# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 12:49:59 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: (1R,2R,4S,5R)-1,4,5-trihydroxy-2-methyl-3-oxocyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C(=O)[C@@H](O)[C@H](O)C[C@]1(O)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
 9PY  9PY  '(1R,2R,4S,5R)-1,4,5-trihydroxy-2-methyl-3-oxocyclohexanecarboxylic 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_9PY
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
 9PY  OAB   O  O      0  -0.581   2.6175  -0.4929   1.3791
 9PY  CAI   C  C      0   0.433   2.3491  -0.4200   0.1724
 9PY  OAD   O  OC    -1  -0.599   3.1407  -0.4789  -0.7953
 9PY  CAN   C  CT     0   0.081   0.8604  -0.2369  -0.2284
 9PY  OAG   O  OH1    0  -0.702   0.7789  -0.1841  -1.6298
 9PY  CAH   C  CH2    0  -0.475   0.0385  -1.4148   0.2997
 9PY  CAL   C  CH1    0   0.054  -1.4293  -1.2942  -0.0661
 9PY  OAE   O  OH1    0  -0.671  -2.1159  -2.3909   0.4911
 9PY  CAM   C  CH1    0  -0.057  -1.9963   0.0309   0.4510
 9PY  OAF   O  OH1    0  -0.668  -3.3213   0.1317   0.0168
 9PY  CAJ   C  C      0   0.372  -1.1309   1.1917  -0.0133
 9PY  OAC   O  O      0  -0.393  -1.6064   2.1190  -0.6265
 9PY  CAK   C  CH1    0  -0.366   0.3244   1.0904   0.3610
 9PY  CAA   C  CH3    0  -0.670   1.1206   2.3123  -0.0631
 9PY  HAG   H  HOH1   0   0.432   1.7173  -0.2645  -1.8935
 9PY  HAH1  H  HCH2   0   0.250   0.4352  -2.3473  -0.1119
 9PY  HAH2  H  HCH2   0   0.237   0.1405  -1.4740   1.3866
 9PY  HAK   H  HCH1   0   0.269   0.3706   0.9886   1.4518
 9PY  HAL   H  HCH1   0   0.214  -1.5289  -1.2964  -1.1610
 9PY  HAE   H  HOH1   0   0.450  -3.0373  -2.3414   0.2170
 9PY  HAM   H  HCH1   0   0.236  -1.9268   0.0119   1.5523
 9PY  HAF   H  HOH1   0   0.456  -3.7063   0.9452   0.3581
 9PY  HAA1  H  HCH3   0   0.227   1.1255   2.4344  -1.1452
 9PY  HAA2  H  HCH3   0   0.235   0.7090   3.2216   0.3738
 9PY  HAA3  H  HCH3   0   0.236   2.1544   2.2332   0.2718

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
 9PY  OAB  CAI   deloc   1.238  0.020  1.238
 9PY  CAI  OAD   deloc   1.252  0.020  1.252
 9PY  CAI  CAN   single  1.553  0.020  1.553
 9PY  CAN  OAG   single  1.405  0.020  1.405
 9PY  CAN  CAH   single  1.530  0.020  1.530
 9PY  CAN  CAK   single  1.548  0.020  1.548
 9PY  CAH  CAL   single  1.518  0.020  1.518
 9PY  CAL  OAE   single  1.409  0.020  1.409
 9PY  CAL  CAM   single  1.531  0.020  1.531
 9PY  CAM  OAF   single  1.398  0.020  1.398
 9PY  CAM  CAJ   single  1.520  0.020  1.520
 9PY  CAJ  OAC   double  1.209  0.020  1.209
 9PY  CAJ  CAK   single  1.506  0.020  1.506
 9PY  CAK  CAA   single  1.519  0.020  1.519
 9PY  OAG  HAG   single  0.850  0.020  0.980
 9PY  CAH  HAH1  single  0.970  0.020  1.090
 9PY  CAH  HAH2  single  0.970  0.020  1.090
 9PY  CAK  HAK   single  0.970  0.020  1.090
 9PY  CAL  HAL   single  0.970  0.020  1.090
 9PY  OAE  HAE   single  0.850  0.020  0.980
 9PY  CAM  HAM   single  0.970  0.020  1.090
 9PY  OAF  HAF   single  0.850  0.020  0.980
 9PY  CAA  HAA1  single  0.970  0.020  1.090
 9PY  CAA  HAA2  single  0.970  0.020  1.090
 9PY  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
 9PY  CAN   CAI  OAD   114.35  3.000
 9PY  CAN   CAI  OAB   117.80  3.000
 9PY  OAD   CAI  OAB   127.85  3.000
 9PY  CAK   CAN  CAH   110.03  3.000
 9PY  CAK   CAN  OAG   109.12  3.000
 9PY  CAH   CAN  OAG   110.00  3.000
 9PY  CAK   CAN  CAI   109.56  3.000
 9PY  CAH   CAN  CAI   109.58  3.000
 9PY  OAG   CAN  CAI   108.52  3.000
 9PY  HAG   OAG  CAN   102.13  3.000
 9PY  HAH2  CAH  HAH1  107.11  3.000
 9PY  HAH2  CAH  CAL   109.53  3.000
 9PY  HAH1  CAH  CAL   109.14  3.000
 9PY  HAH2  CAH  CAN   109.55  3.000
 9PY  HAH1  CAH  CAN   109.36  3.000
 9PY  CAL   CAH  CAN   112.03  3.000
 9PY  HAL   CAL  CAM   107.73  3.000
 9PY  HAL   CAL  OAE   110.38  3.000
 9PY  CAM   CAL  OAE   111.08  3.000
 9PY  HAL   CAL  CAH   109.12  3.000
 9PY  CAM   CAL  CAH   110.22  3.000
 9PY  OAE   CAL  CAH   108.31  3.000
 9PY  HAE   OAE  CAL   108.29  3.000
 9PY  HAM   CAM  CAJ   106.38  3.000
 9PY  HAM   CAM  OAF   111.77  3.000
 9PY  CAJ   CAM  OAF   112.93  3.000
 9PY  HAM   CAM  CAL   107.38  3.000
 9PY  CAJ   CAM  CAL   110.29  3.000
 9PY  OAF   CAM  CAL   107.97  3.000
 9PY  HAF   OAF  CAM   109.26  3.000
 9PY  CAK   CAJ  OAC   123.89  3.000
 9PY  CAK   CAJ  CAM   115.01  3.000
 9PY  OAC   CAJ  CAM   121.10  3.000
 9PY  HAK   CAK  CAA   109.29  3.000
 9PY  HAK   CAK  CAJ   107.11  3.000
 9PY  CAA   CAK  CAJ   112.52  3.000
 9PY  HAK   CAK  CAN   106.53  3.000
 9PY  CAA   CAK  CAN   113.70  3.000
 9PY  CAJ   CAK  CAN   107.31  3.000
 9PY  HAA3  CAA  HAA2  107.21  3.000
 9PY  HAA3  CAA  HAA1  108.02  3.000
 9PY  HAA2  CAA  HAA1  107.86  3.000
 9PY  HAA3  CAA  CAK   110.68  3.000
 9PY  HAA2  CAA  CAK   111.18  3.000
 9PY  HAA1  CAA  CAK   111.71  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
 9PY  chir_01  CAN  OAG  CAH  CAK  positiv
 9PY  chir_02  CAL  OAE  CAM  CAH  negativ
 9PY  chir_03  CAM  OAF  CAL  CAJ  negativ
 9PY  chir_04  CAK  CAA  CAJ  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
 9PY  plan-1  CAM  0.020
 9PY  plan-1  CAJ  0.020
 9PY  plan-1  OAC  0.020
 9PY  plan-1  CAK  0.020
 9PY  plan-2  OAB  0.020
 9PY  plan-2  CAI  0.020
 9PY  plan-2  OAD  0.020
 9PY  plan-2  CAN  0.020

