# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 02:54:46 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N-[3,5-dichloro-2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cc(Cl)cc(Cl)c1Nc2ncc(OCc3c(Cl)c(OC)cc(OC)c3Cl)cn2
#
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
 XL8  XL8  N-[3,5-dichloro-2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)phenyl]propanamide  ligand  54  34  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XL8
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
 XL8  C1   C   CR6   0   0.529   6.0170  -0.4271   0.1392
 XL8  C2   C   CR6   0  -0.272   4.6328  -0.5556   0.0199
 XL8  C3   C   CR6   0   0.272   3.8489   0.4721  -0.4956
 XL8  C4   C   CR6   0  -0.298   4.4765   1.6518  -0.8800
 XL8  C5   C   CR6   0   0.533   5.8625   1.8022  -0.7742
 XL8  C6   C   CR16  0  -0.570   6.6243   0.7583  -0.2628
 XL8  O1   O   O2    0  -0.453   6.6786  -1.4707   0.6429
 XL8  O2   O   O2    0  -0.454   6.3721   2.9678  -1.1778
 XL8  C7   C   CH3   0  -0.444   8.0832  -1.3733   0.8133
 XL8  C8   C   CH3   0  -0.444   7.7713   3.1748  -1.0763
 XL8  CL1  CL  CL    0  -0.099   3.9083  -2.0394   0.5298
 XL8  CL2  CL  CL    0  -0.103   3.5762   2.9912  -1.5036
 XL8  C9   C   CH2   0  -0.264   2.3635   0.2925  -0.5909
 XL8  O3   O   O2    0  -0.459   1.8519   0.3851   0.7292
 XL8  C10  C   CR6   0   0.264   0.5510   0.0889   0.9118
 XL8  C11  C   CR16  0  -0.094   0.0857  -0.0190   2.2217
 XL8  N1   N   N     0  -0.425  -1.1717  -0.2914   2.5059
 XL8  C12  C   CR6   0   0.554  -1.9962  -0.4649   1.4744
 XL8  N2   N   N     0  -0.421  -1.6615  -0.3907   0.1993
 XL8  C13  C   CR16  0  -0.123  -0.3927  -0.1152  -0.0833
 XL8  N3   N   NH1   0  -0.760  -3.3153  -0.7057   1.7826
 XL8  C14  C   CR6   0   0.285  -4.2127  -1.1817   0.8092
 XL8  C15  C   CR6   0   0.358  -5.1044  -0.2803   0.2017
 XL8  C16  C   CR16  0  -0.294  -6.0027  -0.7405  -0.7612
 XL8  C17  C   CR6   0  -0.030  -5.9898  -2.0820  -1.1010
 XL8  C18  C   CR16  0  -0.224  -5.1234  -2.9944  -0.5263
 XL8  C19  C   CR6   0  -0.064  -4.2391  -2.5157   0.4259
 XL8  N4   N   NH1   0  -0.745  -5.0260   1.0361   0.6233
 XL8  C20  C   C     0   0.559  -5.6912   2.1380   0.1672
 XL8  C21  C   CH2   0  -0.589  -5.2856   3.4102   0.8786
 XL8  C22  C   CH3   0  -0.658  -6.0122   4.6433   0.3748
 XL8  O4   O   O     0  -0.456  -6.5193   2.1059  -0.7210
 XL8  CL3  CL  CL    0  -0.092  -3.1298  -3.6117   1.1603
 XL8  CL4  CL  CL    0  -0.108  -7.1099  -2.6406  -2.2948
 XL8  H1   H   HCR6  0   0.322   7.6957   0.8683  -0.1767
 XL8  H2   H   HCH3  0   0.238   8.5973  -1.2284  -0.1392
 XL8  H3   H   HCH3  0   0.238   8.3498  -0.5618   1.4936
 XL8  H4   H   HCH3  0   0.270   8.4021  -2.3173   1.2458
 XL8  H5   H   HCH3  0   0.270   7.9579   4.1745  -1.4582
 XL8  H6   H   HCH3  0   0.238   8.1120   3.1213  -0.0402
 XL8  H7   H   HCH3  0   0.238   8.3314   2.4551  -1.6772
 XL8  H8   H   HCH2  0   0.260   1.9165   1.0523  -1.2341
 XL8  H9   H   HCH2  0   0.256   2.1312  -0.6846  -1.0261
 XL8  H10  H   HCR6  0   0.284   0.7666   0.1230   3.0548
 XL8  H11  H   HCR6  0   0.291  -0.1437  -0.0579  -1.1369
 XL8  H12  H   HNH1  0   0.405  -3.4965  -0.9541   2.7447
 XL8  H13  H   HCR6  0   0.307  -6.6977  -0.0705  -1.2379
 XL8  H14  H   HCR6  0   0.302  -5.1290  -4.0368  -0.8099
 XL8  H15  H   HNH1  0   0.421  -4.3674   1.1812   1.3771
 XL8  H16  H   HCH2  0   0.276  -5.4569   3.2756   1.9508
 XL8  H17  H   HCH2  0   0.274  -4.2041   3.5338   0.7680
 XL8  H18  H   HCH3  0   0.231  -7.0884   4.5662   0.5235
 XL8  H19  H   HCH3  0   0.238  -5.6645   5.5220   0.9164
 XL8  H20  H   HCH3  0   0.231  -5.8298   4.8124  -0.6857

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
 XL8  C22  C21  single    1.517  0.020  1.517
 XL8  C21  C20  single    1.513  0.020  1.513
 XL8  O4   C20  double    1.215  0.020  1.215
 XL8  C20  N4   single    1.365  0.020  1.365
 XL8  CL2  C4   single    1.730  0.020  1.730
 XL8  N4   C15  single    1.385  0.020  1.385
 XL8  O2   C8   single    1.418  0.020  1.418
 XL8  O2   C5   single    1.335  0.020  1.335
 XL8  C13  N2   aromatic  1.329  0.020  1.329
 XL8  C13  C10  aromatic  1.386  0.020  1.386
 XL8  O3   C10  single    1.347  0.020  1.347
 XL8  O3   C9   single    1.419  0.020  1.419
 XL8  C5   C4   aromatic  1.398  0.020  1.398
 XL8  C5   C6   aromatic  1.390  0.020  1.390
 XL8  C4   C3   aromatic  1.390  0.020  1.390
 XL8  N2   C12  aromatic  1.320  0.020  1.320
 XL8  C10  C11  aromatic  1.394  0.020  1.394
 XL8  C15  C16  aromatic  1.395  0.020  1.395
 XL8  C15  C14  aromatic  1.406  0.020  1.406
 XL8  C12  N3   single    1.376  0.020  1.376
 XL8  C12  N1   aromatic  1.332  0.020  1.332
 XL8  C9   C3   single    1.499  0.020  1.499
 XL8  C11  N1   aromatic  1.318  0.020  1.318
 XL8  C16  C17  aromatic  1.384  0.020  1.384
 XL8  C6   C1   aromatic  1.391  0.020  1.391
 XL8  C3   C2   aromatic  1.392  0.020  1.392
 XL8  N3   C14  single    1.407  0.020  1.407
 XL8  C14  C19  aromatic  1.388  0.020  1.388
 XL8  C1   C2   aromatic  1.395  0.020  1.395
 XL8  C1   O1   single    1.334  0.020  1.334
 XL8  C2   CL1  single    1.728  0.020  1.728
 XL8  C7   O1   single    1.418  0.020  1.418
 XL8  C17  CL4  single    1.730  0.020  1.730
 XL8  C17  C18  aromatic  1.383  0.020  1.383
 XL8  C19  C18  aromatic  1.385  0.020  1.385
 XL8  C19  CL3  single    1.724  0.020  1.724
 XL8  C6   H1   single    0.930  0.020  1.080
 XL8  C7   H2   single    0.970  0.020  1.090
 XL8  C7   H3   single    0.970  0.020  1.090
 XL8  C7   H4   single    0.970  0.020  1.090
 XL8  C8   H5   single    0.970  0.020  1.090
 XL8  C8   H6   single    0.970  0.020  1.090
 XL8  C8   H7   single    0.970  0.020  1.090
 XL8  C9   H8   single    0.970  0.020  1.090
 XL8  C9   H9   single    0.970  0.020  1.090
 XL8  C11  H10  single    0.930  0.020  1.080
 XL8  C13  H11  single    0.930  0.020  1.080
 XL8  N3   H12  single    0.890  0.020  1.040
 XL8  C16  H13  single    0.930  0.020  1.080
 XL8  C18  H14  single    0.930  0.020  1.080
 XL8  N4   H15  single    0.860  0.020  1.020
 XL8  C21  H16  single    0.970  0.020  1.090
 XL8  C21  H17  single    0.970  0.020  1.090
 XL8  C22  H18  single    0.970  0.020  1.090
 XL8  C22  H19  single    0.970  0.020  1.090
 XL8  C22  H20  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
 XL8  O1   C1   C6   123.99  3.000
 XL8  O1   C1   C2   116.88  3.000
 XL8  C6   C1   C2   119.13  3.000
 XL8  CL1  C2   C3   120.48  3.000
 XL8  CL1  C2   C1   118.02  3.000
 XL8  C3   C2   C1   121.50  3.000
 XL8  C9   C3   C4   122.09  3.000
 XL8  C9   C3   C2   119.55  3.000
 XL8  C4   C3   C2   118.34  3.000
 XL8  CL2  C4   C5   117.38  3.000
 XL8  C5   C4   C3   121.18  3.000
 XL8  CL2  C4   C3   121.44  3.000
 XL8  O2   C5   C6   123.91  3.000
 XL8  C6   C5   C4   119.37  3.000
 XL8  O2   C5   C4   116.72  3.000
 XL8  H1   C6   C5   119.77  3.000
 XL8  H1   C6   C1   119.77  3.000
 XL8  C5   C6   C1   120.46  3.000
 XL8  C7   O1   C1   118.86  3.000
 XL8  C8   O2   C5   118.86  3.000
 XL8  H4   C7   H3   109.03  3.000
 XL8  H4   C7   H2   108.93  3.000
 XL8  H3   C7   H2   109.26  3.000
 XL8  H4   C7   O1   106.19  3.000
 XL8  H3   C7   O1   111.58  3.000
 XL8  H2   C7   O1   111.75  3.000
 XL8  H7   C8   H6   109.26  3.000
 XL8  H7   C8   H5   108.96  3.000
 XL8  H6   C8   H5   108.97  3.000
 XL8  H7   C8   O2   111.74  3.000
 XL8  H6   C8   O2   111.63  3.000
 XL8  H5   C8   O2   106.18  3.000
 XL8  H9   C9   H8   107.47  3.000
 XL8  H9   C9   O3   110.59  3.000
 XL8  H8   C9   O3   110.81  3.000
 XL8  H9   C9   C3   110.03  3.000
 XL8  H8   C9   C3   111.09  3.000
 XL8  O3   C9   C3   106.88  3.000
 XL8  C10  O3   C9   117.39  3.000
 XL8  C13  C10  C11  115.83  3.000
 XL8  C11  C10  O3   117.82  3.000
 XL8  C13  C10  O3   126.34  3.000
 XL8  H10  C11  N1   117.39  3.000
 XL8  H10  C11  C10  120.12  3.000
 XL8  N1   C11  C10  122.49  3.000
 XL8  C12  N1   C11  116.78  3.000
 XL8  N3   C12  N2   117.98  3.000
 XL8  N3   C12  N1   116.29  3.000
 XL8  N2   C12  N1   125.71  3.000
 XL8  C13  N2   C12  117.33  3.000
 XL8  H11  C13  N2   115.92  3.000
 XL8  H11  C13  C10  122.23  3.000
 XL8  N2   C13  C10  121.86  3.000
 XL8  H12  N3   C14  117.48  3.000
 XL8  H12  N3   C12  115.36  3.000
 XL8  C14  N3   C12  121.05  3.000
 XL8  C19  C14  C15  119.00  3.000
 XL8  C19  C14  N3   121.89  3.000
 XL8  C15  C14  N3   119.12  3.000
 XL8  N4   C15  C16  124.08  3.000
 XL8  C16  C15  C14  119.68  3.000
 XL8  N4   C15  C14  116.24  3.000
 XL8  H13  C16  C17  120.04  3.000
 XL8  H13  C16  C15  121.06  3.000
 XL8  C17  C16  C15  118.90  3.000
 XL8  CL4  C17  C18  118.64  3.000
 XL8  C18  C17  C16  122.90  3.000
 XL8  CL4  C17  C16  118.45  3.000
 XL8  H14  C18  C19  121.16  3.000
 XL8  H14  C18  C17  121.61  3.000
 XL8  C19  C18  C17  117.23  3.000
 XL8  CL3  C19  C18  118.95  3.000
 XL8  CL3  C19  C14  118.76  3.000
 XL8  C18  C19  C14  122.29  3.000
 XL8  H15  N4   C20  116.76  3.000
 XL8  H15  N4   C15  113.59  3.000
 XL8  C20  N4   C15  129.64  3.000
 XL8  O4   C20  C21  123.28  3.000
 XL8  O4   C20  N4   123.71  3.000
 XL8  C21  C20  N4   113.01  3.000
 XL8  H17  C21  H16  105.53  3.000
 XL8  H17  C21  C22  110.36  3.000
 XL8  H16  C21  C22  110.51  3.000
 XL8  H17  C21  C20  108.20  3.000
 XL8  H16  C21  C20  108.39  3.000
 XL8  C22  C21  C20  113.50  3.000
 XL8  H20  C22  H19  107.78  3.000
 XL8  H20  C22  H18  108.02  3.000
 XL8  H19  C22  H18  107.74  3.000
 XL8  H20  C22  C21  111.67  3.000
 XL8  H19  C22  C21  109.73  3.000
 XL8  H18  C22  C21  111.73  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
 XL8  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 XL8  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 XL8  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 XL8  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 XL8  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 XL8  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 XL8  CONST_07  C12  N2   C13  C10     0.00   0.0  0
 XL8  CONST_08  C12  N1   C11  C10     0.00   0.0  0
 XL8  CONST_09  N2   C13  C10  C11     0.00   0.0  0
 XL8  CONST_10  N2   C12  N1   C11     0.00   0.0  0
 XL8  CONST_11  C13  N2   C12  N1      0.00   0.0  0
 XL8  CONST_12  C13  C10  C11  N1      0.00   0.0  0
 XL8  CONST_13  C17  C16  C15  C14     0.00   0.0  0
 XL8  CONST_14  C17  C18  C19  C14     0.00   0.0  0
 XL8  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 XL8  CONST_16  C18  C19  C14  C15     0.00   0.0  0
 XL8  CONST_17  C19  C14  C15  C16     0.00   0.0  0
 XL8  CONST_18  C19  C18  C17  C16     0.00   0.0  0
 XL8  CONST_19  O2   C5   C6   C1    180.00   0.0  0
 XL8  CONST_20  C9   C3   C2   C1    180.00   0.0  0
 XL8  CONST_21  CL2  C4   C3   C2    180.00   0.0  0
 XL8  CONST_22  O2   C5   C4   C3    180.00   0.0  0
 XL8  CONST_23  O1   C1   C2   C3    180.00   0.0  0
 XL8  CONST_24  CL1  C2   C3   C4    180.00   0.0  0
 XL8  CONST_25  C9   C3   C4   C5    180.00   0.0  0
 XL8  CONST_26  O1   C1   C6   C5    180.00   0.0  0
 XL8  CONST_27  CL2  C4   C5   C6    180.00   0.0  0
 XL8  CONST_28  CL1  C2   C1   C6    180.00   0.0  0
 XL8  CONST_29  N2   C13  C10  O3    180.00   0.0  0
 XL8  CONST_30  N1   C11  C10  O3    180.00   0.0  0
 XL8  CONST_31  N3   C12  N1   C11   180.00   0.0  0
 XL8  CONST_32  N3   C12  N2   C13   180.00   0.0  0
 XL8  CONST_33  C16  C15  C14  N3    180.00   0.0  0
 XL8  CONST_34  C18  C19  C14  N3    180.00   0.0  0
 XL8  CONST_35  CL4  C17  C16  C15   180.00   0.0  0
 XL8  CONST_36  CL3  C19  C14  C15   180.00   0.0  0
 XL8  CONST_37  N4   C15  C16  C17   180.00   0.0  0
 XL8  CONST_38  CL3  C19  C18  C17   180.00   0.0  0
 XL8  CONST_39  N4   C15  C14  C19   180.00   0.0  0
 XL8  CONST_40  CL4  C17  C18  C19   180.00   0.0  0
 XL8  CONST_41  H1   C6   C1   C2    180.00   0.0  0
 XL8  CONST_42  H11  C13  C10  C11   180.00   0.0  0
 XL8  CONST_43  H10  C11  N1   C12   180.00   0.0  0
 XL8  CONST_44  H13  C16  C15  C14   180.00   0.0  0
 XL8  CONST_45  H14  C18  C19  C14   180.00   0.0  0
 XL8  CONST_46  C20  N4   C15  C14   180.00   0.0  0
 XL8  CONST_47  C20  N4   C15  C16     0.00   0.0  0
 XL8  CONST_48  H15  N4   C15  C14     0.00   0.0  0
 XL8  CONST_49  C21  C20  N4   C15   180.00   0.0  0
 XL8  CONST_50  O4   C20  N4   C15     0.00   0.0  0
 XL8  Var_01    C14  N3   C12  N1   -166.32  30.0  2
 XL8  Var_02    C15  C14  N3   C12  -101.41  30.0  2
 XL8  Var_03    O3   C9   C3   C2     73.49  30.0  2
 XL8  Var_04    C13  C10  O3   C9     -9.85  30.0  2
 XL8  Var_05    H2   C7   O1   C1    -62.28  30.0  3
 XL8  Var_06    H5   C8   O2   C5    179.87  30.0  3
 XL8  Var_07    C22  C21  C20  N4    179.66  30.0  1
 XL8  Var_08    H18  C22  C21  C20    61.39  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
 XL8  plan-1  C1   0.020
 XL8  plan-1  C2   0.020
 XL8  plan-1  C3   0.020
 XL8  plan-1  C4   0.020
 XL8  plan-1  C5   0.020
 XL8  plan-1  C6   0.020
 XL8  plan-1  O1   0.020
 XL8  plan-1  O2   0.020
 XL8  plan-1  CL1  0.020
 XL8  plan-1  CL2  0.020
 XL8  plan-1  C9   0.020
 XL8  plan-1  H1   0.020
 XL8  plan-2  O3   0.020
 XL8  plan-2  C10  0.020
 XL8  plan-2  C11  0.020
 XL8  plan-2  N1   0.020
 XL8  plan-2  C12  0.020
 XL8  plan-2  N2   0.020
 XL8  plan-2  C13  0.020
 XL8  plan-2  N3   0.020
 XL8  plan-2  H10  0.020
 XL8  plan-2  H11  0.020
 XL8  plan-3  N3   0.020
 XL8  plan-3  C14  0.020
 XL8  plan-3  C15  0.020
 XL8  plan-3  C16  0.020
 XL8  plan-3  C17  0.020
 XL8  plan-3  C18  0.020
 XL8  plan-3  C19  0.020
 XL8  plan-3  N4   0.020
 XL8  plan-3  CL3  0.020
 XL8  plan-3  CL4  0.020
 XL8  plan-3  H13  0.020
 XL8  plan-3  H14  0.020
 XL8  plan-4  C15  0.020
 XL8  plan-4  N4   0.020
 XL8  plan-4  C20  0.020
 XL8  plan-4  C21  0.020
 XL8  plan-4  O4   0.020
 XL8  plan-4  H15  0.020

