# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 08:15:52 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 9,10-dimethoxy-5,6-dihydro[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinolin-7-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2cc3c4cc5OCOc5cc4CC[n+]3cc2c1OC
#
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
 BER  BER  9,10-dimethoxy-5,6-dihydro[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinolin-7-ium  ligand  43  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BER
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
 BER  C1    C  CR66  0   0.399  -0.6407  -0.0806  -0.0006
 BER  C2    C  CR66  0   0.059  -2.1041  -0.1064   0.0108
 BER  N1    N  N     1  -0.502   0.0327  -1.2818  -0.0582
 BER  C3    C  CR16  0  -0.445   0.1013   1.0661   0.0792
 BER  C4    C  CR66  0   0.101  -2.7650  -1.2586   0.4376
 BER  C5    C  CR16  0  -0.422  -2.8258   1.0476  -0.3559
 BER  C6    C  CR16  0   0.064   1.3494  -1.3592  -0.0502
 BER  C7    C  C     0  -0.319  -0.7557  -2.5233  -0.1623
 BER  C8    C  CR66  0   0.272   1.5053   1.0395   0.0796
 BER  C9    C  CR16  0  -0.399  -4.1594  -1.2923   0.5366
 BER  C10   C  C     0  -0.538  -1.9348  -2.4585   0.7785
 BER  C11   C  CR56  0   0.322  -4.1860   0.9895  -0.2487
 BER  C12   C  CR66  0  -0.099   2.1535  -0.2192   0.0065
 BER  C13   C  CR16  0  -0.313   2.2982   2.1962   0.1633
 BER  C14   C  CR56  0   0.323  -4.8418  -0.1528   0.1943
 BER  O1    O  O     0  -0.482  -5.1006   1.9328  -0.5686
 BER  C15   C  CR6   0   0.244   3.5613  -0.3152   0.0245
 BER  C16   C  CR16  0  -0.353   3.6633   2.0942   0.1789
 BER  O2    O  O     0  -0.476  -6.1714   0.0574   0.1717
 BER  C17   C  CH2   0   0.065  -6.3531   1.4422  -0.1105
 BER  C18   C  CR6   0   0.349   4.3173   0.8414   0.1092
 BER  O3    O  O2    0  -0.477   4.1371  -1.5345  -0.0158
 BER  O4    O  O2    0  -0.455   5.6434   0.6906   0.1288
 BER  C19   C  CH3   0  -0.418   4.6331  -1.9323  -1.2963
 BER  C20   C  CH3   0  -0.446   6.4691   1.8335   0.2856
 BER  H31   H  HCR6  0   0.297  -0.4028   2.0177   0.1696
 BER  H51   H  HCR6  0   0.282  -2.3356   1.9357  -0.7301
 BER  H61   H  HCR6  0   0.344   1.7711  -2.3530  -0.0868
 BER  H71   H  H     0   0.301  -0.0969  -3.3562   0.0666
 BER  H72   H  H     0   0.305  -1.0878  -2.6157  -1.1976
 BER  H91   H  HCR6  0   0.282  -4.6713  -2.1876   0.8641
 BER  H101  H  H     0   0.284  -1.5871  -2.4168   1.8151
 BER  H102  H  H     0   0.293  -2.5150  -3.3747   0.6719
 BER  H131  H  HCR6  0   0.283   1.8286   3.1688   0.2208
 BER  H161  H  HCR6  0   0.311   4.2477   3.0019   0.2462
 BER  H171  H  HCH2  0   0.242  -6.6494   1.9677   0.8029
 BER  H172  H  HCH2  0   0.253  -7.1058   1.5637  -0.8878
 BER  H191  H  HCH3  0   0.251   4.9923  -2.9527  -1.1888
 BER  H192  H  HCH3  0   0.230   3.8415  -1.9109  -2.0485
 BER  H193  H  HCH3  0   0.240   5.4568  -1.2982  -1.6262
 BER  H201  H  HCH3  0   0.270   7.4917   1.4679   0.2944
 BER  H202  H  HCH3  0   0.240   6.3509   2.5354  -0.5422
 BER  H203  H  HCH3  0   0.240   6.2691   2.3502   1.2265

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
 BER  C1   C2    aromatic  1.464  0.020  1.464
 BER  C1   N1    aromatic  1.378  0.020  1.378
 BER  C1   C3    aromatic  1.368  0.020  1.368
 BER  C2   C4    aromatic  1.395  0.020  1.395
 BER  C2   C5    aromatic  1.410  0.020  1.410
 BER  N1   C6    aromatic  1.319  0.020  1.319
 BER  N1   C7    single    1.474  0.020  1.474
 BER  C3   C8    aromatic  1.404  0.020  1.404
 BER  C3   H31   single    0.930  0.020  1.080
 BER  C4   C9    aromatic  1.398  0.020  1.398
 BER  C4   C10   single    1.498  0.020  1.498
 BER  C5   C11   aromatic  1.366  0.020  1.366
 BER  C5   H51   single    0.930  0.020  1.080
 BER  C6   C12   aromatic  1.396  0.020  1.396
 BER  C6   H61   single    0.930  0.020  1.080
 BER  C7   C10   single    1.510  0.020  1.510
 BER  C7   H71   single    0.970  0.020  1.090
 BER  C7   H72   single    0.970  0.020  1.090
 BER  C8   C12   aromatic  1.418  0.020  1.418
 BER  C8   C13   aromatic  1.405  0.020  1.405
 BER  C9   C14   aromatic  1.372  0.020  1.372
 BER  C9   H91   single    0.930  0.020  1.080
 BER  C10  H101  single    0.970  0.020  1.090
 BER  C10  H102  single    0.970  0.020  1.090
 BER  C11  C14   aromatic  1.390  0.020  1.390
 BER  C11  O1    single    1.352  0.020  1.352
 BER  C12  C15   aromatic  1.411  0.020  1.411
 BER  C13  C16   aromatic  1.369  0.020  1.369
 BER  C13  H131  single    0.930  0.020  1.080
 BER  C14  O2    single    1.346  0.020  1.346
 BER  O1   C17   single    1.421  0.020  1.421
 BER  C15  C18   aromatic  1.384  0.020  1.384
 BER  C15  O3    single    1.349  0.020  1.349
 BER  C16  C18   aromatic  1.415  0.020  1.415
 BER  C16  H161  single    0.930  0.020  1.080
 BER  O2   C17   single    1.425  0.020  1.425
 BER  C17  H171  single    0.970  0.020  1.090
 BER  C17  H172  single    0.970  0.020  1.090
 BER  C18  O4    single    1.335  0.020  1.335
 BER  O3   C19   single    1.430  0.020  1.430
 BER  O4   C20   single    1.419  0.020  1.419
 BER  C19  H191  single    0.970  0.020  1.090
 BER  C19  H192  single    0.970  0.020  1.090
 BER  C19  H193  single    0.970  0.020  1.090
 BER  C20  H201  single    0.970  0.020  1.090
 BER  C20  H202  single    0.970  0.020  1.090
 BER  C20  H203  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
 BER  C3    C1   N1    117.90  3.000
 BER  C3    C1   C2    123.81  3.000
 BER  N1    C1   C2    118.26  3.000
 BER  C5    C2   C4    120.87  3.000
 BER  C5    C2   C1    119.70  3.000
 BER  C4    C2   C1    119.38  3.000
 BER  C7    N1   C6    119.00  3.000
 BER  C7    N1   C1    118.40  3.000
 BER  C6    N1   C1    122.59  3.000
 BER  H31   C3   C8    118.88  3.000
 BER  H31   C3   C1    119.34  3.000
 BER  C8    C3   C1    121.76  3.000
 BER  C10   C4   C9    121.14  3.000
 BER  C10   C4   C2    117.93  3.000
 BER  C9    C4   C2    120.93  3.000
 BER  H51   C5   C11   120.91  3.000
 BER  H51   C5   C2    122.03  3.000
 BER  C11   C5   C2    117.05  3.000
 BER  H61   C6   C12   121.86  3.000
 BER  H61   C6   N1    116.33  3.000
 BER  C12   C6   N1    121.81  3.000
 BER  H72   C7   H71   108.64  3.000
 BER  H72   C7   C10   110.92  3.000
 BER  H71   C7   C10   112.03  3.000
 BER  H72   C7   N1    107.53  3.000
 BER  H71   C7   N1    107.85  3.000
 BER  C10   C7   N1    109.72  3.000
 BER  C13   C8   C12   118.43  3.000
 BER  C13   C8   C3    123.28  3.000
 BER  C12   C8   C3    118.29  3.000
 BER  H91   C9   C14   121.83  3.000
 BER  H91   C9   C4    120.88  3.000
 BER  C14   C9   C4    117.29  3.000
 BER  H102  C10  H101  107.09  3.000
 BER  H102  C10  C7    108.59  3.000
 BER  H101  C10  C7    110.11  3.000
 BER  H102  C10  C4    110.86  3.000
 BER  H101  C10  C4    111.16  3.000
 BER  C7    C10  C4    108.98  3.000
 BER  O1    C11  C14   109.25  3.000
 BER  O1    C11  C5    128.71  3.000
 BER  C14   C11  C5    122.01  3.000
 BER  C15   C12  C8    121.05  3.000
 BER  C15   C12  C6    121.30  3.000
 BER  C8    C12  C6    117.63  3.000
 BER  H131  C13  C16   119.96  3.000
 BER  H131  C13  C8    119.90  3.000
 BER  C16   C13  C8    120.13  3.000
 BER  O2    C14  C11   109.41  3.000
 BER  O2    C14  C9    128.71  3.000
 BER  C11   C14  C9    121.84  3.000
 BER  C17   O1   C11   106.20  3.000
 BER  O3    C15  C18   121.60  3.000
 BER  O3    C15  C12   119.14  3.000
 BER  C18   C15  C12   119.25  3.000
 BER  H161  C16  C18   119.76  3.000
 BER  H161  C16  C13   118.48  3.000
 BER  C18   C16  C13   121.75  3.000
 BER  C17   O2   C14   106.32  3.000
 BER  H172  C17  H171  110.79  3.000
 BER  H172  C17  O2    109.75  3.000
 BER  H171  C17  O2    109.62  3.000
 BER  H172  C17  O1    109.91  3.000
 BER  H171  C17  O1    109.99  3.000
 BER  O2    C17  O1    106.68  3.000
 BER  O4    C18  C16   123.95  3.000
 BER  O4    C18  C15   116.68  3.000
 BER  C16   C18  C15   119.37  3.000
 BER  C19   O3   C15   115.23  3.000
 BER  C20   O4   C18   119.27  3.000
 BER  H193  C19  H192  109.12  3.000
 BER  H193  C19  H191  109.03  3.000
 BER  H192  C19  H191  109.02  3.000
 BER  H193  C19  O3    111.79  3.000
 BER  H192  C19  O3    111.10  3.000
 BER  H191  C19  O3    106.69  3.000
 BER  H203  C20  H202  109.23  3.000
 BER  H203  C20  H201  108.95  3.000
 BER  H202  C20  H201  108.94  3.000
 BER  H203  C20  O4    111.70  3.000
 BER  H202  C20  O4    111.79  3.000
 BER  H201  C20  O4    106.12  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
 BER  CONST_01  C9    C4   C2   C1    180.00   0.0  0
 BER  CONST_02  C11   C5   C2   C1    180.00   0.0  0
 BER  CONST_03  C12   C6   N1   C1      0.00   0.0  0
 BER  CONST_04  C12   C8   C3   C1      0.00   0.0  0
 BER  CONST_05  C13   C8   C3   C1    180.00   0.0  0
 BER  CONST_06  C6    N1   C1   C2    180.00   0.0  0
 BER  CONST_07  C8    C3   C1   C2    180.00   0.0  0
 BER  CONST_08  C14   C9   C4   C2      0.00   0.0  0
 BER  CONST_09  C14   C11  C5   C2      0.00   0.0  0
 BER  CONST_12  C8    C3   C1   N1      0.00   0.0  0
 BER  CONST_13  C8    C12  C6   N1      0.00   0.0  0
 BER  CONST_14  C15   C12  C6   N1    180.00   0.0  0
 BER  CONST_17  C6    N1   C1   C3      0.00   0.0  0
 BER  CONST_18  C6    C12  C8   C3      0.00   0.0  0
 BER  CONST_19  C15   C12  C8   C3    180.00   0.0  0
 BER  CONST_20  C16   C13  C8   C3    180.00   0.0  0
 BER  CONST_21  C11   C5   C2   C4      0.00   0.0  0
 BER  CONST_22  C11   C14  C9   C4      0.00   0.0  0
 BER  CONST_23  C9    C4   C2   C5      0.00   0.0  0
 BER  CONST_24  C9    C14  C11  C5      0.00   0.0  0
 BER  CONST_25  C13   C8   C12  C6    180.00   0.0  0
 BER  CONST_26  C18   C15  C12  C6    180.00   0.0  0
 BER  CONST_27  C18   C15  C12  C8      0.00   0.0  0
 BER  CONST_28  C18   C16  C13  C8      0.00   0.0  0
 BER  CONST_29  C16   C13  C8   C12     0.00   0.0  0
 BER  CONST_30  C16   C18  C15  C12     0.00   0.0  0
 BER  CONST_31  C15   C12  C8   C13     0.00   0.0  0
 BER  CONST_32  C15   C18  C16  C13     0.00   0.0  0
 BER  CONST_33  O3    C15  C12  C6      0.00   0.0  0
 BER  CONST_34  O3    C15  C12  C8    180.00   0.0  0
 BER  CONST_35  O4    C18  C15  C12   180.00   0.0  0
 BER  CONST_36  O4    C18  C16  C13   180.00   0.0  0
 BER  CONST_37  O3    C15  C18  C16   180.00   0.0  0
 BER  CONST_38  H51   C5   C2   C1      0.00   0.0  0
 BER  CONST_39  H61   C6   N1   C1    180.00   0.0  0
 BER  CONST_40  H31   C3   C1   C2      0.00   0.0  0
 BER  CONST_41  H91   C9   C4   C2    180.00   0.0  0
 BER  CONST_42  H131  C13  C8   C3      0.00   0.0  0
 BER  CONST_43  H161  C16  C13  C8    180.00   0.0  0
 BER  Var_01    C10   C7   N1   C1    -43.02  30.0  1
 BER  Var_02    C7    C10  C4   C2    -35.81  30.0  1
 BER  Var_03    C4    C10  C7   N1     58.00  30.0  1
 BER  Var_04    O2    C17  O1   C11   -14.37  30.0  1
 BER  Var_05    O1    C17  O2   C14    14.06  30.0  1
 BER  Var_06    H191  C19  O3   C15  -175.69  30.0  3
 BER  Var_07    H201  C20  O4   C18   178.76  30.0  3

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
 BER  plan-1  C1    0.020
 BER  plan-1  C2    0.020
 BER  plan-1  N1    0.020
 BER  plan-1  C3    0.020
 BER  plan-1  C6    0.020
 BER  plan-1  C7    0.020
 BER  plan-1  C8    0.020
 BER  plan-1  C12   0.020
 BER  plan-1  C13   0.020
 BER  plan-1  C15   0.020
 BER  plan-1  C16   0.020
 BER  plan-1  C18   0.020
 BER  plan-1  O3    0.020
 BER  plan-1  O4    0.020
 BER  plan-1  H31   0.020
 BER  plan-1  H61   0.020
 BER  plan-1  H131  0.020
 BER  plan-1  H161  0.020
 BER  plan-2  C1    0.020
 BER  plan-2  C2    0.020
 BER  plan-2  C4    0.020
 BER  plan-2  C5    0.020
 BER  plan-2  C9    0.020
 BER  plan-2  C10   0.020
 BER  plan-2  C11   0.020
 BER  plan-2  C14   0.020
 BER  plan-2  O1    0.020
 BER  plan-2  O2    0.020
 BER  plan-2  H51   0.020
 BER  plan-2  H91   0.020

