 6CS  HN    NAG  CAI   119.04  3.000
 6CS  CG2   NAG  CAI   121.47  3.000
 6CS  HG22  CG2  HG21  107.40  3.000
 6CS  HG22  CG2  CB    110.71  3.000
 6CS  HG21  CG2  CB    109.70  3.000
 6CS  HG22  CG2  NAG   109.03  3.000
 6CS  HG21  CG2  NAG   111.90  3.000
 6CS  CB    CG2  NAG   108.11  3.000
 6CS  HB    CB   OG1   111.23  3.000
 6CS  HB    CB   CG2   108.37  3.000
 6CS  OG1   CB   CG2   111.63  3.000
 6CS  HB    CB   CA    108.07  3.000
 6CS  OG1   CB   CA    108.07  3.000
 6CS  CG2   CB   CA    109.40  3.000
 6CS  HOG1  OG1  CB    108.46  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
 6CS  CONST_01  NAG   CAI  N    CA     0.00   0.0  0
 6CS  CONST_02  CG2   NAG  CAI  N      0.00   0.0  0
 6CS  CONST_03  CAA   CAI  N    CA   180.00   0.0  0
 6CS  CONST_04  CG2   NAG  CAI  CAA  180.00   0.0  0
 6CS  CONST_05  HN    NAG  CAI  N    180.00   0.0  0
 6CS  Var_01    CB    CG2  NAG  CAI  -30.40  30.0  1
 6CS  Var_02    HAA1  CAA  CAI  N      3.38  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
 6CS  chir_01  CA  C    N   CB   negativ
 6CS  chir_02  CB  OG1  CA  CG2  positiv

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
 6CS  plan-1  CA   0.020
 6CS  plan-1  N    0.020
 6CS  plan-1  CAI  0.020
 6CS  plan-1  CAA  0.020
 6CS  plan-1  NAG  0.020
 6CS  plan-1  CG2  0.020
 6CS  plan-1  HN   0.020
 6CS  plan-2  O    0.020
 6CS  plan-2  C    0.020
 6CS  plan-2  OXT  0.020
 6CS  plan-2  CA   0.020

