# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 23:31:11 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-hydroxy-4-methoxy-3-(3-methylbut-2-en-1-yl)-6-pentylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCc1cc(OC)c(CC=C(C)C)c(O)c1C(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
 YFD  YFD  '2-hydroxy-4-methoxy-3-(3-methylbut-2-en-1-yl)-6-pentylbenzoic acid'  ligand  48  22  .  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_YFD
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
 YFD  CAA   C  CH3   0  -0.662   7.1441   1.6364  -0.1892
 YFD  CAJ   C  CH2   0  -0.420   5.7329   1.3220  -0.6663
 YFD  CAL   C  CH2   0  -0.410   4.7975   0.9178   0.4664
 YFD  CAM   C  CH2   0  -0.411   3.3872   0.6039  -0.0148
 YFD  CAN   C  CH2   0  -0.537   2.4265   0.2673   1.1292
 YFD  CAS   C  CR6   0   0.162   1.0402  -0.0082   0.6130
 YFD  CAV   C  CR6   0  -0.212   0.6461  -1.2658   0.1683
 YFD  CAQ   C  C     0   0.462   1.5464  -2.4468   0.2813
 YFD  OAF   O  OH1   0  -0.580   1.9225  -2.9045  -0.9054
 YFD  OAE   O  O     0  -0.431   1.9148  -2.9311   1.3232
 YFD  CAR   C  CR6   0   0.348  -0.6297  -1.4438  -0.3855
 YFD  OAG   O  OH1   0  -0.618  -0.9408  -2.7098  -0.7277
 YFD  CAI   C  CR16  0  -0.480   0.1609   1.0620   0.4762
 YFD  CAT   C  CR6   0   0.409  -1.0947   0.8799  -0.0904
 YFD  OAO   O  O2    0  -0.453  -1.9821   1.8713  -0.2512
 YFD  CAB   C  CH3   0  -0.436  -1.6458   3.1770   0.1699
 YFD  CAU   C  CR6   0  -0.109  -1.5153  -0.3821  -0.5380
 YFD  CAK   C  CH2   0  -0.611  -2.8992  -0.5444  -1.1227
 YFD  CAH   C  C1    0  -0.225  -3.9538  -0.6098  -0.0554
 YFD  CAP   C  C     0   0.090  -4.9550   0.2476   0.1543
 YFD  CAD   C  CH3   0  -0.715  -5.2302   1.4692  -0.6693
 YFD  CAC   C  CH3   0  -0.715  -5.9165   0.0370   1.2886
 YFD  HAA1  H  HCH3  0   0.216   7.1423   2.4484   0.5404
 YFD  HAA2  H  HCH3  0   0.216   7.6049   0.7684   0.2856
 YFD  HAA3  H  HCH3  0   0.226   7.7870   1.9391  -1.0168
 YFD  HAJ1  H  HCH2  0   0.211   5.3190   2.1957  -1.1792
 YFD  HAJ2  H  HCH2  0   0.212   5.7678   0.5221  -1.4124
 YFD  HAL1  H  HCH2  0   0.211   5.2090   0.0456   0.9859
 YFD  HAL2  H  HCH2  0   0.211   4.7575   1.7228   1.2086
 YFD  HAM1  H  HCH2  0   0.222   2.9902   1.4614  -0.5665
 YFD  HAM2  H  HCH2  0   0.220   3.4178  -0.2275  -0.7266
 YFD  HAN1  H  HCH2  0   0.247   2.8127  -0.5784   1.6991
 YFD  HAN2  H  HCH2  0   0.247   2.3866   1.1112   1.8223
 YFD  HAI   H  HCR6  0   0.271   0.4855   2.0391   0.8080
 YFD  HAF   H  HOH1  0   0.483   2.4855  -3.6868  -0.7963
 YFD  HAG   H  HOH1  0   0.475  -1.8269  -2.7668  -1.0998
 YFD  HAB1  H  HCH3  0   0.259  -2.5083   3.8004  -0.0521
 YFD  HAB2  H  HCH3  0   0.229  -1.4459   3.2225   1.2434
 YFD  HAB3  H  HCH3  0   0.230  -0.7788   3.5692  -0.3678
 YFD  HAK1  H  HCH2  0   0.280  -3.0916   0.2670  -1.8238
 YFD  HAK2  H  HCH2  0   0.242  -2.9584  -1.4469  -1.7419
 YFD  HAH   H  H     0   0.228  -3.8610  -1.4542   0.6236
 YFD  HAD1  H  HCH3  0   0.230  -6.2372   1.4240  -1.0918
 YFD  HAD2  H  HCH3  0   0.233  -5.1978   2.3631  -0.0412
 YFD  HAD3  H  HCH3  0   0.244  -4.5284   1.6150  -1.4859
 YFD  HAC1  H  HCH3  0   0.234  -5.8905   0.8832   1.9799
 YFD  HAC2  H  HCH3  0   0.235  -6.9440  -0.0322   0.9220
 YFD  HAC3  H  HCH3  0   0.239  -5.6974  -0.8690   1.8535

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
 YFD  CAA  CAJ   single    1.522  0.020  1.522
 YFD  CAJ  CAL   single    1.524  0.020  1.524
 YFD  CAL  CAM   single    1.523  0.020  1.523
 YFD  CAM  CAN   single    1.531  0.020  1.531
 YFD  CAN  CAS   single    1.505  0.020  1.505
 YFD  CAS  CAV   aromatic  1.391  0.020  1.391
 YFD  CAS  CAI   aromatic  1.392  0.020  1.392
 YFD  CAV  CAQ   single    1.489  0.020  1.489
 YFD  CAV  CAR   aromatic  1.402  0.020  1.402
 YFD  CAQ  OAF   single    1.326  0.020  1.326
 YFD  CAQ  OAE   double    1.207  0.020  1.207
 YFD  CAR  OAG   single    1.348  0.020  1.348
 YFD  CAR  CAU   aromatic  1.391  0.020  1.391
 YFD  CAI  CAT   aromatic  1.390  0.020  1.390
 YFD  CAT  OAO   single    1.340  0.020  1.340
 YFD  CAT  CAU   aromatic  1.403  0.020  1.403
 YFD  OAO  CAB   single    1.413  0.020  1.413
 YFD  CAU  CAK   single    1.511  0.020  1.511
 YFD  CAK  CAH   single    1.502  0.020  1.502
 YFD  CAH  CAP   double    1.335  0.020  1.335
 YFD  CAP  CAD   single    1.499  0.020  1.499
 YFD  CAP  CAC   single    1.502  0.020  1.502
 YFD  CAA  HAA1  single    0.970  0.020  1.090
 YFD  CAA  HAA2  single    0.970  0.020  1.090
 YFD  CAA  HAA3  single    0.970  0.020  1.090
 YFD  CAJ  HAJ1  single    0.970  0.020  1.090
 YFD  CAJ  HAJ2  single    0.970  0.020  1.090
 YFD  CAL  HAL1  single    0.970  0.020  1.090
 YFD  CAL  HAL2  single    0.970  0.020  1.090
 YFD  CAM  HAM1  single    0.970  0.020  1.090
 YFD  CAM  HAM2  single    0.970  0.020  1.090
 YFD  CAN  HAN1  single    0.970  0.020  1.090
 YFD  CAN  HAN2  single    0.970  0.020  1.090
 YFD  CAI  HAI   single    0.930  0.020  1.080
 YFD  OAF  HAF   single    0.850  0.020  0.980
 YFD  OAG  HAG   single    0.850  0.020  0.980
 YFD  CAB  HAB1  single    0.970  0.020  1.090
 YFD  CAB  HAB2  single    0.970  0.020  1.090
 YFD  CAB  HAB3  single    0.970  0.020  1.090
 YFD  CAK  HAK1  single    0.970  0.020  1.090
 YFD  CAK  HAK2  single    0.970  0.020  1.090
 YFD  CAH  HAH   single    0.930  0.020  1.080
 YFD  CAD  HAD1  single    0.970  0.020  1.090
 YFD  CAD  HAD2  single    0.970  0.020  1.090
 YFD  CAD  HAD3  single    0.970  0.020  1.090
 YFD  CAC  HAC1  single    0.970  0.020  1.090
 YFD  CAC  HAC2  single    0.970  0.020  1.090
 YFD  CAC  HAC3  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
 YFD  HAA3  CAA  HAA2  107.57  3.000
 YFD  HAA3  CAA  HAA1  107.56  3.000
 YFD  HAA2  CAA  HAA1  107.55  3.000
 YFD  HAA3  CAA  CAJ   111.46  3.000
 YFD  HAA2  CAA  CAJ   111.31  3.000
 YFD  HAA1  CAA  CAJ   111.19  3.000
 YFD  HAJ2  CAJ  HAJ1  106.02  3.000
 YFD  HAJ2  CAJ  CAL   109.42  3.000
 YFD  HAJ1  CAJ  CAL   109.15  3.000
 YFD  HAJ2  CAJ  CAA   109.58  3.000
 YFD  HAJ1  CAJ  CAA   109.42  3.000
 YFD  CAL   CAJ  CAA   113.01  3.000
 YFD  HAL2  CAL  HAL1  106.11  3.000
 YFD  HAL2  CAL  CAM   109.37  3.000
 YFD  HAL1  CAL  CAM   109.49  3.000
 YFD  HAL2  CAL  CAJ   109.33  3.000
 YFD  HAL1  CAL  CAJ   109.46  3.000
 YFD  CAM   CAL  CAJ   112.85  3.000
 YFD  HAM2  CAM  HAM1  106.10  3.000
 YFD  HAM2  CAM  CAN   109.65  3.000
 YFD  HAM1  CAM  CAN   108.74  3.000
 YFD  HAM2  CAM  CAL   109.64  3.000
 YFD  HAM1  CAM  CAL   109.50  3.000
 YFD  CAN   CAM  CAL   112.97  3.000
 YFD  HAN2  CAN  HAN1  106.29  3.000
 YFD  HAN2  CAN  CAS   108.99  3.000
 YFD  HAN1  CAN  CAS   111.32  3.000
 YFD  HAN2  CAN  CAM   109.08  3.000
 YFD  HAN1  CAN  CAM   109.79  3.000
 YFD  CAS   CAN  CAM   111.22  3.000
 YFD  CAI   CAS  CAV   119.00  3.000
 YFD  CAI   CAS  CAN   118.36  3.000
 YFD  CAV   CAS  CAN   122.43  3.000
 YFD  CAR   CAV  CAQ   118.64  3.000
 YFD  CAR   CAV  CAS   119.92  3.000
 YFD  CAQ   CAV  CAS   121.43  3.000
 YFD  OAE   CAQ  OAF   123.19  3.000
 YFD  OAE   CAQ  CAV   124.64  3.000
 YFD  OAF   CAQ  CAV   112.16  3.000
 YFD  HAF   OAF  CAQ   110.02  3.000
 YFD  CAU   CAR  OAG   122.83  3.000
 YFD  CAU   CAR  CAV   121.71  3.000
 YFD  OAG   CAR  CAV   115.44  3.000
 YFD  HAG   OAG  CAR   111.49  3.000
 YFD  HAI   CAI  CAT   120.97  3.000
 YFD  HAI   CAI  CAS   118.35  3.000
 YFD  CAT   CAI  CAS   120.68  3.000
 YFD  CAU   CAT  OAO   115.37  3.000
 YFD  CAU   CAT  CAI   121.24  3.000
 YFD  OAO   CAT  CAI   123.38  3.000
 YFD  CAB   OAO  CAT   119.37  3.000
 YFD  HAB3  CAB  HAB2  108.86  3.000
 YFD  HAB3  CAB  HAB1  108.85  3.000
 YFD  HAB2  CAB  HAB1  108.78  3.000
 YFD  HAB3  CAB  OAO   111.95  3.000
 YFD  HAB2  CAB  OAO   112.01  3.000
 YFD  HAB1  CAB  OAO   106.28  3.000
 YFD  CAK   CAU  CAT   119.63  3.000
 YFD  CAK   CAU  CAR   122.92  3.000
 YFD  CAT   CAU  CAR   117.43  3.000
 YFD  HAK2  CAK  HAK1  103.89  3.000
 YFD  HAK2  CAK  CAH   109.12  3.000
 YFD  HAK1  CAK  CAH   111.46  3.000
 YFD  HAK2  CAK  CAU   110.89  3.000
 YFD  HAK1  CAK  CAU   109.32  3.000
 YFD  CAH   CAK  CAU   111.89  3.000
 YFD  HAH   CAH  CAP   117.68  3.000
 YFD  HAH   CAH  CAK   114.69  3.000
 YFD  CAP   CAH  CAK   127.62  3.000
 YFD  CAC   CAP  CAD   114.31  3.000
 YFD  CAC   CAP  CAH   120.59  3.000
 YFD  CAD   CAP  CAH   125.10  3.000
 YFD  HAD3  CAD  HAD2  107.63  3.000
 YFD  HAD3  CAD  HAD1  108.07  3.000
 YFD  HAD2  CAD  HAD1  106.46  3.000
 YFD  HAD3  CAD  CAP   113.81  3.000
 YFD  HAD2  CAD  CAP   110.20  3.000
 YFD  HAD1  CAD  CAP   110.36  3.000
 YFD  HAC3  CAC  HAC2  108.07  3.000
 YFD  HAC3  CAC  HAC1  108.12  3.000
 YFD  HAC2  CAC  HAC1  106.47  3.000
 YFD  HAC3  CAC  CAP   112.29  3.000
 YFD  HAC2  CAC  CAP   110.94  3.000
 YFD  HAC1  CAC  CAP   110.72  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
 YFD  CONST_01  CAU   CAR  CAV  CAS     0.00   0.0  0
 YFD  CONST_02  CAU   CAT  CAI  CAS     0.00   0.0  0
 YFD  CONST_03  CAT   CAI  CAS  CAV     0.00   0.0  0
 YFD  CONST_04  CAT   CAU  CAR  CAV     0.00   0.0  0
 YFD  CONST_05  CAI   CAS  CAV  CAR     0.00   0.0  0
 YFD  CONST_06  CAI   CAT  CAU  CAR     0.00   0.0  0
 YFD  CONST_07  CAR   CAV  CAS  CAN   180.00   0.0  0
 YFD  CONST_08  CAT   CAI  CAS  CAN   180.00   0.0  0
 YFD  CONST_09  OAG   CAR  CAV  CAS   180.00   0.0  0
 YFD  CONST_10  OAO   CAT  CAI  CAS   180.00   0.0  0
 YFD  CONST_11  CAK   CAU  CAR  CAV   180.00   0.0  0
 YFD  CONST_12  CAI   CAS  CAV  CAQ   180.00   0.0  0
 YFD  CONST_13  CAU   CAR  CAV  CAQ   180.00   0.0  0
 YFD  CONST_14  OAO   CAT  CAU  CAR   180.00   0.0  0
 YFD  CONST_15  CAT   CAU  CAR  OAG   180.00   0.0  0
 YFD  CONST_16  CAK   CAU  CAT  CAI   180.00   0.0  0
 YFD  CONST_17  HAI   CAI  CAS  CAV   180.00   0.0  0
 YFD  CONST_18  HAF   OAF  CAQ  CAV   180.00   0.0  0
 YFD  Var_01    CAV   CAS  CAN  CAM    85.89  30.0  2
 YFD  Var_02    OAF   CAQ  CAV  CAS  -113.97  30.0  2
 YFD  Var_03    CAH   CAK  CAU  CAR    99.85  30.0  2
 YFD  Var_04    CAU   CAT  OAO  CAB  -179.98  30.0  1
 YFD  Var_05    CAS   CAN  CAM  CAL   178.84  30.0  3
 YFD  Var_06    CAP   CAH  CAK  CAU   116.65  30.0  3
 YFD  Var_07    HAB1  CAB  OAO  CAT  -179.64  30.0  3
 YFD  Var_08    CAD   CAP  CAH  CAK     0.56   0.0  2
 YFD  Var_09    CAM   CAL  CAJ  CAA  -179.99  30.0  3
 YFD  Var_10    CAN   CAM  CAL  CAJ  -177.04  30.0  3
 YFD  Var_11    HAA1  CAA  CAJ  CAL   -59.01  30.0  3
 YFD  Var_12    HAD1  CAD  CAP  CAH   121.76  30.0  3
 YFD  Var_13    HAC1  CAC  CAP  CAH   119.69  30.0  3

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
 YFD  plan-1  CAN  0.020
 YFD  plan-1  CAS  0.020
 YFD  plan-1  CAV  0.020
 YFD  plan-1  CAQ  0.020
 YFD  plan-1  CAR  0.020
 YFD  plan-1  OAG  0.020
 YFD  plan-1  CAI  0.020
 YFD  plan-1  CAT  0.020
 YFD  plan-1  OAO  0.020
 YFD  plan-1  CAU  0.020
 YFD  plan-1  CAK  0.020
 YFD  plan-1  HAI  0.020
 YFD  plan-2  CAV  0.020
 YFD  plan-2  CAQ  0.020
 YFD  plan-2  OAF  0.020
 YFD  plan-2  OAE  0.020
 YFD  plan-2  HAF  0.020
 YFD  plan-3  CAK  0.020
 YFD  plan-3  CAH  0.020
 YFD  plan-3  CAP  0.020
 YFD  plan-3  CAD  0.020
 YFD  plan-3  CAC  0.020
 YFD  plan-3  HAH  0.020

