# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 10:30:01 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-[(1R,2S,5S,8S,9R)-5-(hydroxymethyl)-8,9-dimethyl-3-oxabicyclo[3.3.1]non-2-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CC[C@]2(CO)CO[C@@H]([C@H]1[C@H]2C)c3ccc(O)cc3
#
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
 459  459  4-[(1R,2S,5S,8S,9R)-5-(hydroxymethyl)-8,9-dimethyl-3-oxabicyclo[3.3.1]non-2-yl]phenol  ligand  44  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_459
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
 459  CAT   C  CH3   0  -0.684   2.2010  -1.7711   1.7393
 459  CAK   C  CH1   0  -0.228   1.9890  -0.3818   1.1360
 459  CAJ   C  CH1   0  -0.257   0.5070   0.0149   1.0768
 459  CAN   C  CH1   0  -0.214   0.3529   1.5225   0.8190
 459  CAQ   C  CH3   0  -0.665   0.7784   2.3429   2.0375
 459  CAP   C  CH2   0  -0.431   1.1072   1.9580  -0.4445
 459  CAO   C  CH2   0  -0.406   2.4979   1.3351  -0.5819
 459  CAL   C  CT    0  -0.143   2.5699  -0.1721  -0.2767
 459  CAR   C  CH2   0  -0.134   4.0245  -0.6288  -0.3142
 459  OAS   O  OH1   0  -0.673   4.5929  -0.3380  -1.5729
 459  CAM   C  CH2   0  -0.151   1.7592  -1.0060  -1.2730
 459  OAH   O  O2    0  -0.495   0.3735  -0.7433  -1.2393
 459  CAI   C  CH1   0   0.034  -0.2059  -0.8699   0.0371
 459  CAD   C  CR6   0   0.062  -1.6793  -0.5732  -0.0654
 459  CAC   C  CR16  0  -0.298  -2.2371   0.1487  -1.1138
 459  CAB   C  CR16  0  -0.369  -3.5975   0.4278  -1.1505
 459  CAA   C  CR6   0   0.337  -4.4321  -0.0126  -0.1293
 459  OAG   O  OH1   0  -0.636  -5.7606   0.2275  -0.1142
 459  CAF   C  CR16  0  -0.324  -3.8875  -0.7400   0.9269
 459  CAE   C  CR16  0  -0.290  -2.5304  -1.0127   0.9464
 459  HAT1  H  HCH3  0   0.223   1.8821  -2.5863   1.0888
 459  HAT2  H  HCH3  0   0.236   3.2494  -1.9453   1.9827
 459  HAT3  H  HCH3  0   0.234   1.6362  -1.8591   2.6695
 459  HAK   H  HCH1  0   0.235   2.5002   0.3197   1.8048
 459  HAJ   H  HCH1  0   0.230   0.0494  -0.2160   2.0462
 459  HAN   H  HCH1  0   0.231  -0.7100   1.7311   0.6626
 459  HAQ1  H  HCH3  0   0.228   0.5074   3.3910   1.9003
 459  HAQ2  H  HCH3  0   0.222   0.2853   1.9912   2.9464
 459  HAQ3  H  HCH3  0   0.218   1.8545   2.3129   2.2171
 459  HAP1  H  HCH2  0   0.230   0.5114   1.7192  -1.3249
 459  HAP2  H  HCH2  0   0.217   1.2105   3.0476  -0.4444
 459  HAO1  H  HCH2  0   0.231   2.8759   1.5356  -1.5866
 459  HAO2  H  HCH2  0   0.212   3.1896   1.8357   0.1055
 459  HAR1  H  HCH2  0   0.196   4.5666  -0.1206   0.4975
 459  HAR2  H  HCH2  0   0.208   4.0823  -1.7053  -0.1083
 459  HAS   H  HOH1  0   0.454   5.4868  -0.6906  -1.5831
 459  HAM1  H  HCH2  0   0.235   2.0820  -0.8016  -2.2952
 459  HAM2  H  HCH2  0   0.201   1.9419  -2.0753  -1.0844
 459  HAI   H  HCH1  0   0.226  -0.1089  -1.9146   0.3771
 459  HAC   H  HCR6  0   0.251  -1.6181   0.5048  -1.9261
 459  HAB   H  HCR6  0   0.266  -4.0050   0.9891  -1.9841
 459  HAG   H  HOH1  0   0.472  -6.0175   0.7269  -0.8972
 459  HAF   H  HCR6  0   0.260  -4.5280  -1.0973   1.7237
 459  HAE   H  HCR6  0   0.246  -2.1274  -1.5854   1.7744

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
 459  CAT  CAK   single    1.529  0.020  1.529
 459  CAT  HAT1  single    0.970  0.020  1.090
 459  CAT  HAT2  single    0.970  0.020  1.090
 459  CAT  HAT3  single    0.970  0.020  1.090
 459  CAK  CAJ   single    1.535  0.020  1.535
 459  CAK  CAL   single    1.542  0.020  1.542
 459  CAK  HAK   single    0.970  0.020  1.090
 459  CAJ  CAN   single    1.537  0.020  1.537
 459  CAJ  CAI   single    1.540  0.020  1.540
 459  CAJ  HAJ   single    0.970  0.020  1.090
 459  CAN  CAQ   single    1.529  0.020  1.529
 459  CAN  CAP   single    1.535  0.020  1.535
 459  CAN  HAN   single    0.970  0.020  1.090
 459  CAQ  HAQ1  single    0.970  0.020  1.090
 459  CAQ  HAQ2  single    0.970  0.020  1.090
 459  CAQ  HAQ3  single    0.970  0.020  1.090
 459  CAP  CAO   single    1.530  0.020  1.530
 459  CAP  HAP1  single    0.970  0.020  1.090
 459  CAP  HAP2  single    0.970  0.020  1.090
 459  CAO  CAL   single    1.539  0.020  1.539
 459  CAO  HAO1  single    0.970  0.020  1.090
 459  CAO  HAO2  single    0.970  0.020  1.090
 459  CAL  CAR   single    1.525  0.020  1.525
 459  CAL  CAM   single    1.531  0.020  1.531
 459  CAR  OAS   single    1.411  0.020  1.411
 459  CAR  HAR1  single    0.970  0.020  1.090
 459  CAR  HAR2  single    0.970  0.020  1.090
 459  OAS  HAS   single    0.850  0.020  0.980
 459  CAM  OAH   single    1.411  0.020  1.411
 459  CAM  HAM1  single    0.970  0.020  1.090
 459  CAM  HAM2  single    0.970  0.020  1.090
 459  OAH  CAI   single    1.407  0.020  1.407
 459  CAI  CAD   single    1.506  0.020  1.506
 459  CAI  HAI   single    0.970  0.020  1.090
 459  CAD  CAC   aromatic  1.390  0.020  1.390
 459  CAD  CAE   aromatic  1.393  0.020  1.393
 459  CAC  CAB   aromatic  1.389  0.020  1.389
 459  CAC  HAC   single    0.930  0.020  1.080
 459  CAB  CAA   aromatic  1.390  0.020  1.390
 459  CAB  HAB   single    0.930  0.020  1.080
 459  CAA  OAG   single    1.350  0.020  1.350
 459  CAA  CAF   aromatic  1.393  0.020  1.393
 459  OAG  HAG   single    0.850  0.020  0.980
 459  CAF  CAE   aromatic  1.384  0.020  1.384
 459  CAF  HAF   single    0.930  0.020  1.080
 459  CAE  HAE   single    0.930  0.020  1.080

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
 459  HAT3  CAT  HAT2  107.12  3.000
 459  HAT3  CAT  HAT1  107.26  3.000
 459  HAT2  CAT  HAT1  107.15  3.000
 459  HAT3  CAT  CAK   109.73  3.000
 459  HAT2  CAT  CAK   111.50  3.000
 459  HAT1  CAT  CAK   113.77  3.000
 459  HAK   CAK  CAL   107.24  3.000
 459  HAK   CAK  CAJ   107.97  3.000
 459  CAL   CAK  CAJ   107.05  3.000
 459  HAK   CAK  CAT   106.03  3.000
 459  CAL   CAK  CAT   115.65  3.000
 459  CAJ   CAK  CAT   112.57  3.000
 459  HAJ   CAJ  CAI   106.42  3.000
 459  HAJ   CAJ  CAN   108.23  3.000
 459  CAI   CAJ  CAN   113.82  3.000
 459  HAJ   CAJ  CAK   108.32  3.000
 459  CAI   CAJ  CAK   108.93  3.000
 459  CAN   CAJ  CAK   110.89  3.000
 459  HAN   CAN  CAP   107.80  3.000
 459  HAN   CAN  CAQ   106.37  3.000
 459  CAP   CAN  CAQ   111.53  3.000
 459  HAN   CAN  CAJ   107.95  3.000
 459  CAP   CAN  CAJ   111.54  3.000
 459  CAQ   CAN  CAJ   111.38  3.000
 459  HAQ3  CAQ  HAQ2  107.42  3.000
 459  HAQ3  CAQ  HAQ1  106.98  3.000
 459  HAQ2  CAQ  HAQ1  107.57  3.000
 459  HAQ3  CAQ  CAN   113.00  3.000
 459  HAQ2  CAQ  CAN   111.39  3.000
 459  HAQ1  CAQ  CAN   110.24  3.000
 459  HAP2  CAP  HAP1  105.66  3.000
 459  HAP2  CAP  CAO   108.63  3.000
 459  HAP1  CAP  CAO   109.58  3.000
 459  HAP2  CAP  CAN   109.20  3.000
 459  HAP1  CAP  CAN   109.53  3.000
 459  CAO   CAP  CAN   113.90  3.000
 459  HAO2  CAO  HAO1  105.94  3.000
 459  HAO2  CAO  CAL   107.06  3.000
 459  HAO1  CAO  CAL   110.24  3.000
 459  HAO2  CAO  CAP   109.35  3.000
 459  HAO1  CAO  CAP   108.82  3.000
 459  CAL   CAO  CAP   115.04  3.000
 459  CAM   CAL  CAR   109.01  3.000
 459  CAM   CAL  CAO   112.30  3.000
 459  CAR   CAL  CAO   109.44  3.000
 459  CAM   CAL  CAK   108.82  3.000
 459  CAR   CAL  CAK   109.95  3.000
 459  CAO   CAL  CAK   107.29  3.000
 459  HAR2  CAR  HAR1  106.78  3.000
 459  HAR2  CAR  OAS   110.38  3.000
 459  HAR1  CAR  OAS   111.37  3.000
 459  HAR2  CAR  CAL   109.83  3.000
 459  HAR1  CAR  CAL   108.26  3.000
 459  OAS   CAR  CAL   110.14  3.000
 459  HAS   OAS  CAR   107.96  3.000
 459  HAM2  CAM  HAM1  107.05  3.000
 459  HAM2  CAM  OAH   109.86  3.000
 459  HAM1  CAM  OAH   106.14  3.000
 459  HAM2  CAM  CAL   109.24  3.000
 459  HAM1  CAM  CAL   110.54  3.000
 459  OAH   CAM  CAL   113.77  3.000
 459  CAI   OAH  CAM   114.16  3.000
 459  HAI   CAI  CAD   107.07  3.000
 459  HAI   CAI  OAH   109.18  3.000
 459  CAD   CAI  OAH   108.86  3.000
 459  HAI   CAI  CAJ   107.18  3.000
 459  CAD   CAI  CAJ   112.67  3.000
 459  OAH   CAI  CAJ   111.71  3.000
 459  CAE   CAD  CAC   117.80  3.000
 459  CAE   CAD  CAI   119.07  3.000
 459  CAC   CAD  CAI   123.11  3.000
 459  HAC   CAC  CAB   118.32  3.000
 459  HAC   CAC  CAD   120.52  3.000
 459  CAB   CAC  CAD   121.16  3.000
 459  HAB   CAB  CAA   120.20  3.000
 459  HAB   CAB  CAC   119.49  3.000
 459  CAA   CAB  CAC   120.31  3.000
 459  CAF   CAA  OAG   117.97  3.000
 459  CAF   CAA  CAB   119.18  3.000
 459  OAG   CAA  CAB   122.85  3.000
 459  HAG   OAG  CAA   110.21  3.000
 459  HAF   CAF  CAE   120.29  3.000
 459  HAF   CAF  CAA   119.92  3.000
 459  CAE   CAF  CAA   119.78  3.000
 459  HAE   CAE  CAF   118.63  3.000
 459  HAE   CAE  CAD   119.60  3.000
 459  CAF   CAE  CAD   121.76  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
 459  CONST_01  CAA   CAB  CAC  CAD     0.00   0.0  0
 459  CONST_02  CAA   CAF  CAE  CAD     0.00   0.0  0
 459  CONST_03  CAF   CAE  CAD  CAC     0.00   0.0  0
 459  CONST_04  CAF   CAA  CAB  CAC     0.00   0.0  0
 459  CONST_05  CAE   CAD  CAC  CAB     0.00   0.0  0
 459  CONST_06  CAE   CAF  CAA  CAB     0.00   0.0  0
 459  CONST_07  CAB   CAC  CAD  CAI   180.00   0.0  0
 459  CONST_08  CAF   CAE  CAD  CAI   180.00   0.0  0
 459  CONST_09  OAG   CAA  CAB  CAC   180.00   0.0  0
 459  CONST_10  CAE   CAF  CAA  OAG   180.00   0.0  0
 459  CONST_11  HAC   CAC  CAD  CAI     0.00   0.0  0
 459  CONST_12  HAE   CAE  CAD  CAI     0.00   0.0  0
 459  CONST_13  HAB   CAB  CAC  CAD   180.00   0.0  0
 459  CONST_14  HAF   CAF  CAE  CAD   180.00   0.0  0
 459  Var_01    CAL   CAO  CAP  CAN    44.62  30.0  1
 459  Var_02    HAM1  CAM  OAH  CAI  -176.01  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
 459  chir_01  CAK  CAT  CAJ  CAL  positiv
 459  chir_02  CAJ  CAK  CAN  CAI  negativ
 459  chir_03  CAN  CAJ  CAQ  CAP  negativ
 459  chir_04  CAL  CAO  CAK  CAM  negativ
 459  chir_05  CAI  OAH  CAJ  CAD  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
 459  plan-1  CAI  0.020
 459  plan-1  CAD  0.020
 459  plan-1  CAC  0.020
 459  plan-1  CAB  0.020
 459  plan-1  CAA  0.020
 459  plan-1  OAG  0.020
 459  plan-1  CAF  0.020
 459  plan-1  CAE  0.020
 459  plan-1  HAC  0.020
 459  plan-1  HAB  0.020
 459  plan-1  HAF  0.020
 459  plan-1  HAE  0.020

