# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:26:41 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (5S,12bS)-5-methyl-6,7,12b,13-tetrahydro-2H,4H,10H-[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquinolino[3,2-a]isoquinolin-5-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N@@+]12CCc3cc4OCOc4cc3[C@@H]1Cc5ccc6OCOc6c5C2
#
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
 SYT  SYT  (5S,12bS)-5-methyl-6,7,12b,13-tetrahydro-2H,4H,10H-[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquinolino[3,2-a]isoquinolin-5-ium  ligand  45  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SYT
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
 SYT  C07   C  CH3   0  -0.550  -0.3362   2.3131  -1.3472
 SYT  N7    N  NT    1  -0.418   0.2829   1.2915  -0.4515
 SYT  C8    C  CH2   0  -0.356   1.7250   1.2082  -0.8403
 SYT  C8A   C  CR6   0  -0.068   2.4443   0.0557  -0.2202
 SYT  C9    C  CR6   0   0.284   3.8166   0.0640  -0.1226
 SYT  O18   O  O2    0  -0.481   4.6712   1.0420  -0.5011
 SYT  C15   C  CH2   0   0.068   5.9530   0.6453  -0.0223
 SYT  O19   O  O2    0  -0.485   5.8545  -0.7303   0.3208
 SYT  C10   C  CR6   0   0.301   4.5296  -1.0118   0.3718
 SYT  C11   C  CR16  0  -0.338   3.9026  -2.1586   0.7937
 SYT  C12   C  CR16  0  -0.320   2.5087  -2.1798   0.7038
 SYT  C12A  C  CR6   0   0.102   1.7856  -1.1046   0.2058
 SYT  C13   C  CH2   0  -0.527   0.2855  -1.1376   0.1979
 SYT  C13A  C  CH1   0  -0.185  -0.3820  -0.0508  -0.6445
 SYT  C13B  C  CR6   0   0.057  -1.8388   0.0374  -0.2841
 SYT  C4A   C  CR6   0   0.057  -2.2522   0.8649   0.7502
 SYT  C5    C  CH2   0  -0.548  -1.3057   1.8380   1.4036
 SYT  C6    C  CH2   0  -0.338   0.1494   1.7058   0.9828
 SYT  C1    C  CR16  0  -0.379  -2.7361  -0.8080  -0.9556
 SYT  C2    C  CR56  0   0.306  -4.0399  -0.7864  -0.5416
 SYT  O16   O  O     0  -0.484  -5.0890  -1.5086  -0.9972
 SYT  C14   C  CH2   0   0.068  -6.2436  -0.9825  -0.3544
 SYT  O17   O  O     0  -0.483  -5.7844  -0.1451   0.7000
 SYT  C3    C  CR56  0   0.314  -4.4616   0.0398   0.4909
 SYT  C4    C  CR16  0  -0.369  -3.5997   0.8766   1.1473
 SYT  H1    H  HCH3  0   0.301  -0.2854   1.9554  -2.3720
 SYT  H2    H  HCH3  0   0.308  -1.3718   2.4861  -1.0793
 SYT  H3    H  HCH3  0   0.300   0.2269   3.2382  -1.2564
 SYT  H4    H  HCH2  0   0.332   1.7525   1.1299  -1.9293
 SYT  H5    H  HCH2  0   0.319   2.1787   2.1613  -0.5680
 SYT  H6    H  HCH2  0   0.251   6.6955   0.7800  -0.8077
 SYT  H7    H  HCR6  0   0.279   4.4536  -3.0067   1.1761
 SYT  H8    H  HCR6  0   0.261   1.9771  -3.0610   1.0397
 SYT  H9    H  HCH2  0   0.306  -0.0731  -2.0913  -0.1937
 SYT  H10   H  HCH2  0   0.283  -0.0880  -1.0839   1.2243
 SYT  H11   H  HCH1  0   0.330  -0.2605  -0.2814  -1.7056
 SYT  H12   H  HCH2  0   0.283  -1.6561   2.8532   1.2018
 SYT  H13   H  HCH2  0   0.303  -1.3391   1.7241   2.4886
 SYT  H14   H  HCH2  0   0.318   0.6806   0.9729   1.5860
 SYT  H15   H  HCH2  0   0.321   0.6695   2.6554   1.0944
 SYT  H16   H  HCR6  0   0.278  -2.4041  -1.4465  -1.7642
 SYT  H17   H  HCH2  0   0.238  -6.8293  -0.3935  -1.0673
 SYT  H18   H  HCR6  0   0.277  -3.9382   1.5253   1.9453
 SYT  H19   H  HCH2  0   0.238   6.2149   1.2337   0.8634
 SYT  H20   H  HCH2  0   0.249  -6.8419  -1.7962   0.0545

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
 SYT  C14   O17   single    1.423  0.020  1.423
 SYT  C14   O16   single    1.422  0.020  1.422
 SYT  O17   C3    single    1.352  0.020  1.352
 SYT  O16   C2    single    1.353  0.020  1.353
 SYT  C3    C2    aromatic  1.388  0.020  1.388
 SYT  C3    C4    aromatic  1.369  0.020  1.369
 SYT  C2    C1    aromatic  1.368  0.020  1.368
 SYT  C4    C4A   aromatic  1.405  0.020  1.405
 SYT  C1    C13B  aromatic  1.404  0.020  1.404
 SYT  C4A   C13B  aromatic  1.388  0.020  1.388
 SYT  C4A   C5    single    1.507  0.020  1.507
 SYT  C13B  C13A  single    1.503  0.020  1.503
 SYT  C5    C6    single    1.520  0.020  1.520
 SYT  C13A  C13   single    1.528  0.020  1.528
 SYT  C13A  N7    single    1.510  0.020  1.510
 SYT  C13   C12A  single    1.500  0.020  1.500
 SYT  C6    N7    single    1.499  0.020  1.499
 SYT  C07   N7    single    1.493  0.020  1.493
 SYT  N7    C8    single    1.496  0.020  1.496
 SYT  C12A  C12   aromatic  1.388  0.020  1.388
 SYT  C12A  C8A   aromatic  1.401  0.020  1.401
 SYT  C12   C11   aromatic  1.397  0.020  1.397
 SYT  C8    C8A   single    1.493  0.020  1.493
 SYT  C8A   C9    aromatic  1.376  0.020  1.376
 SYT  C11   C10   aromatic  1.373  0.020  1.373
 SYT  C9    C10   aromatic  1.382  0.020  1.382
 SYT  C9    O18   single    1.353  0.020  1.353
 SYT  C10   O19   single    1.355  0.020  1.355
 SYT  O18   C15   single    1.425  0.020  1.425
 SYT  O19   C15   single    1.421  0.020  1.421
 SYT  C07   H1    single    0.970  0.020  1.090
 SYT  C07   H2    single    0.970  0.020  1.090
 SYT  C07   H3    single    0.970  0.020  1.090
 SYT  C8    H4    single    0.970  0.020  1.090
 SYT  C8    H5    single    0.970  0.020  1.090
 SYT  C15   H6    single    0.970  0.020  1.090
 SYT  C11   H7    single    0.930  0.020  1.080
 SYT  C12   H8    single    0.930  0.020  1.080
 SYT  C13   H9    single    0.970  0.020  1.090
 SYT  C13   H10   single    0.970  0.020  1.090
 SYT  C13A  H11   single    0.970  0.020  1.090
 SYT  C5    H12   single    0.970  0.020  1.090
 SYT  C5    H13   single    0.970  0.020  1.090
 SYT  C6    H14   single    0.970  0.020  1.090
 SYT  C6    H15   single    0.970  0.020  1.090
 SYT  C1    H16   single    0.930  0.020  1.080
 SYT  C14   H17   single    0.970  0.020  1.090
 SYT  C4    H18   single    0.930  0.020  1.080
 SYT  C15   H19   single    0.970  0.020  1.090
 SYT  C14   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
 SYT  H3    C07   H2    109.79  3.000
 SYT  H3    C07   H1    109.55  3.000
 SYT  H2    C07   H1    109.29  3.000
 SYT  H3    C07   N7    108.51  3.000
 SYT  H2    C07   N7    110.93  3.000
 SYT  H1    C07   N7    108.74  3.000
 SYT  C6    N7    C13A  109.19  3.000
 SYT  C6    N7    C8    110.49  3.000
 SYT  C13A  N7    C8    109.98  3.000
 SYT  C8    N7    C07   106.37  3.000
 SYT  C6    N7    C07   110.37  3.000
 SYT  C13A  N7    C07   110.42  3.000
 SYT  H5    C8    H4    107.54  3.000
 SYT  H5    C8    C8A   111.75  3.000
 SYT  H4    C8    C8A   110.27  3.000
 SYT  H5    C8    N7    106.71  3.000
 SYT  H4    C8    N7    106.71  3.000
 SYT  C8A   C8    N7    113.54  3.000
 SYT  C12A  C8A   C9    116.91  3.000
 SYT  C9    C8A   C8    120.35  3.000
 SYT  C12A  C8A   C8    122.62  3.000
 SYT  C10   C9    O18   109.69  3.000
 SYT  O18   C9    C8A   127.93  3.000
 SYT  C10   C9    C8A   122.36  3.000
 SYT  C15   O18   C9    105.85  3.000
 SYT  H19   C15   H6    110.72  3.000
 SYT  H19   C15   O19   109.96  3.000
 SYT  H6    C15   O19   109.94  3.000
 SYT  H19   C15   O18   109.71  3.000
 SYT  H6    C15   O18   109.67  3.000
 SYT  O19   C15   O18   106.76  3.000
 SYT  C10   O19   C15   106.13  3.000
 SYT  C11   C10   O19   129.14  3.000
 SYT  O19   C10   C9    109.22  3.000
 SYT  C11   C10   C9    121.62  3.000
 SYT  H7    C11   C12   121.29  3.000
 SYT  H7    C11   C10   122.07  3.000
 SYT  C12   C11   C10   116.64  3.000
 SYT  H8    C12   C12A  119.08  3.000
 SYT  H8    C12   C11   118.84  3.000
 SYT  C12A  C12   C11   122.08  3.000
 SYT  C13   C12A  C12   120.37  3.000
 SYT  C12   C12A  C8A   120.38  3.000
 SYT  C13   C12A  C8A   119.14  3.000
 SYT  H10   C13   H9    105.51  3.000
 SYT  H10   C13   C13A  109.46  3.000
 SYT  H9    C13   C13A  106.26  3.000
 SYT  H10   C13   C12A  109.60  3.000
 SYT  H9    C13   C12A  110.46  3.000
 SYT  C13A  C13   C12A  115.08  3.000
 SYT  H11   C13A  C13B  110.67  3.000
 SYT  H11   C13A  C13   109.67  3.000
 SYT  C13B  C13A  C13   109.44  3.000
 SYT  H11   C13A  N7    105.23  3.000
 SYT  C13   C13A  N7    111.67  3.000
 SYT  C13B  C13A  N7    110.11  3.000
 SYT  C1    C13B  C4A   121.69  3.000
 SYT  C4A   C13B  C13A  120.16  3.000
 SYT  C1    C13B  C13A  118.00  3.000
 SYT  C4    C4A   C5    118.34  3.000
 SYT  C5    C4A   C13B  121.42  3.000
 SYT  C4    C4A   C13B  120.09  3.000
 SYT  H13   C5    H12   105.71  3.000
 SYT  H13   C5    C6    107.18  3.000
 SYT  H12   C5    C6    109.67  3.000
 SYT  H13   C5    C4A   110.15  3.000
 SYT  H12   C5    C4A   108.57  3.000
 SYT  C6    C5    C4A   115.15  3.000
 SYT  H15   C6    H14   107.31  3.000
 SYT  H15   C6    C5    110.67  3.000
 SYT  H14   C6    C5    111.87  3.000
 SYT  H15   C6    N7    107.26  3.000
 SYT  H14   C6    N7    107.51  3.000
 SYT  C5    C6    N7    111.97  3.000
 SYT  H16   C1    C2    121.84  3.000
 SYT  H16   C1    C13B  121.10  3.000
 SYT  C2    C1    C13B  117.06  3.000
 SYT  C3    C2    O16   109.43  3.000
 SYT  C3    C2    C1    121.60  3.000
 SYT  O16   C2    C1    128.96  3.000
 SYT  C14   O16   C2    106.25  3.000
 SYT  H20   C14   H17   110.63  3.000
 SYT  H20   C14   O17   109.79  3.000
 SYT  H17   C14   O17   109.79  3.000
 SYT  H20   C14   O16   109.82  3.000
 SYT  H17   C14   O16   109.82  3.000
 SYT  O17   C14   O16   106.90  3.000
 SYT  C3    O17   C14   106.36  3.000
 SYT  C4    C3    O17   128.71  3.000
 SYT  C4    C3    C2    121.96  3.000
 SYT  O17   C3    C2    109.33  3.000
 SYT  H18   C4    C3    121.53  3.000
 SYT  H18   C4    C4A   120.87  3.000
 SYT  C3    C4    C4A   117.60  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
 SYT  CONST_01  C11   C12   C12A  C8A      0.00   0.0  0
 SYT  CONST_02  C11   C10   C9    C8A      0.00   0.0  0
 SYT  CONST_03  C12   C12A  C8A   C9       0.00   0.0  0
 SYT  CONST_04  C12   C11   C10   C9       0.00   0.0  0
 SYT  CONST_05  C12A  C12   C11   C10      0.00   0.0  0
 SYT  CONST_06  C12A  C8A   C9    C10      0.00   0.0  0
 SYT  CONST_07  C3    C2    C1    C13B     0.00   0.0  0
 SYT  CONST_08  C3    C4    C4A   C13B     0.00   0.0  0
 SYT  CONST_09  C2    C3    C4    C4A      0.00   0.0  0
 SYT  CONST_10  C2    C1    C13B  C4A      0.00   0.0  0
 SYT  CONST_11  C4    C3    C2    C1       0.00   0.0  0
 SYT  CONST_12  C4    C4A   C13B  C1       0.00   0.0  0
 SYT  CONST_13  H8    C12   C12A  C8A    180.00   0.0  0
 SYT  CONST_14  H7    C11   C10   C9     180.00   0.0  0
 SYT  CONST_15  H16   C1    C13B  C13A     0.00   0.0  0
 SYT  CONST_16  H18   C4    C4A   C13B   180.00   0.0  0
 SYT  Var_01    C4A   C5    C6    N7      33.92  30.0  1
 SYT  Var_02    C12A  C8A   C8    N7      24.68  30.0  1
 SYT  Var_03    C13A  C13   C12A  C8A     16.74  30.0  1
 SYT  Var_04    O19   C15   O18   C9      14.99  30.0  1
 SYT  Var_05    C10   C9    O18   C15     -9.58  30.0  1
 SYT  Var_06    C11   C10   O19   C15   -172.47  30.0  1
 SYT  Var_07    C6    C5    C4A   C13B    -8.06  30.0  1
 SYT  Var_08    O17   C14   O16   C2     -12.85  30.0  1
 SYT  Var_09    C4    C3    O17   C14    172.51  30.0  1
 SYT  Var_10    C3    C2    O16   C14      8.19  30.0  1

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
 SYT  chir_01  N7    C6  C13A  C8   positiv
 SYT  chir_02  C13A  N7  C13B  C13  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
 SYT  plan-1  C8    0.020
 SYT  plan-1  C8A   0.020
 SYT  plan-1  C9    0.020
 SYT  plan-1  O18   0.020
 SYT  plan-1  O19   0.020
 SYT  plan-1  C10   0.020
 SYT  plan-1  C11   0.020
 SYT  plan-1  C12   0.020
 SYT  plan-1  C12A  0.020
 SYT  plan-1  C13   0.020
 SYT  plan-1  H7    0.020
 SYT  plan-1  H8    0.020
 SYT  plan-2  C13A  0.020
 SYT  plan-2  C13B  0.020
 SYT  plan-2  C4A   0.020
 SYT  plan-2  C5    0.020
 SYT  plan-2  C1    0.020
 SYT  plan-2  C2    0.020
 SYT  plan-2  O16   0.020
 SYT  plan-2  O17   0.020
 SYT  plan-2  C3    0.020
 SYT  plan-2  C4    0.020
 SYT  plan-2  H16   0.020
 SYT  plan-2  H18   0.020

