# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:47:11 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: (2R,3R,4S,5R,6E)-3,4,5-trihydroxy-2-methoxy-8,8-dimethyl-N-[2-(2,4,6-trimethylphenoxy)ethyl]non-6-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]([C@H](O)[C@@H](O)[C@H](O)\C=C\C(C)(C)C)C(=O)NCCOc1c(C)cc(C)cc1C
#
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
 Y02  Y02  (2R,3R,4S,5R,6E)-3,4,5-trihydroxy-2-methoxy-8,8-dimethyl-N-[2-(2,4,6-trimethylphenoxy)ethyl]non-6-enamide  ligand  67  30  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y02
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
 Y02  N     N  NH1   0  -0.627  -1.5460   2.5890   0.0274
 Y02  O1    O  OH1   0  -0.657   3.2463  -0.6681  -2.2456
 Y02  O2    O  OH1   0  -0.665   0.6285   0.4518  -1.4158
 Y02  O3    O  OH1   0  -0.677   2.1994  -0.3966   0.5366
 Y02  O4    O  O     0  -0.493  -0.3096   3.5355  -1.6187
 Y02  O5    O  O2    0  -0.483   1.7567   3.3582   0.3678
 Y02  O6    O  O2    0  -0.497  -3.9305   1.0727   0.5138
 Y02  C01   C  CT    0  -0.137   6.2232  -2.5659   0.3028
 Y02  C04   C  CH1   0  -0.012   3.7954   0.1360  -1.2352
 Y02  C05   C  CH1   0  -0.036   2.7501   0.6534  -0.2311
 Y02  C06   C  CH1   0   0.006   1.5651   1.3611  -0.8960
 Y02  C07   C  CH1   0  -0.075   0.8653   2.3194   0.0794
 Y02  C08   C  CH3   0  -0.658   7.0778  -1.6391   1.1628
 Y02  C09   C  CH3   0  -0.634   5.4803  -3.5598   1.2060
 Y02  C10   C  CH3   0  -0.636   7.1261  -3.3429  -0.6626
 Y02  C11   C  C     0   0.535  -0.3944   2.8736  -0.5956
 Y02  C19   C  CH2   0  -0.324  -2.8554   2.9567  -0.4580
 Y02  C20   C  CH2   0  -0.174  -3.7206   1.7446  -0.7233
 Y02  C22   C  CR6   0   0.262  -4.4033  -0.2082   0.4146
 Y02  C23   C  CR6   0   0.054  -3.4892  -1.2611   0.4235
 Y02  C24   C  CR16  0  -0.378  -3.9775  -2.5620   0.3469
 Y02  C25   C  CR6   0   0.119  -5.3392  -2.8312   0.2653
 Y02  C26   C  CR16  0  -0.369  -6.2214  -1.7550   0.2701
 Y02  C27   C  CR6   0   0.040  -5.7778  -0.4382   0.3439
 Y02  C28   C  CH3   0  -0.745  -2.0166  -0.9970   0.5372
 Y02  C29   C  CH3   0  -0.723  -5.8474  -4.2434   0.2097
 Y02  C30   C  CH3   0  -0.722  -6.7571   0.6995   0.3666
 Y02  HN    H  HNH1  0   0.402  -1.5108   2.0707   0.8906
 Y02  HO1   H  HOH1  0   0.442   2.7133  -1.3607  -1.8410
 Y02  HO2   H  HOH1  0   0.450   0.5549  -0.2807  -0.7927
 Y02  HO3   H  HOH1  0   0.459   2.9173  -0.9143   0.9209
 Y02  H02   H  H     0   0.231   4.6224  -2.4680  -1.1819
 Y02  H03   H  H     0   0.255   5.4527   0.1325   0.1981
 Y02  H04   H  HCH1  0   0.252   4.2076   1.0186  -1.7374
 Y02  H05   H  HCH1  0   0.239   3.2691   1.3800   0.4076
 Y02  H06   H  HCH1  0   0.253   1.9383   1.9613  -1.7315
 Y02  H07   H  HCH1  0   0.227   0.5933   1.7749   0.9994
 Y02  H08   H  HCH3  0   0.232   7.8114  -2.2199   1.7250
 Y02  H08A  H  HCH3  0   0.227   7.6234  -0.9156   0.5541
 Y02  H08B  H  HCH3  0   0.226   6.4763  -1.0853   1.8860
 Y02  H09   H  HCH3  0   0.226   4.8327  -3.0381   1.9138
 Y02  H09A  H  HCH3  0   0.226   4.8562  -4.2402   0.6227
 Y02  H09B  H  HCH3  0   0.227   6.1867  -4.1649   1.7782
 Y02  H10   H  HCH3  0   0.226   7.8432  -3.9556  -0.1117
 Y02  H10A  H  HCH3  0   0.225   6.5441  -4.0096  -1.3027
 Y02  H10B  H  HCH3  0   0.228   7.6890  -2.6666  -1.3082
 Y02  H19   H  HCH2  0   0.257  -3.3477   3.6148   0.2624
 Y02  H19A  H  HCH2  0   0.264  -2.7421   3.5180  -1.3834
 Y02  H20   H  HCH2  0   0.227  -3.2305   1.0831  -1.4458
 Y02  H20A  H  HCH2  0   0.237  -4.6713   2.0698  -1.1581
 Y02  H21   H  HCH3  0   0.244   2.1462   4.9050   1.6134
 Y02  H21A  H  HCH3  0   0.214   0.4332   4.7439   1.2037
 Y02  H21B  H  HCH3  0   0.214   1.1783   3.6143   2.3499
 Y02  H24   H  HCR6  0   0.241  -3.2709  -3.3848   0.3507
 Y02  H26   H  HCR6  0   0.239  -7.2891  -1.9404   0.2146
 Y02  H28   H  HCH3  0   0.247  -1.7683  -0.4994   1.4766
 Y02  H28A  H  HCH3  0   0.251  -1.4530  -1.9286   0.5022
 Y02  H28B  H  HCH3  0   0.234  -1.6526  -0.3607  -0.2701
 Y02  H29   H  HCH3  0   0.246  -6.1932  -4.5764   1.1904
 Y02  H29A  H  HCH3  0   0.242  -6.6879  -4.3414  -0.4775
 Y02  H29B  H  HCH3  0   0.242  -5.0689  -4.9350  -0.1113
 Y02  H30   H  HCH3  0   0.246  -6.5657   1.3832   1.1941
 Y02  H30A  H  HCH3  0   0.245  -6.7204   1.2895  -0.5510
 Y02  H30B  H  HCH3  0   0.248  -7.7753   0.3276   0.4693
 Y02  C21   C  CH3   0  -0.409   1.3483   4.1870   1.4318
 Y02  C03   C  C1    0  -0.315   4.9029  -0.5317  -0.4626
 Y02  C02   C  C1    0  -0.160   5.1869  -1.8293  -0.5054

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
 Y02  N    C19   single    1.444  0.020  1.444
 Y02  N    C11   single    1.340  0.020  1.340
 Y02  N    HN    single    0.860  0.020  1.020
 Y02  O1   C04   single    1.403  0.020  1.403
 Y02  O1   HO1   single    0.850  0.020  0.980
 Y02  O2   C06   single    1.405  0.020  1.405
 Y02  O2   HO2   single    0.850  0.020  0.980
 Y02  O3   C05   single    1.412  0.020  1.412
 Y02  O3   HO3   single    0.850  0.020  0.980
 Y02  C11  O4    double    1.221  0.020  1.221
 Y02  C07  O5    single    1.399  0.020  1.399
 Y02  C21  O5    single    1.409  0.020  1.409
 Y02  C20  O6    single    1.423  0.020  1.423
 Y02  C22  O6    single    1.369  0.020  1.369
 Y02  C02  C01   single    1.507  0.020  1.507
 Y02  C01  C08   single    1.526  0.020  1.526
 Y02  C01  C09   single    1.535  0.020  1.535
 Y02  C01  C10   single    1.533  0.020  1.533
 Y02  C03  C02   double    1.329  0.020  1.329
 Y02  C02  H02   single    0.930  0.020  1.080
 Y02  C04  C03   single    1.506  0.020  1.506
 Y02  C03  H03   single    0.930  0.020  1.080
 Y02  C05  C04   single    1.539  0.020  1.539
 Y02  C04  H04   single    0.970  0.020  1.090
 Y02  C05  C06   single    1.532  0.020  1.532
 Y02  C05  H05   single    0.970  0.020  1.090
 Y02  C06  C07   single    1.536  0.020  1.536
 Y02  C06  H06   single    0.970  0.020  1.090
 Y02  C07  C11   single    1.533  0.020  1.533
 Y02  C07  H07   single    0.970  0.020  1.090
 Y02  C08  H08   single    0.970  0.020  1.090
 Y02  C08  H08A  single    0.970  0.020  1.090
 Y02  C08  H08B  single    0.970  0.020  1.090
 Y02  C09  H09   single    0.970  0.020  1.090
 Y02  C09  H09A  single    0.970  0.020  1.090
 Y02  C09  H09B  single    0.970  0.020  1.090
 Y02  C10  H10   single    0.970  0.020  1.090
 Y02  C10  H10A  single    0.970  0.020  1.090
 Y02  C10  H10B  single    0.970  0.020  1.090
 Y02  C20  C19   single    1.513  0.020  1.513
 Y02  C19  H19   single    0.970  0.020  1.090
 Y02  C19  H19A  single    0.970  0.020  1.090
 Y02  C20  H20   single    0.970  0.020  1.090
 Y02  C20  H20A  single    0.970  0.020  1.090
 Y02  C21  H21   single    0.970  0.020  1.090
 Y02  C21  H21A  single    0.970  0.020  1.090
 Y02  C21  H21B  single    0.970  0.020  1.090
 Y02  C27  C22   aromatic  1.395  0.020  1.395
 Y02  C22  C23   aromatic  1.394  0.020  1.394
 Y02  C24  C23   aromatic  1.392  0.020  1.392
 Y02  C23  C28   single    1.500  0.020  1.500
 Y02  C25  C24   aromatic  1.390  0.020  1.390
 Y02  C24  H24   single    0.930  0.020  1.080
 Y02  C26  C25   aromatic  1.392  0.020  1.392
 Y02  C29  C25   single    1.502  0.020  1.502
 Y02  C26  C27   aromatic  1.392  0.020  1.392
 Y02  C26  H26   single    0.930  0.020  1.080
 Y02  C30  C27   single    1.501  0.020  1.501
 Y02  C28  H28   single    0.970  0.020  1.090
 Y02  C28  H28A  single    0.970  0.020  1.090
 Y02  C28  H28B  single    0.970  0.020  1.090
 Y02  C29  H29   single    0.970  0.020  1.090
 Y02  C29  H29A  single    0.970  0.020  1.090
 Y02  C29  H29B  single    0.970  0.020  1.090
 Y02  C30  H30   single    0.970  0.020  1.090
 Y02  C30  H30A  single    0.970  0.020  1.090
 Y02  C30  H30B  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
 Y02  HN    N    C19   116.79  3.000
 Y02  HN    N    C11   118.53  3.000
 Y02  C19   N    C11   124.67  3.000
 Y02  HO1   O1   C04   109.04  3.000
 Y02  HO2   O2   C06   107.66  3.000
 Y02  HO3   O3   C05   108.98  3.000
 Y02  C21   O5   C07   114.06  3.000
 Y02  C22   O6   C20   115.44  3.000
 Y02  C10   C01  C09   109.10  3.000
 Y02  C10   C01  C08   109.44  3.000
 Y02  C09   C01  C08   109.44  3.000
 Y02  C10   C01  C02   108.36  3.000
 Y02  C09   C01  C02   107.42  3.000
 Y02  C08   C01  C02   112.99  3.000
 Y02  H04   C04  C05   106.48  3.000
 Y02  H04   C04  C03   108.39  3.000
 Y02  C05   C04  C03   108.29  3.000
 Y02  H04   C04  O1    106.19  3.000
 Y02  C05   C04  O1    113.37  3.000
 Y02  C03   C04  O1    113.77  3.000
 Y02  H05   C05  C06   108.21  3.000
 Y02  H05   C05  C04   106.31  3.000
 Y02  C06   C05  C04   113.42  3.000
 Y02  H05   C05  O3    111.11  3.000
 Y02  C06   C05  O3    106.13  3.000
 Y02  C04   C05  O3    111.68  3.000
 Y02  H06   C06  C07   107.34  3.000
 Y02  H06   C06  C05   108.72  3.000
 Y02  C07   C06  C05   111.41  3.000
 Y02  H06   C06  O2    107.44  3.000
 Y02  C07   C06  O2    109.57  3.000
 Y02  C05   C06  O2    112.16  3.000
 Y02  H07   C07  C11   110.06  3.000
 Y02  H07   C07  C06   109.51  3.000
 Y02  C11   C07  C06   108.68  3.000
 Y02  H07   C07  O5    110.60  3.000
 Y02  C11   C07  O5    110.24  3.000
 Y02  C06   C07  O5    107.69  3.000
 Y02  H08B  C08  H08A  107.97  3.000
 Y02  H08B  C08  H08   107.40  3.000
 Y02  H08A  C08  H08   107.69  3.000
 Y02  H08B  C08  C01   111.90  3.000
 Y02  H08A  C08  C01   111.60  3.000
 Y02  H08   C08  C01   110.09  3.000
 Y02  H09B  C09  H09A  107.72  3.000
 Y02  H09B  C09  H09   107.98  3.000
 Y02  H09A  C09  H09   107.75  3.000
 Y02  H09B  C09  C01   110.74  3.000
 Y02  H09A  C09  C01   111.46  3.000
 Y02  H09   C09  C01   111.04  3.000
 Y02  H10B  C10  H10A  107.85  3.000
 Y02  H10B  C10  H10   107.90  3.000
 Y02  H10A  C10  H10   107.64  3.000
 Y02  H10B  C10  C01   111.23  3.000
 Y02  H10A  C10  C01   111.38  3.000
 Y02  H10   C10  C01   110.68  3.000
 Y02  C07   C11  O4    120.51  3.000
 Y02  C07   C11  N     115.13  3.000
 Y02  O4    C11  N     124.35  3.000
 Y02  H19A  C19  H19   107.27  3.000
 Y02  H19A  C19  C20   108.89  3.000
 Y02  H19   C19  C20   109.90  3.000
 Y02  H19A  C19  N     108.83  3.000
 Y02  H19   C19  N     109.89  3.000
 Y02  C20   C19  N     111.94  3.000
 Y02  H20A  C20  H20   107.82  3.000
 Y02  H20A  C20  C19   109.17  3.000
 Y02  H20   C20  C19   110.10  3.000
 Y02  H20A  C20  O6    110.94  3.000
 Y02  H20   C20  O6    110.75  3.000
 Y02  C19   C20  O6    108.07  3.000
 Y02  C27   C22  C23   121.44  3.000
 Y02  C23   C22  O6    118.66  3.000
 Y02  C27   C22  O6    119.87  3.000
 Y02  C28   C23  C24   120.87  3.000
 Y02  C28   C23  C22   120.73  3.000
 Y02  C24   C23  C22   118.39  3.000
 Y02  H24   C24  C25   119.43  3.000
 Y02  H24   C24  C23   118.71  3.000
 Y02  C25   C24  C23   121.86  3.000
 Y02  C29   C25  C26   120.85  3.000
 Y02  C29   C25  C24   121.04  3.000
 Y02  C26   C25  C24   118.09  3.000
 Y02  H26   C26  C27   118.56  3.000
 Y02  H26   C26  C25   119.44  3.000
 Y02  C27   C26  C25   122.00  3.000
 Y02  C30   C27  C26   120.67  3.000
 Y02  C30   C27  C22   121.12  3.000
 Y02  C26   C27  C22   118.21  3.000
 Y02  H28B  C28  H28A  107.60  3.000
 Y02  H28B  C28  H28   107.16  3.000
 Y02  H28A  C28  H28   107.45  3.000
 Y02  H28B  C28  C23   111.98  3.000
 Y02  H28A  C28  C23   110.79  3.000
 Y02  H28   C28  C23   111.63  3.000
 Y02  H29B  C29  H29A  107.95  3.000
 Y02  H29B  C29  H29   107.30  3.000
 Y02  H29A  C29  H29   107.13  3.000
 Y02  H29B  C29  C25   111.46  3.000
 Y02  H29A  C29  C25   111.64  3.000
 Y02  H29   C29  C25   111.14  3.000
 Y02  H30B  C30  H30A  107.18  3.000
 Y02  H30B  C30  H30   107.86  3.000
 Y02  H30A  C30  H30   107.05  3.000
 Y02  H30B  C30  C27   110.65  3.000
 Y02  H30A  C30  C27   112.03  3.000
 Y02  H30   C30  C27   111.85  3.000
 Y02  H21B  C21  H21A  108.11  3.000
 Y02  H21B  C21  H21   108.58  3.000
 Y02  H21A  C21  H21   108.17  3.000
 Y02  H21B  C21  O5    111.74  3.000
 Y02  H21A  C21  O5    112.58  3.000
 Y02  H21   C21  O5    107.54  3.000
 Y02  H03   C03  C04   114.40  3.000
 Y02  H03   C03  C02   120.56  3.000
 Y02  C04   C03  C02   124.98  3.000
 Y02  H02   C02  C03   118.83  3.000
 Y02  H02   C02  C01   113.79  3.000
 Y02  C03   C02  C01   127.38  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
 Y02  CONST_01  C25  C26  C27  C22     0.00   0.0  0
 Y02  CONST_02  C25  C24  C23  C22     0.00   0.0  0
 Y02  CONST_03  C26  C27  C22  C23     0.00   0.0  0
 Y02  CONST_04  C26  C25  C24  C23     0.00   0.0  0
 Y02  CONST_05  C27  C22  C23  C24     0.00   0.0  0
 Y02  CONST_06  C27  C26  C25  C24     0.00   0.0  0
 Y02  CONST_07  C26  C27  C22  O6    180.00   0.0  0
 Y02  CONST_08  C24  C23  C22  O6    180.00   0.0  0
 Y02  CONST_09  C30  C27  C22  C23   180.00   0.0  0
 Y02  CONST_10  C29  C25  C24  C23   180.00   0.0  0
 Y02  CONST_11  C28  C23  C24  C25   180.00   0.0  0
 Y02  CONST_12  C30  C27  C26  C25   180.00   0.0  0
 Y02  CONST_13  C28  C23  C22  C27   180.00   0.0  0
 Y02  CONST_14  C29  C25  C26  C27   180.00   0.0  0
 Y02  CONST_15  H26  C26  C27  C22   180.00   0.0  0
 Y02  CONST_16  H24  C24  C23  C22   180.00   0.0  0
 Y02  CONST_17  C19  N    C11  O4      0.00   0.0  0
 Y02  CONST_18  C19  N    C11  C07   180.00   0.0  0
 Y02  CONST_19  HN   N    C11  O4    180.00   0.0  0
 Y02  Var_01    C27  C22  O6   C20   -87.44  30.0  2
 Y02  Var_02    H30  C30  C27  C22   -50.35  30.0  2
 Y02  Var_03    H28  C28  C23  C22    61.76  30.0  2
 Y02  Var_04    H29  C29  C25  C24    99.40  30.0  2
 Y02  Var_05    H20  C20  O6   C22   -43.70  30.0  2
 Y02  Var_06    C04  C03  C02  C01  -176.02   0.0  2
 Y02  Var_07    O6   C20  C19  N      63.42  30.0  2
 Y02  Var_08    C08  C01  C02  C03    -5.15  30.0  3
 Y02  Var_09    C20  C19  N    C11   118.81  30.0  3
 Y02  Var_10    H08  C08  C01  C02  -179.90  30.0  3
 Y02  Var_11    H09  C09  C01  C02   -63.22  30.0  3
 Y02  Var_12    H10  C10  C01  C02  -175.47  30.0  3
 Y02  Var_13    H21  C21  O5   C07   175.80  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
 Y02  chir_01  C04  O1  C03  C05  positiv
 Y02  chir_02  C05  O3  C04  C06  negativ
 Y02  chir_03  C06  O2  C07  C05  negativ
 Y02  chir_04  C07  O5  C06  C11  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
 Y02  plan-1  O6   0.020
 Y02  plan-1  C22  0.020
 Y02  plan-1  C23  0.020
 Y02  plan-1  C24  0.020
 Y02  plan-1  C25  0.020
 Y02  plan-1  C26  0.020
 Y02  plan-1  C27  0.020
 Y02  plan-1  C28  0.020
 Y02  plan-1  C29  0.020
 Y02  plan-1  C30  0.020
 Y02  plan-1  H24  0.020
 Y02  plan-1  H26  0.020
 Y02  plan-2  N    0.020
 Y02  plan-2  O4   0.020
 Y02  plan-2  C07  0.020
 Y02  plan-2  C11  0.020
 Y02  plan-2  C19  0.020
 Y02  plan-2  HN   0.020
 Y02  plan-3  C01  0.020
 Y02  plan-3  C04  0.020
 Y02  plan-3  H02  0.020
 Y02  plan-3  H03  0.020
 Y02  plan-3  C03  0.020
 Y02  plan-3  C02  0.020

