# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:58:14 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+]1(C)CCc2cc3OCOc3cc2[C@H]1[C@@H]4OC(=O)c5c6OCOc6ccc45
#
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
 J94  J94  (5S)-6,6-dimethyl-5-[(6R)-8-oxo-6,8-dihydrofuro[3,4-e][1,3]benzodioxol-6-yl]-5,6,7,8-tetrahydro[1,3]dioxolo[4,5-g]isoquinolin-6-ium  ligand  48  28  .  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_J94
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
 J94  C01  C  CH3   0  -0.565  -2.7728   3.3214   0.5978
 J94  N02  N  NT    1  -0.414  -2.8129   1.9247   0.0733
 J94  C03  C  CH3   0  -0.575  -3.0672   1.9717  -1.3990
 J94  C04  C  CH2   0  -0.346  -3.9604   1.2339   0.7557
 J94  C05  C  CH2   0  -0.551  -4.1786  -0.1434   0.1920
 J94  C06  C  CR6   0   0.055  -2.9066  -0.9361   0.2145
 J94  C07  C  CR6   0   0.099  -1.6757  -0.3116   0.3751
 J94  C08  C  CR16  0  -0.381  -0.5118  -1.0890   0.5517
 J94  C09  C  CR56  0   0.314  -0.6309  -2.4468   0.4729
 J94  O10  O  O     0  -0.482   0.3290  -3.3868   0.6182
 J94  C11  C  CH2   0   0.068  -0.2815  -4.6361   0.3165
 J94  O12  O  O     0  -0.481  -1.6836  -4.4033   0.2326
 J94  C13  C  CR56  0   0.317  -1.8519  -3.0648   0.2463
 J94  C14  C  CR16  0  -0.380  -3.0018  -2.3370   0.1321
 J94  C15  C  CH1   0  -0.173  -1.5251   1.1991   0.4282
 J94  C16  C  CR15  0  -0.030  -0.3594   1.7424  -0.4230
 J94  O17  O  O     0  -0.458  -0.2457   1.0484  -1.6608
 J94  C18  C  CR5   0   0.571   1.0134   0.6168  -1.8924
 J94  O19  O  O     0  -0.393   1.3112   0.0425  -2.8998
 J94  C20  C  CR56  0  -0.191   1.8193   0.9846  -0.7323
 J94  C21  C  CR56  0   0.303   3.1407   0.7842  -0.4245
 J94  O22  O  O     0  -0.457   4.1145   0.1918  -1.1202
 J94  C23  C  CH2   0   0.066   5.3140   0.3481  -0.3548
 J94  O24  O  O     0  -0.477   4.9340   0.9137   0.8924
 J94  C25  C  CR56  0   0.304   3.6243   1.2297   0.7999
 J94  C26  C  CR16  0  -0.329   2.8308   1.8654   1.7248
 J94  C27  C  CR16  0  -0.347   1.4773   2.0743   1.4097
 J94  C28  C  CR56  0   0.050   1.0033   1.6296   0.1990
 J94  H1   H  HCH3  0   0.305  -1.9562   3.8792   0.1498
 J94  H2   H  HCH3  0   0.306  -3.7088   3.8089   0.3408
 J94  H3   H  HCH3  0   0.304  -2.6560   3.2973   1.6780
 J94  H4   H  HCH3  0   0.309  -2.3820   2.6689  -1.8703
 J94  H5   H  HCH3  0   0.308  -2.9477   0.9863  -1.8360
 J94  H6   H  HCH3  0   0.310  -4.0830   2.3242  -1.5548
 J94  H7   H  HCH2  0   0.318  -3.7178   1.1903   1.8180
 J94  H8   H  HCH2  0   0.305  -4.9255  -0.6298   0.8214
 J94  H9   H  HCR6  0   0.289   0.4477  -0.6505   0.7797
 J94  H10  H  HCH2  0   0.241   0.0896  -5.0088  -0.6425
 J94  H11  H  HCH2  0   0.250  -0.0736  -5.3507   1.1130
 J94  H12  H  HCR6  0   0.279  -3.9657  -2.8124   0.0036
 J94  H13  H  HCH1  0   0.341  -1.3284   1.5014   1.4612
 J94  H14  H  HCR5  0   0.329  -0.5354   2.7959  -0.6558
 J94  H15  H  HCH2  0   0.258   5.7734  -0.6277  -0.1980
 J94  H16  H  HCH2  0   0.253   5.9949   1.0204  -0.8818
 J94  H17  H  HCR6  0   0.296   3.2344   2.2000   2.6705
 J94  H18  H  HCR6  0   0.272   0.8393   2.5789   2.1232
 J94  H19  H  HCH2  0   0.319  -4.8367   1.8673   0.6293
 J94  H20  H  HCH2  0   0.287  -4.6137  -0.1012  -0.8093

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
 J94  O12  C11  single    1.424  0.020  1.424
 J94  O12  C13  single    1.349  0.020  1.349
 J94  C11  O10  single    1.423  0.020  1.423
 J94  C14  C13  aromatic  1.366  0.020  1.366
 J94  C14  C06  aromatic  1.407  0.020  1.407
 J94  C13  C09  aromatic  1.387  0.020  1.387
 J94  C05  C06  single    1.499  0.020  1.499
 J94  C05  C04  single    1.504  0.020  1.504
 J94  O10  C09  single    1.351  0.020  1.351
 J94  C06  C07  aromatic  1.390  0.020  1.390
 J94  C09  C08  aromatic  1.365  0.020  1.365
 J94  C04  N02  single    1.503  0.020  1.503
 J94  C07  C08  aromatic  1.411  0.020  1.411
 J94  C07  C15  single    1.519  0.020  1.519
 J94  O19  C18  double    1.197  0.020  1.197
 J94  C01  N02  single    1.492  0.020  1.492
 J94  N02  C15  single    1.520  0.020  1.520
 J94  N02  C03  single    1.495  0.020  1.495
 J94  O17  C18  single    1.351  0.020  1.351
 J94  O17  C16  single    1.424  0.020  1.424
 J94  C18  C20  single    1.460  0.020  1.460
 J94  C15  C16  single    1.542  0.020  1.542
 J94  C16  C28  single    1.502  0.020  1.502
 J94  C20  C21  aromatic  1.372  0.020  1.372
 J94  C20  C28  aromatic  1.396  0.020  1.396
 J94  O22  C21  single    1.335  0.020  1.335
 J94  O22  C23  single    1.431  0.020  1.431
 J94  C21  C25  aromatic  1.390  0.020  1.390
 J94  C28  C27  aromatic  1.374  0.020  1.374
 J94  C23  O24  single    1.421  0.020  1.421
 J94  C25  O24  single    1.350  0.020  1.350
 J94  C25  C26  aromatic  1.375  0.020  1.375
 J94  C27  C26  aromatic  1.405  0.020  1.405
 J94  C01  H1   single    0.970  0.020  1.090
 J94  C01  H2   single    0.970  0.020  1.090
 J94  C01  H3   single    0.970  0.020  1.090
 J94  C03  H4   single    0.970  0.020  1.090
 J94  C03  H5   single    0.970  0.020  1.090
 J94  C03  H6   single    0.970  0.020  1.090
 J94  C04  H7   single    0.970  0.020  1.090
 J94  C05  H8   single    0.970  0.020  1.090
 J94  C08  H9   single    0.930  0.020  1.080
 J94  C11  H10  single    0.970  0.020  1.090
 J94  C11  H11  single    0.970  0.020  1.090
 J94  C14  H12  single    0.930  0.020  1.080
 J94  C15  H13  single    0.970  0.020  1.090
 J94  C16  H14  single    0.970  0.020  1.090
 J94  C23  H15  single    0.970  0.020  1.090
 J94  C23  H16  single    0.970  0.020  1.090
 J94  C26  H17  single    0.930  0.020  1.080
 J94  C27  H18  single    0.930  0.020  1.080
 J94  C04  H19  single    0.970  0.020  1.090
 J94  C05  H20  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
 J94  H3   C01  H2   109.74  3.000
 J94  H3   C01  H1   109.92  3.000
 J94  H2   C01  H1   108.66  3.000
 J94  H3   C01  N02  109.36  3.000
 J94  H2   C01  N02  108.28  3.000
 J94  H1   C01  N02  110.86  3.000
 J94  C15  N02  C04  108.74  3.000
 J94  C15  N02  C03  112.89  3.000
 J94  C04  N02  C03  109.38  3.000
 J94  C03  N02  C01  108.74  3.000
 J94  C15  N02  C01  109.99  3.000
 J94  C04  N02  C01  106.92  3.000
 J94  H6   C03  H5   109.87  3.000
 J94  H6   C03  H4   108.64  3.000
 J94  H5   C03  H4   109.83  3.000
 J94  H6   C03  N02  108.09  3.000
 J94  H5   C03  N02  110.46  3.000
 J94  H4   C03  N02  109.91  3.000
 J94  H19  C04  H7   108.39  3.000
 J94  H19  C04  C05  111.87  3.000
 J94  H7   C04  C05  111.15  3.000
 J94  H19  C04  N02  107.12  3.000
 J94  H7   C04  N02  106.90  3.000
 J94  C05  C04  N02  111.19  3.000
 J94  H20  C05  H8   105.86  3.000
 J94  H20  C05  C06  111.85  3.000
 J94  H8   C05  C06  109.66  3.000
 J94  H20  C05  C04  111.47  3.000
 J94  H8   C05  C04  106.94  3.000
 J94  C06  C05  C04  110.82  3.000
 J94  C14  C06  C07  120.95  3.000
 J94  C07  C06  C05  121.05  3.000
 J94  C14  C06  C05  117.93  3.000
 J94  C15  C07  C08  117.51  3.000
 J94  C15  C07  C06  122.60  3.000
 J94  C08  C07  C06  119.84  3.000
 J94  H9   C08  C09  119.59  3.000
 J94  H9   C08  C07  122.41  3.000
 J94  C09  C08  C07  117.96  3.000
 J94  C13  C09  O10  109.45  3.000
 J94  O10  C09  C08  128.58  3.000
 J94  C13  C09  C08  121.96  3.000
 J94  C11  O10  C09  106.45  3.000
 J94  H11  C11  H10  110.64  3.000
 J94  H11  C11  O12  109.76  3.000
 J94  H10  C11  O12  109.77  3.000
 J94  H11  C11  O10  109.80  3.000
 J94  H10  C11  O10  109.85  3.000
 J94  O12  C11  O10  106.95  3.000
 J94  C13  O12  C11  106.53  3.000
 J94  C14  C13  O12  129.27  3.000
 J94  C14  C13  C09  121.16  3.000
 J94  O12  C13  C09  109.50  3.000
 J94  H12  C14  C13  121.71  3.000
 J94  H12  C14  C06  120.31  3.000
 J94  C13  C14  C06  117.97  3.000
 J94  H13  C15  C16  106.72  3.000
 J94  H13  C15  C07  109.01  3.000
 J94  C16  C15  C07  113.95  3.000
 J94  H13  C15  N02  103.94  3.000
 J94  C16  C15  N02  110.07  3.000
 J94  C07  C15  N02  112.50  3.000
 J94  H14  C16  C28  107.85  3.000
 J94  H14  C16  O17  107.31  3.000
 J94  C28  C16  O17  104.53  3.000
 J94  H14  C16  C15  109.60  3.000
 J94  C28  C16  C15  115.51  3.000
 J94  O17  C16  C15  111.63  3.000
 J94  C18  O17  C16  112.29  3.000
 J94  C20  C18  O19  130.72  3.000
 J94  C20  C18  O17  107.32  3.000
 J94  O19  C18  O17  121.96  3.000
 J94  C28  C20  C21  118.74  3.000
 J94  C28  C20  C18  108.90  3.000
 J94  C21  C20  C18  132.34  3.000
 J94  C25  C21  O22  110.33  3.000
 J94  C25  C21  C20  119.09  3.000
 J94  O22  C21  C20  130.58  3.000
 J94  C23  O22  C21  106.51  3.000
 J94  H16  C23  H15  110.96  3.000
 J94  H16  C23  O24  110.18  3.000
 J94  H15  C23  O24  110.05  3.000
 J94  H16  C23  O22  109.36  3.000
 J94  H15  C23  O22  109.41  3.000
 J94  O24  C23  O22  106.77  3.000
 J94  C25  O24  C23  106.99  3.000
 J94  C26  C25  O24  128.46  3.000
 J94  C26  C25  C21  122.70  3.000
 J94  O24  C25  C21  108.84  3.000
 J94  H17  C26  C27  120.64  3.000
 J94  H17  C26  C25  121.07  3.000
 J94  C27  C26  C25  118.29  3.000
 J94  H18  C27  C28  121.91  3.000
 J94  H18  C27  C26  119.30  3.000
 J94  C28  C27  C26  118.80  3.000
 J94  C27  C28  C20  122.39  3.000
 J94  C27  C28  C16  130.80  3.000
 J94  C20  C28  C16  106.78  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
 J94  CONST_01  C09  C13  C14  C06     0.00   0.0  0
 J94  CONST_02  C09  C08  C07  C06     0.00   0.0  0
 J94  CONST_03  C13  C14  C06  C07     0.00   0.0  0
 J94  CONST_04  C13  C09  C08  C07     0.00   0.0  0
 J94  CONST_05  C14  C13  C09  C08     0.00   0.0  0
 J94  CONST_06  C14  C06  C07  C08     0.00   0.0  0
 J94  CONST_07  C26  C25  C21  C20     0.00   0.0  0
 J94  CONST_08  C26  C27  C28  C20     0.00   0.0  0
 J94  CONST_09  C27  C28  C20  C21     0.00   0.0  0
 J94  CONST_10  C27  C26  C25  C21     0.00   0.0  0
 J94  CONST_11  C28  C20  C21  C25     0.00   0.0  0
 J94  CONST_12  C28  C27  C26  C25     0.00   0.0  0
 J94  CONST_13  H12  C14  C06  C05     0.00   0.0  0
 J94  CONST_14  H9   C08  C07  C06   180.00   0.0  0
 J94  CONST_15  H18  C27  C28  C16     0.00   0.0  0
 J94  CONST_16  H17  C26  C25  C21   180.00   0.0  0
 J94  Var_01    C06  C05  C04  N02    52.85  30.0  1
 J94  Var_02    C14  C06  C05  C04   160.26  30.0  1
 J94  Var_03    C15  N02  C04  C05   -67.16  30.0  1
 J94  Var_04    O12  C11  O10  C09   -10.48  30.0  1
 J94  Var_05    C14  C13  O12  C11   177.02  30.0  1
 J94  Var_06    C13  C09  O10  C11     6.92  30.0  1
 J94  Var_07    C20  C18  O17  C16     2.13  30.0  1
 J94  Var_08    C21  C20  C18  O17   179.08  30.0  1
 J94  Var_09    O24  C23  O22  C21     7.22  30.0  1
 J94  Var_10    C25  C21  O22  C23    -4.46  30.0  1
 J94  Var_11    C26  C25  O24  C23  -176.16  30.0  1
 J94  Var_12    H1   C01  N02  C04   179.53  30.0  3
 J94  Var_13    H4   C03  N02  C04   166.21  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
 J94  chir_01  C15  C07  N02  C16  positiv
 J94  chir_02  C16  O17  C15  C28  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
 J94  plan-1  C05  0.020
 J94  plan-1  C06  0.020
 J94  plan-1  C07  0.020
 J94  plan-1  C08  0.020
 J94  plan-1  C09  0.020
 J94  plan-1  O10  0.020
 J94  plan-1  O12  0.020
 J94  plan-1  C13  0.020
 J94  plan-1  C14  0.020
 J94  plan-1  C15  0.020
 J94  plan-1  H9   0.020
 J94  plan-1  H12  0.020
 J94  plan-2  C16  0.020
 J94  plan-2  C18  0.020
 J94  plan-2  C20  0.020
 J94  plan-2  C21  0.020
 J94  plan-2  O22  0.020
 J94  plan-2  O24  0.020
 J94  plan-2  C25  0.020
 J94  plan-2  C26  0.020
 J94  plan-2  C27  0.020
 J94  plan-2  C28  0.020
 J94  plan-2  H17  0.020
 J94  plan-2  H18  0.020
 J94  plan-3  O17  0.020
 J94  plan-3  C18  0.020
 J94  plan-3  O19  0.020
 J94  plan-3  C20  0.020

