# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 06:03:16 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: (1R,4R,5R)-1,4,5-trihydroxy-3-(2-hydroxyethyl)cyclohex-2-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCC1=C[C@](O)(C[C@@H](O)[C@@H]1O)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
 XH2  XH2  '(1R,4R,5R)-1,4,5-trihydroxy-3-(2-hydroxyethyl)cyclohex-2-ene-1-carboxylic acid'  ligand  29  15  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XH2
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
 XH2  OAF   O  OH1   0  -0.665   2.2211   1.7524   0.1531
 XH2  CAC   C  CH1   0  -0.042   0.9720   1.2255   0.5510
 XH2  CAB   C  CH1   0   0.053  -0.0976   1.8658  -0.3224
 XH2  OAG   O  OH1   0  -0.674  -0.1929   3.2516  -0.0954
 XH2  CAA   C  CH2   0  -0.488  -1.4414   1.2438   0.0031
 XH2  CAI   C  CT    0   0.069  -1.4578  -0.2362  -0.3659
 XH2  CAH   C  C     0   0.535  -2.5926  -0.9451   0.3863
 XH2  OAO   O  O     0  -0.432  -2.8979  -0.7018   1.5265
 XH2  OAN   O  OH1   0  -0.585  -3.1585  -1.8974  -0.3361
 XH2  OAM   O  OH1   0  -0.657  -1.6344  -0.3246  -1.7607
 XH2  CAE   C  C1    0  -0.285  -0.1814  -0.9203   0.0631
 XH2  CAD   C  C     0   0.081   0.9233  -0.2833   0.4483
 XH2  CAL   C  CH2   0  -0.547   2.1648  -1.0594   0.7971
 XH2  CAK   C  CH2   0  -0.131   3.0287  -1.3168  -0.4308
 XH2  OAJ   O  OH1   0  -0.673   4.1659  -2.0500  -0.0294
 XH2  HAF   H  HOH1  0   0.462   2.8125   1.7723   0.9105
 XH2  HAC   H  HCH1  0   0.239   0.7627   1.4964   1.5974
 XH2  HAB   H  HCH1  0   0.211   0.1554   1.6613  -1.3734
 XH2  HAG   H  HOH1  0   0.448   0.6632   3.6431  -0.2982
 XH2  HAA1  H  HCH2  0   0.257  -1.6407   1.3628   1.0697
 XH2  HAA2  H  HCH2  0   0.268  -2.2417   1.7571  -0.5361
 XH2  HAM   H  HOH1  0   0.455  -1.3699  -1.1978  -2.0699
 XH2  HAE   H  H     0   0.272  -0.1746  -2.0072   0.0161
 XH2  HAN   H  HOH1  0   0.485  -3.8249  -2.3622   0.1930
 XH2  HAL1  H  HCH2  0   0.242   2.7530  -0.5318   1.5539
 XH2  HAL2  H  HCH2  0   0.252   1.8800  -2.0190   1.2348
 XH2  HAK1  H  HCH2  0   0.193   2.4319  -1.8695  -1.1676
 XH2  HAK2  H  HCH2  0   0.202   3.3058  -0.3632  -0.8922
 XH2  HAJ   H  HOH1  0   0.454   4.7123  -2.2007  -0.8059

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
 XH2  OAF  CAC   single  1.413  0.020  1.413
 XH2  CAC  CAB   single  1.522  0.020  1.522
 XH2  CAC  CAD   single  1.513  0.020  1.513
 XH2  CAB  OAG   single  1.407  0.020  1.407
 XH2  CAB  CAA   single  1.516  0.020  1.516
 XH2  CAA  CAI   single  1.525  0.020  1.525
 XH2  CAI  CAH   single  1.535  0.020  1.535
 XH2  CAI  OAM   single  1.409  0.020  1.409
 XH2  CAI  CAE   single  1.510  0.020  1.510
 XH2  CAH  OAO   double  1.205  0.020  1.205
 XH2  CAH  OAN   single  1.323  0.020  1.323
 XH2  CAE  CAD   double  1.332  0.020  1.332
 XH2  CAD  CAL   single  1.505  0.020  1.505
 XH2  CAL  CAK   single  1.523  0.020  1.523
 XH2  CAK  OAJ   single  1.411  0.020  1.411
 XH2  OAF  HAF   single  0.850  0.020  0.980
 XH2  CAC  HAC   single  0.970  0.020  1.090
 XH2  CAB  HAB   single  0.970  0.020  1.090
 XH2  OAG  HAG   single  0.850  0.020  0.980
 XH2  CAA  HAA1  single  0.970  0.020  1.090
 XH2  CAA  HAA2  single  0.970  0.020  1.090
 XH2  OAM  HAM   single  0.850  0.020  0.980
 XH2  CAE  HAE   single  0.930  0.020  1.080
 XH2  OAN  HAN   single  0.850  0.020  0.980
 XH2  CAL  HAL1  single  0.970  0.020  1.090
 XH2  CAL  HAL2  single  0.970  0.020  1.090
 XH2  CAK  HAK1  single  0.970  0.020  1.090
 XH2  CAK  HAK2  single  0.970  0.020  1.090
 XH2  OAJ  HAJ   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
 XH2  HAF   OAF  CAC   109.26  3.000
 XH2  HAC   CAC  CAD   107.69  3.000
 XH2  HAC   CAC  CAB   107.95  3.000
 XH2  CAD   CAC  CAB   110.97  3.000
 XH2  HAC   CAC  OAF   110.12  3.000
 XH2  CAD   CAC  OAF   112.41  3.000
 XH2  CAB   CAC  OAF   107.63  3.000
 XH2  HAB   CAB  CAA   109.43  3.000
 XH2  HAB   CAB  OAG   110.64  3.000
 XH2  CAA   CAB  OAG   108.02  3.000
 XH2  HAB   CAB  CAC   107.96  3.000
 XH2  CAA   CAB  CAC   109.09  3.000
 XH2  OAG   CAB  CAC   111.67  3.000
 XH2  HAG   OAG  CAB   107.83  3.000
 XH2  HAA2  CAA  HAA1  107.29  3.000
 XH2  HAA2  CAA  CAI   109.18  3.000
 XH2  HAA1  CAA  CAI   109.89  3.000
 XH2  HAA2  CAA  CAB   110.51  3.000
 XH2  HAA1  CAA  CAB   109.07  3.000
 XH2  CAI   CAA  CAB   110.83  3.000
 XH2  CAE   CAI  OAM   111.02  3.000
 XH2  CAE   CAI  CAH   106.05  3.000
 XH2  OAM   CAI  CAH   111.31  3.000
 XH2  CAE   CAI  CAA   111.21  3.000
 XH2  OAM   CAI  CAA   107.56  3.000
 XH2  CAH   CAI  CAA   109.72  3.000
 XH2  OAN   CAH  OAO   123.63  3.000
 XH2  OAN   CAH  CAI   112.41  3.000
 XH2  OAO   CAH  CAI   123.89  3.000
 XH2  HAN   OAN  CAH   109.95  3.000
 XH2  HAM   OAM  CAI   109.90  3.000
 XH2  HAE   CAE  CAD   119.02  3.000
 XH2  HAE   CAE  CAI   116.46  3.000
 XH2  CAD   CAE  CAI   124.50  3.000
 XH2  CAL   CAD  CAE   120.30  3.000
 XH2  CAL   CAD  CAC   118.16  3.000
 XH2  CAE   CAD  CAC   121.54  3.000
 XH2  HAL2  CAL  HAL1  106.65  3.000
 XH2  HAL2  CAL  CAK   108.81  3.000
 XH2  HAL1  CAL  CAK   109.52  3.000
 XH2  HAL2  CAL  CAD   109.32  3.000
 XH2  HAL1  CAL  CAD   110.80  3.000
 XH2  CAK   CAL  CAD   111.60  3.000
 XH2  HAK2  CAK  HAK1  107.06  3.000
 XH2  HAK2  CAK  OAJ   111.61  3.000
 XH2  HAK1  CAK  OAJ   111.56  3.000
 XH2  HAK2  CAK  CAL   109.64  3.000
 XH2  HAK1  CAK  CAL   108.53  3.000
 XH2  OAJ   CAK  CAL   108.39  3.000
 XH2  HAJ   OAJ  CAK   108.04  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
 XH2  CONST_01  HAN  OAN  CAH  CAI   180.00   0.0  0
 XH2  Var_01    CAI  CAE  CAD  CAC     2.91  30.0  1
 XH2  Var_02    CAK  CAL  CAD  CAC   -92.19  30.0  3
 XH2  Var_03    OAJ  CAK  CAL  CAD  -179.76  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
 XH2  chir_01  CAC  OAF  CAB  CAD  negativ
 XH2  chir_02  CAB  OAG  CAC  CAA  negativ
 XH2  chir_03  CAI  CAA  CAH  CAE  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
 XH2  plan-1  CAI  0.020
 XH2  plan-1  CAH  0.020
 XH2  plan-1  OAO  0.020
 XH2  plan-1  OAN  0.020
 XH2  plan-1  HAN  0.020

