# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:56:01 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (3aS,4R,9bR)-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCc1cc(O)cc2[C@@H]3CCC[C@@H]3[C@@H](Oc12)c4ccc(O)cc4
#
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
 JJ3  JJ3  (3aS,4R,9bR)-4-(4-hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol  ligand  46  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JJ3
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
 JJ3  C1    C  CR6   0   0.373  -4.0295   0.6208   0.2596
 JJ3  C2    C  CR16  0  -0.456  -3.6305  -0.7035   0.0967
 JJ3  C3    C  CR6   0  -0.088  -2.2850  -1.0356   0.1197
 JJ3  C4    C  CR6   0   0.311  -1.3348  -0.0261   0.2991
 JJ3  O5    O  O2    0  -0.500  -0.0387  -0.4347   0.3152
 JJ3  C6    C  CH1   0   0.022   0.9252   0.4657   0.8332
 JJ3  C8    C  CH1   0  -0.295   0.7139   1.8646   0.2743
 JJ3  C10   C  CH2   0  -0.434   0.8095   1.9955  -1.2457
 JJ3  C11   C  CH2   0  -0.443   0.0726   3.3041  -1.5629
 JJ3  C12   C  CH2   0  -0.443  -0.8490   3.5855  -0.3549
 JJ3  C13   C  CH1   0  -0.291  -0.6830   2.3951   0.6072
 JJ3  C15   C  CR6   0   0.071  -1.7159   1.3066   0.4290
 JJ3  C16   C  CR16  0  -0.414  -3.0751   1.6115   0.4221
 JJ3  C17   C  CR6   0   0.061   2.2910  -0.0831   0.5250
 JJ3  C18   C  CR16  0  -0.292   3.3512   0.2074   1.3790
 JJ3  C19   C  CR16  0  -0.325   4.6399  -0.2207   1.1064
 JJ3  C20   C  CR6   0   0.342   4.8924  -0.9670  -0.0426
 JJ3  O21   O  OH1   0  -0.633   6.1597  -1.3678  -0.2719
 JJ3  C22   C  CR16  0  -0.371   3.8402  -1.2715  -0.9010
 JJ3  C23   C  CR16  0  -0.291   2.5556  -0.8308  -0.6171
 JJ3  C24   C  CH2   0  -0.135  -1.8102  -2.4544  -0.0356
 JJ3  O25   O  O2    0  -0.488  -2.8949  -3.3046  -0.2786
 JJ3  C26   C  CH3   0  -0.394  -2.5039  -4.6475  -0.4104
 JJ3  O27   O  OH1   0  -0.646  -5.3333   0.9882   0.2642
 JJ3  H2    H  HCR6  0   0.265  -4.3760  -1.4779  -0.0363
 JJ3  H16   H  HCR6  0   0.254  -3.3958   2.6400   0.5443
 JJ3  H27   H  HOH1  0   0.470  -5.8968   0.2153   0.1521
 JJ3  H241  H  HCH2  0   0.219  -1.0800  -2.5160  -0.8562
 JJ3  H242  H  HCH2  0   0.218  -1.2716  -2.7622   0.8737
 JJ3  H6    H  HCH1  0   0.243   0.8077   0.5195   1.9255
 JJ3  H8    H  HCH1  0   0.259   1.4579   2.5206   0.7380
 JJ3  H101  H  HCH2  0   0.240   1.8421   2.0008  -1.5953
 JJ3  H102  H  HCH2  0   0.230   0.3154   1.1531  -1.7359
 JJ3  H13   H  HCH1  0   0.267  -0.7282   2.7396   1.6448
 JJ3  H111  H  HCH2  0   0.229   0.7840   4.1215  -1.6893
 JJ3  H112  H  HCH2  0   0.232  -0.4865   3.2323  -2.4961
 JJ3  H121  H  HCH2  0   0.238  -0.5370   4.4996   0.1527
 JJ3  H122  H  HCH2  0   0.238  -1.8858   3.7394  -0.6527
 JJ3  H18   H  HCR6  0   0.250   3.1697   0.7826   2.2801
 JJ3  H23   H  HCR6  0   0.252   1.7581  -1.0818  -1.3039
 JJ3  H19   H  HCR6  0   0.262   5.4500   0.0154   1.7851
 JJ3  H21   H  HOH1  0   0.473   6.2066  -1.8760  -1.0894
 JJ3  H22   H  HCR6  0   0.269   4.0208  -1.8565  -1.7960
 JJ3  H261  H  HCH3  0   0.237  -3.3951  -5.2368  -0.6222
 JJ3  H262  H  HCH3  0   0.206  -1.7913  -4.7889  -1.2318
 JJ3  H263  H  HCH3  0   0.207  -2.0420  -5.0325   0.5063

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
 JJ3  C1   C2    aromatic  1.393  0.020  1.393
 JJ3  C1   C16   aromatic  1.385  0.020  1.385
 JJ3  C1   O27   single    1.355  0.020  1.355
 JJ3  C2   C3    aromatic  1.386  0.020  1.386
 JJ3  C2   H2    single    0.930  0.020  1.080
 JJ3  C3   C4    aromatic  1.398  0.020  1.398
 JJ3  C3   C24   single    1.504  0.020  1.504
 JJ3  C4   O5    single    1.359  0.020  1.359
 JJ3  C4   C15   aromatic  1.392  0.020  1.392
 JJ3  O5   C6    single    1.417  0.020  1.417
 JJ3  C6   C8    single    1.521  0.020  1.521
 JJ3  C6   C17   single    1.504  0.020  1.504
 JJ3  C6   H6    single    0.970  0.020  1.090
 JJ3  C8   C10   single    1.529  0.020  1.529
 JJ3  C8   C13   single    1.531  0.020  1.531
 JJ3  C8   H8    single    0.970  0.020  1.090
 JJ3  C10  C11   single    1.535  0.020  1.535
 JJ3  C10  H101  single    0.970  0.020  1.090
 JJ3  C10  H102  single    0.970  0.020  1.090
 JJ3  C11  C12   single    1.545  0.020  1.545
 JJ3  C11  H111  single    0.970  0.020  1.090
 JJ3  C11  H112  single    0.970  0.020  1.090
 JJ3  C12  C13   single    1.540  0.020  1.540
 JJ3  C12  H121  single    0.970  0.020  1.090
 JJ3  C12  H122  single    0.970  0.020  1.090
 JJ3  C13  C15   single    1.511  0.020  1.511
 JJ3  C13  H13   single    0.970  0.020  1.090
 JJ3  C15  C16   aromatic  1.393  0.020  1.393
 JJ3  C16  H16   single    0.930  0.020  1.080
 JJ3  C17  C18   aromatic  1.392  0.020  1.392
 JJ3  C17  C23   aromatic  1.390  0.020  1.390
 JJ3  C18  C19   aromatic  1.385  0.020  1.385
 JJ3  C18  H18   single    0.930  0.020  1.080
 JJ3  C19  C20   aromatic  1.393  0.020  1.393
 JJ3  C19  H19   single    0.930  0.020  1.080
 JJ3  C20  O21   single    1.349  0.020  1.349
 JJ3  C20  C22   aromatic  1.392  0.020  1.392
 JJ3  O21  H21   single    0.850  0.020  0.980
 JJ3  C22  C23   aromatic  1.387  0.020  1.387
 JJ3  C22  H22   single    0.930  0.020  1.080
 JJ3  C23  H23   single    0.930  0.020  1.080
 JJ3  C24  O25   single    1.399  0.020  1.399
 JJ3  C24  H241  single    0.970  0.020  1.090
 JJ3  C24  H242  single    0.970  0.020  1.090
 JJ3  O25  C26   single    1.405  0.020  1.405
 JJ3  C26  H261  single    0.970  0.020  1.090
 JJ3  C26  H262  single    0.970  0.020  1.090
 JJ3  C26  H263  single    0.970  0.020  1.090
 JJ3  O27  H27   single    0.850  0.020  0.980

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
 JJ3  O27   C1   C16   117.96  3.000
 JJ3  O27   C1   C2    122.28  3.000
 JJ3  C16   C1   C2    119.76  3.000
 JJ3  H2    C2   C3    119.93  3.000
 JJ3  H2    C2   C1    119.80  3.000
 JJ3  C3    C2   C1    120.26  3.000
 JJ3  C24   C3   C4    118.68  3.000
 JJ3  C24   C3   C2    122.05  3.000
 JJ3  C4    C3   C2    119.27  3.000
 JJ3  C15   C4   O5    123.21  3.000
 JJ3  C15   C4   C3    121.15  3.000
 JJ3  O5    C4   C3    115.63  3.000
 JJ3  C6    O5   C4    117.51  3.000
 JJ3  H6    C6   C17   108.57  3.000
 JJ3  H6    C6   C8    107.76  3.000
 JJ3  C17   C6   C8    112.73  3.000
 JJ3  H6    C6   O5    108.75  3.000
 JJ3  C17   C6   O5    108.11  3.000
 JJ3  C8    C6   O5    110.83  3.000
 JJ3  H8    C8   C13   108.68  3.000
 JJ3  H8    C8   C10   109.11  3.000
 JJ3  C13   C8   C10   104.10  3.000
 JJ3  H8    C8   C6    107.52  3.000
 JJ3  C13   C8   C6    111.44  3.000
 JJ3  C10   C8   C6    115.81  3.000
 JJ3  H102  C10  H101  106.75  3.000
 JJ3  H102  C10  C11   110.34  3.000
 JJ3  H101  C10  C11   112.60  3.000
 JJ3  H102  C10  C8    110.59  3.000
 JJ3  H101  C10  C8    112.24  3.000
 JJ3  C11   C10  C8    104.39  3.000
 JJ3  H112  C11  H111  106.54  3.000
 JJ3  H112  C11  C12   112.04  3.000
 JJ3  H111  C11  C12   110.06  3.000
 JJ3  H112  C11  C10   111.52  3.000
 JJ3  H111  C11  C10   110.47  3.000
 JJ3  C12   C11  C10   106.26  3.000
 JJ3  H122  C12  H121  106.32  3.000
 JJ3  H122  C12  C13   112.50  3.000
 JJ3  H121  C12  C13   109.04  3.000
 JJ3  H122  C12  C11   112.31  3.000
 JJ3  H121  C12  C11   110.22  3.000
 JJ3  C13   C12  C11   106.46  3.000
 JJ3  H13   C13  C15   108.08  3.000
 JJ3  H13   C13  C12   110.16  3.000
 JJ3  C15   C13  C12   114.18  3.000
 JJ3  H13   C13  C8    110.67  3.000
 JJ3  C15   C13  C8    110.39  3.000
 JJ3  C12   C13  C8    103.32  3.000
 JJ3  C16   C15  C13   120.65  3.000
 JJ3  C16   C15  C4    118.44  3.000
 JJ3  C13   C15  C4    120.89  3.000
 JJ3  H16   C16  C15   119.72  3.000
 JJ3  H16   C16  C1    119.20  3.000
 JJ3  C15   C16  C1    121.08  3.000
 JJ3  C23   C17  C18   118.11  3.000
 JJ3  C23   C17  C6    122.51  3.000
 JJ3  C18   C17  C6    119.32  3.000
 JJ3  H18   C18  C19   118.90  3.000
 JJ3  H18   C18  C17   119.54  3.000
 JJ3  C19   C18  C17   121.56  3.000
 JJ3  H19   C19  C20   119.88  3.000
 JJ3  H19   C19  C18   120.35  3.000
 JJ3  C20   C19  C18   119.77  3.000
 JJ3  C22   C20  O21   122.72  3.000
 JJ3  C22   C20  C19   119.27  3.000
 JJ3  O21   C20  C19   118.01  3.000
 JJ3  H21   O21  C20   110.28  3.000
 JJ3  H22   C22  C23   119.64  3.000
 JJ3  H22   C22  C20   120.08  3.000
 JJ3  C23   C22  C20   120.28  3.000
 JJ3  H23   C23  C22   118.61  3.000
 JJ3  H23   C23  C17   120.38  3.000
 JJ3  C22   C23  C17   121.01  3.000
 JJ3  H242  C24  H241  106.01  3.000
 JJ3  H242  C24  O25   110.66  3.000
 JJ3  H241  C24  O25   110.54  3.000
 JJ3  H242  C24  C3    109.44  3.000
 JJ3  H241  C24  C3    109.83  3.000
 JJ3  O25   C24  C3    110.26  3.000
 JJ3  C26   O25  C24   112.41  3.000
 JJ3  H263  C26  H262  107.90  3.000
 JJ3  H263  C26  H261  108.50  3.000
 JJ3  H262  C26  H261  108.44  3.000
 JJ3  H263  C26  O25   111.99  3.000
 JJ3  H262  C26  O25   111.98  3.000
 JJ3  H261  C26  O25   107.92  3.000
 JJ3  H27   O27  C1    110.19  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
 JJ3  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 JJ3  CONST_02  C4    C15  C16  C1      0.00   0.0  0
 JJ3  CONST_03  C15   C16  C1   C2      0.00   0.0  0
 JJ3  CONST_04  C15   C4   C3   C2      0.00   0.0  0
 JJ3  CONST_05  C16   C1   C2   C3      0.00   0.0  0
 JJ3  CONST_06  C16   C15  C4   C3      0.00   0.0  0
 JJ3  CONST_07  C20   C19  C18  C17     0.00   0.0  0
 JJ3  CONST_08  C20   C22  C23  C17     0.00   0.0  0
 JJ3  CONST_09  C22   C23  C17  C18     0.00   0.0  0
 JJ3  CONST_10  C22   C20  C19  C18     0.00   0.0  0
 JJ3  CONST_11  C23   C17  C18  C19     0.00   0.0  0
 JJ3  CONST_12  C23   C22  C20  C19     0.00   0.0  0
 JJ3  CONST_13  C19   C18  C17  C6    180.00   0.0  0
 JJ3  CONST_14  C22   C23  C17  C6    180.00   0.0  0
 JJ3  CONST_15  C24   C3   C2   C1    180.00   0.0  0
 JJ3  CONST_16  O27   C1   C2   C3    180.00   0.0  0
 JJ3  CONST_17  C24   C3   C4   O5      0.00   0.0  0
 JJ3  CONST_18  C24   C3   C4   C15   180.00   0.0  0
 JJ3  CONST_19  O27   C1   C16  C15   180.00   0.0  0
 JJ3  CONST_20  O21   C20  C19  C18   180.00   0.0  0
 JJ3  CONST_21  C23   C22  C20  O21   180.00   0.0  0
 JJ3  CONST_22  H16   C16  C1   C2    180.00   0.0  0
 JJ3  CONST_23  H2    C2   C3   C4    180.00   0.0  0
 JJ3  CONST_24  H18   C18  C17  C6      0.00   0.0  0
 JJ3  CONST_25  H23   C23  C17  C6      0.00   0.0  0
 JJ3  CONST_26  H19   C19  C18  C17   180.00   0.0  0
 JJ3  CONST_27  H22   C22  C23  C17   180.00   0.0  0
 JJ3  Var_01    C15   C4   O5   C6     17.11  30.0  1
 JJ3  Var_02    C12   C11  C10  C8    -20.92  30.0  1
 JJ3  Var_03    C13   C12  C11  C10    -2.89  30.0  1
 JJ3  Var_04    O25   C24  C3   C2      3.64  30.0  2
 JJ3  Var_05    H261  C26  O25  C24  -178.55  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
 JJ3  chir_01  C6   O5  C8   C17  positiv
 JJ3  chir_02  C8   C6  C10  C13  negativ
 JJ3  chir_03  C13  C8  C12  C15  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
 JJ3  plan-1  C6   0.020
 JJ3  plan-1  C17  0.020
 JJ3  plan-1  C18  0.020
 JJ3  plan-1  C19  0.020
 JJ3  plan-1  C20  0.020
 JJ3  plan-1  O21  0.020
 JJ3  plan-1  C22  0.020
 JJ3  plan-1  C23  0.020
 JJ3  plan-1  H18  0.020
 JJ3  plan-1  H23  0.020
 JJ3  plan-1  H19  0.020
 JJ3  plan-1  H22  0.020
 JJ3  plan-2  C1   0.020
 JJ3  plan-2  C2   0.020
 JJ3  plan-2  C3   0.020
 JJ3  plan-2  C4   0.020
 JJ3  plan-2  O5   0.020
 JJ3  plan-2  C13  0.020
 JJ3  plan-2  C15  0.020
 JJ3  plan-2  C16  0.020
 JJ3  plan-2  C24  0.020
 JJ3  plan-2  O27  0.020
 JJ3  plan-2  H2   0.020
 JJ3  plan-2  H16  0.020

