# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 12:35:09 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (5R,5aR,8aR,9R)-9-hydroxy-5-(3,4,5-trimethoxyphenyl)-5,8,8a,9-tetrahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5aH)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1OC)[C@H]2[C@@H]3[C@H](COC3=O)[C@@H](O)c4cc5OCOc5cc24
#
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
 POD  POD  (5R,5aR,8aR,9R)-9-hydroxy-5-(3,4,5-trimethoxyphenyl)-5,8,8a,9-tetrahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-6(5aH)-one  ligand  52  30  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_POD
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
 POD  O5    O  O     0  -0.420  -2.8969  -1.6985   2.0502
 POD  C13   C  C     0   0.618  -2.9873  -0.8421   1.2152
 POD  O4    O  O2    0  -0.448  -3.8453   0.1758   1.3429
 POD  C10   C  CH1   0  -0.462  -2.2838  -0.7167  -0.1103
 POD  C9    C  CH1   0  -0.354  -2.4575   0.7481  -0.4410
 POD  C12   C  CH2   0  -0.141  -3.8068   1.0422   0.1912
 POD  C11   C  CH1   0  -0.378  -0.8382  -1.1668  -0.2732
 POD  C5    C  CR6   0   0.101  -0.3942  -0.7593  -1.6675
 POD  C6    C  CR6   0   0.023  -1.0451   0.2249  -2.4139
 POD  C8    C  CH1   0   0.016  -2.3056   0.9407  -1.9275
 POD  O3    O  OH1   0  -0.660  -2.2821   2.3209  -2.2022
 POD  C7    C  CR16  0  -0.397  -0.5625   0.5745  -3.6903
 POD  C2    C  CR56  0   0.308   0.5465  -0.0716  -4.1600
 POD  C3    C  CR56  0   0.307   1.1939  -1.0454  -3.4148
 POD  C4    C  CR16  0  -0.373   0.7476  -1.4065  -2.1752
 POD  O2    O  O     0  -0.487   1.2006   0.1036  -5.3338
 POD  C1    C  CH2   0   0.068   2.1736  -0.9308  -5.4036
 POD  O1    O  O     0  -0.487   2.2659  -1.5024  -4.1047
 POD  C14   C  CR6   0   0.176   0.0889  -0.6245   0.8000
 POD  C15   C  CR16  0  -0.463   0.2829  -1.3675   1.9579
 POD  C16   C  CR6   0   0.347   1.1026  -0.8815   2.9736
 POD  O6    O  O2    0  -0.465   1.3384  -1.5263   4.1299
 POD  C20   C  CH3   0  -0.438   0.6877  -2.7614   4.3533
 POD  C17   C  CR6   0   0.163   1.7500   0.3471   2.8234
 POD  O7    O  O2    0  -0.481   2.5804   0.8065   3.7964
 POD  C21   C  CH3   0  -0.408   1.9388   1.6111   4.7770
 POD  C18   C  CR6   0   0.351   1.5578   1.0876   1.6553
 POD  C19   C  CR16  0  -0.470   0.7342   0.5971   0.6444
 POD  O8    O  O2    0  -0.463   2.2190   2.2573   1.5911
 POD  C22   C  CH3   0  -0.439   2.0665   3.0523   0.4329
 POD  H10   H  HCH1  0   0.319  -2.8925  -1.3107  -0.8102
 POD  H9    H  HCH1  0   0.286  -1.6890   1.3314   0.0792
 POD  H121  H  HCH2  0   0.265  -3.9276   2.0660   0.5366
 POD  H122  H  HCH2  0   0.244  -4.6392   0.7880  -0.4712
 POD  H11   H  HCH1  0   0.285  -0.8076  -2.2585  -0.2127
 POD  H8    H  HCH1  0   0.234  -3.1673   0.4712  -2.4242
 POD  HO3   H  HOH1  0   0.462  -2.6035   2.4723  -3.0953
 POD  H7    H  HCR6  0   0.260  -1.0488   1.3300  -4.2936
 POD  H4    H  HCR6  0   0.268   1.2562  -2.1599  -1.5867
 POD  H11A  H  HCH2  0   0.234   1.8545  -1.6928  -6.1225
 POD  H12   H  HCH2  0   0.247   3.1377  -0.5128  -5.6921
 POD  H15   H  HCR6  0   0.273  -0.2161  -2.3204   2.0612
 POD  H201  H  HCH3  0   0.261   0.9894  -3.0936   5.3435
 POD  H202  H  HCH3  0   0.228  -0.4006  -2.6599   4.3323
 POD  H203  H  HCH3  0   0.228   0.9854  -3.5183   3.6231
 POD  H211  H  HCH3  0   0.236   2.7024   1.9204   5.4889
 POD  H212  H  HCH3  0   0.221   1.4886   2.5044   4.3373
 POD  H213  H  HCH3  0   0.221   1.1659   1.0558   5.3139
 POD  H19   H  HCR6  0   0.266   0.6061   1.1554  -0.2732
 POD  H221  H  HCH3  0   0.263   2.6800   3.9370   0.5834
 POD  H222  H  HCH3  0   0.227   2.4102   2.5357  -0.4670
 POD  H223  H  HCH3  0   0.226   1.0297   3.3667   0.2855

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
 POD  O5   C13   double    1.200  0.020  1.200
 POD  C13  O4    single    1.337  0.020  1.337
 POD  C13  C10   single    1.506  0.020  1.506
 POD  O4   C12   single    1.442  0.020  1.442
 POD  C10  C9    single    1.512  0.020  1.512
 POD  C10  C11   single    1.523  0.020  1.523
 POD  C10  H10   single    0.970  0.020  1.090
 POD  C9   C12   single    1.519  0.020  1.519
 POD  C9   C8    single    1.507  0.020  1.507
 POD  C9   H9    single    0.970  0.020  1.090
 POD  C12  H121  single    0.970  0.020  1.090
 POD  C12  H122  single    0.970  0.020  1.090
 POD  C11  C5    single    1.519  0.020  1.519
 POD  C11  C14   single    1.518  0.020  1.518
 POD  C11  H11   single    0.970  0.020  1.090
 POD  C5   C6    aromatic  1.396  0.020  1.396
 POD  C5   C4    aromatic  1.407  0.020  1.407
 POD  C6   C8    single    1.529  0.020  1.529
 POD  C6   C7    aromatic  1.409  0.020  1.409
 POD  C8   O3    single    1.408  0.020  1.408
 POD  C8   H8    single    0.970  0.020  1.090
 POD  O3   HO3   single    0.850  0.020  0.980
 POD  C7   C2    aromatic  1.367  0.020  1.367
 POD  C7   H7    single    0.930  0.020  1.080
 POD  C2   C3    aromatic  1.387  0.020  1.387
 POD  C2   O2    single    1.355  0.020  1.355
 POD  C3   C4    aromatic  1.366  0.020  1.366
 POD  C3   O1    single    1.354  0.020  1.354
 POD  C4   H4    single    0.930  0.020  1.080
 POD  O2   C1    single    1.422  0.020  1.422
 POD  C1   O1    single    1.422  0.020  1.422
 POD  C1   H11A  single    0.970  0.020  1.090
 POD  C1   H12   single    0.970  0.020  1.090
 POD  C14  C15   aromatic  1.389  0.020  1.389
 POD  C14  C19   aromatic  1.390  0.020  1.390
 POD  C15  C16   aromatic  1.393  0.020  1.393
 POD  C15  H15   single    0.930  0.020  1.080
 POD  C16  O6    single    1.345  0.020  1.345
 POD  C16  C17   aromatic  1.397  0.020  1.397
 POD  O6   C20   single    1.414  0.020  1.414
 POD  C20  H201  single    0.970  0.020  1.090
 POD  C20  H202  single    0.970  0.020  1.090
 POD  C20  H203  single    0.970  0.020  1.090
 POD  C17  O7    single    1.359  0.020  1.359
 POD  C17  C18   aromatic  1.396  0.020  1.396
 POD  O7   C21   single    1.421  0.020  1.421
 POD  C21  H211  single    0.970  0.020  1.090
 POD  C21  H212  single    0.970  0.020  1.090
 POD  C21  H213  single    0.970  0.020  1.090
 POD  C18  C19   aromatic  1.393  0.020  1.393
 POD  C18  O8    single    1.345  0.020  1.345
 POD  C19  H19   single    0.930  0.020  1.080
 POD  O8   C22   single    1.413  0.020  1.413
 POD  C22  H221  single    0.970  0.020  1.090
 POD  C22  H222  single    0.970  0.020  1.090
 POD  C22  H223  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
 POD  C10   C13  O4    108.69  3.000
 POD  C10   C13  O5    129.57  3.000
 POD  O4    C13  O5    121.68  3.000
 POD  C12   O4   C13   111.34  3.000
 POD  H10   C10  C11   107.29  3.000
 POD  H10   C10  C9    108.66  3.000
 POD  C11   C10  C9    111.85  3.000
 POD  H10   C10  C13   104.85  3.000
 POD  C11   C10  C13   120.87  3.000
 POD  C9    C10  C13   102.68  3.000
 POD  H9    C9   C8    109.24  3.000
 POD  H9    C9   C12   108.81  3.000
 POD  C8    C9   C12   118.40  3.000
 POD  H9    C9   C10   109.34  3.000
 POD  C8    C9   C10   109.15  3.000
 POD  C12   C9   C10   101.46  3.000
 POD  H122  C12  H121  109.06  3.000
 POD  H122  C12  C9    112.27  3.000
 POD  H121  C12  C9    114.41  3.000
 POD  H122  C12  O4    108.89  3.000
 POD  H121  C12  O4    108.01  3.000
 POD  C9    C12  O4    103.88  3.000
 POD  H11   C11  C14   107.48  3.000
 POD  H11   C11  C5    108.08  3.000
 POD  C14   C11  C5    112.00  3.000
 POD  H11   C11  C10   108.40  3.000
 POD  C14   C11  C10   113.48  3.000
 POD  C5    C11  C10   107.24  3.000
 POD  C4    C5   C6    120.63  3.000
 POD  C4    C5   C11   116.42  3.000
 POD  C6    C5   C11   122.93  3.000
 POD  C7    C6   C8    117.03  3.000
 POD  C7    C6   C5    119.98  3.000
 POD  C8    C6   C5    122.97  3.000
 POD  H8    C8   O3    110.09  3.000
 POD  H8    C8   C6    107.60  3.000
 POD  O3    C8   C6    112.53  3.000
 POD  H8    C8   C9    108.18  3.000
 POD  O3    C8   C9    108.64  3.000
 POD  C6    C8   C9    109.71  3.000
 POD  HO3   O3   C8    109.28  3.000
 POD  H7    C7   C2    120.20  3.000
 POD  H7    C7   C6    121.63  3.000
 POD  C2    C7   C6    118.17  3.000
 POD  O2    C2   C3    109.32  3.000
 POD  O2    C2   C7    128.92  3.000
 POD  C3    C2   C7    121.75  3.000
 POD  O1    C3   C4    129.17  3.000
 POD  O1    C3   C2    109.44  3.000
 POD  C4    C3   C2    121.38  3.000
 POD  H4    C4   C3    121.57  3.000
 POD  H4    C4   C5    120.33  3.000
 POD  C3    C4   C5    118.09  3.000
 POD  C1    O2   C2    106.19  3.000
 POD  H12   C1   H11A  110.54  3.000
 POD  H12   C1   O1    109.79  3.000
 POD  H11A  C1   O1    109.80  3.000
 POD  H12   C1   O2    109.84  3.000
 POD  H11A  C1   O2    109.82  3.000
 POD  O1    C1   O2    106.98  3.000
 POD  C1    O1   C3    106.16  3.000
 POD  C19   C14  C15   119.89  3.000
 POD  C19   C14  C11   121.21  3.000
 POD  C15   C14  C11   118.90  3.000
 POD  H15   C15  C16   120.65  3.000
 POD  H15   C15  C14   119.12  3.000
 POD  C16   C15  C14   120.22  3.000
 POD  C17   C16  O6    115.65  3.000
 POD  C17   C16  C15   120.09  3.000
 POD  O6    C16  C15   124.26  3.000
 POD  C20   O6   C16   118.30  3.000
 POD  H203  C20  H202  108.82  3.000
 POD  H203  C20  H201  108.75  3.000
 POD  H202  C20  H201  108.79  3.000
 POD  H203  C20  O6    111.96  3.000
 POD  H202  C20  O6    111.97  3.000
 POD  H201  C20  O6    106.45  3.000
 POD  C18   C17  O7    120.24  3.000
 POD  C18   C17  C16   119.51  3.000
 POD  O7    C17  C16   120.23  3.000
 POD  C21   O7   C17   114.17  3.000
 POD  H213  C21  H212  108.76  3.000
 POD  H213  C21  H211  108.62  3.000
 POD  H212  C21  H211  108.65  3.000
 POD  H213  C21  O7    111.75  3.000
 POD  H212  C21  O7    111.78  3.000
 POD  H211  C21  O7    107.17  3.000
 POD  O8    C18  C19   124.20  3.000
 POD  O8    C18  C17   115.69  3.000
 POD  C19   C18  C17   120.11  3.000
 POD  H19   C19  C18   120.25  3.000
 POD  H19   C19  C14   119.57  3.000
 POD  C18   C19  C14   120.17  3.000
 POD  C22   O8   C18   118.38  3.000
 POD  H223  C22  H222  108.85  3.000
 POD  H223  C22  H221  108.66  3.000
 POD  H222  C22  H221  108.73  3.000
 POD  H223  C22  O8    112.00  3.000
 POD  H222  C22  O8    112.02  3.000
 POD  H221  C22  O8    106.46  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
 POD  CONST_01  C2    C7   C6   C5      0.00   0.0  0
 POD  CONST_02  C2    C3   C4   C5      0.00   0.0  0
 POD  CONST_03  C3    C4   C5   C6      0.00   0.0  0
 POD  CONST_04  C3    C2   C7   C6      0.00   0.0  0
 POD  CONST_05  C4    C5   C6   C7      0.00   0.0  0
 POD  CONST_06  C4    C3   C2   C7      0.00   0.0  0
 POD  CONST_07  C17   C16  C15  C14     0.00   0.0  0
 POD  CONST_08  C17   C18  C19  C14     0.00   0.0  0
 POD  CONST_09  C18   C19  C14  C15     0.00   0.0  0
 POD  CONST_10  C18   C17  C16  C15     0.00   0.0  0
 POD  CONST_11  C19   C14  C15  C16     0.00   0.0  0
 POD  CONST_12  C19   C18  C17  C16     0.00   0.0  0
 POD  CONST_13  C16   C15  C14  C11   180.00   0.0  0
 POD  CONST_14  C18   C19  C14  C11   180.00   0.0  0
 POD  CONST_15  O6    C16  C15  C14   180.00   0.0  0
 POD  CONST_16  O8    C18  C19  C14   180.00   0.0  0
 POD  CONST_17  O7    C17  C16  C15   180.00   0.0  0
 POD  CONST_18  O8    C18  C17  C16   180.00   0.0  0
 POD  CONST_19  C18   C17  C16  O6    180.00   0.0  0
 POD  CONST_20  C19   C18  C17  O7    180.00   0.0  0
 POD  CONST_21  H4    C4   C5   C11     0.00   0.0  0
 POD  CONST_22  H15   C15  C14  C11     0.00   0.0  0
 POD  CONST_23  H19   C19  C14  C11     0.00   0.0  0
 POD  CONST_24  H7    C7   C6   C5    180.00   0.0  0
 POD  Var_01    C9    C12  O4   C13   -20.96  30.0  1
 POD  Var_02    O1    C1   O2   C2    -13.49  30.0  1
 POD  Var_03    O2    C1   O1   C3     13.45  30.0  1
 POD  Var_04    C17   C16  O6   C20   178.61  30.0  2
 POD  Var_05    C18   C17  O7   C21    90.63  30.0  2
 POD  Var_06    H201  C20  O6   C16  -178.39  30.0  3
 POD  Var_07    H211  C21  O7   C17  -179.59  30.0  3
 POD  Var_08    H221  C22  O8   C18  -179.74  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
 POD  chir_01  C10  C13  C9   C11  negativ
 POD  chir_02  C9   C8   C12  C10  negativ
 POD  chir_03  C11  C10  C5   C14  negativ
 POD  chir_04  C8   O3   C6   C9   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
 POD  plan-1  C11  0.020
 POD  plan-1  C14  0.020
 POD  plan-1  C15  0.020
 POD  plan-1  C16  0.020
 POD  plan-1  O6   0.020
 POD  plan-1  C17  0.020
 POD  plan-1  O7   0.020
 POD  plan-1  C18  0.020
 POD  plan-1  C19  0.020
 POD  plan-1  O8   0.020
 POD  plan-1  H15  0.020
 POD  plan-1  H19  0.020
 POD  plan-2  C11  0.020
 POD  plan-2  C5   0.020
 POD  plan-2  C6   0.020
 POD  plan-2  C8   0.020
 POD  plan-2  C7   0.020
 POD  plan-2  C2   0.020
 POD  plan-2  C3   0.020
 POD  plan-2  C4   0.020
 POD  plan-2  O2   0.020
 POD  plan-2  O1   0.020
 POD  plan-2  H7   0.020
 POD  plan-2  H4   0.020
 POD  plan-3  O5   0.020
 POD  plan-3  C13  0.020
 POD  plan-3  O4   0.020
 POD  plan-3  C10  0.020

