# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 15:32:30 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 1-{[2-(diethylamino)ethyl]amino}-4-(hydroxymethyl)-9H-thioxanthen-9-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)CCNc1ccc(CO)c2Sc3ccccc3C(=O)c12
#
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
 QHM  QHM  1-{[2-(diethylamino)ethyl]amino}-4-(hydroxymethyl)-9H-thioxanthen-9-one  ligand  49  25  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QHM
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
 QHM  N1   N  NH1   0  -0.703  -1.5334   0.1380   0.2172
 QHM  C4   C  CR6   0  -0.000   1.7219  -2.4946   0.4011
 QHM  C5   C  CR16  0  -0.265   4.9091   1.6182  -0.1106
 QHM  C6   C  CR16  0  -0.239   5.0204   2.9835  -0.2635
 QHM  C7   C  CR16  0  -0.248   3.8746   3.7766  -0.3191
 QHM  C8   C  CR16  0  -0.266   2.6315   3.1904  -0.2225
 QHM  C10  C  CR66  0  -0.018   0.8844  -0.1811   0.1900
 QHM  C13  C  CR66  0   0.097   2.4892   1.8037  -0.0679
 QHM  C15  C  CH2   0  -0.264  -2.9023  -0.3136   0.2321
 QHM  C17  C  CH2   0  -0.292  -5.5844   0.0314  -1.3787
 QHM  C20  C  CH3   0  -0.665  -6.1472   1.4324   2.0434
 QHM  C9   C  CR6   0   0.378   1.1197   1.2510   0.0288
 QHM  C3   C  CR16  0  -0.288   0.4048  -2.9283   0.4880
 QHM  C2   C  CR16  0  -0.367  -0.6585  -2.0584   0.4306
 QHM  C12  C  CR66  0  -0.211   3.6446   1.0295  -0.0133
 QHM  C11  C  CR66  0  -0.265   1.9378  -1.1233   0.2582
 QHM  C1   C  CR6   0   0.399  -0.4645  -0.6754   0.2769
 QHM  N2   N  NT    0  -0.415  -5.2160   0.4412  -0.0300
 QHM  O1   O  O     0  -0.468   0.1864   2.0538  -0.0327
 QHM  C16  C  CH2   0  -0.324  -3.8359   0.8763   0.0518
 QHM  C18  C  CH3   0  -0.661  -6.6890  -1.0121  -1.3920
 QHM  C19  C  CH2   0  -0.287  -6.1479   1.4121   0.5237
 QHM  O2   O  OH1   0  -0.664   2.3827  -4.7765   0.5452
 QHM  S1   S  S2    0   0.156   3.6261  -0.6909   0.1763
 QHM  H1   H  HNH1  0   0.413  -1.3375   1.1214   0.0965
 QHM  H2   H  HCR6  0   0.278   5.7984   1.0017  -0.0647
 QHM  H3   H  HCR6  0   0.275   6.0011   3.4339  -0.3400
 QHM  H4   H  HCR6  0   0.267   3.9602   4.8482  -0.4358
 QHM  H5   H  HCR6  0   0.268   1.7456   3.8076  -0.2657
 QHM  H6   H  HCH2  0   0.230  -3.0706  -1.0484  -0.5632
 QHM  H7   H  HCH2  0   0.231  -3.1466  -0.8093   1.1774
 QHM  H8   H  HCH2  0   0.201  -5.8740   0.8978  -1.9949
 QHM  H9   H  HCH2  0   0.230  -4.7054  -0.3968  -1.8646
 QHM  H10  H  HCH3  0   0.221  -6.4054   0.4508   2.4420
 QHM  H11  H  HCH3  0   0.223  -5.1781   1.7172   2.4554
 QHM  H12  H  HCH3  0   0.226  -6.8794   2.1520   2.4113
 QHM  H13  H  HCR6  0   0.268   0.1992  -3.9830   0.6067
 QHM  H14  H  HCR6  0   0.277  -1.6602  -2.4552   0.5107
 QHM  H16  H  HCH2  0   0.216   3.5093  -3.3363  -0.4255
 QHM  H17  H  HCH2  0   0.219   3.5097  -3.2256   1.3293
 QHM  H19  H  HCH2  0   0.248  -3.7108   1.5409   0.9092
 QHM  H20  H  HCH2  0   0.213  -3.5323   1.4561  -0.8348
 QHM  H21  H  HCH3  0   0.221  -6.3750  -1.9076  -0.8550
 QHM  H22  H  HCH3  0   0.222  -7.6086  -0.6497  -0.9309
 QHM  H23  H  HCH3  0   0.224  -6.9303  -1.2980  -2.4163
 QHM  H24  H  HCH2  0   0.230  -7.1526   1.1502   0.1875
 QHM  H25  H  HCH2  0   0.197  -5.9538   2.4251   0.1352
 QHM  H26  H  HOH1  0   0.465   3.1348  -5.3703   0.6224
 QHM  C14  C  CH2   0  -0.184   2.8737  -3.4652   0.4637

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
 QHM  C6   C7   aromatic  1.395  0.020  1.395
 QHM  C6   C5   aromatic  1.378  0.020  1.378
 QHM  C7   C8   aromatic  1.378  0.020  1.378
 QHM  C5   C12  aromatic  1.398  0.020  1.398
 QHM  C8   C13  aromatic  1.403  0.020  1.403
 QHM  C12  C13  aromatic  1.392  0.020  1.392
 QHM  C12  S1   single    1.731  0.020  1.731
 QHM  C13  C9   single    1.480  0.020  1.480
 QHM  S1   C11  single    1.745  0.020  1.745
 QHM  C9   O1   double    1.233  0.020  1.233
 QHM  C9   C10  single    1.460  0.020  1.460
 QHM  C11  C10  aromatic  1.415  0.020  1.415
 QHM  C11  C4   aromatic  1.396  0.020  1.396
 QHM  C10  C1   aromatic  1.439  0.020  1.439
 QHM  C14  C4   single    1.508  0.020  1.508
 QHM  C14  O2   single    1.403  0.020  1.403
 QHM  C4   C3   aromatic  1.389  0.020  1.389
 QHM  C1   N1   single    1.344  0.020  1.344
 QHM  C1   C2   aromatic  1.405  0.020  1.405
 QHM  N1   C15  single    1.442  0.020  1.442
 QHM  C3   C2   aromatic  1.375  0.020  1.375
 QHM  C15  C16  single    1.523  0.020  1.523
 QHM  C16  N2   single    1.449  0.020  1.449
 QHM  N2   C19  single    1.455  0.020  1.455
 QHM  N2   C17  single    1.457  0.020  1.457
 QHM  C19  C20  single    1.520  0.020  1.520
 QHM  C17  C18  single    1.520  0.020  1.520
 QHM  N1   H1   single    0.860  0.020  1.020
 QHM  C5   H2   single    0.930  0.020  1.080
 QHM  C6   H3   single    0.930  0.020  1.080
 QHM  C7   H4   single    0.930  0.020  1.080
 QHM  C8   H5   single    0.930  0.020  1.080
 QHM  C15  H6   single    0.970  0.020  1.090
 QHM  C15  H7   single    0.970  0.020  1.090
 QHM  C17  H8   single    0.970  0.020  1.090
 QHM  C17  H9   single    0.970  0.020  1.090
 QHM  C20  H10  single    0.970  0.020  1.090
 QHM  C20  H11  single    0.970  0.020  1.090
 QHM  C20  H12  single    0.970  0.020  1.090
 QHM  C3   H13  single    0.930  0.020  1.080
 QHM  C2   H14  single    0.930  0.020  1.080
 QHM  C14  H16  single    0.970  0.020  1.090
 QHM  C14  H17  single    0.970  0.020  1.090
 QHM  C16  H19  single    0.970  0.020  1.090
 QHM  C16  H20  single    0.970  0.020  1.090
 QHM  C18  H21  single    0.970  0.020  1.090
 QHM  C18  H22  single    0.970  0.020  1.090
 QHM  C18  H23  single    0.970  0.020  1.090
 QHM  C19  H24  single    0.970  0.020  1.090
 QHM  C19  H25  single    0.970  0.020  1.090
 QHM  O2   H26  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
 QHM  H1   N1   C1   116.12  3.000
 QHM  H1   N1   C15  119.36  3.000
 QHM  C1   N1   C15  124.40  3.000
 QHM  C14  C4   C11  121.25  3.000
 QHM  C14  C4   C3   121.38  3.000
 QHM  C11  C4   C3   117.37  3.000
 QHM  H2   C5   C12  120.00  3.000
 QHM  H2   C5   C6   120.14  3.000
 QHM  C12  C5   C6   119.86  3.000
 QHM  H3   C6   C7   120.34  3.000
 QHM  H3   C6   C5   119.57  3.000
 QHM  C7   C6   C5   120.09  3.000
 QHM  H4   C7   C8   120.04  3.000
 QHM  H4   C7   C6   120.19  3.000
 QHM  C8   C7   C6   119.77  3.000
 QHM  H5   C8   C13  119.08  3.000
 QHM  H5   C8   C7   119.60  3.000
 QHM  C13  C8   C7   121.32  3.000
 QHM  C1   C10  C11  117.78  3.000
 QHM  C1   C10  C9   119.64  3.000
 QHM  C11  C10  C9   122.58  3.000
 QHM  C12  C13  C9   123.91  3.000
 QHM  C9   C13  C8   118.05  3.000
 QHM  C12  C13  C8   118.04  3.000
 QHM  H7   C15  H6   106.78  3.000
 QHM  H7   C15  C16  108.61  3.000
 QHM  H6   C15  C16  110.11  3.000
 QHM  H7   C15  N1   111.26  3.000
 QHM  H6   C15  N1   110.39  3.000
 QHM  C16  C15  N1   109.64  3.000
 QHM  H9   C17  H8   105.73  3.000
 QHM  H9   C17  C18  108.18  3.000
 QHM  H8   C17  C18  110.12  3.000
 QHM  H9   C17  N2   108.58  3.000
 QHM  H8   C17  N2   111.29  3.000
 QHM  C18  C17  N2   112.65  3.000
 QHM  H12  C20  H11  107.26  3.000
 QHM  H12  C20  H10  108.16  3.000
 QHM  H11  C20  H10  107.89  3.000
 QHM  H12  C20  C19  110.23  3.000
 QHM  H11  C20  C19  112.43  3.000
 QHM  H10  C20  C19  110.70  3.000
 QHM  O1   C9   C13  117.01  3.000
 QHM  O1   C9   C10  121.48  3.000
 QHM  C13  C9   C10  121.51  3.000
 QHM  H13  C3   C2   118.34  3.000
 QHM  H13  C3   C4   119.45  3.000
 QHM  C2   C3   C4   122.21  3.000
 QHM  H14  C2   C1   119.85  3.000
 QHM  H14  C2   C3   118.78  3.000
 QHM  C1   C2   C3   121.37  3.000
 QHM  S1   C12  C13  123.25  3.000
 QHM  S1   C12  C5   115.83  3.000
 QHM  C13  C12  C5   120.92  3.000
 QHM  S1   C11  C10  123.58  3.000
 QHM  C10  C11  C4   122.97  3.000
 QHM  S1   C11  C4   113.45  3.000
 QHM  C2   C1   C10  118.31  3.000
 QHM  C2   C1   N1   119.38  3.000
 QHM  C10  C1   N1   122.32  3.000
 QHM  C19  N2   C16  112.83  3.000
 QHM  C19  N2   C17  112.20  3.000
 QHM  C16  N2   C17  112.18  3.000
 QHM  H20  C16  H19  106.25  3.000
 QHM  H20  C16  N2   112.02  3.000
 QHM  H19  C16  N2   109.64  3.000
 QHM  H20  C16  C15  109.72  3.000
 QHM  H19  C16  C15  108.20  3.000
 QHM  N2   C16  C15  110.84  3.000
 QHM  H23  C18  H22  107.32  3.000
 QHM  H23  C18  H21  108.12  3.000
 QHM  H22  C18  H21  107.91  3.000
 QHM  H23  C18  C17  110.43  3.000
 QHM  H22  C18  C17  112.39  3.000
 QHM  H21  C18  C17  110.51  3.000
 QHM  H25  C19  H24  105.91  3.000
 QHM  H25  C19  N2   111.49  3.000
 QHM  H24  C19  N2   108.19  3.000
 QHM  H25  C19  C20  109.88  3.000
 QHM  H24  C19  C20  108.16  3.000
 QHM  N2   C19  C20  112.89  3.000
 QHM  H26  O2   C14  107.96  3.000
 QHM  C11  S1   C12  105.18  3.000
 QHM  H17  C14  H16  106.04  3.000
 QHM  H17  C14  O2   111.11  3.000
 QHM  H16  C14  O2   111.02  3.000
 QHM  H17  C14  C4   109.51  3.000
 QHM  H16  C14  C4   109.40  3.000
 QHM  O2   C14  C4   109.69  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
 QHM  CONST_01  C1   C10  C11  C4      0.00   0.0  0
 QHM  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 QHM  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 QHM  CONST_04  C8   C13  C12  C5      0.00   0.0  0
 QHM  CONST_05  C13  C8   C7   C6      0.00   0.0  0
 QHM  CONST_06  C13  C12  C5   C6      0.00   0.0  0
 QHM  CONST_07  C12  C5   C6   C7      0.00   0.0  0
 QHM  CONST_08  C12  C13  C8   C7      0.00   0.0  0
 QHM  CONST_09  C3   C4   C11  C10     0.00   0.0  0
 QHM  CONST_10  C3   C2   C1   C10     0.00   0.0  0
 QHM  CONST_11  C11  C10  C1   C2      0.00   0.0  0
 QHM  CONST_12  C11  C4   C3   C2      0.00   0.0  0
 QHM  CONST_13  C9   C10  C1   N1      0.00   0.0  0
 QHM  CONST_14  C11  C10  C1   N1    180.00   0.0  0
 QHM  CONST_15  C3   C2   C1   N1    180.00   0.0  0
 QHM  CONST_16  C14  C4   C11  C10   180.00   0.0  0
 QHM  CONST_17  C14  C4   C3   C2    180.00   0.0  0
 QHM  CONST_18  S1   C11  C4   C14     0.00   0.0  0
 QHM  CONST_19  H14  C2   C3   C4    180.00   0.0  0
 QHM  CONST_20  H4   C7   C6   C5    180.00   0.0  0
 QHM  CONST_21  H5   C8   C7   C6    180.00   0.0  0
 QHM  CONST_22  H2   C5   C6   C7    180.00   0.0  0
 QHM  CONST_23  H3   C6   C7   C8    180.00   0.0  0
 QHM  CONST_24  H13  C3   C4   C11   180.00   0.0  0
 QHM  CONST_25  C15  N1   C1   C10   180.00   0.0  0
 QHM  CONST_26  C2   C1   N1   C15     0.00   0.0  0
 QHM  CONST_27  H1   N1   C1   C10     0.00   0.0  0
 QHM  Var_01    C10  C9   C13  C8    179.97  30.0  1
 QHM  Var_02    C11  C10  C9   C13    -0.25  30.0  1
 QHM  Var_03    O2   C14  C4   C3      2.98  30.0  2
 QHM  Var_04    C16  C15  N1   C1   -176.05  30.0  3
 QHM  Var_05    N2   C16  C15  N1    176.04  30.0  3
 QHM  Var_06    C19  N2   C16  C15   148.02  30.0  3
 QHM  Var_07    C20  C19  N2   C17   156.55  30.0  3
 QHM  Var_08    C18  C17  N2   C16   151.84  30.0  3
 QHM  Var_09    H10  C20  C19  N2    -58.73  30.0  3
 QHM  Var_10    H21  C18  C17  N2    -59.97  30.0  3

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
 QHM  plan-1  C5   0.020
 QHM  plan-1  C6   0.020
 QHM  plan-1  C7   0.020
 QHM  plan-1  C8   0.020
 QHM  plan-1  C13  0.020
 QHM  plan-1  C9   0.020
 QHM  plan-1  C12  0.020
 QHM  plan-1  S1   0.020
 QHM  plan-1  H2   0.020
 QHM  plan-1  H3   0.020
 QHM  plan-1  H4   0.020
 QHM  plan-1  H5   0.020
 QHM  plan-2  N1   0.020
 QHM  plan-2  C4   0.020
 QHM  plan-2  C10  0.020
 QHM  plan-2  C9   0.020
 QHM  plan-2  C3   0.020
 QHM  plan-2  C2   0.020
 QHM  plan-2  C11  0.020
 QHM  plan-2  C1   0.020
 QHM  plan-2  S1   0.020
 QHM  plan-2  H13  0.020
 QHM  plan-2  H14  0.020
 QHM  plan-2  C14  0.020
 QHM  plan-3  N1   0.020
 QHM  plan-3  C15  0.020
 QHM  plan-3  C1   0.020
 QHM  plan-3  H1   0.020
 QHM  plan-4  C10  0.020
 QHM  plan-4  C13  0.020
 QHM  plan-4  C9   0.020
 QHM  plan-4  O1   0.020

