# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 01:24:50 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2S)-2-(3,4-dihydroxyphenyl)-6-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-5,7-dihydroxy-2,3-dihydro-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)=CCC\C(C)=C\Cc1c(O)cc2O[C@@H](CC(=O)c2c1O)c3ccc(O)c(O)c3
#
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
 L2E  L2E  (2S)-2-(3,4-dihydroxyphenyl)-6-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-5,7-dihydroxy-2,3-dihydro-4H-chromen-4-one  ligand  59  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L2E
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
 L2E  CAA  C  CH3   0  -0.705   7.5293   4.4964  -0.4748
 L2E  CAT  C  C     0   0.078   6.3896   3.5376  -0.2826
 L2E  CAB  C  CH3   0  -0.720   5.0718   4.0350  -0.7986
 L2E  CAI  C  C1    0  -0.256   6.5796   2.3556   0.3096
 L2E  CAO  C  CH2   0  -0.484   5.5721   1.2825   0.5797
 L2E  CAQ  C  CH2   0  -0.497   5.8374   0.0194  -0.2540
 L2E  CAU  C  C     0   0.121   4.9417  -1.1213   0.1411
 L2E  CAC  C  CH3   0  -0.755   5.2085  -1.7434   1.4888
 L2E  CAJ  C  C1    0  -0.250   3.9580  -1.5284  -0.6623
 L2E  CAP  C  CH2   0  -0.545   2.9701  -2.6210  -0.3681
 L2E  CBC  C  CR6   0  -0.119   1.5504  -2.1179  -0.4412
 L2E  CAZ  C  CR6   0   0.399   0.9564  -1.4982   0.6527
 L2E  OAH  O  OH1   0  -0.616   1.6651  -1.3697   1.7678
 L2E  CAY  C  CR6   0   0.369   0.7978  -2.1984  -1.6177
 L2E  OAG  O  OH1   0  -0.611   1.3882  -2.7618  -2.6765
 L2E  CAN  C  CR16  0  -0.539  -0.5167  -1.7311  -1.7054
 L2E  CBB  C  CR6   0   0.428  -1.0943  -1.1428  -0.6006
 L2E  OAS  O  O2    0  -0.479  -2.3582  -0.7099  -0.7173
 L2E  CBD  C  CR6   0  -0.340  -0.3702  -0.9971   0.5976
 L2E  CAV  C  C     0   0.450  -0.9342  -0.2633   1.7029
 L2E  OAD  O  O     0  -0.470  -0.3320  -0.0866   2.7634
 L2E  CAR  C  CH2   0  -0.590  -2.2955   0.3266   1.4675
 L2E  CBE  C  CH1   0  -0.049  -3.0910  -0.5302   0.4975
 L2E  CBA  C  CR6   0   0.100  -4.4228   0.0689   0.1531
 L2E  CAM  C  CR16  0  -0.405  -5.5811  -0.4971   0.6761
 L2E  CAX  C  CR6   0   0.312  -6.8258   0.0555   0.4183
 L2E  OAF  O  OH1   0  -0.634  -7.9207  -0.5251   0.9515
 L2E  CAW  C  CR6   0   0.248  -6.9168   1.1942  -0.3915
 L2E  OAE  O  OH1   0  -0.642  -8.1618   1.6726  -0.6098
 L2E  CAK  C  CR16  0  -0.358  -5.7630   1.7565  -0.9154
 L2E  CAL  C  CR16  0  -0.313  -4.5194   1.2028  -0.6427
 L2E  H1   H  HCH3  0   0.230   7.6950   4.7022  -1.5356
 L2E  H2   H  HCH3  0   0.229   7.3129   5.4595  -0.0045
 L2E  H3   H  HCH3  0   0.235   8.4613   4.1179  -0.0559
 L2E  H5   H  HCH3  0   0.240   4.2665   3.3089  -0.7129
 L2E  H6   H  HCH3  0   0.235   4.7666   4.9382  -0.2637
 L2E  H7   H  HCH3  0   0.233   5.1553   4.3157  -1.8515
 L2E  H8   H  H     0   0.220   7.5917   2.1142   0.6289
 L2E  H10  H  HCH2  0   0.234   5.6126   1.0234   1.6432
 L2E  H11  H  HCH2  0   0.236   4.5529   1.6225   0.3887
 L2E  H12  H  HCH2  0   0.232   5.7046   0.2594  -1.3118
 L2E  H13  H  HCH2  0   0.228   6.8853  -0.2762  -0.1271
 L2E  H14  H  HCH3  0   0.239   6.0388  -1.2536   1.9978
 L2E  H15  H  HCH3  0   0.248   4.3383  -1.6798   2.1426
 L2E  H16  H  HCH3  0   0.242   5.4672  -2.8004   1.4018
 L2E  H17  H  H     0   0.223   3.8318  -1.0307  -1.6210
 L2E  H18  H  HCH2  0   0.257   3.1015  -3.4361  -1.0834
 L2E  H19  H  HCH2  0   0.257   3.1574  -3.0520   0.6153
 L2E  H20  H  HOH1  0   0.475   1.1126  -0.8803   2.4225
 L2E  H21  H  HOH1  0   0.485   0.7934  -2.7742  -3.4357
 L2E  H22  H  HCR6  0   0.282  -1.0827  -1.8361  -2.6234
 L2E  H25  H  HCH2  0   0.294  -2.8324   0.4221   2.4118
 L2E  H26  H  HCH2  0   0.296  -2.1618   1.3378   1.0654
 L2E  H27  H  HCH1  0   0.269  -3.2460  -1.5183   0.9495
 L2E  H28  H  HCR6  0   0.264  -5.5232  -1.3831   1.2986
 L2E  H29  H  HOH1  0   0.473  -8.7164  -0.0424   0.6991
 L2E  H30  H  HOH1  0   0.483  -8.1377   2.4570  -1.1688
 L2E  H31  H  HCR6  0   0.277  -5.8353   2.6372  -1.5435
 L2E  H32  H  HCR6  0   0.256  -3.6348   1.6657  -1.0609

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
 L2E  OAH  CAZ  single    1.328  0.020  1.328
 L2E  OAD  CAV  double    1.232  0.020  1.232
 L2E  CAC  CAU  single    1.508  0.020  1.508
 L2E  CAU  CAQ  single    1.503  0.020  1.503
 L2E  CAU  CAJ  double    1.334  0.020  1.334
 L2E  CAP  CAJ  single    1.502  0.020  1.502
 L2E  CAP  CBC  single    1.508  0.020  1.508
 L2E  CAQ  CAO  single    1.537  0.020  1.537
 L2E  CAB  CAT  single    1.500  0.020  1.500
 L2E  CAO  CAI  single    1.497  0.020  1.497
 L2E  CAZ  CBC  aromatic  1.390  0.020  1.390
 L2E  CAZ  CBD  aromatic  1.419  0.020  1.419
 L2E  CAV  CBD  single    1.442  0.020  1.442
 L2E  CAV  CAR  single    1.502  0.020  1.502
 L2E  CBC  CAY  aromatic  1.399  0.020  1.399
 L2E  CBD  CBB  aromatic  1.408  0.020  1.408
 L2E  CAR  CBE  single    1.519  0.020  1.519
 L2E  CAT  CAI  double    1.336  0.020  1.336
 L2E  CAT  CAA  single    1.502  0.020  1.502
 L2E  CAY  OAG  single    1.337  0.020  1.337
 L2E  CAY  CAN  aromatic  1.398  0.020  1.398
 L2E  CBE  OAS  single    1.430  0.020  1.430
 L2E  CBE  CBA  single    1.500  0.020  1.500
 L2E  CBB  CAN  aromatic  1.378  0.020  1.378
 L2E  CBB  OAS  single    1.341  0.020  1.341
 L2E  CAL  CBA  aromatic  1.389  0.020  1.389
 L2E  CAL  CAK  aromatic  1.388  0.020  1.388
 L2E  CBA  CAM  aromatic  1.391  0.020  1.391
 L2E  CAK  CAW  aromatic  1.386  0.020  1.386
 L2E  CAM  CAX  aromatic  1.386  0.020  1.386
 L2E  CAW  CAX  aromatic  1.400  0.020  1.400
 L2E  CAW  OAE  single    1.351  0.020  1.351
 L2E  CAX  OAF  single    1.349  0.020  1.349
 L2E  CAA  H1   single    0.970  0.020  1.090
 L2E  CAA  H2   single    0.970  0.020  1.090
 L2E  CAA  H3   single    0.970  0.020  1.090
 L2E  CAB  H5   single    0.970  0.020  1.090
 L2E  CAB  H6   single    0.970  0.020  1.090
 L2E  CAB  H7   single    0.970  0.020  1.090
 L2E  CAI  H8   single    0.930  0.020  1.080
 L2E  CAO  H10  single    0.970  0.020  1.090
 L2E  CAO  H11  single    0.970  0.020  1.090
 L2E  CAQ  H12  single    0.970  0.020  1.090
 L2E  CAQ  H13  single    0.970  0.020  1.090
 L2E  CAC  H14  single    0.970  0.020  1.090
 L2E  CAC  H15  single    0.970  0.020  1.090
 L2E  CAC  H16  single    0.970  0.020  1.090
 L2E  CAJ  H17  single    0.930  0.020  1.080
 L2E  CAP  H18  single    0.970  0.020  1.090
 L2E  CAP  H19  single    0.970  0.020  1.090
 L2E  OAH  H20  single    0.850  0.020  0.980
 L2E  OAG  H21  single    0.850  0.020  0.980
 L2E  CAN  H22  single    0.930  0.020  1.080
 L2E  CAR  H25  single    0.970  0.020  1.090
 L2E  CAR  H26  single    0.970  0.020  1.090
 L2E  CBE  H27  single    0.970  0.020  1.090
 L2E  CAM  H28  single    0.930  0.020  1.080
 L2E  OAF  H29  single    0.850  0.020  0.980
 L2E  OAE  H30  single    0.850  0.020  0.980
 L2E  CAK  H31  single    0.930  0.020  1.080
 L2E  CAL  H32  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
 L2E  H3   CAA  H2   108.06  3.000
 L2E  H3   CAA  H1   107.98  3.000
 L2E  H2   CAA  H1   106.35  3.000
 L2E  H3   CAA  CAT  112.22  3.000
 L2E  H2   CAA  CAT  110.93  3.000
 L2E  H1   CAA  CAT  111.06  3.000
 L2E  CAI  CAT  CAB  124.81  3.000
 L2E  CAI  CAT  CAA  120.92  3.000
 L2E  CAB  CAT  CAA  114.27  3.000
 L2E  H7   CAB  H6   106.30  3.000
 L2E  H7   CAB  H5   107.70  3.000
 L2E  H6   CAB  H5   107.84  3.000
 L2E  H7   CAB  CAT  110.45  3.000
 L2E  H6   CAB  CAT  110.54  3.000
 L2E  H5   CAB  CAT  113.69  3.000
 L2E  H8   CAI  CAO  114.46  3.000
 L2E  H8   CAI  CAT  117.30  3.000
 L2E  CAO  CAI  CAT  128.23  3.000
 L2E  H11  CAO  H10  106.15  3.000
 L2E  H11  CAO  CAQ  108.81  3.000
 L2E  H10  CAO  CAQ  109.02  3.000
 L2E  H11  CAO  CAI  111.95  3.000
 L2E  H10  CAO  CAI  108.67  3.000
 L2E  CAQ  CAO  CAI  112.04  3.000
 L2E  H13  CAQ  H12  106.70  3.000
 L2E  H13  CAQ  CAU  109.55  3.000
 L2E  H12  CAQ  CAU  110.40  3.000
 L2E  H13  CAQ  CAO  108.90  3.000
 L2E  H12  CAQ  CAO  108.89  3.000
 L2E  CAU  CAQ  CAO  112.23  3.000
 L2E  CAJ  CAU  CAC  122.88  3.000
 L2E  CAJ  CAU  CAQ  120.85  3.000
 L2E  CAC  CAU  CAQ  116.26  3.000
 L2E  H16  CAC  H15  107.06  3.000
 L2E  H16  CAC  H14  106.96  3.000
 L2E  H15  CAC  H14  107.56  3.000
 L2E  H16  CAC  CAU  111.72  3.000
 L2E  H15  CAC  CAU  111.75  3.000
 L2E  H14  CAC  CAU  111.51  3.000
 L2E  H17  CAJ  CAP  115.42  3.000
 L2E  H17  CAJ  CAU  118.49  3.000
 L2E  CAP  CAJ  CAU  126.09  3.000
 L2E  H19  CAP  H18  105.97  3.000
 L2E  H19  CAP  CBC  109.72  3.000
 L2E  H18  CAP  CBC  109.30  3.000
 L2E  H19  CAP  CAJ  110.57  3.000
 L2E  H18  CAP  CAJ  109.60  3.000
 L2E  CBC  CAP  CAJ  111.53  3.000
 L2E  CAY  CBC  CAZ  117.22  3.000
 L2E  CAY  CBC  CAP  121.87  3.000
 L2E  CAZ  CBC  CAP  120.85  3.000
 L2E  CBD  CAZ  OAH  119.83  3.000
 L2E  CBD  CAZ  CBC  121.75  3.000
 L2E  OAH  CAZ  CBC  118.42  3.000
 L2E  H20  OAH  CAZ  107.85  3.000
 L2E  CAN  CAY  OAG  120.43  3.000
 L2E  CAN  CAY  CBC  122.64  3.000
 L2E  OAG  CAY  CBC  116.92  3.000
 L2E  H21  OAG  CAY  110.88  3.000
 L2E  H22  CAN  CBB  120.09  3.000
 L2E  H22  CAN  CAY  120.80  3.000
 L2E  CBB  CAN  CAY  119.11  3.000
 L2E  CBD  CBB  OAS  121.70  3.000
 L2E  OAS  CBB  CAN  117.58  3.000
 L2E  CBD  CBB  CAN  120.72  3.000
 L2E  CBE  OAS  CBB  116.72  3.000
 L2E  CAV  CBD  CBB  120.27  3.000
 L2E  CBB  CBD  CAZ  118.51  3.000
 L2E  CAV  CBD  CAZ  121.04  3.000
 L2E  CAR  CAV  OAD  121.43  3.000
 L2E  CAR  CAV  CBD  115.74  3.000
 L2E  OAD  CAV  CBD  122.79  3.000
 L2E  H26  CAR  H25  107.27  3.000
 L2E  H26  CAR  CBE  110.48  3.000
 L2E  H25  CAR  CBE  110.15  3.000
 L2E  H26  CAR  CAV  108.01  3.000
 L2E  H25  CAR  CAV  110.18  3.000
 L2E  CBE  CAR  CAV  110.67  3.000
 L2E  H27  CBE  CBA  109.18  3.000
 L2E  H27  CBE  CAR  108.59  3.000
 L2E  CBA  CBE  CAR  112.71  3.000
 L2E  H27  CBE  OAS  108.01  3.000
 L2E  CBA  CBE  OAS  108.06  3.000
 L2E  CAR  CBE  OAS  110.18  3.000
 L2E  CAL  CBA  CAM  119.32  3.000
 L2E  CAM  CBA  CBE  119.36  3.000
 L2E  CAL  CBA  CBE  121.29  3.000
 L2E  H28  CAM  CAX  118.71  3.000
 L2E  H28  CAM  CBA  120.25  3.000
 L2E  CAX  CAM  CBA  121.04  3.000
 L2E  CAW  CAX  OAF  121.72  3.000
 L2E  OAF  CAX  CAM  118.93  3.000
 L2E  CAW  CAX  CAM  119.34  3.000
 L2E  H29  OAF  CAX  110.54  3.000
 L2E  CAK  CAW  OAE  124.20  3.000
 L2E  OAE  CAW  CAX  116.17  3.000
 L2E  CAK  CAW  CAX  119.63  3.000
 L2E  H30  OAE  CAW  111.03  3.000
 L2E  H31  CAK  CAL  119.84  3.000
 L2E  H31  CAK  CAW  119.53  3.000
 L2E  CAL  CAK  CAW  120.63  3.000
 L2E  H32  CAL  CAK  119.05  3.000
 L2E  H32  CAL  CBA  120.91  3.000
 L2E  CAK  CAL  CBA  120.04  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
 L2E  CONST_01  CBB  CBD  CAZ  CBC     0.00   0.0  0
 L2E  CONST_02  CBB  CAN  CAY  CBC     0.00   0.0  0
 L2E  CONST_03  CAN  CAY  CBC  CAZ     0.00   0.0  0
 L2E  CONST_04  CAN  CBB  CBD  CAZ     0.00   0.0  0
 L2E  CONST_05  CBD  CAZ  CBC  CAY     0.00   0.0  0
 L2E  CONST_06  CBD  CBB  CAN  CAY     0.00   0.0  0
 L2E  CONST_07  CAW  CAK  CAL  CBA     0.00   0.0  0
 L2E  CONST_08  CAW  CAX  CAM  CBA     0.00   0.0  0
 L2E  CONST_09  CAK  CAL  CBA  CAM     0.00   0.0  0
 L2E  CONST_10  CAK  CAW  CAX  CAM     0.00   0.0  0
 L2E  CONST_11  CAL  CBA  CAM  CAX     0.00   0.0  0
 L2E  CONST_12  CAL  CAK  CAW  CAX     0.00   0.0  0
 L2E  CONST_13  CAK  CAL  CBA  CBE   180.00   0.0  0
 L2E  CONST_14  CAX  CAM  CBA  CBE   180.00   0.0  0
 L2E  CONST_15  CBD  CAZ  CBC  CAP   180.00   0.0  0
 L2E  CONST_16  CAN  CAY  CBC  CAP   180.00   0.0  0
 L2E  CONST_17  OAG  CAY  CBC  CAZ   180.00   0.0  0
 L2E  CONST_18  CAY  CBC  CAZ  OAH   180.00   0.0  0
 L2E  CONST_19  CAV  CBD  CAZ  OAH     0.00   0.0  0
 L2E  CONST_20  CBB  CBD  CAZ  OAH   180.00   0.0  0
 L2E  CONST_21  CBB  CAN  CAY  OAG   180.00   0.0  0
 L2E  CONST_22  OAF  CAX  CAM  CBA   180.00   0.0  0
 L2E  CONST_23  OAE  CAW  CAX  CAM   180.00   0.0  0
 L2E  CONST_24  CAK  CAW  CAX  OAF   180.00   0.0  0
 L2E  CONST_25  CAL  CAK  CAW  OAE   180.00   0.0  0
 L2E  CONST_26  H22  CAN  CAY  CBC   180.00   0.0  0
 L2E  CONST_27  H32  CAL  CBA  CBE     0.00   0.0  0
 L2E  CONST_28  H28  CAM  CBA  CBE     0.00   0.0  0
 L2E  CONST_29  H31  CAK  CAL  CBA   180.00   0.0  0
 L2E  Var_01    CAR  CAV  CBD  CAZ   174.27  30.0  1
 L2E  Var_02    CBE  CAR  CAV  CBD    30.64  30.0  1
 L2E  Var_03    CAZ  CBC  CAP  CAJ   -84.45  30.0  2
 L2E  Var_04    CBC  CAP  CAJ  CAU   122.66  30.0  1
 L2E  Var_05    CAO  CAI  CAT  CAA  -179.80   0.0  2
 L2E  Var_06    CAP  CAJ  CAU  CAQ  -177.91   0.0  2
 L2E  Var_07    CAQ  CAO  CAI  CAT   112.55  30.0  1
 L2E  Var_08    CAU  CAQ  CAO  CAI   172.55  30.0  2
 L2E  Var_09    CAC  CAU  CAQ  CAO   -70.09  30.0  1
 L2E  Var_10    H5   CAB  CAT  CAA   176.28  30.0  3
 L2E  Var_11    H1   CAA  CAT  CAB   -61.13  30.0  3
 L2E  Var_12    H14  CAC  CAU  CAQ     0.25  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
 L2E  chir_01  CBE  CAR  OAS  CBA  positiv

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
 L2E  plan-1  CBE  0.020
 L2E  plan-1  CBA  0.020
 L2E  plan-1  CAM  0.020
 L2E  plan-1  CAX  0.020
 L2E  plan-1  OAF  0.020
 L2E  plan-1  CAW  0.020
 L2E  plan-1  OAE  0.020
 L2E  plan-1  CAK  0.020
 L2E  plan-1  CAL  0.020
 L2E  plan-1  H28  0.020
 L2E  plan-1  H31  0.020
 L2E  plan-1  H32  0.020
 L2E  plan-2  CAP  0.020
 L2E  plan-2  CBC  0.020
 L2E  plan-2  CAZ  0.020
 L2E  plan-2  OAH  0.020
 L2E  plan-2  CAY  0.020
 L2E  plan-2  OAG  0.020
 L2E  plan-2  CAN  0.020
 L2E  plan-2  CBB  0.020
 L2E  plan-2  OAS  0.020
 L2E  plan-2  CBD  0.020
 L2E  plan-2  CAV  0.020
 L2E  plan-2  H22  0.020
 L2E  plan-3  CBD  0.020
 L2E  plan-3  CAV  0.020
 L2E  plan-3  OAD  0.020
 L2E  plan-3  CAR  0.020
 L2E  plan-4  CAQ  0.020
 L2E  plan-4  CAU  0.020
 L2E  plan-4  CAC  0.020
 L2E  plan-4  CAJ  0.020
 L2E  plan-4  CAP  0.020
 L2E  plan-4  H17  0.020
 L2E  plan-5  CAA  0.020
 L2E  plan-5  CAT  0.020
 L2E  plan-5  CAB  0.020
 L2E  plan-5  CAI  0.020
 L2E  plan-5  CAO  0.020
 L2E  plan-5  H8   0.020

