# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:27:58 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 2,7-dimethoxy-9-piperidin-4-ylsulfanyl-acridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc3ccc(OC)cc3c(SC4CCNCC4)c2c1
#
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
 H7C  H7C  "2,7-dimethoxy-9-piperidin-4-ylsulfanyl-acridine"
  ligand  47  25  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H7C
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
 H7C  C10  C  CR16  0  -0.482  83.0269  140.5258  15.1840
 H7C  C11  C  CR16  0  -0.480  81.0692  143.7414  18.4381
 H7C  C12  C  CR6   0   0.415  81.0270  145.0329  18.8824
 H7C  C13  C  CR16  0  -0.336  81.7845  146.0500  18.2275
 H7C  C14  C  CR16  0  -0.274  82.5638  145.7414  17.1639
 H7C  C16  C  CH1   0  -0.373  79.4494  140.7381  16.5929
 H7C  C19  C  CH3   0  -0.440  79.5100  144.5240  20.6247
 H7C  C21  C  CH2   0  -0.431  78.6615  142.0440  16.6799
 H7C  C22  C  CH2   0  -0.315  77.5577  142.0773  15.6013
 H7C  C24  C  CH2   0  -0.294  78.2040  140.0170  14.5494
 H7C  C25  C  CH2   0  -0.453  79.6008  140.3058  15.1442
 H7C  C01  C  CR6   0  -0.163  81.9468  142.0853  16.7978
 H7C  C02  C  CR66  0   0.176  81.8703  143.3879  17.3178
 H7C  C03  C  CR66  0   0.135  82.6439  144.4045  16.6731
 H7C  C05  C  CR66  0   0.137  83.5401  142.9270  15.1750
 H7C  C06  C  CR66  0   0.185  82.8197  141.8217  15.7295
 H7C  C07  C  CR16  0  -0.274  84.4153  142.6920  14.0736
 H7C  C08  C  CR16  0  -0.336  84.5827  141.4474  13.5668
 H7C  C09  C  CR6   0   0.413  83.8829  140.3410  14.1346
 H7C  C20  C  CH3   0  -0.442  83.4863  138.0103  14.0506
 H7C  N04  N  N     0  -0.458  83.4349  144.1675  15.6345
 H7C  N23  N  NH1   0  -0.585  77.1175  140.7632  15.1733
 H7C  O18  O  O2    0  -0.462  80.3062  145.4618  19.9277
 H7C  S15  S  S2    0  -0.002  81.0189  140.7694  17.5442
 H7C  H1   H  HCR6  0   0.280  82.4970  139.6972  15.6296
 H7C  H2   H  HCR6  0   0.283  80.5017  142.9597  18.9216
 H7C  H3   H  HCR6  0   0.272  81.7271  147.0660  18.5975
 H7C  H4   H  HCR6  0   0.266  83.1463  146.5032  16.6623
 H7C  H5   H  HCH1  0   0.280  78.9092  139.9543  17.1354
 H7C  H6   H  HCH3  0   0.263  79.0123  145.0712  21.4211
 H7C  H7   H  HCH3  0   0.231  78.7537  144.0740  19.9759
 H7C  H8   H  HCH3  0   0.231  80.1148  143.7271  21.0649
 H7C  H9   H  HCH2  0   0.243  79.3235  142.8993  16.5339
 H7C  H10  H  HCH2  0   0.237  78.2343  142.1431  17.6798
 H7C  H11  H  HCH2  0   0.227  77.9241  142.6064  14.7172
 H7C  H12  H  HCH2  0   0.240  76.7008  142.6478  15.9636
 H7C  H13  H  HCH2  0   0.233  77.9766  138.9541  14.6451
 H7C  H14  H  HCH2  0   0.222  78.2250  140.2356  13.4776
 H7C  H15  H  HCH2  0   0.250  80.2263  139.4162  15.0618
 H7C  H16  H  HCH2  0   0.235  80.1042  141.0973  14.5826
 H7C  H17  H  HCR6  0   0.265  84.9465  143.5380  13.6571
 H7C  H18  H  HCR6  0   0.272  85.2507  141.2730  12.7326
 H7C  H19  H  HCH3  0   0.263  83.8245  137.1749  13.4430
 H7C  H20  H  HCH3  0   0.231  83.7415  137.8160  15.0956
 H7C  H21  H  HCH3  0   0.233  82.4000  138.0965  13.9633
 H7C  H22  H  HNH1  0   0.344  76.7694  140.2501  15.9733
 H7C  O17  O  O2    0  -0.462  84.1440  139.1605  13.5557

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
 H7C  O17  C20  single    1.414  0.020  1.414
 H7C  O17  C09  single    1.340  0.020  1.340
 H7C  C08  C09  aromatic  1.427  0.020  1.427
 H7C  C08  C07  aromatic  1.354  0.020  1.354
 H7C  C09  C10  aromatic  1.367  0.020  1.367
 H7C  C07  C05  aromatic  1.426  0.020  1.426
 H7C  C22  N23  single    1.450  0.020  1.450
 H7C  C22  C21  single    1.544  0.020  1.544
 H7C  N23  C24  single    1.458  0.020  1.458
 H7C  C10  C06  aromatic  1.421  0.020  1.421
 H7C  C05  C06  aromatic  1.431  0.020  1.431
 H7C  C05  N04  aromatic  1.327  0.020  1.327
 H7C  C24  C25  single    1.545  0.020  1.545
 H7C  C06  C01  aromatic  1.404  0.020  1.404
 H7C  N04  C03  aromatic  1.327  0.020  1.327
 H7C  C25  C16  single    1.519  0.020  1.519
 H7C  C21  C16  single    1.528  0.020  1.528
 H7C  C01  C02  aromatic  1.405  0.020  1.405
 H7C  C01  S15  single    1.775  0.020  1.775
 H7C  C16  S15  single    1.836  0.020  1.836
 H7C  C03  C02  aromatic  1.431  0.020  1.431
 H7C  C03  C14  aromatic  1.426  0.020  1.426
 H7C  C02  C11  aromatic  1.422  0.020  1.422
 H7C  C14  C13  aromatic  1.354  0.020  1.354
 H7C  C11  C12  aromatic  1.367  0.020  1.367
 H7C  C13  C12  aromatic  1.427  0.020  1.427
 H7C  C12  O18  single    1.340  0.020  1.340
 H7C  O18  C19  single    1.414  0.020  1.414
 H7C  C10  H1   single    0.930  0.020  1.080
 H7C  C11  H2   single    0.930  0.020  1.080
 H7C  C13  H3   single    0.930  0.020  1.080
 H7C  C14  H4   single    0.930  0.020  1.080
 H7C  C16  H5   single    0.970  0.020  1.090
 H7C  C19  H6   single    0.970  0.020  1.090
 H7C  C19  H7   single    0.970  0.020  1.090
 H7C  C19  H8   single    0.970  0.020  1.090
 H7C  C21  H9   single    0.970  0.020  1.090
 H7C  C21  H10  single    0.970  0.020  1.090
 H7C  C22  H11  single    0.970  0.020  1.090
 H7C  C22  H12  single    0.970  0.020  1.090
 H7C  C24  H13  single    0.970  0.020  1.090
 H7C  C24  H14  single    0.970  0.020  1.090
 H7C  C25  H15  single    0.970  0.020  1.090
 H7C  C25  H16  single    0.970  0.020  1.090
 H7C  C07  H17  single    0.930  0.020  1.080
 H7C  C08  H18  single    0.930  0.020  1.080
 H7C  C20  H19  single    0.970  0.020  1.090
 H7C  C20  H20  single    0.970  0.020  1.090
 H7C  C20  H21  single    0.970  0.020  1.090
 H7C  N23  H22  single    0.890  0.020  1.040

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
 H7C  H1   C10  C09  121.36  3.000
 H7C  H1   C10  C06  118.02  3.000
 H7C  C09  C10  C06  120.62  3.000
 H7C  H2   C11  C02  117.95  3.000
 H7C  H2   C11  C12  121.48  3.000
 H7C  C02  C11  C12  120.57  3.000
 H7C  O18  C12  C13  114.54  3.000
 H7C  O18  C12  C11  124.94  3.000
 H7C  C13  C12  C11  120.52  3.000
 H7C  H3   C13  C14  120.84  3.000
 H7C  H3   C13  C12  118.93  3.000
 H7C  C14  C13  C12  120.23  3.000
 H7C  H4   C14  C03  118.03  3.000
 H7C  H4   C14  C13  120.89  3.000
 H7C  C03  C14  C13  121.08  3.000
 H7C  H5   C16  S15  100.20  3.000
 H7C  H5   C16  C25  108.53  3.000
 H7C  S15  C16  C25  114.44  3.000
 H7C  H5   C16  C21  109.21  3.000
 H7C  S15  C16  C21  113.38  3.000
 H7C  C25  C16  C21  110.42  3.000
 H7C  H8   C19  H7   108.77  3.000
 H7C  H8   C19  H6   108.98  3.000
 H7C  H7   C19  H6   108.98  3.000
 H7C  H8   C19  O18  111.75  3.000
 H7C  H7   C19  O18  111.72  3.000
 H7C  H6   C19  O18  106.56  3.000
 H7C  H10  C21  H9   106.78  3.000
 H7C  H10  C21  C22  110.99  3.000
 H7C  H9   C21  C22  108.86  3.000
 H7C  H10  C21  C16  109.36  3.000
 H7C  H9   C21  C16  110.46  3.000
 H7C  C22  C21  C16  110.33  3.000
 H7C  H12  C22  H11  106.17  3.000
 H7C  H12  C22  N23  109.46  3.000
 H7C  H11  C22  N23  107.55  3.000
 H7C  H12  C22  C21  109.92  3.000
 H7C  H11  C22  C21  109.62  3.000
 H7C  N23  C22  C21  113.81  3.000
 H7C  H14  C24  H13  106.53  3.000
 H7C  H14  C24  N23  109.34  3.000
 H7C  H13  C24  N23  107.80  3.000
 H7C  H14  C24  C25  108.80  3.000
 H7C  H13  C24  C25  109.67  3.000
 H7C  N23  C24  C25  114.40  3.000
 H7C  H16  C25  H15  106.72  3.000
 H7C  H16  C25  C24  110.72  3.000
 H7C  H15  C25  C24  109.69  3.000
 H7C  H16  C25  C16  109.25  3.000
 H7C  H15  C25  C16  111.18  3.000
 H7C  C24  C25  C16  109.27  3.000
 H7C  S15  C01  C06  120.38  3.000
 H7C  S15  C01  C02  120.22  3.000
 H7C  C06  C01  C02  119.31  3.000
 H7C  C03  C02  C01  117.55  3.000
 H7C  C03  C02  C11  118.88  3.000
 H7C  C01  C02  C11  123.57  3.000
 H7C  N04  C03  C02  123.23  3.000
 H7C  C02  C03  C14  118.72  3.000
 H7C  N04  C03  C14  118.05  3.000
 H7C  N04  C05  C07  118.04  3.000
 H7C  N04  C05  C06  123.22  3.000
 H7C  C07  C05  C06  118.74  3.000
 H7C  C05  C06  C01  117.56  3.000
 H7C  C01  C06  C10  123.62  3.000
 H7C  C05  C06  C10  118.83  3.000
 H7C  H17  C07  C08  120.91  3.000
 H7C  H17  C07  C05  118.01  3.000
 H7C  C08  C07  C05  121.08  3.000
 H7C  H18  C08  C09  118.96  3.000
 H7C  H18  C08  C07  120.83  3.000
 H7C  C09  C08  C07  120.20  3.000
 H7C  C08  C09  O17  114.55  3.000
 H7C  C08  C09  C10  120.52  3.000
 H7C  O17  C09  C10  124.94  3.000
 H7C  H21  C20  H20  108.81  3.000
 H7C  H21  C20  H19  108.97  3.000
 H7C  H20  C20  H19  108.98  3.000
 H7C  H21  C20  O17  111.71  3.000
 H7C  H20  C20  O17  111.75  3.000
 H7C  H19  C20  O17  106.54  3.000
 H7C  C05  N04  C03  119.03  3.000
 H7C  H22  N23  C24  109.57  3.000
 H7C  H22  N23  C22  109.30  3.000
 H7C  C24  N23  C22  111.33  3.000
 H7C  C19  O18  C12  118.36  3.000
 H7C  C01  S15  C16  103.99  3.000
 H7C  C20  O17  C09  118.33  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
 H7C  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 H7C  CONST_02  C07  C05  C06  C10     0.00   0.0  0
 H7C  CONST_03  N04  C05  C06  C10   180.00   0.0  0
 H7C  CONST_04  C02  C01  C06  C10   180.00   0.0  0
 H7C  CONST_05  C06  C01  C02  C11   180.00   0.0  0
 H7C  CONST_06  N04  C03  C02  C11   180.00   0.0  0
 H7C  CONST_07  C14  C03  C02  C11     0.00   0.0  0
 H7C  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 H7C  CONST_09  C01  C02  C11  C12   180.00   0.0  0
 H7C  CONST_10  C03  C02  C11  C12     0.00   0.0  0
 H7C  CONST_11  C03  C14  C13  C12     0.00   0.0  0
 H7C  CONST_12  N04  C03  C14  C13   180.00   0.0  0
 H7C  CONST_13  C02  C03  C14  C13     0.00   0.0  0
 H7C  CONST_14  C02  C11  C12  C13     0.00   0.0  0
 H7C  CONST_15  C05  N04  C03  C14   180.00   0.0  0
 H7C  CONST_16  C01  C02  C03  C14   180.00   0.0  0
 H7C  CONST_17  C09  C10  C06  C01   180.00   0.0  0
 H7C  CONST_18  C07  C05  C06  C01   180.00   0.0  0
 H7C  CONST_19  N04  C05  C06  C01     0.00   0.0  0
 H7C  CONST_20  N04  C03  C02  C01     0.00   0.0  0
 H7C  CONST_21  C05  C06  C01  C02     0.00   0.0  0
 H7C  CONST_22  C05  N04  C03  C02     0.00   0.0  0
 H7C  CONST_23  C07  C05  N04  C03   180.00   0.0  0
 H7C  CONST_24  C06  C05  N04  C03     0.00   0.0  0
 H7C  CONST_25  C06  C01  C02  C03     0.00   0.0  0
 H7C  CONST_26  C09  C08  C07  C05     0.00   0.0  0
 H7C  CONST_27  C09  C10  C06  C05     0.00   0.0  0
 H7C  CONST_28  C08  C09  C10  C06     0.00   0.0  0
 H7C  CONST_29  C08  C07  C05  C06     0.00   0.0  0
 H7C  CONST_30  N04  C05  C07  C08   180.00   0.0  0
 H7C  CONST_31  S15  C01  C06  C10     0.00   0.0  0
 H7C  CONST_32  S15  C01  C02  C11     0.00   0.0  0
 H7C  CONST_33  O18  C12  C13  C14   180.00   0.0  0
 H7C  CONST_34  C07  C08  C09  O17   180.00   0.0  0
 H7C  CONST_35  C06  C10  C09  O17   180.00   0.0  0
 H7C  CONST_36  O18  C12  C11  C02   180.00   0.0  0
 H7C  CONST_37  S15  C01  C02  C03   180.00   0.0  0
 H7C  CONST_38  S15  C01  C06  C05   180.00   0.0  0
 H7C  CONST_39  H18  C08  C09  C10   180.00   0.0  0
 H7C  CONST_40  H3   C13  C12  C11   180.00   0.0  0
 H7C  CONST_41  H4   C14  C13  C12   180.00   0.0  0
 H7C  CONST_42  H2   C11  C12  C13   180.00   0.0  0
 H7C  CONST_43  H1   C10  C06  C01     0.00   0.0  0
 H7C  CONST_44  H2   C11  C02  C01     0.00   0.0  0
 H7C  CONST_45  H4   C14  C03  C02   180.00   0.0  0
 H7C  CONST_46  H2   C11  C02  C03   180.00   0.0  0
 H7C  CONST_47  H3   C13  C14  C03   180.00   0.0  0
 H7C  CONST_48  H18  C08  C07  C05   180.00   0.0  0
 H7C  CONST_49  H1   C10  C06  C05   180.00   0.0  0
 H7C  CONST_50  H17  C07  C05  C06   180.00   0.0  0
 H7C  CONST_51  H1   C10  C09  C08   180.00   0.0  0
 H7C  CONST_52  H17  C07  C08  C09   180.00   0.0  0
 H7C  CONST_53  H17  C07  C05  N04     0.00   0.0  0
 H7C  CONST_54  H4   C14  C03  N04     0.00   0.0  0
 H7C  Var_01    N23  C24  C25  C16    27.26  30.0  1
 H7C  Var_02    N23  C22  C21  C16    25.40  30.0  1
 H7C  Var_03    C24  N23  C22  C21   -62.65  30.0  1
 H7C  Var_04    C25  C24  N23  C22    33.49  30.0  1
 H7C  Var_05    C06  C01  S15  C16   -90.80  30.0  2
 H7C  Var_06    C02  C01  S15  C16    92.69  30.0  2
 H7C  Var_07    H13  C24  C25  C16   -93.98  30.0  1
 H7C  Var_08    H14  C24  C25  C16   149.86  30.0  1
 H7C  Var_09    H11  C22  C21  C16   -95.07  30.0  1
 H7C  Var_10    H12  C22  C21  C16   148.58  30.0  1
 H7C  Var_11    H22  N23  C22  C21    58.54  30.0  1
 H7C  Var_12    H13  C24  N23  C22   155.76  30.0  1
 H7C  Var_13    H14  C24  N23  C22   -88.80  30.0  1
 H7C  Var_14    H11  C22  N23  C24    58.98  30.0  1
 H7C  Var_15    H12  C22  N23  C24   173.92  30.0  1
 H7C  Var_16    H22  N23  C24  C25   -87.53  30.0  1
 H7C  Var_17    H9   C21  C22  N23   146.77  30.0  1
 H7C  Var_18    H10  C21  C22  N23   -95.99  30.0  1
 H7C  Var_19    H15  C25  C24  N23   149.38  30.0  1
 H7C  Var_20    H16  C25  C24  N23   -93.11  30.0  1
 H7C  Var_21    C20  O17  C09  C10     0.40  30.0  2
 H7C  Var_22    C19  O18  C12  C11    -0.85  30.0  2
 H7C  Var_23    C19  O18  C12  C13   179.13  30.0  2
 H7C  Var_24    C20  O17  C09  C08  -179.61  30.0  2
 H7C  Var_25    H6   C19  O18  C12  -179.78  30.0  3
 H7C  Var_26    H7   C19  O18  C12   -60.85  30.0  3
 H7C  Var_27    H8   C19  O18  C12    61.28  30.0  3
 H7C  Var_28    H19  C20  O17  C09   179.30  30.0  3
 H7C  Var_29    H20  C20  O17  C09   -61.78  30.0  3
 H7C  Var_30    H21  C20  O17  C09    60.39  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
 H7C  chir_01  C16  C25  C21  S15  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
 H7C  plan-1  C10  0.020
 H7C  plan-1  C11  0.020
 H7C  plan-1  C12  0.020
 H7C  plan-1  C13  0.020
 H7C  plan-1  C14  0.020
 H7C  plan-1  C01  0.020
 H7C  plan-1  C02  0.020
 H7C  plan-1  C03  0.020
 H7C  plan-1  C05  0.020
 H7C  plan-1  C06  0.020
 H7C  plan-1  C07  0.020
 H7C  plan-1  C08  0.020
 H7C  plan-1  C09  0.020
 H7C  plan-1  N04  0.020
 H7C  plan-1  O18  0.020
 H7C  plan-1  S15  0.020
 H7C  plan-1  H1   0.020
 H7C  plan-1  H2   0.020
 H7C  plan-1  H3   0.020
 H7C  plan-1  H4   0.020
 H7C  plan-1  H17  0.020
 H7C  plan-1  H18  0.020
 H7C  plan-1  O17  0.020

