# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 08:11:10 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (1R,2S,3R,4S,5R)-1,2,3,4,5-pentahydroxycyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@](O)([C@@H](O)[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
 9C4  9C4  '(1R,2S,3R,4S,5R)-1,2,3,4,5-pentahydroxycyclohexanecarboxylic acid'  ligand  25  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9C4
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
 9C4  OAA   O  OC    -1  -0.673   3.2234  -0.4496  -0.6535
 9C4  CAI   C  C      0   0.470   2.3764  -0.3485   0.2619
 9C4  OAB   O  O      0  -0.575   2.5856  -0.2858   1.4808
 9C4  CAN   C  CT     0   0.018   0.9029  -0.3187  -0.2304
 9C4  OAG   O  OH1    0  -0.690   0.9116  -0.3984  -1.6339
 9C4  CAH   C  CH2    0  -0.524   0.1267  -1.4997   0.3580
 9C4  CAJ   C  CH1    0   0.064  -1.3324  -1.4827  -0.0670
 9C4  OAC   O  OH1    0  -0.654  -1.9795  -2.5875   0.5284
 9C4  CAK   C  CH1    0  -0.047  -1.9840  -0.1692   0.3466
 9C4  OAD   O  OH1    0  -0.738  -3.3228  -0.1955  -0.1063
 9C4  CAL   C  CH1    0   0.034  -1.2193   1.0206  -0.2259
 9C4  OAE   O  OH1    0  -0.694  -1.7779   2.2436   0.2262
 9C4  CAM   C  CH1    0   0.069   0.2365   0.9816   0.2231
 9C4  OAF   O  OH1    0  -0.706   0.9649   2.0670  -0.2940
 9C4  HAG   H  HOH1   0   0.424   1.8710  -0.4323  -1.8230
 9C4  HAH1  H  HCH2   0   0.250   0.5905  -2.4357   0.0334
 9C4  HAH2  H  HCH2   0   0.262   0.1888  -1.4738   1.4493
 9C4  HAM   H  HCH1   0   0.248   0.2554   0.9952   1.3243
 9C4  HAJ   H  HCH1   0   0.242  -1.3845  -1.5605  -1.1635
 9C4  HAC   H  HOH1   0   0.421  -2.9119  -2.5433   0.2921
 9C4  HAK   H  HCH1   0   0.236  -1.9511  -0.1053   1.4461
 9C4  HAD   H  HOH1   0   0.434  -3.8166   0.4919   0.3503
 9C4  HAL   H  HCH1   0   0.242  -1.2533   0.9735  -1.3224
 9C4  HAE   H  HOH1   0   0.450  -2.4378   2.5370  -0.4076
 9C4  HAF   H  HOH1   0   0.437   0.4714   2.8681  -0.0884

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
 9C4  OAA  CAI   deloc   1.251  0.020  1.251
 9C4  CAI  OAB   deloc   1.238  0.020  1.238
 9C4  CAI  CAN   single  1.554  0.020  1.554
 9C4  CAN  OAG   single  1.406  0.020  1.406
 9C4  CAN  CAH   single  1.531  0.020  1.531
 9C4  CAN  CAM   single  1.530  0.020  1.530
 9C4  CAH  CAJ   single  1.520  0.020  1.520
 9C4  CAJ  OAC   single  1.412  0.020  1.412
 9C4  CAJ  CAK   single  1.523  0.020  1.523
 9C4  CAK  OAD   single  1.414  0.020  1.414
 9C4  CAK  CAL   single  1.526  0.020  1.526
 9C4  CAL  OAE   single  1.419  0.020  1.419
 9C4  CAL  CAM   single  1.524  0.020  1.524
 9C4  CAM  OAF   single  1.406  0.020  1.406
 9C4  OAG  HAG   single  0.850  0.020  0.980
 9C4  CAH  HAH1  single  0.970  0.020  1.090
 9C4  CAH  HAH2  single  0.970  0.020  1.090
 9C4  CAM  HAM   single  0.970  0.020  1.090
 9C4  CAJ  HAJ   single  0.970  0.020  1.090
 9C4  OAC  HAC   single  0.850  0.020  0.980
 9C4  CAK  HAK   single  0.970  0.020  1.090
 9C4  OAD  HAD   single  0.850  0.020  0.980
 9C4  CAL  HAL   single  0.970  0.020  1.090
 9C4  OAE  HAE   single  0.850  0.020  0.980
 9C4  OAF  HAF   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
 9C4  CAN   CAI  OAB   118.11  3.000
 9C4  CAN   CAI  OAA   114.31  3.000
 9C4  OAB   CAI  OAA   127.57  3.000
 9C4  CAM   CAN  CAH   108.72  3.000
 9C4  CAM   CAN  OAG   110.29  3.000
 9C4  CAH   CAN  OAG   110.07  3.000
 9C4  CAM   CAN  CAI   109.60  3.000
 9C4  CAH   CAN  CAI   110.13  3.000
 9C4  OAG   CAN  CAI   108.02  3.000
 9C4  HAG   OAG  CAN   101.60  3.000
 9C4  HAH2  CAH  HAH1  107.00  3.000
 9C4  HAH2  CAH  CAJ   109.48  3.000
 9C4  HAH1  CAH  CAJ   109.49  3.000
 9C4  HAH2  CAH  CAN   109.67  3.000
 9C4  HAH1  CAH  CAN   109.33  3.000
 9C4  CAJ   CAH  CAN   111.75  3.000
 9C4  HAJ   CAJ  CAK   108.13  3.000
 9C4  HAJ   CAJ  OAC   110.07  3.000
 9C4  CAK   CAJ  OAC   111.35  3.000
 9C4  HAJ   CAJ  CAH   108.86  3.000
 9C4  CAK   CAJ  CAH   110.14  3.000
 9C4  OAC   CAJ  CAH   108.25  3.000
 9C4  HAC   OAC  CAJ   107.72  3.000
 9C4  HAK   CAK  CAL   108.31  3.000
 9C4  HAK   CAK  OAD   110.44  3.000
 9C4  CAL   CAK  OAD   111.65  3.000
 9C4  HAK   CAK  CAJ   107.95  3.000
 9C4  CAL   CAK  CAJ   110.86  3.000
 9C4  OAD   CAK  CAJ   107.58  3.000
 9C4  HAD   OAD  CAK   108.71  3.000
 9C4  HAL   CAL  CAM   108.83  3.000
 9C4  HAL   CAL  OAE   110.06  3.000
 9C4  CAM   CAL  OAE   107.72  3.000
 9C4  HAL   CAL  CAK   109.01  3.000
 9C4  CAM   CAL  CAK   110.38  3.000
 9C4  OAE   CAL  CAK   110.81  3.000
 9C4  HAE   OAE  CAL   108.88  3.000
 9C4  HAM   CAM  OAF   110.45  3.000
 9C4  HAM   CAM  CAL   108.10  3.000
 9C4  OAF   CAM  CAL   111.52  3.000
 9C4  HAM   CAM  CAN   107.42  3.000
 9C4  OAF   CAM  CAN   108.75  3.000
 9C4  CAL   CAM  CAN   110.52  3.000
 9C4  HAF   OAF  CAM   107.35  3.000

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
 9C4  chir_01  CAN  OAG  CAH  CAM  positiv
 9C4  chir_02  CAJ  OAC  CAH  CAK  positiv
 9C4  chir_03  CAK  OAD  CAJ  CAL  negativ
 9C4  chir_04  CAL  OAE  CAK  CAM  positiv
 9C4  chir_05  CAM  OAF  CAL  CAN  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
 9C4  plan-1  OAA  0.020
 9C4  plan-1  CAI  0.020
 9C4  plan-1  OAB  0.020
 9C4  plan-1  CAN  0.020

