# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 20:03:50 2021
#   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  21  11  .  2021-08-05  2022-11-17
;
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  -0.443  16.9539  24.6932  32.4936
 6CS  C     C  C     0   0.551  16.6081  23.6491  32.0011
 6CS  OXT   O  OH1   0  -0.591  15.7466  23.5667  30.9968
 6CS  CA    C  CH1   0  -0.232  17.1460  22.2859  32.3963
 6CS  N     N  N     0  -0.484  18.2740  22.0461  31.5138
 6CS  CAI   C  C     0   0.435  19.2396  21.3350  31.9708
 6CS  CAA   C  CH3   0  -0.734  20.4327  21.0722  31.1021
 6CS  NAG   N  NH1   0  -0.646  19.2869  20.7769  33.2003
 6CS  CG2   C  CH2   0  -0.279  18.2112  20.9242  34.1511
 6CS  CB    C  CH1   0   0.011  17.4964  22.2402  33.8749
 6CS  OG1   O  OH1   0  -0.668  16.2994  22.3533  34.6023
 6CS  HXT   H  HOH1  0   0.479  15.4691  24.4537  30.7208
 6CS  HA    H  HCH1  0   0.260  16.3635  21.5378  32.2103
 6CS  HN    H  HNH1  0   0.400  20.0906  20.2311  33.4593
 6CS  HAA1  H  HCH3  0   0.255  20.3214  21.5760  30.1462
 6CS  HAA2  H  HCH3  0   0.255  21.3462  21.4263  31.5821
 6CS  HAA3  H  HCH3  0   0.256  20.5519  20.0027  30.9233
 6CS  HG21  H  HCH2  0   0.233  17.4971  20.0963  34.0838
 6CS  HG22  H  HCH2  0   0.258  18.6261  20.9202  35.1603
 6CS  HB    H  HCH1  0   0.226  18.1858  23.0631  34.1012
 6CS  HOG1  H  HOH1  0   0.457  16.5132  22.5446  35.5206

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     double  1.205  0.020  1.205
 6CS  C    OXT   single  1.326  0.020  1.326
 6CS  C    CA    single  1.518  0.020  1.518
 6CS  OXT  HXT   single  0.850  0.020  0.980
 6CS  CA   N     single  1.452  0.020  1.452
 6CS  CA   CB    single  1.520  0.020  1.520
 6CS  CA   HA    single  0.970  0.020  1.090
 6CS  N    CAI   double  1.283  0.020  1.283
 6CS  CAI  CAA   single  1.499  0.020  1.499
 6CS  CAI  NAG   single  1.351  0.020  1.351
 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  1.443  0.020  1.443
 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  1.405  0.020  1.405
 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   111.82  3.000
 6CS  CA    C    O     124.75  3.000
 6CS  OXT   C    O     123.37  3.000
 6CS  HXT   OXT  C     110.16  3.000
 6CS  HA    CA   CB    107.96  3.000
 6CS  HA    CA   N     109.76  3.000
 6CS  CB    CA   N     114.02  3.000
 6CS  HA    CA   C     108.37  3.000
 6CS  CB    CA   C     111.22  3.000
 6CS  N     CA   C     105.39  3.000
 6CS  CAI   N    CA    117.36  3.000
 6CS  NAG   CAI  CAA   115.28  3.000
 6CS  NAG   CAI  N     125.40  3.000
 6CS  CAA   CAI  N     119.32  3.000
 6CS  HAA3  CAA  HAA2  107.39  3.000
 6CS  HAA3  CAA  HAA1  108.76  3.000
 6CS  HAA2  CAA  HAA1  108.81  3.000
 6CS  HAA3  CAA  CAI   110.72  3.000
 6CS  HAA2  CAA  CAI   110.77  3.000
 6CS  HAA1  CAA  CAI   110.31  3.000
 6CS  HN    NAG  CG2   118.78  3.000
 6CS  HN    NAG  CAI   119.12  3.000
 6CS  CG2   NAG  CAI   122.09  3.000
 6CS  HG22  CG2  HG21  107.58  3.000
 6CS  HG22  CG2  CB    110.45  3.000
 6CS  HG21  CG2  CB    109.63  3.000
 6CS  HG22  CG2  NAG   109.00  3.000
 6CS  HG21  CG2  NAG   111.61  3.000
 6CS  CB    CG2  NAG   108.58  3.000
 6CS  HB    CB   OG1   111.60  3.000
 6CS  HB    CB   CG2   108.41  3.000
 6CS  OG1   CB   CG2   112.05  3.000
 6CS  HB    CB   CA    108.84  3.000
 6CS  OG1   CB   CA    107.74  3.000
 6CS  CG2   CB   CA    108.09  3.000
 6CS  HOG1  OG1  CB    108.71  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  CONST_06  HXT   OXT  C    CA   180.00   0.0  0
 6CS  Var_01    CB    CG2  NAG  CAI  -28.20  30.0  1
 6CS  Var_02    HAA1  CAA  CAI  N      1.57  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
 6CS  plan-2  HXT  0.020

