# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 19:15:35 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (1S)-1-[(2R)-6-oxotetrahydro-2H-pyran-2-yl]undecyl acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC[C@H](OC(C)=O)[C@H]1CCCC(=O)O1
#
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
 3OG  3OG  '(1S)-1-[(2R)-6-oxotetrahydro-2H-pyran-2-yl]undecyl acetate'  ligand  54  22  .  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_3OG
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
 3OG  OAA   O  O     0  -0.446    2.6829  -2.6772  -1.4415
 3OG  OAB   O  O2    0  -0.470    2.3851  -1.6550   0.5336
 3OG  CAC   C  C     0   0.567    2.5215  -2.7264  -0.2489
 3OG  CAD   C  CH3   0  -0.773    2.4125  -3.9912   0.5483
 3OG  CAE   C  CH2   0  -0.457    6.1155   0.5237   0.4775
 3OG  CAF   C  CH2   0  -0.495    4.9292  -0.3930   0.2375
 3OG  CAG   C  CH1   0   0.058    3.6442   0.3696   0.4923
 3OG  CAH   C  CH1   0  -0.003    2.3835  -0.3339  -0.0232
 3OG  CAI   C  CH2   0  -0.434    1.0953   0.3453   0.4123
 3OG  CAJ   C  CH2   0  -0.427   -0.1592  -0.2683  -0.1980
 3OG  CAK   C  CH2   0  -0.414   -1.4291   0.4004   0.3136
 3OG  CAL   C  CH2   0  -0.414   -2.7028  -0.1707  -0.2955
 3OG  CAM   C  CH2   0  -0.412   -3.9665   0.4671   0.2676
 3OG  CAN   C  CH2   0  -0.412   -5.2507  -0.0941  -0.3285
 3OG  CAO   C  CH2   0  -0.411   -6.5065   0.5356   0.2611
 3OG  CAP   C  CH2   0  -0.406   -7.7983  -0.0230  -0.3207
 3OG  CAQ   C  CH2   0  -0.419   -9.0491   0.6053   0.2813
 3OG  CAR   C  CH3   0  -0.662  -10.3381   0.0415  -0.2995
 3OG  CAS   C  CH2   0  -0.598    6.0428   1.6801  -0.5024
 3OG  CAT   C  C     0   0.548    4.6881   2.3285  -0.5781
 3OG  OAU   O  O2    0  -0.453    3.6224   1.6635  -0.1368
 3OG  OAV   O  O     0  -0.447    4.5074   3.4227  -1.0502
 3OG  HAD   H  HCH3  0   0.279    1.3590  -4.2037   0.7413
 3OG  HADA  H  HCH3  0   0.265    2.8310  -4.8256  -0.0074
 3OG  HADB  H  HCH3  0   0.267    2.9102  -3.9058   1.5125
 3OG  HAEA  H  HCH2  0   0.262    7.0541  -0.0148   0.3489
 3OG  HAF   H  HCH2  0   0.245    4.9564  -0.7802  -0.7858
 3OG  HAFA  H  HCH2  0   0.267    4.9621  -1.2480   0.9126
 3OG  HAG   H  HCH1  0   0.251    3.5452   0.5463   1.5696
 3OG  HAH   H  HCH1  0   0.254    2.4368  -0.3849  -1.1143
 3OG  HAI   H  HCH2  0   0.229    1.0313   0.3197   1.5055
 3OG  HAIA  H  HCH2  0   0.243    1.1470   1.3996   0.1327
 3OG  HAJ   H  HCH2  0   0.218   -0.1116  -0.1834  -1.2888
 3OG  HAJA  H  HCH2  0   0.218   -0.2097  -1.3383   0.0256
 3OG  HAK   H  HCH2  0   0.211   -1.4730   0.2977   1.4035
 3OG  HAKA  H  HCH2  0   0.211   -1.3813   1.4766   0.1145
 3OG  HAL   H  HCH2  0   0.209   -2.6788  -0.0384  -1.3828
 3OG  HALA  H  HCH2  0   0.208   -2.7355  -1.2523  -0.1238
 3OG  HAM   H  HCH2  0   0.207   -3.9837   0.3312   1.3549
 3OG  HAMA  H  HCH2  0   0.207   -3.9323   1.5496   0.1015
 3OG  HAN   H  HCH2  0   0.207   -5.2438   0.0530  -1.4143
 3OG  HANA  H  HCH2  0   0.206   -5.2810  -1.1782  -0.1717
 3OG  HAO   H  HCH2  0   0.206   -6.5065   0.3906   1.3473
 3OG  HAOA  H  HCH2  0   0.206   -6.4764   1.6196   0.1035
 3OG  HAP   H  HCH2  0   0.206   -7.8042   0.1261  -1.4064
 3OG  HAPA  H  HCH2  0   0.205   -7.8281  -1.1076  -0.1664
 3OG  HAQ   H  HCH2  0   0.210   -9.0404   0.4574   1.3657
 3OG  HAQA  H  HCH2  0   0.210   -9.0194   1.6883   0.1252
 3OG  HAR   H  HCH3  0   0.216  -10.4104  -1.0344  -0.1291
 3OG  HARA  H  HCH3  0   0.225  -11.2170   0.5063   0.1487
 3OG  HARB  H  HCH3  0   0.216  -10.3910   0.2056  -1.3776
 3OG  HAS   H  HCH2  0   0.289    6.7741   2.4591  -0.2847
 3OG  HASA  H  HCH2  0   0.287    6.2696   1.3229  -1.5126
 3OG  HAE   H  HCH2  0   0.243    6.1009   0.8936   1.5061

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
 3OG  CAC  OAA   double  1.205  0.020  1.205
 3OG  CAH  OAB   single  1.434  0.020  1.434
 3OG  OAB  CAC   single  1.334  0.020  1.334
 3OG  CAC  CAD   single  1.499  0.020  1.499
 3OG  CAD  HAD   single  0.970  0.020  1.090
 3OG  CAD  HADA  single  0.970  0.020  1.090
 3OG  CAD  HADB  single  0.970  0.020  1.090
 3OG  CAE  CAF   single  1.518  0.020  1.518
 3OG  CAE  CAS   single  1.518  0.020  1.518
 3OG  CAE  HAE   single  0.970  0.020  1.090
 3OG  CAE  HAEA  single  0.970  0.020  1.090
 3OG  CAF  CAG   single  1.516  0.020  1.516
 3OG  CAF  HAF   single  0.970  0.020  1.090
 3OG  CAF  HAFA  single  0.970  0.020  1.090
 3OG  CAG  OAU   single  1.439  0.020  1.439
 3OG  CAG  CAH   single  1.533  0.020  1.533
 3OG  CAG  HAG   single  0.970  0.020  1.090
 3OG  CAI  CAH   single  1.520  0.020  1.520
 3OG  CAH  HAH   single  0.970  0.020  1.090
 3OG  CAI  CAJ   single  1.524  0.020  1.524
 3OG  CAI  HAI   single  0.970  0.020  1.090
 3OG  CAI  HAIA  single  0.970  0.020  1.090
 3OG  CAK  CAJ   single  1.524  0.020  1.524
 3OG  CAJ  HAJ   single  0.970  0.020  1.090
 3OG  CAJ  HAJA  single  0.970  0.020  1.090
 3OG  CAL  CAK   single  1.523  0.020  1.523
 3OG  CAK  HAK   single  0.970  0.020  1.090
 3OG  CAK  HAKA  single  0.970  0.020  1.090
 3OG  CAM  CAL   single  1.523  0.020  1.523
 3OG  CAL  HAL   single  0.970  0.020  1.090
 3OG  CAL  HALA  single  0.970  0.020  1.090
 3OG  CAN  CAM   single  1.523  0.020  1.523
 3OG  CAM  HAM   single  0.970  0.020  1.090
 3OG  CAM  HAMA  single  0.970  0.020  1.090
 3OG  CAN  CAO   single  1.523  0.020  1.523
 3OG  CAN  HAN   single  0.970  0.020  1.090
 3OG  CAN  HANA  single  0.970  0.020  1.090
 3OG  CAP  CAO   single  1.523  0.020  1.523
 3OG  CAO  HAO   single  0.970  0.020  1.090
 3OG  CAO  HAOA  single  0.970  0.020  1.090
 3OG  CAP  CAQ   single  1.524  0.020  1.524
 3OG  CAP  HAP   single  0.970  0.020  1.090
 3OG  CAP  HAPA  single  0.970  0.020  1.090
 3OG  CAR  CAQ   single  1.522  0.020  1.522
 3OG  CAQ  HAQ   single  0.970  0.020  1.090
 3OG  CAQ  HAQA  single  0.970  0.020  1.090
 3OG  CAR  HAR   single  0.970  0.020  1.090
 3OG  CAR  HARA  single  0.970  0.020  1.090
 3OG  CAR  HARB  single  0.970  0.020  1.090
 3OG  CAS  CAT   single  1.504  0.020  1.504
 3OG  CAS  HAS   single  0.970  0.020  1.090
 3OG  CAS  HASA  single  0.970  0.020  1.090
 3OG  OAU  CAT   single  1.331  0.020  1.331
 3OG  CAT  OAV   double  1.205  0.020  1.205

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
 3OG  CAH   OAB  CAC   120.84  3.000
 3OG  CAD   CAC  OAB   111.00  3.000
 3OG  CAD   CAC  OAA   124.80  3.000
 3OG  OAB   CAC  OAA   124.18  3.000
 3OG  HADB  CAD  HADA  109.71  3.000
 3OG  HADB  CAD  HAD   107.44  3.000
 3OG  HADA  CAD  HAD   108.21  3.000
 3OG  HADB  CAD  CAC   111.82  3.000
 3OG  HADA  CAD  CAC   110.37  3.000
 3OG  HAD   CAD  CAC   109.17  3.000
 3OG  HAEA  CAE  HAE   106.84  3.000
 3OG  HAEA  CAE  CAS   109.98  3.000
 3OG  HAE   CAE  CAS   110.42  3.000
 3OG  HAEA  CAE  CAF   110.85  3.000
 3OG  HAE   CAE  CAF   110.04  3.000
 3OG  CAS   CAE  CAF   108.70  3.000
 3OG  HAFA  CAF  HAF   107.51  3.000
 3OG  HAFA  CAF  CAG   108.43  3.000
 3OG  HAF   CAF  CAG   110.87  3.000
 3OG  HAFA  CAF  CAE   110.62  3.000
 3OG  HAF   CAF  CAE   109.99  3.000
 3OG  CAG   CAF  CAE   109.39  3.000
 3OG  HAG   CAG  OAU   106.46  3.000
 3OG  HAG   CAG  CAH   109.28  3.000
 3OG  OAU   CAG  CAH   104.66  3.000
 3OG  HAG   CAG  CAF   108.84  3.000
 3OG  CAH   CAG  CAF   114.19  3.000
 3OG  OAU   CAG  CAF   113.07  3.000
 3OG  HAH   CAH  CAI   110.36  3.000
 3OG  HAH   CAH  CAG   108.47  3.000
 3OG  CAI   CAH  CAG   113.30  3.000
 3OG  HAH   CAH  OAB   110.15  3.000
 3OG  CAI   CAH  OAB   107.54  3.000
 3OG  CAG   CAH  OAB   106.94  3.000
 3OG  HAIA  CAI  HAI   106.31  3.000
 3OG  HAIA  CAI  CAJ   108.98  3.000
 3OG  HAI   CAI  CAJ   110.01  3.000
 3OG  HAIA  CAI  CAH   108.53  3.000
 3OG  HAI   CAI  CAH   108.97  3.000
 3OG  CAJ   CAI  CAH   113.77  3.000
 3OG  HAJA  CAJ  HAJ   106.34  3.000
 3OG  HAJA  CAJ  CAK   108.79  3.000
 3OG  HAJ   CAJ  CAK   109.67  3.000
 3OG  HAJA  CAJ  CAI   110.48  3.000
 3OG  HAJ   CAJ  CAI   109.38  3.000
 3OG  CAK   CAJ  CAI   112.02  3.000
 3OG  HAKA  CAK  HAK   105.94  3.000
 3OG  HAKA  CAK  CAL   109.40  3.000
 3OG  HAK   CAK  CAL   109.22  3.000
 3OG  HAKA  CAK  CAJ   109.50  3.000
 3OG  HAK   CAK  CAJ   109.04  3.000
 3OG  CAL   CAK  CAJ   113.46  3.000
 3OG  HALA  CAL  HAL   105.98  3.000
 3OG  HALA  CAL  CAM   109.30  3.000
 3OG  HAL   CAL  CAM   109.54  3.000
 3OG  HALA  CAL  CAK   109.42  3.000
 3OG  HAL   CAL  CAK   109.48  3.000
 3OG  CAM   CAL  CAK   112.89  3.000
 3OG  HAMA  CAM  HAM   105.87  3.000
 3OG  HAMA  CAM  CAN   109.33  3.000
 3OG  HAM   CAM  CAN   109.23  3.000
 3OG  HAMA  CAM  CAL   109.37  3.000
 3OG  HAM   CAM  CAL   109.14  3.000
 3OG  CAN   CAM  CAL   113.61  3.000
 3OG  HANA  CAN  HAN   105.95  3.000
 3OG  HANA  CAN  CAO   109.31  3.000
 3OG  HAN   CAN  CAO   109.46  3.000
 3OG  HANA  CAN  CAM   109.38  3.000
 3OG  HAN   CAN  CAM   109.46  3.000
 3OG  CAO   CAN  CAM   113.03  3.000
 3OG  HAOA  CAO  HAO   105.86  3.000
 3OG  HAOA  CAO  CAP   109.34  3.000
 3OG  HAO   CAO  CAP   109.27  3.000
 3OG  HAOA  CAO  CAN   109.31  3.000
 3OG  HAO   CAO  CAN   109.20  3.000
 3OG  CAP   CAO  CAN   113.56  3.000
 3OG  HAPA  CAP  HAP   105.91  3.000
 3OG  HAPA  CAP  CAQ   109.28  3.000
 3OG  HAP   CAP  CAQ   109.32  3.000
 3OG  HAPA  CAP  CAO   109.40  3.000
 3OG  HAP   CAP  CAO   109.46  3.000
 3OG  CAQ   CAP  CAO   113.21  3.000
 3OG  HAQA  CAQ  HAQ   105.95  3.000
 3OG  HAQA  CAQ  CAR   109.58  3.000
 3OG  HAQ   CAQ  CAR   109.56  3.000
 3OG  HAQA  CAQ  CAP   109.24  3.000
 3OG  HAQ   CAQ  CAP   109.22  3.000
 3OG  CAR   CAQ  CAP   113.06  3.000
 3OG  HARB  CAR  HARA  107.62  3.000
 3OG  HARB  CAR  HAR   107.40  3.000
 3OG  HARA  CAR  HAR   107.61  3.000
 3OG  HARB  CAR  CAQ   111.23  3.000
 3OG  HARA  CAR  CAQ   111.58  3.000
 3OG  HAR   CAR  CAQ   111.20  3.000
 3OG  HASA  CAS  HAS   106.15  3.000
 3OG  HASA  CAS  CAT   106.31  3.000
 3OG  HAS   CAS  CAT   107.83  3.000
 3OG  HASA  CAS  CAE   109.70  3.000
 3OG  HAS   CAS  CAE   112.54  3.000
 3OG  CAT   CAS  CAE   113.85  3.000
 3OG  OAV   CAT  OAU   117.60  3.000
 3OG  OAV   CAT  CAS   123.10  3.000
 3OG  OAU   CAT  CAS   119.28  3.000
 3OG  CAT   OAU  CAG   125.58  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
 3OG  Var_01  OAU  CAT  CAS  CAE   -19.08  30.0  1
 3OG  Var_02  CAT  CAS  CAE  CAF    47.87  30.0  1
 3OG  Var_03  CAS  CAE  CAF  CAG   -61.82  30.0  1
 3OG  Var_04  CAK  CAJ  CAI  CAH   177.39  30.0  3
 3OG  Var_05  CAL  CAK  CAJ  CAI   178.93  30.0  1
 3OG  Var_06  CAM  CAL  CAK  CAJ   177.61  30.0  1
 3OG  Var_07  CAN  CAM  CAL  CAK  -179.89  30.0  1
 3OG  Var_08  CAO  CAN  CAM  CAL   179.00  30.0  1
 3OG  Var_09  CAP  CAO  CAN  CAM  -179.65  30.0  3
 3OG  Var_10  CAQ  CAP  CAO  CAN   179.60  30.0  1
 3OG  Var_11  CAR  CAQ  CAP  CAO  -179.82  30.0  3
 3OG  Var_12  HAD  CAD  CAC  OAA   -99.26  30.0  3
 3OG  Var_13  HAR  CAR  CAQ  CAP    59.76  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
 3OG  chir_01  CAG  CAF  OAU  CAH  negativ
 3OG  chir_02  CAH  OAB  CAI  CAG  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
 3OG  plan-1  CAS  0.020
 3OG  plan-1  CAT  0.020
 3OG  plan-1  OAU  0.020
 3OG  plan-1  OAV  0.020
 3OG  plan-2  OAA  0.020
 3OG  plan-2  OAB  0.020
 3OG  plan-2  CAC  0.020
 3OG  plan-2  CAD  0.020

