# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:41:44 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: (4S)-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](CCN1)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
 4CS  4CS  '(4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  19  10  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4CS
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
 4CS  O     O  O      0  -0.600   2.0682  -1.3930   0.6476
 4CS  C     C  C      0   0.391   1.9776  -0.3149   0.0351
 4CS  OXT   O  OC    -1  -0.632   2.9168   0.4632  -0.2429
 4CS  CA    C  CH1    0  -0.224   0.5801   0.1633  -0.4181
 4CS  CB    C  CH2    0  -0.485   0.2042   1.4326   0.3544
 4CS  CAD   C  CH2    0  -0.261  -1.2183   1.8411   0.0186
 4CS  NAG   N  NH1    0  -0.642  -2.0762   0.6949   0.1998
 4CS  CAI   C  C      0   0.400  -1.6206  -0.5646  -0.0497
 4CS  CAA   C  CH3    0  -0.736  -2.6738  -1.6328   0.0286
 4CS  N     N  N      0  -0.455  -0.4145  -0.8843  -0.3217
 4CS  HA    H  HCH1   0   0.207   0.6773   0.4448  -1.4768
 4CS  HB1   H  HCH2   0   0.222   0.2805   1.2480   1.4309
 4CS  HB2   H  HCH2   0   0.236   0.8934   2.2420   0.1150
 4CS  HAD1  H  HCH2   0   0.240  -1.5574   2.6458   0.6733
 4CS  HAD2  H  HCH2   0   0.216  -1.2673   2.2211  -1.0092
 4CS  HNAG  H  HNH1   0   0.385  -3.0700   0.8432   0.2375
 4CS  HAA1  H  HCH3   0   0.246  -3.4227  -1.4938  -0.7536
 4CS  HAA2  H  HCH3   0   0.247  -2.2242  -2.6148  -0.0923
 4CS  HAA3  H  HCH3   0   0.244  -3.1968  -1.6016   0.9861

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
 4CS  O    C     deloc   1.243  0.020  1.243
 4CS  C    OXT   deloc   1.251  0.020  1.251
 4CS  C    CA    single  1.545  0.020  1.545
 4CS  CA   CB    single  1.533  0.020  1.533
 4CS  CA   N     single  1.448  0.020  1.448
 4CS  CA   HA    single  0.970  0.020  1.090
 4CS  CB   CAD   single  1.518  0.020  1.518
 4CS  CB   HB1   single  0.970  0.020  1.090
 4CS  CB   HB2   single  0.970  0.020  1.090
 4CS  CAD  NAG   single  1.443  0.020  1.443
 4CS  CAD  HAD1  single  0.970  0.020  1.090
 4CS  CAD  HAD2  single  0.970  0.020  1.090
 4CS  NAG  CAI   single  1.362  0.020  1.362
 4CS  NAG  HNAG  single  0.860  0.020  1.020
 4CS  CAI  CAA   single  1.502  0.020  1.502
 4CS  CAI  N     double  1.277  0.020  1.277
 4CS  CAA  HAA1  single  0.970  0.020  1.090
 4CS  CAA  HAA2  single  0.970  0.020  1.090
 4CS  CAA  HAA3  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
 4CS  CA    C    OXT   114.92  3.000
 4CS  CA    C    O     118.61  3.000
 4CS  OXT   C    O     126.45  3.000
 4CS  HA    CA   N     108.06  3.000
 4CS  HA    CA   CB    107.15  3.000
 4CS  N     CA   CB    113.40  3.000
 4CS  HA    CA   C     106.35  3.000
 4CS  N     CA   C     112.20  3.000
 4CS  CB    CA   C     109.29  3.000
 4CS  HB2   CB   HB1   107.29  3.000
 4CS  HB2   CB   CAD   110.14  3.000
 4CS  HB1   CB   CAD   109.16  3.000
 4CS  HB2   CB   CA    110.44  3.000
 4CS  HB1   CB   CA    109.80  3.000
 4CS  CAD   CB   CA    109.96  3.000
 4CS  HAD2  CAD  HAD1  107.02  3.000
 4CS  HAD2  CAD  NAG   111.48  3.000
 4CS  HAD1  CAD  NAG   109.00  3.000
 4CS  HAD2  CAD  CB    110.02  3.000
 4CS  HAD1  CAD  CB    110.92  3.000
 4CS  NAG   CAD  CB    108.40  3.000
 4CS  HNAG  NAG  CAI   118.28  3.000
 4CS  HNAG  NAG  CAD   118.37  3.000
 4CS  CAI   NAG  CAD   120.82  3.000
 4CS  N     CAI  CAA   119.69  3.000
 4CS  N     CAI  NAG   125.89  3.000
 4CS  CAA   CAI  NAG   114.42  3.000
 4CS  HAA3  CAA  HAA2  108.76  3.000
 4CS  HAA3  CAA  HAA1  107.23  3.000
 4CS  HAA2  CAA  HAA1  108.60  3.000
 4CS  HAA3  CAA  CAI   111.18  3.000
 4CS  HAA2  CAA  CAI   110.29  3.000
 4CS  HAA1  CAA  CAI   110.68  3.000
 4CS  CAI   N    CA    118.81  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
 4CS  CONST_01  NAG   CAI  N    CA     0.00   0.0  0
 4CS  CONST_02  N     CAI  NAG  CAD    0.00   0.0  0
 4CS  CONST_03  CAA   CAI  N    CA   180.00   0.0  0
 4CS  CONST_04  CAA   CAI  NAG  CAD  180.00   0.0  0
 4CS  CONST_05  HNAG  NAG  CAI  N    180.00   0.0  0
 4CS  Var_01    NAG   CAD  CB   CA    51.40  30.0  1
 4CS  Var_02    CAI   NAG  CAD  CB   -32.97  30.0  1
 4CS  Var_03    HAA1  CAA  CAI  NAG   64.87  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
 4CS  chir_01  CA  C  CB  N  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
 4CS  plan-1  CA    0.020
 4CS  plan-1  CAD   0.020
 4CS  plan-1  NAG   0.020
 4CS  plan-1  CAI   0.020
 4CS  plan-1  CAA   0.020
 4CS  plan-1  N     0.020
 4CS  plan-1  HNAG  0.020
 4CS  plan-2  O     0.020
 4CS  plan-2  C     0.020
 4CS  plan-2  OXT   0.020
 4CS  plan-2  CA    0.020

