# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 17:06:30 2020
#   Inital geometry file: a 156 line input string
#   Ligand name: (9aS)-8-ethanoyl-1,7-dihydroxy-3-methoxy-9a-methyl-N-(naphthalen-1-ylmethyl)-9-oxo-dibenzofuran-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)c2c(OC3=CC(=C(C(C)=O)C(=O)[C@@]23C)O)c1C(=O)NCc4cccc5ccccc45
#
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
 CEK  CEK  (9aS)-8-ethanoyl-1,7-dihydroxy-3-methoxy-9a-methyl-N-(naphthalen-1-ylmethyl)-9-oxo-dibenzofuran-4-carboxamide  ligand  59  36  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CEK
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
 CEK  C1    C  CH3   0  -0.765   4.9505  -2.2188  -2.4633
 CEK  C2    C  C     0   0.392   4.0995  -2.8545  -1.3949
 CEK  O3    O  O     0  -0.405   4.3075  -4.0024  -1.0551
 CEK  C4    C  C     0  -0.352   2.9992  -2.0660  -0.7888
 CEK  C5    C  C     0   0.508   3.1285  -0.6464  -0.5870
 CEK  C6    C  CR5   0  -0.482   2.1122  -0.0022   0.3297
 CEK  C7    C  CR5   0   0.544   0.7907  -0.6814   0.3046
 CEK  C8    C  C1    0  -0.535   0.6416  -1.9835   0.0480
 CEK  C9    C  C     0   0.476   1.8090  -2.6920  -0.4134
 CEK  O10   O  O     0  -0.454  -0.2010   0.1926   0.5065
 CEK  C11   C  CR56  0   0.474   0.3136   1.4543   0.3121
 CEK  C12   C  CR56  0  -0.080   1.6762   1.4126   0.0835
 CEK  C13   C  CR6   0  -0.315  -0.4504   2.5948   0.3624
 CEK  C14   C  CR6   0   0.396   0.2545   3.7986   0.1597
 CEK  C15   C  CR16  0  -0.522   1.6220   3.8000  -0.0979
 CEK  C16   C  CR6   0   0.345   2.3510   2.6038  -0.1314
 CEK  C17   C  CH3   0  -0.594   2.7035  -0.1321   1.7665
 CEK  O18   O  O     0  -0.463   4.0653   0.0451  -0.9805
 CEK  O19   O  OH1   0  -0.555   1.6859  -3.9857  -0.6024
 CEK  O20   O  OH1   0  -0.637   3.6604   2.6587  -0.3722
 CEK  O21   O  O2    0  -0.457  -0.4935   4.9058   0.1890
 CEK  C22   C  CH3   0  -0.441   0.1243   6.1609  -0.0368
 CEK  C23   C  C     0   0.519  -1.9123   2.5491   0.6709
 CEK  O24   O  O     0  -0.477  -2.3908   3.0919   1.6542
 CEK  N25   N  NH1   0  -0.604  -2.6225   1.8247  -0.2070
 CEK  C26   C  CH2   0  -0.382  -4.0111   1.4460  -0.0369
 CEK  C27   C  CR6   0   0.069  -4.2065   0.0193  -0.4779
 CEK  C28   C  CR66  0   0.096  -3.6786  -1.0673   0.2808
 CEK  C29   C  CR66  0   0.113  -3.8059  -2.3875  -0.2296
 CEK  C30   C  CR16  0  -0.327  -4.4751  -2.6000  -1.4588
 CEK  C31   C  CR16  0  -0.247  -4.9952  -1.5473  -2.1551
 CEK  C32   C  CR16  0  -0.317  -4.8498  -0.2347  -1.6613
 CEK  C33   C  CR16  0  -0.309  -3.2661  -3.4720   0.5011
 CEK  C34   C  CR16  0  -0.270  -2.6375  -3.2667   1.6988
 CEK  C35   C  CR16  0  -0.247  -2.5280  -1.9618   2.2186
 CEK  C36   C  CR16  0  -0.310  -3.0313  -0.8928   1.5276
 CEK  H1    H  HCH3  0   0.253   5.4437  -3.0020  -3.0366
 CEK  H1A   H  HCH3  0   0.252   4.3720  -1.5872  -3.1351
 CEK  H1B   H  HCH3  0   0.268   5.7209  -1.5917  -2.0139
 CEK  H15   H  HCR6  0   0.294   2.1520   4.7224  -0.2926
 CEK  H17   H  HCH3  0   0.263   3.6191   0.4537   1.8311
 CEK  H17A  H  HCH3  0   0.265   1.9959   0.2577   2.4965
 CEK  H17B  H  HCH3  0   0.265   2.9271  -1.1700   2.0094
 CEK  HO19  H  HOH1  0   0.496   0.8037  -4.2973  -0.3614
 CEK  HO20  H  HOH1  0   0.480   3.9869   1.7530  -0.5746
 CEK  H22   H  HCH3  0   0.236   0.8925   6.3738   0.7096
 CEK  H22A  H  HCH3  0   0.236   0.5685   6.2184  -1.0330
 CEK  H22B  H  HCH3  0   0.267  -0.6621   6.9060   0.0441
 CEK  HN25  H  HNH1  0   0.407  -2.1585   1.4877  -1.0358
 CEK  H26   H  HCH2  0   0.268  -4.2848   1.5898   1.0087
 CEK  H26A  H  HCH2  0   0.272  -4.6606   2.1008  -0.6225
 CEK  H30   H  HCR6  0   0.257  -4.5723  -3.6111  -1.8352
 CEK  H31   H  HCR6  0   0.259  -5.5119  -1.7114  -3.0914
 CEK  H32   H  HCR6  0   0.258  -5.2500   0.5917  -2.2365
 CEK  H33   H  HCR6  0   0.257  -3.3652  -4.4729   0.0985
 CEK  H34   H  HCR6  0   0.259  -2.2285  -4.1033   2.2502
 CEK  H35   H  HCR6  0   0.259  -2.0375  -1.8025   3.1698
 CEK  H36   H  HCR6  0   0.244  -2.9292   0.0954   1.9542
 CEK  H8    H  H     0   0.297  -0.3270  -2.4707   0.0673

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
 CEK  C1   C2    single    1.507  0.020  1.507
 CEK  C2   O3    double    1.215  0.020  1.215
 CEK  C2   C4    single    1.483  0.020  1.483
 CEK  C4   C5    single    1.440  0.020  1.440
 CEK  C4   C9    double    1.396  0.020  1.396
 CEK  C5   C6    single    1.513  0.020  1.513
 CEK  C5   O18   double    1.229  0.020  1.229
 CEK  C6   C7    single    1.486  0.020  1.486
 CEK  C6   C12   single    1.501  0.020  1.501
 CEK  C6   C17   single    1.559  0.020  1.559
 CEK  C7   C8    double    1.335  0.020  1.335
 CEK  C7   O10   single    1.337  0.020  1.337
 CEK  C8   C9    single    1.441  0.020  1.441
 CEK  C9   O19   single    1.313  0.020  1.313
 CEK  O10  C11   single    1.376  0.020  1.376
 CEK  C11  C12   aromatic  1.382  0.020  1.382
 CEK  C11  C13   aromatic  1.374  0.020  1.374
 CEK  C12  C16   aromatic  1.386  0.020  1.386
 CEK  C13  C14   aromatic  1.410  0.020  1.410
 CEK  C13  C23   single    1.495  0.020  1.495
 CEK  C14  C15   aromatic  1.392  0.020  1.392
 CEK  C14  O21   single    1.337  0.020  1.337
 CEK  C15  C16   aromatic  1.401  0.020  1.401
 CEK  C16  O20   single    1.332  0.020  1.332
 CEK  O21  C22   single    1.417  0.020  1.417
 CEK  C23  O24   double    1.221  0.020  1.221
 CEK  C23  N25   single    1.342  0.020  1.342
 CEK  N25  C26   single    1.449  0.020  1.449
 CEK  C26  C27   single    1.506  0.020  1.506
 CEK  C27  C28   aromatic  1.427  0.020  1.427
 CEK  C27  C32   aromatic  1.371  0.020  1.371
 CEK  C28  C29   aromatic  1.421  0.020  1.421
 CEK  C28  C36   aromatic  1.416  0.020  1.416
 CEK  C29  C30   aromatic  1.416  0.020  1.416
 CEK  C29  C33   aromatic  1.415  0.020  1.415
 CEK  C30  C31   aromatic  1.365  0.020  1.365
 CEK  C31  C32   aromatic  1.410  0.020  1.410
 CEK  C33  C34   aromatic  1.368  0.020  1.368
 CEK  C34  C35   aromatic  1.409  0.020  1.409
 CEK  C35  C36   aromatic  1.369  0.020  1.369
 CEK  C1   H1    single    0.970  0.020  1.090
 CEK  C1   H1A   single    0.970  0.020  1.090
 CEK  C1   H1B   single    0.970  0.020  1.090
 CEK  C15  H15   single    0.930  0.020  1.080
 CEK  C17  H17   single    0.970  0.020  1.090
 CEK  C17  H17A  single    0.970  0.020  1.090
 CEK  C17  H17B  single    0.970  0.020  1.090
 CEK  O19  HO19  single    0.850  0.020  0.980
 CEK  O20  HO20  single    0.850  0.020  0.980
 CEK  C22  H22   single    0.970  0.020  1.090
 CEK  C22  H22A  single    0.970  0.020  1.090
 CEK  C22  H22B  single    0.970  0.020  1.090
 CEK  N25  HN25  single    0.860  0.020  1.020
 CEK  C26  H26   single    0.970  0.020  1.090
 CEK  C26  H26A  single    0.970  0.020  1.090
 CEK  C30  H30   single    0.930  0.020  1.080
 CEK  C31  H31   single    0.930  0.020  1.080
 CEK  C32  H32   single    0.930  0.020  1.080
 CEK  C33  H33   single    0.930  0.020  1.080
 CEK  C34  H34   single    0.930  0.020  1.080
 CEK  C35  H35   single    0.930  0.020  1.080
 CEK  C36  H36   single    0.930  0.020  1.080
 CEK  C8   H8    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
 CEK  H1B   C1   H1A   107.23  3.000
 CEK  H1B   C1   H1    108.11  3.000
 CEK  H1A   C1   H1    109.46  3.000
 CEK  H1B   C1   C2    110.46  3.000
 CEK  H1A   C1   C2    112.47  3.000
 CEK  H1    C1   C2    109.01  3.000
 CEK  C4    C2   O3    120.99  3.000
 CEK  C4    C2   C1    118.98  3.000
 CEK  O3    C2   C1    120.02  3.000
 CEK  C9    C4   C5    118.74  3.000
 CEK  C9    C4   C2    120.26  3.000
 CEK  C5    C4   C2    120.99  3.000
 CEK  O18   C5   C6    117.81  3.000
 CEK  O18   C5   C4    125.33  3.000
 CEK  C6    C5   C4    116.40  3.000
 CEK  C17   C6   C12   109.87  3.000
 CEK  C17   C6   C7    108.35  3.000
 CEK  C12   C6   C7     99.77  3.000
 CEK  C17   C6   C5    105.56  3.000
 CEK  C12   C6   C5    119.82  3.000
 CEK  C7    C6   C5    113.12  3.000
 CEK  O10   C7   C8    125.70  3.000
 CEK  O10   C7   C6    110.99  3.000
 CEK  C8    C7   C6    123.24  3.000
 CEK  H8    C8   C9    120.55  3.000
 CEK  H8    C8   C7    122.30  3.000
 CEK  C9    C8   C7    116.77  3.000
 CEK  O19   C9   C8    117.03  3.000
 CEK  O19   C9   C4    118.87  3.000
 CEK  C8    C9   C4    123.79  3.000
 CEK  C11   O10  C7    107.49  3.000
 CEK  C13   C11  C12   125.41  3.000
 CEK  C13   C11  O10   123.22  3.000
 CEK  C12   C11  O10   111.36  3.000
 CEK  C16   C12  C11   118.67  3.000
 CEK  C16   C12  C6    133.97  3.000
 CEK  C11   C12  C6    106.72  3.000
 CEK  C23   C13  C14   123.02  3.000
 CEK  C23   C13  C11   121.74  3.000
 CEK  C14   C13  C11   115.18  3.000
 CEK  O21   C14  C15   123.59  3.000
 CEK  O21   C14  C13   115.11  3.000
 CEK  C15   C14  C13   121.26  3.000
 CEK  H15   C15  C16   117.96  3.000
 CEK  H15   C15  C14   121.05  3.000
 CEK  C16   C15  C14   120.99  3.000
 CEK  O20   C16  C15   118.71  3.000
 CEK  O20   C16  C12   122.82  3.000
 CEK  C15   C16  C12   118.47  3.000
 CEK  H17B  C17  H17A  108.96  3.000
 CEK  H17B  C17  H17   109.07  3.000
 CEK  H17A  C17  H17   108.30  3.000
 CEK  H17B  C17  C6    111.27  3.000
 CEK  H17A  C17  C6    109.98  3.000
 CEK  H17   C17  C6    109.20  3.000
 CEK  HO19  O19  C9    111.55  3.000
 CEK  HO20  O20  C16   108.99  3.000
 CEK  C22   O21  C14   119.10  3.000
 CEK  H22B  C22  H22A  109.03  3.000
 CEK  H22B  C22  H22   108.95  3.000
 CEK  H22A  C22  H22   109.09  3.000
 CEK  H22B  C22  O21   106.26  3.000
 CEK  H22A  C22  O21   111.67  3.000
 CEK  H22   C22  O21   111.75  3.000
 CEK  N25   C23  O24   124.03  3.000
 CEK  N25   C23  C13   113.52  3.000
 CEK  O24   C23  C13   122.41  3.000
 CEK  HN25  N25  C26   116.76  3.000
 CEK  HN25  N25  C23   118.36  3.000
 CEK  C26   N25  C23   124.85  3.000
 CEK  H26A  C26  H26   106.60  3.000
 CEK  H26A  C26  C27   109.49  3.000
 CEK  H26   C26  C27   111.91  3.000
 CEK  H26A  C26  N25   110.50  3.000
 CEK  H26   C26  N25   108.58  3.000
 CEK  C27   C26  N25   109.72  3.000
 CEK  C32   C27  C28   119.45  3.000
 CEK  C32   C27  C26   119.29  3.000
 CEK  C28   C27  C26   121.19  3.000
 CEK  C36   C28  C29   118.15  3.000
 CEK  C36   C28  C27   122.94  3.000
 CEK  C29   C28  C27   118.91  3.000
 CEK  C33   C29  C30   120.92  3.000
 CEK  C33   C29  C28   119.50  3.000
 CEK  C30   C29  C28   119.58  3.000
 CEK  H30   C30  C31   120.55  3.000
 CEK  H30   C30  C29   118.96  3.000
 CEK  C31   C30  C29   120.48  3.000
 CEK  H31   C31  C32   119.57  3.000
 CEK  H31   C31  C30   120.43  3.000
 CEK  C32   C31  C30   120.00  3.000
 CEK  H32   C32  C31   119.08  3.000
 CEK  H32   C32  C27   119.36  3.000
 CEK  C31   C32  C27   121.55  3.000
 CEK  H33   C33  C34   120.40  3.000
 CEK  H33   C33  C29   118.77  3.000
 CEK  C34   C33  C29   120.83  3.000
 CEK  H34   C34  C35   119.91  3.000
 CEK  H34   C34  C33   120.24  3.000
 CEK  C35   C34  C33   119.85  3.000
 CEK  H35   C35  C36   119.70  3.000
 CEK  H35   C35  C34   119.73  3.000
 CEK  C36   C35  C34   120.57  3.000
 CEK  H36   C36  C35   118.68  3.000
 CEK  H36   C36  C28   120.23  3.000
 CEK  C35   C36  C28   121.10  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
 CEK  CONST_01  C15   C16  C12  C11     0.00   0.0  0
 CEK  CONST_02  C15   C14  C13  C11     0.00   0.0  0
 CEK  CONST_03  C14   C13  C11  C12     0.00   0.0  0
 CEK  CONST_04  C14   C15  C16  C12     0.00   0.0  0
 CEK  CONST_05  C16   C12  C11  C13     0.00   0.0  0
 CEK  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 CEK  CONST_07  C30   C29  C28  C27     0.00   0.0  0
 CEK  CONST_08  C33   C29  C28  C27   180.00   0.0  0
 CEK  CONST_09  C35   C36  C28  C27   180.00   0.0  0
 CEK  CONST_10  C30   C31  C32  C27     0.00   0.0  0
 CEK  CONST_11  C31   C32  C27  C28     0.00   0.0  0
 CEK  CONST_12  C31   C30  C29  C28     0.00   0.0  0
 CEK  CONST_13  C34   C33  C29  C28     0.00   0.0  0
 CEK  CONST_14  C34   C35  C36  C28     0.00   0.0  0
 CEK  CONST_15  C32   C27  C28  C29     0.00   0.0  0
 CEK  CONST_16  C35   C36  C28  C29     0.00   0.0  0
 CEK  CONST_17  C32   C31  C30  C29     0.00   0.0  0
 CEK  CONST_18  C35   C34  C33  C29     0.00   0.0  0
 CEK  CONST_19  C36   C28  C29  C30   180.00   0.0  0
 CEK  CONST_20  C34   C33  C29  C30   180.00   0.0  0
 CEK  CONST_21  C33   C29  C30  C31   180.00   0.0  0
 CEK  CONST_22  C36   C28  C27  C32   180.00   0.0  0
 CEK  CONST_23  C36   C28  C29  C33     0.00   0.0  0
 CEK  CONST_24  C36   C35  C34  C33     0.00   0.0  0
 CEK  CONST_25  O20   C16  C12  C6      0.00   0.0  0
 CEK  CONST_26  C23   C13  C11  O10     0.00   0.0  0
 CEK  CONST_27  O20   C16  C12  C11   180.00   0.0  0
 CEK  CONST_28  O21   C14  C13  C11   180.00   0.0  0
 CEK  CONST_29  C23   C13  C11  C12   180.00   0.0  0
 CEK  CONST_30  O20   C16  C15  C14   180.00   0.0  0
 CEK  CONST_31  C23   C13  C14  C15   180.00   0.0  0
 CEK  CONST_32  O21   C14  C15  C16   180.00   0.0  0
 CEK  CONST_33  C29   C28  C27  C26   180.00   0.0  0
 CEK  CONST_34  C36   C28  C27  C26     0.00   0.0  0
 CEK  CONST_35  C31   C32  C27  C26   180.00   0.0  0
 CEK  CONST_36  H15   C15  C16  C12   180.00   0.0  0
 CEK  CONST_37  H36   C36  C28  C27     0.00   0.0  0
 CEK  CONST_38  H31   C31  C32  C27   180.00   0.0  0
 CEK  CONST_39  H32   C32  C27  C28   180.00   0.0  0
 CEK  CONST_40  H30   C30  C29  C28   180.00   0.0  0
 CEK  CONST_41  H33   C33  C29  C28   180.00   0.0  0
 CEK  CONST_42  H35   C35  C36  C28   180.00   0.0  0
 CEK  CONST_43  H34   C34  C33  C29   180.00   0.0  0
 CEK  CONST_44  C26   N25  C23  C13   180.00   0.0  0
 CEK  CONST_45  HN25  N25  C23  C13     0.00   0.0  0
 CEK  CONST_46  C26   N25  C23  O24     0.00   0.0  0
 CEK  Var_01    C7    C8   C9   C4     -9.88  30.0  1
 CEK  Var_02    C8    C9   C4   C5      6.30  30.0  1
 CEK  Var_03    C9    C4   C5   C6     15.02  30.0  1
 CEK  Var_04    C9    C8   C7   C6     -9.27  30.0  1
 CEK  Var_05    C12   C11  O10  C7     -4.73  30.0  1
 CEK  Var_06    C5    C4   C2   C1    -34.66  30.0  2
 CEK  Var_07    O24   C23  C13  C11   117.79  30.0  2
 CEK  Var_08    C28   C27  C26  N25    70.57  30.0  2
 CEK  Var_09    C27   C26  N25  C23  -138.54  30.0  3
 CEK  Var_10    H1    C1   C2   C4   -159.73  30.0  3
 CEK  Var_11    H22   C22  O21  C14   -60.68  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
 CEK  chir_01  C6  C7  C12  C5  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
 CEK  plan-1  C26   0.020
 CEK  plan-1  C27   0.020
 CEK  plan-1  C28   0.020
 CEK  plan-1  C29   0.020
 CEK  plan-1  C30   0.020
 CEK  plan-1  C31   0.020
 CEK  plan-1  C32   0.020
 CEK  plan-1  C33   0.020
 CEK  plan-1  C34   0.020
 CEK  plan-1  C35   0.020
 CEK  plan-1  C36   0.020
 CEK  plan-1  H30   0.020
 CEK  plan-1  H31   0.020
 CEK  plan-1  H32   0.020
 CEK  plan-1  H33   0.020
 CEK  plan-1  H34   0.020
 CEK  plan-1  H35   0.020
 CEK  plan-1  H36   0.020
 CEK  plan-2  C6    0.020
 CEK  plan-2  O10   0.020
 CEK  plan-2  C11   0.020
 CEK  plan-2  C12   0.020
 CEK  plan-2  C13   0.020
 CEK  plan-2  C14   0.020
 CEK  plan-2  C15   0.020
 CEK  plan-2  C16   0.020
 CEK  plan-2  O20   0.020
 CEK  plan-2  O21   0.020
 CEK  plan-2  C23   0.020
 CEK  plan-2  H15   0.020
 CEK  plan-3  C13   0.020
 CEK  plan-3  C23   0.020
 CEK  plan-3  O24   0.020
 CEK  plan-3  N25   0.020
 CEK  plan-3  C26   0.020
 CEK  plan-3  HN25  0.020
 CEK  plan-4  C1    0.020
 CEK  plan-4  C2    0.020
 CEK  plan-4  O3    0.020
 CEK  plan-4  C4    0.020
 CEK  plan-5  C4    0.020
 CEK  plan-5  C5    0.020
 CEK  plan-5  C6    0.020
 CEK  plan-5  O18   0.020

