# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 08:41:10 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2S)-1-(pyrrolidin-1-yl)-3-(9H-thioxanthen-9-yl)propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CC1c2ccccc2Sc3ccccc13)CN4CCCC4
#
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
 0LU  0LU  (2S)-1-(pyrrolidin-1-yl)-3-(9H-thioxanthen-9-yl)propan-2-ol  ligand  46  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0LU
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
 0LU  C1   C  CR66  0   0.264  -1.1208   1.2590   0.7883
 0LU  C2   C  CR16  0  -0.465  -0.9257  -0.2332   0.8883
 0LU  C3   C  CR66  0  -0.202  -1.8051   1.8114  -0.2928
 0LU  C4   C  CR16  0  -0.298  -0.6400   2.1208   1.7692
 0LU  C5   C  CR66  0   0.250  -2.2227  -0.9506   0.6060
 0LU  C6   C  CH2   0  -0.435   0.1667  -0.7814  -0.0548
 0LU  S7   S  S2    0   0.076  -2.5311   0.7657  -1.5166
 0LU  C8   C  CR16  0  -0.253  -1.9504   3.1904  -0.4239
 0LU  C9   C  CR16  0  -0.253  -0.7832   3.4938   1.6530
 0LU  C10  C  CR66  0  -0.196  -3.0008  -0.5970  -0.4955
 0LU  C11  C  CR16  0  -0.320  -2.6451  -2.0116   1.3997
 0LU  C12  C  CH1   0   0.033   1.6029  -0.4579   0.3518
 0LU  C13  C  CR16  0  -0.268  -1.4245   4.0314   0.5429
 0LU  C14  C  CR16  0  -0.253  -4.1552  -1.3057  -0.8140
 0LU  C15  C  CR16  0  -0.246  -3.7918  -2.7280   1.0882
 0LU  C16  C  CH2   0  -0.274   2.5721  -1.1762  -0.5859
 0LU  O17  O  OH1   0  -0.647   1.8439   0.9290   0.4375
 0LU  C18  C  CR16  0  -0.266  -4.5424  -2.3798  -0.0272
 0LU  N19  N  NT    0  -0.435   3.9530  -1.1545  -0.1584
 0LU  C20  C  CH2   0  -0.275   4.7603  -2.1577  -0.8358
 0LU  C21  C  CH2   0  -0.274   4.6661   0.0944  -0.3886
 0LU  C22  C  CH2   0  -0.464   6.1895  -1.8022  -0.4397
 0LU  C23  C  CH2   0  -0.469   6.1440  -0.2762  -0.2234
 0LU  H1   H  HCR6  0   0.274  -0.6240  -0.4696   1.9130
 0LU  H2   H  HCR6  0   0.249  -0.1332   1.7038   2.6306
 0LU  H3   H  HCH2  0   0.245   0.0659  -1.8696  -0.0722
 0LU  H4   H  HCH2  0   0.240  -0.0177  -0.4451  -1.0807
 0LU  H5   H  HCR6  0   0.265  -2.4881   3.6024  -1.2686
 0LU  H6   H  HCR6  0   0.256  -0.3918   4.1445   2.4241
 0LU  H7   H  HCR6  0   0.255  -2.0560  -2.2895   2.2661
 0LU  H8   H  HCH1  0   0.219   1.7739  -0.8437   1.3626
 0LU  H9   H  HCR6  0   0.260  -1.5387   5.1027   0.4414
 0LU  H10  H  HCR6  0   0.267  -4.7566  -1.0111  -1.6651
 0LU  H11  H  HCR6  0   0.259  -4.0995  -3.5553   1.7141
 0LU  H12  H  HCH2  0   0.231   2.2599  -2.2234  -0.6330
 0LU  H13  H  HCH2  0   0.188   2.4563  -0.7757  -1.6117
 0LU  H14  H  HOH1  0   0.440   1.6118   1.3345  -0.4049
 0LU  H15  H  HCR6  0   0.261  -5.4402  -2.9296  -0.2774
 0LU  H17  H  HCH2  0   0.231   4.4670  -3.1651  -0.5329
 0LU  H18  H  HCH2  0   0.188   4.6449  -2.0985  -1.9320
 0LU  H19  H  HCH2  0   0.183   4.4790   0.4709  -1.4093
 0LU  H20  H  HCH2  0   0.234   4.3477   0.8724   0.3018
 0LU  H21  H  HCH2  0   0.232   6.4684  -2.3132   0.4828
 0LU  H22  H  HCH2  0   0.232   6.9062  -2.1013  -1.2043
 0LU  H23  H  HCH2  0   0.231   6.7648   0.2637  -0.9378
 0LU  H24  H  HCH2  0   0.232   6.5050  -0.0152   0.7717

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
 0LU  C23  C22  single    1.542  0.020  1.542
 0LU  C23  C21  single    1.533  0.020  1.533
 0LU  C22  C20  single    1.525  0.020  1.525
 0LU  C21  N19  single    1.456  0.020  1.456
 0LU  C20  N19  single    1.455  0.020  1.455
 0LU  N19  C16  single    1.446  0.020  1.446
 0LU  C16  C12  single    1.528  0.020  1.528
 0LU  O17  C12  single    1.410  0.020  1.410
 0LU  C12  C6   single    1.527  0.020  1.527
 0LU  C6   C2   single    1.544  0.020  1.544
 0LU  C2   C5   single    1.509  0.020  1.509
 0LU  C2   C1   single    1.508  0.020  1.508
 0LU  C11  C15  aromatic  1.388  0.020  1.388
 0LU  C11  C5   aromatic  1.391  0.020  1.391
 0LU  C15  C18  aromatic  1.389  0.020  1.389
 0LU  C5   C10  aromatic  1.394  0.020  1.394
 0LU  C10  C14  aromatic  1.392  0.020  1.392
 0LU  C10  S7   single    1.766  0.020  1.766
 0LU  C18  C14  aromatic  1.387  0.020  1.387
 0LU  S7   C3   single    1.766  0.020  1.766
 0LU  C1   C3   aromatic  1.394  0.020  1.394
 0LU  C1   C4   aromatic  1.391  0.020  1.391
 0LU  C3   C8   aromatic  1.393  0.020  1.393
 0LU  C4   C9   aromatic  1.385  0.020  1.385
 0LU  C8   C13  aromatic  1.385  0.020  1.385
 0LU  C9   C13  aromatic  1.390  0.020  1.390
 0LU  C2   H1   single    0.970  0.020  1.090
 0LU  C4   H2   single    0.930  0.020  1.080
 0LU  C6   H3   single    0.970  0.020  1.090
 0LU  C6   H4   single    0.970  0.020  1.090
 0LU  C8   H5   single    0.930  0.020  1.080
 0LU  C9   H6   single    0.930  0.020  1.080
 0LU  C11  H7   single    0.930  0.020  1.080
 0LU  C12  H8   single    0.970  0.020  1.090
 0LU  C13  H9   single    0.930  0.020  1.080
 0LU  C14  H10  single    0.930  0.020  1.080
 0LU  C15  H11  single    0.930  0.020  1.080
 0LU  C16  H12  single    0.970  0.020  1.090
 0LU  C16  H13  single    0.970  0.020  1.090
 0LU  O17  H14  single    0.850  0.020  0.980
 0LU  C18  H15  single    0.930  0.020  1.080
 0LU  C20  H17  single    0.970  0.020  1.090
 0LU  C20  H18  single    0.970  0.020  1.090
 0LU  C21  H19  single    0.970  0.020  1.090
 0LU  C21  H20  single    0.970  0.020  1.090
 0LU  C22  H21  single    0.970  0.020  1.090
 0LU  C22  H22  single    0.970  0.020  1.090
 0LU  C23  H23  single    0.970  0.020  1.090
 0LU  C23  H24  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
 0LU  C4   C1   C3   118.10  3.000
 0LU  C4   C1   C2   121.42  3.000
 0LU  C3   C1   C2   120.47  3.000
 0LU  H1   C2   C6   107.48  3.000
 0LU  H1   C2   C5   108.03  3.000
 0LU  C6   C2   C5   108.97  3.000
 0LU  H1   C2   C1   108.15  3.000
 0LU  C5   C2   C1   110.29  3.000
 0LU  C6   C2   C1   113.73  3.000
 0LU  C8   C3   S7   118.56  3.000
 0LU  C8   C3   C1   121.11  3.000
 0LU  S7   C3   C1   120.32  3.000
 0LU  H2   C4   C9   119.79  3.000
 0LU  H2   C4   C1   118.95  3.000
 0LU  C9   C4   C1   121.26  3.000
 0LU  C11  C5   C10  118.35  3.000
 0LU  C10  C5   C2   120.46  3.000
 0LU  C11  C5   C2   121.13  3.000
 0LU  H4   C6   H3   105.98  3.000
 0LU  H4   C6   C12  110.04  3.000
 0LU  H3   C6   C12  107.57  3.000
 0LU  H4   C6   C2   110.12  3.000
 0LU  H3   C6   C2   107.34  3.000
 0LU  C12  C6   C2   115.31  3.000
 0LU  C10  S7   C3    99.53  3.000
 0LU  H5   C8   C13  120.14  3.000
 0LU  H5   C8   C3   120.13  3.000
 0LU  C13  C8   C3   119.72  3.000
 0LU  H6   C9   C13  120.22  3.000
 0LU  H6   C9   C4   119.91  3.000
 0LU  C13  C9   C4   119.87  3.000
 0LU  C14  C10  S7   118.76  3.000
 0LU  S7   C10  C5   120.26  3.000
 0LU  C14  C10  C5   120.98  3.000
 0LU  H7   C11  C15  119.75  3.000
 0LU  H7   C11  C5   119.13  3.000
 0LU  C15  C11  C5   121.11  3.000
 0LU  H8   C12  O17  105.29  3.000
 0LU  H8   C12  C16  107.56  3.000
 0LU  O17  C12  C16  113.03  3.000
 0LU  H8   C12  C6   108.53  3.000
 0LU  O17  C12  C6   112.66  3.000
 0LU  C16  C12  C6   109.48  3.000
 0LU  H9   C13  C9   120.43  3.000
 0LU  H9   C13  C8   119.71  3.000
 0LU  C9   C13  C8   119.85  3.000
 0LU  H10  C14  C18  120.11  3.000
 0LU  H10  C14  C10  120.13  3.000
 0LU  C18  C14  C10  119.76  3.000
 0LU  H11  C15  C18  120.17  3.000
 0LU  H11  C15  C11  119.99  3.000
 0LU  C18  C15  C11  119.84  3.000
 0LU  H13  C16  H12  106.06  3.000
 0LU  H13  C16  N19  111.62  3.000
 0LU  H12  C16  N19  107.45  3.000
 0LU  H13  C16  C12  109.39  3.000
 0LU  H12  C16  C12  107.18  3.000
 0LU  N19  C16  C12  114.67  3.000
 0LU  H14  O17  C12  108.64  3.000
 0LU  H15  C18  C15  120.44  3.000
 0LU  H15  C18  C14  119.61  3.000
 0LU  C15  C18  C14  119.94  3.000
 0LU  C21  N19  C20  104.24  3.000
 0LU  C20  N19  C16  112.45  3.000
 0LU  C21  N19  C16  115.71  3.000
 0LU  H18  C20  H17  107.27  3.000
 0LU  H18  C20  C22  110.08  3.000
 0LU  H17  C20  C22  113.25  3.000
 0LU  H18  C20  N19  111.55  3.000
 0LU  H17  C20  N19  110.97  3.000
 0LU  C22  C20  N19  103.79  3.000
 0LU  H20  C21  H19  107.05  3.000
 0LU  H20  C21  C23  112.75  3.000
 0LU  H19  C21  C23  110.21  3.000
 0LU  H20  C21  N19  111.70  3.000
 0LU  H19  C21  N19  110.84  3.000
 0LU  C23  C21  N19  104.35  3.000
 0LU  H22  C22  H21  107.26  3.000
 0LU  H22  C22  C23  112.92  3.000
 0LU  H21  C22  C23  110.64  3.000
 0LU  H22  C22  C20  111.72  3.000
 0LU  H21  C22  C20  110.48  3.000
 0LU  C23  C22  C20  103.86  3.000
 0LU  H24  C23  H23  106.92  3.000
 0LU  H24  C23  C22  110.81  3.000
 0LU  H23  C23  C22  112.43  3.000
 0LU  H24  C23  C21  111.09  3.000
 0LU  H23  C23  C21  111.04  3.000
 0LU  C22  C23  C21  104.63  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
 0LU  CONST_01  C13  C8   C3   C1     0.00   0.0  0
 0LU  CONST_02  C13  C9   C4   C1     0.00   0.0  0
 0LU  CONST_03  C9   C4   C1   C3     0.00   0.0  0
 0LU  CONST_04  C9   C13  C8   C3     0.00   0.0  0
 0LU  CONST_05  C8   C3   C1   C4     0.00   0.0  0
 0LU  CONST_06  C8   C13  C9   C4     0.00   0.0  0
 0LU  CONST_07  C18  C15  C11  C5     0.00   0.0  0
 0LU  CONST_08  C18  C14  C10  C5     0.00   0.0  0
 0LU  CONST_09  C15  C11  C5   C10    0.00   0.0  0
 0LU  CONST_10  C15  C18  C14  C10    0.00   0.0  0
 0LU  CONST_11  C14  C18  C15  C11    0.00   0.0  0
 0LU  CONST_12  C14  C10  C5   C11    0.00   0.0  0
 0LU  CONST_13  H5   C8   C3   C1   180.00   0.0  0
 0LU  CONST_14  H6   C9   C4   C1   180.00   0.0  0
 0LU  CONST_15  H7   C11  C5   C2     0.00   0.0  0
 0LU  CONST_16  H2   C4   C1   C2     0.00   0.0  0
 0LU  CONST_17  H9   C13  C8   C3   180.00   0.0  0
 0LU  CONST_18  H11  C15  C11  C5   180.00   0.0  0
 0LU  CONST_19  H10  C14  C10  C5   180.00   0.0  0
 0LU  CONST_20  H15  C18  C14  C10  180.00   0.0  0
 0LU  Var_01    C5   C10  S7   C3   -33.50  30.0  1
 0LU  Var_02    C22  C23  C21  N19   21.09  30.0  1
 0LU  Var_03    C23  C22  C20  N19  -29.44  30.0  1
 0LU  Var_04    C21  C23  C22  C20    5.01  30.0  1
 0LU  Var_05    C23  C21  N19  C20  -40.64  30.0  1
 0LU  Var_06    C22  C20  N19  C21   44.07  30.0  1
 0LU  Var_07    C21  N19  C16  C12  -77.54  30.0  1

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
 0LU  chir_01  C2   C6   C5   C1  positiv
 0LU  chir_02  C12  O17  C16  C6  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
 0LU  plan-1  C1   0.020
 0LU  plan-1  C2   0.020
 0LU  plan-1  C3   0.020
 0LU  plan-1  C4   0.020
 0LU  plan-1  S7   0.020
 0LU  plan-1  C8   0.020
 0LU  plan-1  C9   0.020
 0LU  plan-1  C13  0.020
 0LU  plan-1  H2   0.020
 0LU  plan-1  H5   0.020
 0LU  plan-1  H6   0.020
 0LU  plan-1  H9   0.020
 0LU  plan-2  C2   0.020
 0LU  plan-2  C5   0.020
 0LU  plan-2  S7   0.020
 0LU  plan-2  C10  0.020
 0LU  plan-2  C11  0.020
 0LU  plan-2  C14  0.020
 0LU  plan-2  C15  0.020
 0LU  plan-2  C18  0.020
 0LU  plan-2  H7   0.020
 0LU  plan-2  H10  0.020
 0LU  plan-2  H11  0.020
 0LU  plan-2  H15  0.020

