# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 00:22:06 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 2,7-dimethoxy-9-(piperidin-4-ylmethylsulfanyl)acridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc3c(cc(OC)cc3c(SCC4CCNCC4)c2c1)C(O)=O
#
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
 H7X  H7X  "2,7-dimethoxy-9-(piperidin-4-ylmethylsulfanyl)acridine-4-carboxylic acid"  ligand  52  29  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H7X
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
 H7X  C10  C  CR66   0   0.110  83.3286  143.1758  15.6885
 H7X  C13  C  CR6    0   0.427  83.7301  140.7181  14.4008
 H7X  C20  C  CH2    0  -0.423  77.9034  141.1183  15.1230
 H7X  C21  C  CH2    0  -0.314  77.8197  140.7936  13.6324
 H7X  C24  C  CH2    0  -0.428  79.4415  139.1747  15.3863
 H7X  C26  C  CH3    0  -0.439  79.8313  146.2396  21.2859
 H7X  C01  C  CR6    0   0.419  80.7420  144.8569  19.5710
 H7X  C02  C  CR16   0  -0.381  81.4379  145.9583  18.9929
 H7X  C03  C  CR16   0  -0.274  82.2266  145.7644  17.9030
 H7X  C04  C  CR66   0   0.151  82.3752  144.4799  17.3126
 H7X  C05  C  CR66   0   0.182  81.6650  143.3761  17.8846
 H7X  C06  C  CR16   0  -0.458  80.8552  143.6061  19.0231
 H7X  C08  C  CR16   0  -0.476  82.8987  140.7689  15.4873
 H7X  C09  C  CR66   0   0.182  82.6691  141.9907  16.1627
 H7X  C11  C  CR6    0  -0.026  84.1956  143.0915  14.5540
 H7X  C12  C  CR16   0  -0.450  84.3903  141.8914  13.9383
 H7X  C16  C  CR6    0  -0.176  81.8197  142.1217  17.2727
 H7X  C18  C  CH3    0  -0.439  84.7270  139.3950  12.6836
 H7X  C19  C  CH2    0  -0.558  79.3132  140.9580  17.1867
 H7X  C23  C  CH2    0  -0.312  79.3084  138.9184  13.8874
 H7X  C25  C  CH1    0  -0.214  79.2428  140.6543  15.6983
 H7X  C27  C  C      0   0.356  84.8832  144.3489  14.0397
 H7X  N07  N  N      0  -0.450  83.1710  144.3636  16.2561
 H7X  N22  N  NH1    0  -0.573  78.0590  139.3952  13.3149
 H7X  O14  O  O2     0  -0.466  79.9601  144.9789  20.6566
 H7X  O15  O  O2     0  -0.469  83.8831  139.5191  13.8120
 H7X  O28  O  OC    -1  -0.588  84.1916  145.0699  13.3029
 H7X  O29  O  O      0  -0.587  86.0631  144.5034  14.3955
 H7X  S17  S  S2     0  -0.016  80.9666  140.7102  17.9256
 H7X  H3   H  HCH2   0   0.213  78.5627  141.3952  13.0965
 H7X  H4   H  HCH2   0   0.232  76.8430  141.0796  13.2360
 H7X  H5   H  HCH2   0   0.212  78.6873  138.5888  15.9257
 H7X  H6   H  HCH2   0   0.233  80.4170  138.8284  15.7370
 H7X  H7   H  HCH3   0   0.261  79.1728  146.0887  22.1376
 H7X  H8   H  HCH3   0   0.231  80.7901  146.6184  21.6483
 H7X  H9   H  HCH3   0   0.231  79.3817  146.9851  20.6255
 H7X  H10  H  HCR6   0   0.286  81.3520  146.9517  19.4111
 H7X  H11  H  HCR6   0   0.266  82.7633  146.5930  17.4592
 H7X  H12  H  HCR6   0   0.265  80.3299  142.7761  19.4775
 H7X  H13  H  HCR6   0   0.262  82.4143  139.8667  15.8343
 H7X  H14  H  HCR6   0   0.278  85.0515  141.8403  13.0824
 H7X  H15  H  HCH3   0   0.260  84.6936  138.3479  12.3925
 H7X  H16  H  HCH3   0   0.230  84.3818  140.0018  11.8429
 H7X  H17  H  HCH3   0   0.230  85.7622  139.6606  12.9110
 H7X  H18  H  HCH2   0   0.278  79.0006  141.9837  17.3932
 H7X  H19  H  HCH2   0   0.272  78.6488  140.2963  17.7489
 H7X  H20  H  HCH2   0   0.231  79.4066  137.8522  13.6738
 H7X  H21  H  HCH2   0   0.211  80.1334  139.4183  13.3668
 H7X  H22  H  HCH1   0   0.232  80.0326  141.2248  15.1934
 H7X  H23  H  HNH1   0   0.335  77.2971  138.8410  13.6899
 H7X  H1   H  HCH2   0   0.227  77.7761  142.1938  15.2768
 H7X  H2   H  HCH2   0   0.213  77.0823  140.6216  15.6538

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
 H7X  C18  O15  single    1.415  0.020  1.415
 H7X  C21  N22  single    1.454  0.020  1.454
 H7X  C21  C20  single    1.528  0.020  1.528
 H7X  O29  C27  deloc     1.242  0.020  1.242
 H7X  O15  C13  single    1.344  0.020  1.344
 H7X  N22  C23  single    1.455  0.020  1.455
 H7X  C12  C13  aromatic  1.424  0.020  1.424
 H7X  C12  C11  aromatic  1.363  0.020  1.363
 H7X  C27  O28  deloc     1.241  0.020  1.241
 H7X  C27  C11  single    1.523  0.020  1.523
 H7X  C13  C08  aromatic  1.369  0.020  1.369
 H7X  C20  C25  single    1.530  0.020  1.530
 H7X  C11  C10  aromatic  1.430  0.020  1.430
 H7X  C23  C24  single    1.526  0.020  1.526
 H7X  C08  C09  aromatic  1.415  0.020  1.415
 H7X  C10  C09  aromatic  1.437  0.020  1.437
 H7X  C10  N07  aromatic  1.326  0.020  1.326
 H7X  C25  C24  single    1.525  0.020  1.525
 H7X  C25  C19  single    1.521  0.020  1.521
 H7X  C09  C16  aromatic  1.404  0.020  1.404
 H7X  N07  C04  aromatic  1.328  0.020  1.328
 H7X  C19  S17  single    1.828  0.020  1.828
 H7X  C16  S17  single    1.774  0.020  1.774
 H7X  C16  C05  aromatic  1.404  0.020  1.404
 H7X  C04  C05  aromatic  1.432  0.020  1.432
 H7X  C04  C03  aromatic  1.421  0.020  1.421
 H7X  C05  C06  aromatic  1.416  0.020  1.416
 H7X  C03  C02  aromatic  1.359  0.020  1.359
 H7X  C06  C01  aromatic  1.370  0.020  1.370
 H7X  C02  C01  aromatic  1.425  0.020  1.425
 H7X  C01  O14  single    1.343  0.020  1.343
 H7X  O14  C26  single    1.415  0.020  1.415
 H7X  C20  H1   single    0.970  0.020  1.090
 H7X  C20  H2   single    0.970  0.020  1.090
 H7X  C21  H3   single    0.970  0.020  1.090
 H7X  C21  H4   single    0.970  0.020  1.090
 H7X  C24  H5   single    0.970  0.020  1.090
 H7X  C24  H6   single    0.970  0.020  1.090
 H7X  C26  H7   single    0.970  0.020  1.090
 H7X  C26  H8   single    0.970  0.020  1.090
 H7X  C26  H9   single    0.970  0.020  1.090
 H7X  C02  H10  single    0.930  0.020  1.080
 H7X  C03  H11  single    0.930  0.020  1.080
 H7X  C06  H12  single    0.930  0.020  1.080
 H7X  C08  H13  single    0.930  0.020  1.080
 H7X  C12  H14  single    0.930  0.020  1.080
 H7X  C18  H15  single    0.970  0.020  1.090
 H7X  C18  H16  single    0.970  0.020  1.090
 H7X  C18  H17  single    0.970  0.020  1.090
 H7X  C19  H18  single    0.970  0.020  1.090
 H7X  C19  H19  single    0.970  0.020  1.090
 H7X  C23  H20  single    0.970  0.020  1.090
 H7X  C23  H21  single    0.970  0.020  1.090
 H7X  C25  H22  single    0.970  0.020  1.090
 H7X  N22  H23  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
 H7X  N07  C10  C11  117.67  3.000
 H7X  N07  C10  C09  122.90  3.000
 H7X  C11  C10  C09  119.43  3.000
 H7X  O15  C13  C12  122.68  3.000
 H7X  C12  C13  C08  120.59  3.000
 H7X  O15  C13  C08  116.73  3.000
 H7X  H2   C20  H1   106.86  3.000
 H7X  H2   C20  C25  109.64  3.000
 H7X  H1   C20  C25  110.32  3.000
 H7X  H2   C20  C21  109.57  3.000
 H7X  H1   C20  C21  109.86  3.000
 H7X  C25  C20  C21  110.51  3.000
 H7X  H4   C21  H3   106.56  3.000
 H7X  H4   C21  N22  108.65  3.000
 H7X  H3   C21  N22  108.04  3.000
 H7X  H4   C21  C20  110.33  3.000
 H7X  H3   C21  C20  108.86  3.000
 H7X  N22  C21  C20  114.11  3.000
 H7X  H6   C24  H5   106.66  3.000
 H7X  H6   C24  C25  110.98  3.000
 H7X  H5   C24  C25  109.15  3.000
 H7X  H6   C24  C23  109.86  3.000
 H7X  H5   C24  C23  109.47  3.000
 H7X  C25  C24  C23  110.64  3.000
 H7X  H9   C26  H8   108.96  3.000
 H7X  H9   C26  H7   108.60  3.000
 H7X  H8   C26  H7   108.65  3.000
 H7X  H9   C26  O14  112.12  3.000
 H7X  H8   C26  O14  112.12  3.000
 H7X  H7   C26  O14  106.25  3.000
 H7X  O14  C01  C06  117.01  3.000
 H7X  O14  C01  C02  122.80  3.000
 H7X  C06  C01  C02  120.19  3.000
 H7X  H10  C02  C03  119.16  3.000
 H7X  H10  C02  C01  120.95  3.000
 H7X  C03  C02  C01  119.89  3.000
 H7X  H11  C03  C04  118.01  3.000
 H7X  H11  C03  C02  120.48  3.000
 H7X  C04  C03  C02  121.51  3.000
 H7X  N07  C04  C05  123.21  3.000
 H7X  C05  C04  C03  118.61  3.000
 H7X  N07  C04  C03  118.18  3.000
 H7X  C16  C05  C06  123.95  3.000
 H7X  C06  C05  C04  118.66  3.000
 H7X  C16  C05  C04  117.38  3.000
 H7X  H12  C06  C05  119.38  3.000
 H7X  H12  C06  C01  119.48  3.000
 H7X  C05  C06  C01  121.13  3.000
 H7X  H13  C08  C09  119.65  3.000
 H7X  H13  C08  C13  119.72  3.000
 H7X  C09  C08  C13  120.63  3.000
 H7X  C16  C09  C08  123.80  3.000
 H7X  C16  C09  C10  117.49  3.000
 H7X  C08  C09  C10  118.70  3.000
 H7X  C27  C11  C12  120.67  3.000
 H7X  C27  C11  C10  119.53  3.000
 H7X  C12  C11  C10  119.80  3.000
 H7X  H14  C12  C11  119.08  3.000
 H7X  H14  C12  C13  120.07  3.000
 H7X  C11  C12  C13  120.85  3.000
 H7X  S17  C16  C09  120.52  3.000
 H7X  S17  C16  C05  119.83  3.000
 H7X  C09  C16  C05  119.64  3.000
 H7X  H17  C18  H16  108.93  3.000
 H7X  H17  C18  H15  108.60  3.000
 H7X  H16  C18  H15  108.61  3.000
 H7X  H17  C18  O15  112.20  3.000
 H7X  H16  C18  O15  112.12  3.000
 H7X  H15  C18  O15  106.24  3.000
 H7X  H19  C19  H18  107.29  3.000
 H7X  H19  C19  S17  105.06  3.000
 H7X  H18  C19  S17  108.05  3.000
 H7X  H19  C19  C25  110.75  3.000
 H7X  H18  C19  C25  111.06  3.000
 H7X  S17  C19  C25  114.24  3.000
 H7X  H21  C23  H20  106.54  3.000
 H7X  H21  C23  N22  108.06  3.000
 H7X  H20  C23  N22  108.68  3.000
 H7X  H21  C23  C24  108.91  3.000
 H7X  H20  C23  C24  110.38  3.000
 H7X  N22  C23  C24  113.98  3.000
 H7X  H22  C25  C19  108.25  3.000
 H7X  H22  C25  C24  108.45  3.000
 H7X  C19  C25  C24  112.83  3.000
 H7X  H22  C25  C20  107.42  3.000
 H7X  C19  C25  C20  110.37  3.000
 H7X  C24  C25  C20  109.35  3.000
 H7X  O29  C27  O28  128.83  3.000
 H7X  O28  C27  C11  115.37  3.000
 H7X  O29  C27  C11  115.79  3.000
 H7X  C04  N07  C10  119.36  3.000
 H7X  H23  N22  C23  108.71  3.000
 H7X  H23  N22  C21  108.74  3.000
 H7X  C23  N22  C21  111.76  3.000
 H7X  C01  O14  C26  119.56  3.000
 H7X  C18  O15  C13  119.70  3.000
 H7X  C19  S17  C16  100.27  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
 H7X  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 H7X  CONST_02  C13  C08  C09  C10     0.00   0.0  0
 H7X  CONST_03  C05  C16  C09  C10     0.00   0.0  0
 H7X  CONST_04  C05  C04  N07  C10     0.00   0.0  0
 H7X  CONST_05  C03  C04  N07  C10   180.00   0.0  0
 H7X  CONST_06  C16  C09  C08  C13   180.00   0.0  0
 H7X  CONST_07  C16  C05  C06  C01   180.00   0.0  0
 H7X  CONST_08  C04  C05  C06  C01     0.00   0.0  0
 H7X  CONST_09  C04  C03  C02  C01     0.00   0.0  0
 H7X  CONST_10  N07  C04  C03  C02   180.00   0.0  0
 H7X  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 H7X  CONST_12  C05  C06  C01  C02     0.00   0.0  0
 H7X  CONST_13  C16  C05  C04  C03   180.00   0.0  0
 H7X  CONST_14  C06  C05  C04  C03     0.00   0.0  0
 H7X  CONST_15  C06  C01  C02  C03     0.00   0.0  0
 H7X  CONST_16  C11  C10  N07  C04   180.00   0.0  0
 H7X  CONST_17  C09  C10  N07  C04     0.00   0.0  0
 H7X  CONST_18  C09  C16  C05  C04     0.00   0.0  0
 H7X  CONST_19  C08  C09  C16  C05   180.00   0.0  0
 H7X  CONST_20  C09  C16  C05  C06   180.00   0.0  0
 H7X  CONST_21  N07  C04  C05  C06   180.00   0.0  0
 H7X  CONST_22  C11  C12  C13  C08     0.00   0.0  0
 H7X  CONST_23  C11  C10  C09  C08     0.00   0.0  0
 H7X  CONST_24  N07  C10  C09  C08   180.00   0.0  0
 H7X  CONST_25  C12  C13  C08  C09     0.00   0.0  0
 H7X  CONST_26  C12  C11  C10  C09     0.00   0.0  0
 H7X  CONST_27  C16  C09  C10  C11   180.00   0.0  0
 H7X  CONST_28  N07  C10  C11  C12   180.00   0.0  0
 H7X  CONST_29  N07  C10  C09  C16     0.00   0.0  0
 H7X  CONST_30  N07  C04  C05  C16     0.00   0.0  0
 H7X  CONST_31  S17  C16  C09  C10   180.00   0.0  0
 H7X  CONST_32  C27  C11  C12  C13   180.00   0.0  0
 H7X  CONST_33  O14  C01  C02  C03   180.00   0.0  0
 H7X  CONST_34  S17  C16  C05  C04   180.00   0.0  0
 H7X  CONST_35  O14  C01  C06  C05   180.00   0.0  0
 H7X  CONST_36  S17  C16  C05  C06     0.00   0.0  0
 H7X  CONST_37  S17  C16  C09  C08     0.00   0.0  0
 H7X  CONST_38  O15  C13  C08  C09   180.00   0.0  0
 H7X  CONST_39  C27  C11  C10  C09   180.00   0.0  0
 H7X  CONST_40  O15  C13  C12  C11   180.00   0.0  0
 H7X  CONST_41  N07  C10  C11  C27     0.00   0.0  0
 H7X  CONST_42  H14  C12  C11  C10   180.00   0.0  0
 H7X  CONST_43  H13  C08  C09  C10   180.00   0.0  0
 H7X  CONST_44  H11  C03  C02  C01   180.00   0.0  0
 H7X  CONST_45  H12  C06  C01  C02   180.00   0.0  0
 H7X  CONST_46  H12  C06  C05  C04   180.00   0.0  0
 H7X  CONST_47  H10  C02  C03  C04   180.00   0.0  0
 H7X  CONST_48  H11  C03  C04  C05   180.00   0.0  0
 H7X  CONST_49  H10  C02  C01  C06   180.00   0.0  0
 H7X  CONST_50  H14  C12  C13  C08   180.00   0.0  0
 H7X  CONST_51  H13  C08  C13  C12   180.00   0.0  0
 H7X  CONST_52  H13  C08  C09  C16     0.00   0.0  0
 H7X  CONST_53  H12  C06  C05  C16     0.00   0.0  0
 H7X  CONST_54  H11  C03  C04  N07     0.00   0.0  0
 H7X  Var_01    C23  N22  C21  C20   -52.78  30.0  1
 H7X  Var_02    C24  C23  N22  C21    52.87  30.0  1
 H7X  Var_03    N22  C21  C20  C25    54.47  30.0  1
 H7X  Var_04    N22  C23  C24  C25   -54.83  30.0  1
 H7X  Var_05    H23  N22  C21  C20    67.22  30.0  1
 H7X  Var_06    H20  C23  N22  C21   176.43  30.0  1
 H7X  Var_07    H21  C23  N22  C21   -68.34  30.0  1
 H7X  Var_08    H23  N22  C23  C24   -67.14  30.0  1
 H7X  Var_09    H3   C21  N22  C23    68.43  30.0  1
 H7X  Var_10    H4   C21  N22  C23  -176.34  30.0  1
 H7X  Var_11    H3   C21  C20  C25   -66.28  30.0  1
 H7X  Var_12    H4   C21  C20  C25   177.11  30.0  1
 H7X  Var_13    H20  C23  C24  C25  -177.46  30.0  1
 H7X  Var_14    H21  C23  C24  C25    65.91  30.0  1
 H7X  Var_15    H1   C20  C21  N22   176.43  30.0  1
 H7X  Var_16    H2   C20  C21  N22   -66.46  30.0  1
 H7X  Var_17    H5   C24  C23  N22    65.49  30.0  1
 H7X  Var_18    H6   C24  C23  N22  -177.70  30.0  1
 H7X  Var_19    O29  C27  C11  C10    99.32  30.0  2
 H7X  Var_20    O28  C27  C11  C10   -81.79  30.0  2
 H7X  Var_21    C06  C01  O14  C26   178.42  30.0  1
 H7X  Var_22    C02  C01  O14  C26    -1.44  30.0  1
 H7X  Var_23    C19  S17  C16  C05    81.01  30.0  2
 H7X  Var_24    C18  O15  C13  C08   179.95  30.0  2
 H7X  Var_25    C19  S17  C16  C09  -100.18  30.0  2
 H7X  Var_26    C18  O15  C13  C12    -0.16  30.0  2
 H7X  Var_27    O29  C27  C11  C12   -81.18  30.0  2
 H7X  Var_28    O28  C27  C11  C12    97.71  30.0  2
 H7X  Var_29    C25  C19  S17  C16    73.67  30.0  2
 H7X  Var_30    H15  C18  O15  C13   179.75  30.0  3
 H7X  Var_31    H16  C18  O15  C13   -61.75  30.0  3
 H7X  Var_32    H17  C18  O15  C13    61.21  30.0  3
 H7X  Var_33    H7   C26  O14  C01  -179.05  30.0  3
 H7X  Var_34    H8   C26  O14  C01   -60.49  30.0  3
 H7X  Var_35    H9   C26  O14  C01    62.45  30.0  3
 H7X  Var_36    H18  C19  S17  C16   -50.47  30.0  2
 H7X  Var_37    H19  C19  S17  C16  -164.77  30.0  2

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
 H7X  chir_01  C25  C20  C24  C19  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
 H7X  plan-1  C10  0.020
 H7X  plan-1  C13  0.020
 H7X  plan-1  C01  0.020
 H7X  plan-1  C02  0.020
 H7X  plan-1  C03  0.020
 H7X  plan-1  C04  0.020
 H7X  plan-1  C05  0.020
 H7X  plan-1  C06  0.020
 H7X  plan-1  C08  0.020
 H7X  plan-1  C09  0.020
 H7X  plan-1  C11  0.020
 H7X  plan-1  C12  0.020
 H7X  plan-1  C16  0.020
 H7X  plan-1  C27  0.020
 H7X  plan-1  N07  0.020
 H7X  plan-1  O14  0.020
 H7X  plan-1  O15  0.020
 H7X  plan-1  S17  0.020
 H7X  plan-1  H10  0.020
 H7X  plan-1  H11  0.020
 H7X  plan-1  H12  0.020
 H7X  plan-1  H13  0.020
 H7X  plan-1  H14  0.020
 H7X  plan-2  C11  0.020
 H7X  plan-2  C27  0.020
 H7X  plan-2  O28  0.020
 H7X  plan-2  O29  0.020

