# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 07:37:51 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 2,7-dimethoxy-9-(piperidin-4-ylmethylsulfanyl)acridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc3ccc(OC)cc3c(SCC4CCNCC4)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
 H5R  H5R  "2,7-dimethoxy-9-(piperidin-4-ylmethylsulfanyl)acridine"
  ligand  50  26  .  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_H5R
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
 H5R  C13  C  CR66  0   0.144  83.5522  143.1282  15.0922
 H5R  C15  C  CR16  0  -0.378  84.5191  141.6508  13.4282
 H5R  C17  C  CH3   0  -0.439  84.7938  139.0263  12.4485
 H5R  C20  C  CH2   0  -0.560  79.6808  141.1009  17.1367
 H5R  C21  C  CH1   0  -0.213  79.4838  140.6865  15.6865
 H5R  C22  C  CH2   0  -0.424  78.0930  141.1047  15.2077
 H5R  C26  C  CH2   0  -0.428  79.6658  139.1876  15.4671
 H5R  C01  C  CH3   0  -0.438  79.8327  144.7122  20.7730
 H5R  C04  C  CR16  0  -0.496  81.2848  143.9219  18.5085
 H5R  C05  C  CR6   0   0.413  81.1673  145.2295  18.8884
 H5R  C06  C  CR16  0  -0.335  81.7870  146.2659  18.1245
 H5R  C07  C  CR16  0  -0.273  82.5115  145.9627  17.0226
 H5R  C08  C  CR66  0   0.193  82.0289  143.5726  17.3464
 H5R  C09  C  CR66  0   0.139  82.6669  144.6104  16.5922
 H5R  C11  C  CR16  0  -0.453  83.1623  140.7142  15.2024
 H5R  C12  C  CR66  0   0.171  82.9530  142.0038  15.7451
 H5R  C14  C  CR16  0  -0.272  84.3378  142.9015  13.9302
 H5R  C16  C  CR6   0   0.419  83.9155  140.5333  14.0720
 H5R  C18  C  CR6   0  -0.168  82.1723  142.2573  16.8871
 H5R  C23  C  CH2   0  -0.314  77.8649  140.6659  13.7624
 H5R  C25  C  CH2   0  -0.313  79.3867  138.8182  14.0122
 H5R  N10  N  N     0  -0.459  83.3973  144.3809  15.5112
 H5R  N24  N  NH1   0  -0.572  78.0818  139.2465  13.5333
 H5R  O02  O  O2    0  -0.466  84.0443  139.2743  13.6224
 H5R  O03  O  O2    0  -0.461  80.4975  145.6625  19.9645
 H5R  S19  S  S2    0  -0.011  81.3922  140.9197  17.7506
 H5R  H1   H  HCR6  0   0.288  85.1227  141.5224  12.5403
 H5R  H2   H  HCH3  0   0.261  84.7459  137.9537  12.2780
 H5R  H3   H  HCH3  0   0.232  84.3750  139.5377  11.5785
 H5R  H4   H  HCH3  0   0.231  85.8416  139.3155  12.5608
 H5R  H5   H  HCH2  0   0.279  79.3737  142.1373  17.2928
 H5R  H6   H  HCH2  0   0.274  79.0752  140.4797  17.8018
 H5R  H7   H  HCH1  0   0.231  80.2180  141.2200  15.0690
 H5R  H8   H  HCH2  0   0.228  77.9736  142.1889  15.2910
 H5R  H9   H  HCH2  0   0.214  77.3308  140.6507  15.8520
 H5R  H10  H  HCH2  0   0.212  78.9745  138.6417  16.1209
 H5R  H11  H  HCH2  0   0.233  80.6743  138.8700  15.7441
 H5R  H12  H  HCH3  0   0.263  79.3530  145.2690  21.5738
 H5R  H13  H  HCH3  0   0.231  79.0689  144.1680  20.2115
 H5R  H14  H  HCH3  0   0.232  80.5295  143.9924  21.2102
 H5R  H15  H  HCR6  0   0.286  80.8350  143.1251  19.0842
 H5R  H16  H  HCR6  0   0.273  81.6704  147.2930  18.4466
 H5R  H17  H  HCR6  0   0.266  82.9904  146.7398  16.4412
 H5R  H18  H  HCR6  0   0.268  82.7155  139.8554  15.6844
 H5R  H19  H  HCR6  0   0.268  84.7916  143.7575  13.4478
 H5R  H20  H  HCH2  0   0.213  78.5471  141.2221  13.1097
 H5R  H21  H  HCH2  0   0.233  76.8520  140.9210  13.4437
 H5R  H22  H  HCH2  0   0.232  79.4740  137.7388  13.8721
 H5R  H23  H  HCH2  0   0.212  80.1504  139.2780  13.3744
 H5R  H24  H  HNH1  0   0.336  77.3673  138.7244  14.0284

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
 H5R  C17  O02  single    1.415  0.020  1.415
 H5R  O02  C16  single    1.343  0.020  1.343
 H5R  C23  N24  single    1.454  0.020  1.454
 H5R  C23  C22  single    1.528  0.020  1.528
 H5R  C15  C16  aromatic  1.424  0.020  1.424
 H5R  C15  C14  aromatic  1.360  0.020  1.360
 H5R  N24  C25  single    1.454  0.020  1.454
 H5R  C16  C11  aromatic  1.370  0.020  1.370
 H5R  C14  C13  aromatic  1.421  0.020  1.421
 H5R  C22  C21  single    1.529  0.020  1.529
 H5R  C25  C26  single    1.527  0.020  1.527
 H5R  C11  C12  aromatic  1.415  0.020  1.415
 H5R  C13  C12  aromatic  1.432  0.020  1.432
 H5R  C13  N10  aromatic  1.330  0.020  1.330
 H5R  C21  C26  single    1.526  0.020  1.526
 H5R  C21  C20  single    1.521  0.020  1.521
 H5R  C12  C18  aromatic  1.406  0.020  1.406
 H5R  N10  C09  aromatic  1.325  0.020  1.325
 H5R  C20  S19  single    1.827  0.020  1.827
 H5R  C18  C08  aromatic  1.401  0.020  1.401
 H5R  C18  S19  single    1.773  0.020  1.773
 H5R  C09  C08  aromatic  1.433  0.020  1.433
 H5R  C09  C07  aromatic  1.428  0.020  1.428
 H5R  C08  C04  aromatic  1.423  0.020  1.423
 H5R  C07  C06  aromatic  1.353  0.020  1.353
 H5R  C04  C05  aromatic  1.367  0.020  1.367
 H5R  C06  C05  aromatic  1.429  0.020  1.429
 H5R  C05  O03  single    1.339  0.020  1.339
 H5R  O03  C01  single    1.414  0.020  1.414
 H5R  C15  H1   single    0.930  0.020  1.080
 H5R  C17  H2   single    0.970  0.020  1.090
 H5R  C17  H3   single    0.970  0.020  1.090
 H5R  C17  H4   single    0.970  0.020  1.090
 H5R  C20  H5   single    0.970  0.020  1.090
 H5R  C20  H6   single    0.970  0.020  1.090
 H5R  C21  H7   single    0.970  0.020  1.090
 H5R  C22  H8   single    0.970  0.020  1.090
 H5R  C22  H9   single    0.970  0.020  1.090
 H5R  C26  H10  single    0.970  0.020  1.090
 H5R  C26  H11  single    0.970  0.020  1.090
 H5R  C01  H12  single    0.970  0.020  1.090
 H5R  C01  H13  single    0.970  0.020  1.090
 H5R  C01  H14  single    0.970  0.020  1.090
 H5R  C04  H15  single    0.930  0.020  1.080
 H5R  C06  H16  single    0.930  0.020  1.080
 H5R  C07  H17  single    0.930  0.020  1.080
 H5R  C11  H18  single    0.930  0.020  1.080
 H5R  C14  H19  single    0.930  0.020  1.080
 H5R  C23  H20  single    0.970  0.020  1.090
 H5R  C23  H21  single    0.970  0.020  1.090
 H5R  C25  H22  single    0.970  0.020  1.090
 H5R  C25  H23  single    0.970  0.020  1.090
 H5R  N24  H24  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
 H5R  N10  C13  C14  118.19  3.000
 H5R  N10  C13  C12  123.19  3.000
 H5R  C14  C13  C12  118.62  3.000
 H5R  H1   C15  C16  120.98  3.000
 H5R  H1   C15  C14  119.13  3.000
 H5R  C16  C15  C14  119.89  3.000
 H5R  H4   C17  H3   108.99  3.000
 H5R  H4   C17  H2   108.63  3.000
 H5R  H3   C17  H2   108.66  3.000
 H5R  H4   C17  O02  112.11  3.000
 H5R  H3   C17  O02  112.06  3.000
 H5R  H2   C17  O02  106.25  3.000
 H5R  H6   C20  H5   107.25  3.000
 H5R  H6   C20  S19  104.96  3.000
 H5R  H5   C20  S19  108.03  3.000
 H5R  H6   C20  C21  110.70  3.000
 H5R  H5   C20  C21  111.00  3.000
 H5R  S19  C20  C21  114.49  3.000
 H5R  H7   C21  C26  108.47  3.000
 H5R  H7   C21  C22  107.41  3.000
 H5R  C26  C21  C22  109.39  3.000
 H5R  H7   C21  C20  108.50  3.000
 H5R  C26  C21  C20  112.91  3.000
 H5R  C22  C21  C20  109.99  3.000
 H5R  H9   C22  H8   106.84  3.000
 H5R  H9   C22  C23  109.47  3.000
 H5R  H8   C22  C23  109.91  3.000
 H5R  H9   C22  C21  109.57  3.000
 H5R  H8   C22  C21  110.27  3.000
 H5R  C23  C22  C21  110.70  3.000
 H5R  H11  C26  H10  106.61  3.000
 H5R  H11  C26  C25  109.87  3.000
 H5R  H10  C26  C25  109.42  3.000
 H5R  H11  C26  C21  111.04  3.000
 H5R  H10  C26  C21  109.15  3.000
 H5R  C25  C26  C21  110.67  3.000
 H5R  H14  C01  H13  108.84  3.000
 H5R  H14  C01  H12  108.90  3.000
 H5R  H13  C01  H12  108.97  3.000
 H5R  H14  C01  O03  111.82  3.000
 H5R  H13  C01  O03  111.68  3.000
 H5R  H12  C01  O03  106.54  3.000
 H5R  H15  C04  C08  118.13  3.000
 H5R  H15  C04  C05  121.42  3.000
 H5R  C08  C04  C05  120.44  3.000
 H5R  O03  C05  C06  114.32  3.000
 H5R  O03  C05  C04  125.14  3.000
 H5R  C06  C05  C04  120.53  3.000
 H5R  H16  C06  C07  120.83  3.000
 H5R  H16  C06  C05  118.84  3.000
 H5R  C07  C06  C05  120.33  3.000
 H5R  H17  C07  C09  118.03  3.000
 H5R  H17  C07  C06  120.90  3.000
 H5R  C09  C07  C06  121.07  3.000
 H5R  C18  C08  C09  117.51  3.000
 H5R  C09  C08  C04  119.00  3.000
 H5R  C18  C08  C04  123.48  3.000
 H5R  N10  C09  C08  123.34  3.000
 H5R  C08  C09  C07  118.61  3.000
 H5R  N10  C09  C07  118.05  3.000
 H5R  H18  C11  C16  119.33  3.000
 H5R  H18  C11  C12  119.46  3.000
 H5R  C16  C11  C12  121.21  3.000
 H5R  C18  C12  C11  123.92  3.000
 H5R  C18  C12  C13  117.45  3.000
 H5R  C11  C12  C13  118.63  3.000
 H5R  H19  C14  C15  120.46  3.000
 H5R  H19  C14  C13  118.05  3.000
 H5R  C15  C14  C13  121.49  3.000
 H5R  O02  C16  C11  116.91  3.000
 H5R  C11  C16  C15  120.16  3.000
 H5R  O02  C16  C15  122.93  3.000
 H5R  S19  C18  C12  120.25  3.000
 H5R  S19  C18  C08  120.25  3.000
 H5R  C12  C18  C08  119.50  3.000
 H5R  H21  C23  H20  106.56  3.000
 H5R  H21  C23  N24  108.69  3.000
 H5R  H20  C23  N24  107.98  3.000
 H5R  H21  C23  C22  110.33  3.000
 H5R  H20  C23  C22  108.95  3.000
 H5R  N24  C23  C22  114.03  3.000
 H5R  H23  C25  H22  106.52  3.000
 H5R  H23  C25  N24  108.06  3.000
 H5R  H22  C25  N24  108.69  3.000
 H5R  H23  C25  C26  109.01  3.000
 H5R  H22  C25  C26  110.29  3.000
 H5R  N24  C25  C26  113.99  3.000
 H5R  C09  N10  C13  118.98  3.000
 H5R  H24  N24  C25  108.65  3.000
 H5R  H24  N24  C23  108.69  3.000
 H5R  C25  N24  C23  111.68  3.000
 H5R  C16  O02  C17  119.53  3.000
 H5R  C05  O03  C01  118.51  3.000
 H5R  C18  S19  C20  100.00  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
 H5R  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 H5R  CONST_02  C16  C11  C12  C13     0.00   0.0  0
 H5R  CONST_03  C08  C18  C12  C13     0.00   0.0  0
 H5R  CONST_04  C08  C09  N10  C13     0.00   0.0  0
 H5R  CONST_05  C07  C09  N10  C13   180.00   0.0  0
 H5R  CONST_06  C12  C11  C16  C15     0.00   0.0  0
 H5R  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 H5R  CONST_08  N10  C13  C14  C15   180.00   0.0  0
 H5R  CONST_09  C12  C18  C08  C04   180.00   0.0  0
 H5R  CONST_10  N10  C09  C08  C04   180.00   0.0  0
 H5R  CONST_11  C07  C09  C08  C04     0.00   0.0  0
 H5R  CONST_12  C07  C06  C05  C04     0.00   0.0  0
 H5R  CONST_13  C18  C08  C04  C05   180.00   0.0  0
 H5R  CONST_14  C09  C08  C04  C05     0.00   0.0  0
 H5R  CONST_15  C09  C07  C06  C05     0.00   0.0  0
 H5R  CONST_16  N10  C09  C07  C06   180.00   0.0  0
 H5R  CONST_17  C08  C09  C07  C06     0.00   0.0  0
 H5R  CONST_18  C08  C04  C05  C06     0.00   0.0  0
 H5R  CONST_19  C18  C08  C09  C07   180.00   0.0  0
 H5R  CONST_20  C11  C12  C18  C08   180.00   0.0  0
 H5R  CONST_21  C14  C13  N10  C09   180.00   0.0  0
 H5R  CONST_22  C12  C13  N10  C09     0.00   0.0  0
 H5R  CONST_23  C12  C18  C08  C09     0.00   0.0  0
 H5R  CONST_24  C14  C15  C16  C11     0.00   0.0  0
 H5R  CONST_25  C14  C13  C12  C11     0.00   0.0  0
 H5R  CONST_26  N10  C13  C12  C11   180.00   0.0  0
 H5R  CONST_27  C18  C12  C13  C14   180.00   0.0  0
 H5R  CONST_28  C18  C12  C11  C16   180.00   0.0  0
 H5R  CONST_29  N10  C13  C12  C18     0.00   0.0  0
 H5R  CONST_30  N10  C09  C08  C18     0.00   0.0  0
 H5R  CONST_31  S19  C18  C12  C13   180.00   0.0  0
 H5R  CONST_32  S19  C18  C08  C04     0.00   0.0  0
 H5R  CONST_33  O03  C05  C06  C07   180.00   0.0  0
 H5R  CONST_34  O03  C05  C04  C08   180.00   0.0  0
 H5R  CONST_35  S19  C18  C08  C09   180.00   0.0  0
 H5R  CONST_36  S19  C18  C12  C11     0.00   0.0  0
 H5R  CONST_37  O02  C16  C11  C12   180.00   0.0  0
 H5R  CONST_38  O02  C16  C15  C14   180.00   0.0  0
 H5R  CONST_39  H1   C15  C14  C13   180.00   0.0  0
 H5R  CONST_40  H18  C11  C12  C13   180.00   0.0  0
 H5R  CONST_41  H18  C11  C16  C15   180.00   0.0  0
 H5R  CONST_42  H16  C06  C05  C04   180.00   0.0  0
 H5R  CONST_43  H17  C07  C06  C05   180.00   0.0  0
 H5R  CONST_44  H15  C04  C05  C06   180.00   0.0  0
 H5R  CONST_45  H17  C07  C09  C08   180.00   0.0  0
 H5R  CONST_46  H15  C04  C08  C09   180.00   0.0  0
 H5R  CONST_47  H16  C06  C07  C09   180.00   0.0  0
 H5R  CONST_48  H1   C15  C16  C11   180.00   0.0  0
 H5R  CONST_49  H19  C14  C13  C12   180.00   0.0  0
 H5R  CONST_50  H19  C14  C15  C16   180.00   0.0  0
 H5R  CONST_51  H18  C11  C12  C18     0.00   0.0  0
 H5R  CONST_52  H15  C04  C08  C18     0.00   0.0  0
 H5R  CONST_53  H19  C14  C13  N10     0.00   0.0  0
 H5R  CONST_54  H17  C07  C09  N10     0.00   0.0  0
 H5R  Var_01    N24  C23  C22  C21    54.41  30.0  1
 H5R  Var_02    N24  C25  C26  C21   -54.83  30.0  1
 H5R  Var_03    C25  N24  C23  C22   -52.95  30.0  1
 H5R  Var_04    C23  N24  C25  C26    53.14  30.0  1
 H5R  Var_05    H20  C23  C22  C21   -66.30  30.0  1
 H5R  Var_06    H21  C23  C22  C21   177.05  30.0  1
 H5R  Var_07    H22  C25  C26  C21  -177.42  30.0  1
 H5R  Var_08    H23  C25  C26  C21    65.97  30.0  1
 H5R  Var_09    H24  N24  C23  C22    66.91  30.0  1
 H5R  Var_10    H24  N24  C25  C26   -66.73  30.0  1
 H5R  Var_11    H22  C25  N24  C23   176.60  30.0  1
 H5R  Var_12    H23  C25  N24  C23   -68.19  30.0  1
 H5R  Var_13    H20  C23  N24  C25    68.29  30.0  1
 H5R  Var_14    H21  C23  N24  C25  -176.49  30.0  1
 H5R  Var_15    H8   C22  C23  N24   176.46  30.0  1
 H5R  Var_16    H9   C22  C23  N24   -66.49  30.0  1
 H5R  Var_17    H10  C26  C25  N24    65.47  30.0  1
 H5R  Var_18    H11  C26  C25  N24  -177.81  30.0  1
 H5R  Var_19    C17  O02  C16  C15    -0.87  30.0  2
 H5R  Var_20    C11  C16  O02  C17   179.09  30.0  2
 H5R  Var_21    C12  C18  S19  C20  -102.04  30.0  3
 H5R  Var_22    C08  C18  S19  C20    78.73  30.0  3
 H5R  Var_23    C18  S19  C20  C21    72.21  30.0  3
 H5R  Var_24    C04  C05  O03  C01    -1.15  30.0  1
 H5R  Var_25    C06  C05  O03  C01   179.06  30.0  1
 H5R  Var_26    H12  C01  O03  C05  -179.50  30.0  3
 H5R  Var_27    H13  C01  O03  C05   -60.62  30.0  3
 H5R  Var_28    H14  C01  O03  C05    61.62  30.0  3
 H5R  Var_29    H2   C17  O02  C16  -179.28  30.0  3
 H5R  Var_30    H3   C17  O02  C16   -60.74  30.0  3
 H5R  Var_31    H4   C17  O02  C16    62.19  30.0  3
 H5R  Var_32    H5   C20  S19  C18   -52.01  30.0  2
 H5R  Var_33    H6   C20  S19  C18  -166.21  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
 H5R  chir_01  C21  C22  C26  C20  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
 H5R  plan-1  C13  0.020
 H5R  plan-1  C15  0.020
 H5R  plan-1  C04  0.020
 H5R  plan-1  C05  0.020
 H5R  plan-1  C06  0.020
 H5R  plan-1  C07  0.020
 H5R  plan-1  C08  0.020
 H5R  plan-1  C09  0.020
 H5R  plan-1  C11  0.020
 H5R  plan-1  C12  0.020
 H5R  plan-1  C14  0.020
 H5R  plan-1  C16  0.020
 H5R  plan-1  C18  0.020
 H5R  plan-1  N10  0.020
 H5R  plan-1  O02  0.020
 H5R  plan-1  O03  0.020
 H5R  plan-1  S19  0.020
 H5R  plan-1  H1   0.020
 H5R  plan-1  H15  0.020
 H5R  plan-1  H16  0.020
 H5R  plan-1  H17  0.020
 H5R  plan-1  H18  0.020
 H5R  plan-1  H19  0.020

