# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 16:32:50 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: (3R,5R)-3,5-dihydroxy-7-[(1S,2S,6R,8S,8aR)-8-hydroxy-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]heptanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](O)[C@@H]2[C@@H](CC[C@@H](O)C[C@@H](O)CC(O)=O)[C@@H](C)C=CC2=C1
#
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
 MJA  MJA  '(3R,5R)-3,5-dihydroxy-7-[(1S,2S,6R,8S,8aR)-8-hydroxy-2,6-dimethyl-1,2,6,7,8,8a-hexahydronaphthalen-1-yl]heptanoic acid'  ligand  54  24  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MJA
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
 MJA  O16   O  O     0  -0.439  -12.1343  28.6291  -32.3046
 MJA  C15   C  C     0   0.545  -11.2978  27.7623  -32.3401
 MJA  O15   O  OH1   0  -0.599  -10.2926  27.7669  -33.2147
 MJA  C14   C  CH2   0  -0.588  -11.2491  26.5665  -31.4326
 MJA  C13   C  CH1   0   0.002  -11.5115  25.2556  -32.1865
 MJA  O13   O  OH1   0  -0.661  -12.6875  25.3386  -32.9608
 MJA  C12   C  CH2   0  -0.503  -11.5498  24.0892  -31.2010
 MJA  C11   C  CH1   0   0.094  -11.4829  22.7071  -31.8618
 MJA  O11   O  OH1   0  -0.683  -12.4795  21.9110  -31.2401
 MJA  C10   C  CH2   0  -0.494  -10.1216  22.0129  -31.7518
 MJA  C9    C  CH2   0  -0.467   -8.9692  22.6388  -32.5444
 MJA  C1    C  CH1   0  -0.226   -8.2867  23.8693  -31.9428
 MJA  C8A   C  CR16  0  -0.327   -7.1230  24.3711  -32.8184
 MJA  C2    C  CH1   0  -0.288   -7.8020  23.6485  -30.4987
 MJA  C2M   C  CH3   0  -0.664   -6.9126  22.4159  -30.3141
 MJA  C3    C  C1    0  -0.214   -7.1126  24.8801  -29.9934
 MJA  C4    C  C1    0  -0.257   -6.5828  25.8015  -30.8012
 MJA  C4A   C  CR6   0   0.127   -6.5575  25.6552  -32.2504
 MJA  C5    C  CR16  0  -0.290   -6.0102  26.6039  -33.0231
 MJA  C6    C  CR16  0  -0.289   -5.8475  26.5245  -34.5089
 MJA  C6M   C  CH3   0  -0.653   -6.5223  27.7100  -35.2074
 MJA  C7    C  C     0  -0.449   -6.2878  25.1561  -35.0422
 MJA  C8    C  CR16  0   0.011   -7.4766  24.5614  -34.2960
 MJA  O8    O  OH1   0  -0.669   -8.6583  25.3201  -34.4772
 MJA  H14   H  HCH2  0   0.272  -10.2658  26.5176  -30.9557
 MJA  H14A  H  HCH2  0   0.272  -11.9896  26.6978  -30.6412
 MJA  H13   H  HCH1  0   0.245  -10.7122  25.0996  -32.9150
 MJA  HO13  H  HOH1  0   0.444  -13.4419  25.4241  -32.3671
 MJA  H12   H  HCH2  0   0.243  -10.7527  24.2039  -30.4622
 MJA  H12A  H  HCH2  0   0.252  -12.4826  24.1638  -30.6317
 MJA  H11   H  HCH1  0   0.201  -11.7151  22.8191  -32.9317
 MJA  HO11  H  HOH1  0   0.444  -12.4443  21.0308  -31.6279
 MJA  H10   H  HCH2  0   0.228   -9.8641  21.8974  -30.6944
 MJA  H10A  H  HCH2  0   0.233  -10.2531  20.9967  -32.1395
 MJA  H9    H  HCH2  0   0.231   -8.2091  21.8677  -32.7033
 MJA  H9A   H  HCH2  0   0.244   -9.3477  22.8868  -33.5393
 MJA  H1    H  HCH1  0   0.225   -9.0132  24.6847  -31.8823
 MJA  H8A   H  HCR6  0   0.248   -6.3308  23.6102  -32.7859
 MJA  H2    H  HCH1  0   0.241   -8.6832  23.5015  -29.8631
 MJA  H2M   H  HCH3  0   0.225   -6.0451  22.4407  -30.9763
 MJA  H2MA  H  HCH3  0   0.237   -6.5408  22.3595  -29.2902
 MJA  H2MB  H  HCH3  0   0.233   -7.4582  21.4930  -30.5139
 MJA  H3    H  H     0   0.241   -7.0502  25.0104  -28.9180
 MJA  H4    H  H     0   0.235   -6.1134  26.6859  -30.3823
 MJA  H5    H  HCR6  0   0.236   -5.6279  27.5030  -32.5453
 MJA  H6    H  HCR6  0   0.248   -4.7754  26.6283  -34.7156
 MJA  H6M   H  HCH3  0   0.229   -6.1323  28.6559  -34.8285
 MJA  H6MA  H  HCH3  0   0.232   -6.3343  27.6786  -36.2816
 MJA  H6MB  H  HCH3  0   0.209   -7.6024  27.7195  -35.0644
 MJA  H7    H  H     0   0.236   -6.5147  25.2223  -36.1095
 MJA  H7A   H  H     0   0.234   -5.4585  24.4492  -34.9488
 MJA  H8    H  HCR6  0   0.241   -7.6901  23.5843  -34.7362
 MJA  HO8   H  HOH1  0   0.440   -8.6317  26.0951  -33.9057
 MJA  H30   H  HOH1  0   0.483  -10.3613  28.5394  -33.7958

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
 MJA  O16  C15   double  1.205  0.020  1.205
 MJA  C15  O15   single  1.332  0.020  1.332
 MJA  C15  C14   single  1.502  0.020  1.502
 MJA  C14  C13   single  1.535  0.020  1.535
 MJA  C14  H14   single  0.970  0.020  1.090
 MJA  C14  H14A  single  0.970  0.020  1.090
 MJA  C13  O13   single  1.410  0.020  1.410
 MJA  C13  C12   single  1.528  0.020  1.528
 MJA  C13  H13   single  0.970  0.020  1.090
 MJA  O13  HO13  single  0.850  0.020  0.980
 MJA  C12  C11   single  1.533  0.020  1.533
 MJA  C12  H12   single  0.970  0.020  1.090
 MJA  C12  H12A  single  0.970  0.020  1.090
 MJA  C11  O11   single  1.419  0.020  1.419
 MJA  C11  C10   single  1.532  0.020  1.532
 MJA  C11  H11   single  0.970  0.020  1.090
 MJA  O11  HO11  single  0.850  0.020  0.980
 MJA  C10  C9    single  1.532  0.020  1.532
 MJA  C10  H10   single  0.970  0.020  1.090
 MJA  C10  H10A  single  0.970  0.020  1.090
 MJA  C9   C1    single  1.530  0.020  1.530
 MJA  C9   H9    single  0.970  0.020  1.090
 MJA  C9   H9A   single  0.970  0.020  1.090
 MJA  C1   C8A   single  1.540  0.020  1.540
 MJA  C1   C2    single  1.539  0.020  1.539
 MJA  C1   H1    single  0.970  0.020  1.090
 MJA  C8A  C4A   single  1.514  0.020  1.514
 MJA  C8A  C8    single  1.531  0.020  1.531
 MJA  C8A  H8A   single  0.970  0.020  1.090
 MJA  C2   C2M   single  1.531  0.020  1.531
 MJA  C2   C3    single  1.499  0.020  1.499
 MJA  C2   H2    single  0.970  0.020  1.090
 MJA  C2M  H2M   single  0.970  0.020  1.090
 MJA  C2M  H2MA  single  0.970  0.020  1.090
 MJA  C2M  H2MB  single  0.970  0.020  1.090
 MJA  C3   C4    double  1.335  0.020  1.335
 MJA  C3   H3    single  0.930  0.020  1.080
 MJA  C4   C4A   single  1.457  0.020  1.457
 MJA  C4   H4    single  0.930  0.020  1.080
 MJA  C4A  C5    double  1.340  0.020  1.340
 MJA  C5   C6    single  1.497  0.020  1.497
 MJA  C5   H5    single  0.930  0.020  1.080
 MJA  C6   C6M   single  1.533  0.020  1.533
 MJA  C6   C7    single  1.533  0.020  1.533
 MJA  C6   H6    single  0.970  0.020  1.090
 MJA  C6M  H6M   single  0.970  0.020  1.090
 MJA  C6M  H6MA  single  0.970  0.020  1.090
 MJA  C6M  H6MB  single  0.970  0.020  1.090
 MJA  C7   C8    single  1.524  0.020  1.524
 MJA  C7   H7    single  0.970  0.020  1.090
 MJA  C7   H7A   single  0.970  0.020  1.090
 MJA  C8   O8    single  1.416  0.020  1.416
 MJA  C8   H8    single  0.970  0.020  1.090
 MJA  O8   HO8   single  0.850  0.020  0.980
 MJA  O15  H30   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
 MJA  C14   C15  O15   112.02  3.000
 MJA  C14   C15  O16   125.26  3.000
 MJA  O15   C15  O16   122.72  3.000
 MJA  H30   O15  C15   110.05  3.000
 MJA  H14A  C14  H14   107.40  3.000
 MJA  H14A  C14  C13   110.05  3.000
 MJA  H14   C14  C13   109.25  3.000
 MJA  H14A  C14  C15   108.68  3.000
 MJA  H14   C14  C15   109.15  3.000
 MJA  C13   C14  C15   112.19  3.000
 MJA  H13   C13  C12   109.84  3.000
 MJA  H13   C13  O13   104.61  3.000
 MJA  C12   C13  O13   112.23  3.000
 MJA  H13   C13  C14   108.93  3.000
 MJA  C12   C13  C14   109.85  3.000
 MJA  O13   C13  C14   111.22  3.000
 MJA  HO13  O13  C13   108.64  3.000
 MJA  H12A  C12  H12   105.23  3.000
 MJA  H12A  C12  C11   108.81  3.000
 MJA  H12   C12  C11   110.74  3.000
 MJA  H12A  C12  C13   107.73  3.000
 MJA  H12   C12  C13   109.74  3.000
 MJA  C11   C12  C13   114.15  3.000
 MJA  H11   C11  C10   107.66  3.000
 MJA  H11   C11  O11   109.56  3.000
 MJA  C10   C11  O11   109.78  3.000
 MJA  H11   C11  C12   108.55  3.000
 MJA  C10   C11  C12   114.60  3.000
 MJA  O11   C11  C12   106.63  3.000
 MJA  HO11  O11  C11   108.11  3.000
 MJA  H10A  C10  H10   105.80  3.000
 MJA  H10A  C10  C9    106.63  3.000
 MJA  H10   C10  C9    111.46  3.000
 MJA  H10A  C10  C11   106.75  3.000
 MJA  H10   C10  C11   109.04  3.000
 MJA  C9    C10  C11   116.49  3.000
 MJA  H9A   C9   H9    105.56  3.000
 MJA  H9A   C9   C1    109.26  3.000
 MJA  H9    C9   C1    108.29  3.000
 MJA  H9A   C9   C10   107.64  3.000
 MJA  H9    C9   C10   108.04  3.000
 MJA  C1    C9   C10   117.42  3.000
 MJA  H1    C1   C2    105.32  3.000
 MJA  H1    C1   C8A   106.88  3.000
 MJA  C2    C1   C8A   110.01  3.000
 MJA  H1    C1   C9    108.96  3.000
 MJA  C2    C1   C9    113.20  3.000
 MJA  C8A   C1   C9    112.05  3.000
 MJA  H8A   C8A  C8    106.32  3.000
 MJA  H8A   C8A  C4A   107.88  3.000
 MJA  C8    C8A  C4A   110.06  3.000
 MJA  H8A   C8A  C1    107.59  3.000
 MJA  C8    C8A  C1    114.49  3.000
 MJA  C4A   C8A  C1    110.20  3.000
 MJA  H2    C2   C3    106.52  3.000
 MJA  H2    C2   C2M   106.80  3.000
 MJA  C3    C2   C2M   110.70  3.000
 MJA  H2    C2   C1    108.06  3.000
 MJA  C3    C2   C1    110.07  3.000
 MJA  C2M   C2   C1    114.30  3.000
 MJA  H2MB  C2M  H2MA  107.38  3.000
 MJA  H2MB  C2M  H2M   107.79  3.000
 MJA  H2MA  C2M  H2M   107.45  3.000
 MJA  H2MB  C2M  C2    111.62  3.000
 MJA  H2MA  C2M  C2    110.66  3.000
 MJA  H2M   C2M  C2    111.73  3.000
 MJA  H3    C3   C4    119.61  3.000
 MJA  H3    C3   C2    117.33  3.000
 MJA  C4    C3   C2    123.06  3.000
 MJA  H4    C4   C4A   117.27  3.000
 MJA  H4    C4   C3    120.03  3.000
 MJA  C4A   C4   C3    122.65  3.000
 MJA  C5    C4A  C4    120.63  3.000
 MJA  C5    C4A  C8A   122.45  3.000
 MJA  C4    C4A  C8A   116.87  3.000
 MJA  H5    C5   C6    116.22  3.000
 MJA  H5    C5   C4A   118.38  3.000
 MJA  C6    C5   C4A   125.39  3.000
 MJA  H6    C6   C7    107.43  3.000
 MJA  H6    C6   C6M   105.75  3.000
 MJA  C7    C6   C6M   113.92  3.000
 MJA  H6    C6   C5    106.76  3.000
 MJA  C7    C6   C5    111.19  3.000
 MJA  C6M   C6   C5    111.32  3.000
 MJA  H6MB  C6M  H6MA  107.47  3.000
 MJA  H6MB  C6M  H6M   107.53  3.000
 MJA  H6MA  C6M  H6M   107.77  3.000
 MJA  H6MB  C6M  C6    112.55  3.000
 MJA  H6MA  C6M  C6    110.53  3.000
 MJA  H6M   C6M  C6    110.79  3.000
 MJA  H7A   C7   H7    106.25  3.000
 MJA  H7A   C7   C8    107.30  3.000
 MJA  H7    C7   C8    109.86  3.000
 MJA  H7A   C7   C6    109.23  3.000
 MJA  H7    C7   C6    110.20  3.000
 MJA  C8    C7   C6    113.70  3.000
 MJA  H8    C8   O8    105.34  3.000
 MJA  H8    C8   C7    107.70  3.000
 MJA  O8    C8   C7    112.28  3.000
 MJA  H8    C8   C8A   108.83  3.000
 MJA  O8    C8   C8A   112.51  3.000
 MJA  C7    C8   C8A   109.92  3.000
 MJA  HO8   O8   C8    109.40  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
 MJA  CONST_01  H30  O15  C15  O16    0.00   0.0  0
 MJA  Var_01    C6   C5   C4A  C8A   -1.68   0.0  0
 MJA  Var_02    C3   C4   C4A  C8A   -2.09  30.0  1
 MJA  Var_03    C4A  C4   C3   C2    -3.69  30.0  1
 MJA  Var_04    C1   C9   C10  C11   79.46  30.0  3
 MJA  Var_05    C13  C14  C15  O16  112.73  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
 MJA  chir_01  C13  C14  O13  C12  positiv
 MJA  chir_02  C11  O11  C12  C10  negativ
 MJA  chir_03  C1   C9   C8A  C2   positiv
 MJA  chir_04  C8A  C1   C4A  C8   positiv
 MJA  chir_05  C2   C1   C2M  C3   negativ
 MJA  chir_06  C6   C5   C6M  C7   positiv
 MJA  chir_07  C8   O8   C8A  C7   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
 MJA  plan-1  O16  0.020
 MJA  plan-1  C15  0.020
 MJA  plan-1  O15  0.020
 MJA  plan-1  C14  0.020
 MJA  plan-1  H30  0.020
 MJA  plan-2  C8A  0.020
 MJA  plan-2  C4   0.020
 MJA  plan-2  C4A  0.020
 MJA  plan-2  C5   0.020
 MJA  plan-2  C6   0.020
 MJA  plan-2  H5   0.020

