# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 15:25:45 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: [2,7-dimethoxy-9-[[(3~{R})-pyrrolidin-3-yl]methylsulfanyl]acridin-4-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc3c(CO)cc(OC)cc3c(SC[C@@H]4CCNC4)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
 H96  H96  "[2,7-dimethoxy-9-[[(3R)-pyrrolidin-3-yl]methylsulfanyl]acridin-4-yl]methanol"  ligand  51  27  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H96
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
 H96  C13  C  CR66  0   0.148  82.4920  144.5988  17.3197
 H96  C15  C  CR16  0  -0.335  81.5781  146.0166  19.0570
 H96  C17  C  CH3   0  -0.440  79.3542  144.1425  21.2465
 H96  C20  C  CH2   0  -0.570  79.2184  141.2501  17.2950
 H96  C21  C  CR15  0  -0.242  78.7313  140.7971  15.9271
 H96  C22  C  CH2   0  -0.291  79.3726  141.5108  14.7077
 H96  C24  C  CH2   0  -0.321  78.9379  139.3021  14.0887
 H96  C26  C  CH2   0  -0.219  85.0471  144.5148  14.0731
 H96  C01  C  CH3   0  -0.441  84.7255  139.6724  12.4619
 H96  C04  C  CR16  0  -0.475  82.8995  140.9804  15.3006
 H96  C05  C  CR6   0   0.436  83.7448  140.9448  14.2250
 H96  C06  C  CR16  0  -0.443  84.4605  142.1130  13.8416
 H96  C07  C  CR6   0   0.073  84.3161  143.2837  14.5239
 H96  C08  C  CR66  0   0.173  82.7180  142.1720  16.0412
 H96  C09  C  CR66  0   0.122  83.4283  143.3504  15.6442
 H96  C11  C  CR16  0  -0.505  80.9298  143.6787  18.9810
 H96  C12  C  CR66  0   0.196  81.7394  143.4919  17.8260
 H96  C14  C  CR16  0  -0.275  82.3751  145.8617  17.9743
 H96  C16  C  CR6   0   0.413  80.8459  144.9058  19.5772
 H96  C18  C  CR6   0  -0.176  81.8502  142.2739  17.1440
 H96  C25  C  CH2   0  -0.438  78.9013  139.3093  15.6155
 H96  N10  N  N     0  -0.453  83.3002  144.5121  16.2744
 H96  N23  N  NR15  0  -0.592  79.6990  140.4886  13.7110
 H96  O02  O  O2    0  -0.461  80.1109  145.1845  20.6617
 H96  O03  O  O2    0  -0.468  83.8482  139.7781  13.5678
 H96  O27  O  OH1   0  -0.662  84.1384  145.3441  13.3800
 H96  S19  S  S2    0  -0.005  80.9586  140.8473  17.7022
 H96  H1   H  HCR6  0   0.273  81.4914  146.9767  19.5500
 H96  H2   H  HCH3  0   0.263  78.8291  144.5784  22.0924
 H96  H3   H  HCH3  0   0.232  78.6220  143.7325  20.5460
 H96  H4   H  HCH3  0   0.232  79.9919  143.3302  21.6048
 H96  H5   H  HCH2  0   0.287  79.0754  142.3232  17.4263
 H96  H6   H  HCH2  0   0.282  78.6393  140.7563  18.0774
 H96  H7   H  HCR5  0   0.250  77.6586  141.0207  15.9252
 H96  H8   H  HCH2  0   0.237  80.2702  142.0682  14.9733
 H96  H9   H  HCH2  0   0.224  78.6662  142.2353  14.2940
 H96  H10  H  HCH2  0   0.215  77.9212  139.3750  13.6892
 H96  H11  H  HCH2  0   0.235  79.3906  138.4049  13.6658
 H96  H12  H  HCH2  0   0.209  85.8829  144.2130  13.4301
 H96  H13  H  HCH2  0   0.213  85.4755  145.0239  14.9417
 H96  H14  H  HCH3  0   0.263  84.6437  138.6484  12.1062
 H96  H15  H  HCH3  0   0.232  84.4463  140.3474  11.6493
 H96  H16  H  HCH3  0   0.232  85.7642  139.8627  12.7423
 H96  H17  H  HCR6  0   0.270  82.3668  140.0846  15.5916
 H96  H18  H  HCR6  0   0.285  85.1306  142.0880  12.9918
 H96  H19  H  HCR6  0   0.290  80.4046  142.8231  19.3811
 H96  H20  H  HCR6  0   0.266  82.9438  146.6933  17.5789
 H96  H21  H  HCH2  0   0.232  78.1023  138.6977  16.0375
 H96  H22  H  HCH2  0   0.223  79.8524  138.9373  16.0069
 H96  H23  H  HNR5  0   0.349  80.6837  140.2675  13.7888
 H96  H25  H  HOH1  0   0.453  84.5384  146.2147  13.2954

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
 H96  C01  O03  single    1.416  0.020  1.416
 H96  O03  C05  single    1.343  0.020  1.343
 H96  N23  C24  single    1.459  0.020  1.459
 H96  N23  C22  single    1.465  0.020  1.465
 H96  C06  C05  aromatic  1.423  0.020  1.423
 H96  C06  C07  aromatic  1.363  0.020  1.363
 H96  C26  O27  single    1.412  0.020  1.412
 H96  C26  C07  single    1.501  0.020  1.501
 H96  C05  C04  aromatic  1.368  0.020  1.368
 H96  C07  C09  aromatic  1.431  0.020  1.431
 H96  C24  C25  single    1.527  0.020  1.527
 H96  C22  C21  single    1.552  0.020  1.552
 H96  C04  C08  aromatic  1.415  0.020  1.415
 H96  C09  C08  aromatic  1.432  0.020  1.432
 H96  C09  N10  aromatic  1.328  0.020  1.328
 H96  C25  C21  single    1.529  0.020  1.529
 H96  C08  C18  aromatic  1.407  0.020  1.407
 H96  C21  C20  single    1.521  0.020  1.521
 H96  N10  C13  aromatic  1.324  0.020  1.324
 H96  C18  S19  single    1.772  0.020  1.772
 H96  C18  C12  aromatic  1.400  0.020  1.400
 H96  C20  S19  single    1.832  0.020  1.832
 H96  C13  C12  aromatic  1.431  0.020  1.431
 H96  C13  C14  aromatic  1.427  0.020  1.427
 H96  C12  C11  aromatic  1.423  0.020  1.423
 H96  C14  C15  aromatic  1.353  0.020  1.353
 H96  C11  C16  aromatic  1.367  0.020  1.367
 H96  C15  C16  aromatic  1.429  0.020  1.429
 H96  C16  O02  single    1.339  0.020  1.339
 H96  O02  C17  single    1.414  0.020  1.414
 H96  C15  H1   single    0.930  0.020  1.080
 H96  C17  H2   single    0.970  0.020  1.090
 H96  C17  H3   single    0.970  0.020  1.090
 H96  C17  H4   single    0.970  0.020  1.090
 H96  C20  H5   single    0.970  0.020  1.090
 H96  C20  H6   single    0.970  0.020  1.090
 H96  C21  H7   single    0.970  0.020  1.090
 H96  C22  H8   single    0.970  0.020  1.090
 H96  C22  H9   single    0.970  0.020  1.090
 H96  C24  H10  single    0.970  0.020  1.090
 H96  C24  H11  single    0.970  0.020  1.090
 H96  C26  H12  single    0.970  0.020  1.090
 H96  C26  H13  single    0.970  0.020  1.090
 H96  C01  H14  single    0.970  0.020  1.090
 H96  C01  H15  single    0.970  0.020  1.090
 H96  C01  H16  single    0.970  0.020  1.090
 H96  C04  H17  single    0.930  0.020  1.080
 H96  C06  H18  single    0.930  0.020  1.080
 H96  C11  H19  single    0.930  0.020  1.080
 H96  C14  H20  single    0.930  0.020  1.080
 H96  C25  H21  single    0.970  0.020  1.090
 H96  C25  H22  single    0.970  0.020  1.090
 H96  N23  H23  single    0.890  0.020  1.040
 H96  O27  H25  single    0.850  0.020  0.980

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
 H96  N10  C13  C14  118.04  3.000
 H96  C14  C13  C12  118.63  3.000
 H96  N10  C13  C12  123.34  3.000
 H96  H1   C15  C16  118.86  3.000
 H96  H1   C15  C14  120.86  3.000
 H96  C16  C15  C14  120.28  3.000
 H96  H4   C17  H3   108.79  3.000
 H96  H4   C17  H2   108.95  3.000
 H96  H3   C17  H2   108.99  3.000
 H96  H4   C17  O02  111.77  3.000
 H96  H3   C17  O02  111.70  3.000
 H96  H2   C17  O02  106.55  3.000
 H96  H6   C20  H5   106.82  3.000
 H96  H6   C20  S19  104.19  3.000
 H96  H5   C20  S19  108.31  3.000
 H96  H6   C20  C21  109.88  3.000
 H96  H5   C20  C21  111.06  3.000
 H96  S19  C20  C21  116.01  3.000
 H96  H7   C21  C25  107.87  3.000
 H96  H7   C21  C22  108.02  3.000
 H96  C25  C21  C22  103.97  3.000
 H96  H7   C21  C20  104.73  3.000
 H96  C25  C21  C20  115.93  3.000
 H96  C22  C21  C20  115.94  3.000
 H96  H9   C22  H8   106.59  3.000
 H96  H9   C22  N23  110.42  3.000
 H96  H8   C22  N23  109.84  3.000
 H96  H9   C22  C21  109.59  3.000
 H96  H8   C22  C21  112.60  3.000
 H96  N23  C22  C21  107.81  3.000
 H96  H11  C24  H10  107.39  3.000
 H96  H11  C24  N23  110.62  3.000
 H96  H10  C24  N23  109.62  3.000
 H96  H11  C24  C25  113.68  3.000
 H96  H10  C24  C25  110.01  3.000
 H96  N23  C24  C25  105.51  3.000
 H96  H13  C26  H12  107.16  3.000
 H96  H13  C26  O27  111.62  3.000
 H96  H12  C26  O27  111.36  3.000
 H96  H13  C26  C07  109.51  3.000
 H96  H12  C26  C07  108.75  3.000
 H96  O27  C26  C07  108.40  3.000
 H96  H16  C01  H15  109.04  3.000
 H96  H16  C01  H14  108.64  3.000
 H96  H15  C01  H14  108.62  3.000
 H96  H16  C01  O03  112.06  3.000
 H96  H15  C01  O03  112.12  3.000
 H96  H14  C01  O03  106.22  3.000
 H96  H17  C04  C08  119.56  3.000
 H96  H17  C04  C05  119.60  3.000
 H96  C08  C04  C05  120.84  3.000
 H96  O03  C05  C06  122.87  3.000
 H96  C06  C05  C04  120.08  3.000
 H96  O03  C05  C04  117.05  3.000
 H96  H18  C06  C07  118.59  3.000
 H96  H18  C06  C05  120.26  3.000
 H96  C07  C06  C05  121.15  3.000
 H96  C09  C07  C06  119.86  3.000
 H96  C09  C07  C26  119.93  3.000
 H96  C06  C07  C26  120.18  3.000
 H96  C18  C08  C09  117.62  3.000
 H96  C18  C08  C04  123.40  3.000
 H96  C09  C08  C04  118.97  3.000
 H96  N10  C09  C08  122.72  3.000
 H96  N10  C09  C07  118.18  3.000
 H96  C08  C09  C07  119.10  3.000
 H96  H19  C11  C16  121.29  3.000
 H96  H19  C11  C12  118.23  3.000
 H96  C16  C11  C12  120.46  3.000
 H96  C18  C12  C11  123.68  3.000
 H96  C11  C12  C13  119.00  3.000
 H96  C18  C12  C13  117.31  3.000
 H96  H20  C14  C15  120.92  3.000
 H96  H20  C14  C13  117.99  3.000
 H96  C15  C14  C13  121.09  3.000
 H96  O02  C16  C11  125.01  3.000
 H96  O02  C16  C15  114.47  3.000
 H96  C11  C16  C15  120.52  3.000
 H96  S19  C18  C12  120.46  3.000
 H96  C12  C18  C08  119.57  3.000
 H96  S19  C18  C08  119.92  3.000
 H96  H22  C25  H21  107.92  3.000
 H96  H22  C25  C24  109.59  3.000
 H96  H21  C25  C24  113.67  3.000
 H96  H22  C25  C21  110.77  3.000
 H96  H21  C25  C21  112.66  3.000
 H96  C24  C25  C21  102.18  3.000
 H96  C09  N10  C13  119.40  3.000
 H96  H23  N23  C24  108.05  3.000
 H96  H23  N23  C22  108.48  3.000
 H96  C24  N23  C22  105.97  3.000
 H96  C16  O02  C17  118.36  3.000
 H96  C05  O03  C01  119.66  3.000
 H96  H25  O27  C26  107.88  3.000
 H96  C18  S19  C20  103.35  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
 H96  CONST_01  C07  C09  N10  C13   180.00   0.0  0
 H96  CONST_02  C08  C09  N10  C13     0.00   0.0  0
 H96  CONST_03  C08  C18  C12  C13     0.00   0.0  0
 H96  CONST_04  C16  C11  C12  C13     0.00   0.0  0
 H96  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 H96  CONST_06  N10  C13  C14  C15   180.00   0.0  0
 H96  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 H96  CONST_08  C12  C11  C16  C15     0.00   0.0  0
 H96  CONST_09  C07  C06  C05  C04     0.00   0.0  0
 H96  CONST_10  C07  C09  C08  C04     0.00   0.0  0
 H96  CONST_11  N10  C09  C08  C04   180.00   0.0  0
 H96  CONST_12  C12  C18  C08  C04   180.00   0.0  0
 H96  CONST_13  C09  C07  C06  C05     0.00   0.0  0
 H96  CONST_14  C09  C08  C04  C05     0.00   0.0  0
 H96  CONST_15  C18  C08  C04  C05   180.00   0.0  0
 H96  CONST_16  C08  C04  C05  C06     0.00   0.0  0
 H96  CONST_17  C08  C09  C07  C06     0.00   0.0  0
 H96  CONST_18  N10  C09  C07  C06   180.00   0.0  0
 H96  CONST_19  C18  C08  C09  C07   180.00   0.0  0
 H96  CONST_20  C11  C12  C18  C08   180.00   0.0  0
 H96  CONST_21  C12  C18  C08  C09     0.00   0.0  0
 H96  CONST_22  C12  C13  N10  C09     0.00   0.0  0
 H96  CONST_23  C14  C13  N10  C09   180.00   0.0  0
 H96  CONST_24  N10  C13  C12  C11   180.00   0.0  0
 H96  CONST_25  C14  C13  C12  C11     0.00   0.0  0
 H96  CONST_26  C14  C15  C16  C11     0.00   0.0  0
 H96  CONST_27  C18  C12  C13  C14   180.00   0.0  0
 H96  CONST_28  C18  C12  C11  C16   180.00   0.0  0
 H96  CONST_29  N10  C09  C08  C18     0.00   0.0  0
 H96  CONST_30  N10  C13  C12  C18     0.00   0.0  0
 H96  CONST_31  S19  C18  C12  C13   180.00   0.0  0
 H96  CONST_32  C05  C06  C07  C26   180.00   0.0  0
 H96  CONST_33  C08  C09  C07  C26   180.00   0.0  0
 H96  CONST_34  N10  C09  C07  C26     0.00   0.0  0
 H96  CONST_35  S19  C18  C08  C04     0.00   0.0  0
 H96  CONST_36  O03  C05  C06  C07   180.00   0.0  0
 H96  CONST_37  O03  C05  C04  C08   180.00   0.0  0
 H96  CONST_38  S19  C18  C08  C09   180.00   0.0  0
 H96  CONST_39  S19  C18  C12  C11     0.00   0.0  0
 H96  CONST_40  O02  C16  C11  C12   180.00   0.0  0
 H96  CONST_41  O02  C16  C15  C14   180.00   0.0  0
 H96  CONST_42  H19  C11  C12  C13   180.00   0.0  0
 H96  CONST_43  H1   C15  C14  C13   180.00   0.0  0
 H96  CONST_44  H19  C11  C16  C15   180.00   0.0  0
 H96  CONST_45  H18  C06  C05  C04   180.00   0.0  0
 H96  CONST_46  H17  C04  C05  C06   180.00   0.0  0
 H96  CONST_47  H18  C06  C07  C09   180.00   0.0  0
 H96  CONST_48  H17  C04  C08  C09   180.00   0.0  0
 H96  CONST_49  H1   C15  C16  C11   180.00   0.0  0
 H96  CONST_50  H20  C14  C13  C12   180.00   0.0  0
 H96  CONST_51  H20  C14  C15  C16   180.00   0.0  0
 H96  CONST_52  H17  C04  C08  C18     0.00   0.0  0
 H96  CONST_53  H19  C11  C12  C18     0.00   0.0  0
 H96  CONST_54  H20  C14  C13  N10     0.00   0.0  0
 H96  Var_01    C24  N23  C22  C21    16.62  30.0  1
 H96  Var_02    N23  C24  C25  C21    38.55  30.0  1
 H96  Var_03    C25  C24  N23  C22   -34.60  30.0  1
 H96  Var_04    H23  N23  C22  C21   -99.19  30.0  1
 H96  Var_05    H10  C24  C25  C21   -79.61  30.0  1
 H96  Var_06    H11  C24  C25  C21   159.94  30.0  1
 H96  Var_07    H10  C24  N23  C22    83.82  30.0  1
 H96  Var_08    H11  C24  N23  C22  -157.94  30.0  1
 H96  Var_09    H8   C22  N23  C24   139.65  30.0  1
 H96  Var_10    H9   C22  N23  C24  -103.07  30.0  1
 H96  Var_11    H23  N23  C24  C25    81.50  30.0  1
 H96  Var_12    H21  C25  C24  N23   160.21  30.0  1
 H96  Var_13    H22  C25  C24  N23   -78.95  30.0  1
 H96  Var_14    C17  O02  C16  C15  -179.88  30.0  2
 H96  Var_15    C11  C16  O02  C17    -0.17  30.0  1
 H96  Var_16    C08  C18  S19  C20  -111.75  30.0  2
 H96  Var_17    C12  C18  S19  C20    70.85  30.0  2
 H96  Var_18    C18  S19  C20  C21    91.07  30.0  3
 H96  Var_19    C06  C05  O03  C01     1.57  30.0  2
 H96  Var_20    C04  C05  O03  C01  -178.84  30.0  2
 H96  Var_21    O27  C26  C07  C06   101.84  30.0  2
 H96  Var_22    O27  C26  C07  C09   -75.94  30.0  2
 H96  Var_23    H12  C26  C07  C06   -19.38  30.0  2
 H96  Var_24    H13  C26  C07  C06  -136.17  30.0  2
 H96  Var_25    H12  C26  C07  C09   162.85  30.0  2
 H96  Var_26    H13  C26  C07  C09    46.05  30.0  2
 H96  Var_27    H14  C01  O03  C05   179.57  30.0  3
 H96  Var_28    H15  C01  O03  C05   -61.93  30.0  3
 H96  Var_29    H16  C01  O03  C05    61.07  30.0  3
 H96  Var_30    H2   C17  O02  C16  -179.24  30.0  3
 H96  Var_31    H3   C17  O02  C16   -60.31  30.0  3
 H96  Var_32    H4   C17  O02  C16    61.85  30.0  3
 H96  Var_33    H5   C20  S19  C18   -34.56  30.0  2
 H96  Var_34    H6   C20  S19  C18  -148.02  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
 H96  chir_01  C21  C22  C25  C20  negativ

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
 H96  plan-1  C13  0.020
 H96  plan-1  C15  0.020
 H96  plan-1  C26  0.020
 H96  plan-1  C04  0.020
 H96  plan-1  C05  0.020
 H96  plan-1  C06  0.020
 H96  plan-1  C07  0.020
 H96  plan-1  C08  0.020
 H96  plan-1  C09  0.020
 H96  plan-1  C11  0.020
 H96  plan-1  C12  0.020
 H96  plan-1  C14  0.020
 H96  plan-1  C16  0.020
 H96  plan-1  C18  0.020
 H96  plan-1  N10  0.020
 H96  plan-1  O02  0.020
 H96  plan-1  O03  0.020
 H96  plan-1  S19  0.020
 H96  plan-1  H1   0.020
 H96  plan-1  H17  0.020
 H96  plan-1  H18  0.020
 H96  plan-1  H19  0.020
 H96  plan-1  H20  0.020

