# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:47:00 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-fluorophenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(F)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
 XL5  XL5  N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-fluorophenyl]propanamide  ligand  54  33  .  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_XL5
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
 XL5  C1   C   CR6   0   0.533   5.6846  -0.3611  -0.4117
 XL5  C2   C   CR6   0  -0.291   4.3357  -0.6693  -0.6074
 XL5  C3   C   CR6   0   0.267   3.3410   0.2789  -0.3961
 XL5  C4   C   CR6   0  -0.277   3.7167   1.5427   0.0484
 XL5  C5   C   CR6   0   0.530   5.0572   1.8750   0.2494
 XL5  C6   C   CR16  0  -0.570   6.0356   0.9148   0.0145
 XL5  O1   O   O2    0  -0.454   6.5644  -1.3367  -0.6475
 XL5  O2   O   O2    0  -0.453   5.3152   3.1167   0.6649
 XL5  C7   C   CH3   0  -0.444   7.9434  -1.0796  -0.4423
 XL5  C8   C   CH3   0  -0.444   6.6592   3.4902   0.9180
 XL5  CL1  CL  CL    0  -0.102   3.9466  -2.2786  -1.1087
 XL5  CL2  CL  CL    0  -0.100   2.5252   2.7513   0.3769
 XL5  C9   C   CH2   0  -0.262   1.8909  -0.0465  -0.5921
 XL5  O3   O   O2    0  -0.459   1.3656  -0.3577   0.6887
 XL5  C10  C   CR6   0   0.261   0.0389  -0.5764   0.7785
 XL5  C11  C   CR16  0  -0.094  -0.5085  -0.7426   2.0498
 XL5  N1   N   N     0  -0.428  -1.7909  -0.9733   2.2438
 XL5  C12  C   CR6   0   0.561  -2.5618  -1.0393   1.1584
 XL5  N2   N   N     0  -0.425  -2.1483  -0.8926  -0.0879
 XL5  C13  C   CR16  0  -0.124  -0.8537  -0.6639  -0.2787
 XL5  N3   N   NH1   0  -0.750  -3.9031  -1.2412   1.3766
 XL5  C14  C   CR6   0   0.020  -4.7573  -1.6550   0.3347
 XL5  C15  C   CR6   0   0.363  -5.6218  -0.7339  -0.2791
 XL5  C16  C   CR16  0  -0.346  -6.4611  -1.1710  -1.3069
 XL5  C17  C   CR16  0  -0.232  -6.4251  -2.4976  -1.7089
 XL5  C18  C   CR16  0  -0.442  -5.5730  -3.4197  -1.1203
 XL5  C19  C   CR6   0   0.560  -4.7535  -2.9671  -0.1081
 XL5  N4   N   NH1   0  -0.742  -5.5699   0.5665   0.2031
 XL5  C20  C   C     0   0.554  -6.2123   1.6844  -0.2394
 XL5  C21  C   CH2   0  -0.589  -5.8346   2.9306   0.5321
 XL5  C22  C   CH3   0  -0.658  -6.5834   4.1719   0.0839
 XL5  O4   O   O     0  -0.460  -7.0031   1.6896  -1.1628
 XL5  F1   F   F     0  -0.304  -3.9051  -3.8185   0.4815
 XL5  H1   H   HCR6  0   0.323   7.0764   1.1607   0.1674
 XL5  H2   H   HCH3  0   0.270   8.4636  -2.0016  -0.6869
 XL5  H3   H   HCH3  0   0.238   8.3079  -0.2833  -1.0949
 XL5  H4   H   HCH3  0   0.238   8.1541  -0.8174   0.5968
 XL5  H5   H   HCH3  0   0.269   6.6282   4.5219   1.2568
 XL5  H6   H   HCH3  0   0.238   7.1084   2.8733   1.6994
 XL5  H7   H   HCH3  0   0.238   7.2734   3.4323   0.0164
 XL5  H8   H   HCH2  0   0.256   1.3668   0.8096  -1.0261
 XL5  H9   H   HCH2  0   0.258   1.7684  -0.8867  -1.2789
 XL5  H10  H   HCR6  0   0.283   0.1269  -0.6859   2.9283
 XL5  H11  H   HCR6  0   0.291  -0.5388  -0.5485  -1.3097
 XL5  H12  H   HNH1  0   0.403  -4.1474  -1.5164   2.3170
 XL5  H13  H   HCR6  0   0.285  -7.1382  -0.4898  -1.7925
 XL5  H14  H   HCR6  0   0.272  -7.0815  -2.8191  -2.5067
 XL5  H15  H   HCR6  0   0.281  -5.5441  -4.4534  -1.4374
 XL5  H16  H   HNH1  0   0.416  -4.9424   0.6863   0.9874
 XL5  H17  H   HCH2  0   0.272  -6.0035   2.7456   1.5971
 XL5  H18  H   HCH2  0   0.273  -4.7554   3.0792   0.4284
 XL5  H19  H   HCH3  0   0.237  -6.2516   5.0313   0.6654
 XL5  H20  H   HCH3  0   0.230  -6.4042   4.3937  -0.9674
 XL5  H21  H   HCH3  0   0.230  -7.6582   4.0693   0.2289

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
 XL5  C22  C21  single    1.517  0.020  1.517
 XL5  C21  C20  single    1.514  0.020  1.514
 XL5  O4   C20  double    1.216  0.020  1.216
 XL5  C20  N4   single    1.363  0.020  1.363
 XL5  CL1  C2   single    1.730  0.020  1.730
 XL5  C7   O1   single    1.418  0.020  1.418
 XL5  N4   C15  single    1.388  0.020  1.388
 XL5  O1   C1   single    1.335  0.020  1.335
 XL5  C13  N2   aromatic  1.328  0.020  1.328
 XL5  C13  C10  aromatic  1.386  0.020  1.386
 XL5  C1   C2   aromatic  1.397  0.020  1.397
 XL5  C1   C6   aromatic  1.390  0.020  1.390
 XL5  C2   C3   aromatic  1.390  0.020  1.390
 XL5  N2   C12  aromatic  1.321  0.020  1.321
 XL5  O3   C10  single    1.348  0.020  1.348
 XL5  O3   C9   single    1.419  0.020  1.419
 XL5  C10  C11  aromatic  1.394  0.020  1.394
 XL5  C15  C16  aromatic  1.397  0.020  1.397
 XL5  C15  C14  aromatic  1.405  0.020  1.405
 XL5  C12  N3   single    1.374  0.020  1.374
 XL5  C12  N1   aromatic  1.333  0.020  1.333
 XL5  N3   C14  single    1.409  0.020  1.409
 XL5  C11  N1   aromatic  1.317  0.020  1.317
 XL5  C6   C5   aromatic  1.391  0.020  1.391
 XL5  C9   C3   single    1.499  0.020  1.499
 XL5  C3   C4   aromatic  1.391  0.020  1.391
 XL5  C16  C17  aromatic  1.387  0.020  1.387
 XL5  C14  C19  aromatic  1.385  0.020  1.385
 XL5  C5   C4   aromatic  1.396  0.020  1.396
 XL5  C5   O2   single    1.335  0.020  1.335
 XL5  C4   CL2  single    1.729  0.020  1.729
 XL5  C8   O2   single    1.418  0.020  1.418
 XL5  C17  C18  aromatic  1.387  0.020  1.387
 XL5  C19  C18  aromatic  1.379  0.020  1.379
 XL5  C19  F1   single    1.339  0.020  1.339
 XL5  C6   H1   single    0.930  0.020  1.080
 XL5  C7   H2   single    0.970  0.020  1.090
 XL5  C7   H3   single    0.970  0.020  1.090
 XL5  C7   H4   single    0.970  0.020  1.090
 XL5  C8   H5   single    0.970  0.020  1.090
 XL5  C8   H6   single    0.970  0.020  1.090
 XL5  C8   H7   single    0.970  0.020  1.090
 XL5  C9   H8   single    0.970  0.020  1.090
 XL5  C9   H9   single    0.970  0.020  1.090
 XL5  C11  H10  single    0.930  0.020  1.080
 XL5  C13  H11  single    0.930  0.020  1.080
 XL5  N3   H12  single    0.890  0.020  1.040
 XL5  C16  H13  single    0.930  0.020  1.080
 XL5  C17  H14  single    0.930  0.020  1.080
 XL5  C18  H15  single    0.930  0.020  1.080
 XL5  N4   H16  single    0.860  0.020  1.020
 XL5  C21  H17  single    0.970  0.020  1.090
 XL5  C21  H18  single    0.970  0.020  1.090
 XL5  C22  H19  single    0.970  0.020  1.090
 XL5  C22  H20  single    0.970  0.020  1.090
 XL5  C22  H21  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
 XL5  O1   C1   C6   123.96  3.000
 XL5  C6   C1   C2   119.28  3.000
 XL5  O1   C1   C2   116.76  3.000
 XL5  CL1  C2   C3   121.17  3.000
 XL5  C3   C2   C1   121.26  3.000
 XL5  CL1  C2   C1   117.57  3.000
 XL5  C9   C3   C4   120.01  3.000
 XL5  C4   C3   C2   118.34  3.000
 XL5  C9   C3   C2   121.61  3.000
 XL5  CL2  C4   C5   117.91  3.000
 XL5  CL2  C4   C3   120.64  3.000
 XL5  C5   C4   C3   121.45  3.000
 XL5  O2   C5   C6   123.98  3.000
 XL5  O2   C5   C4   116.88  3.000
 XL5  C6   C5   C4   119.14  3.000
 XL5  H1   C6   C5   119.77  3.000
 XL5  H1   C6   C1   119.71  3.000
 XL5  C5   C6   C1   120.52  3.000
 XL5  C7   O1   C1   118.88  3.000
 XL5  C8   O2   C5   118.95  3.000
 XL5  H4   C7   H3   109.21  3.000
 XL5  H4   C7   H2   109.00  3.000
 XL5  H3   C7   H2   108.93  3.000
 XL5  H4   C7   O1   111.64  3.000
 XL5  H3   C7   O1   111.74  3.000
 XL5  H2   C7   O1   106.22  3.000
 XL5  H7   C8   H6   109.22  3.000
 XL5  H7   C8   H5   108.89  3.000
 XL5  H6   C8   H5   108.97  3.000
 XL5  H7   C8   O2   111.82  3.000
 XL5  H6   C8   O2   111.64  3.000
 XL5  H5   C8   O2   106.19  3.000
 XL5  H9   C9   H8   107.39  3.000
 XL5  H9   C9   O3   110.94  3.000
 XL5  H8   C9   O3   110.64  3.000
 XL5  H9   C9   C3   110.96  3.000
 XL5  H8   C9   C3   110.22  3.000
 XL5  O3   C9   C3   106.72  3.000
 XL5  C10  O3   C9   117.40  3.000
 XL5  C13  C10  C11  115.79  3.000
 XL5  C11  C10  O3   117.82  3.000
 XL5  C13  C10  O3   126.39  3.000
 XL5  H10  C11  N1   117.37  3.000
 XL5  H10  C11  C10  120.12  3.000
 XL5  N1   C11  C10  122.51  3.000
 XL5  C12  N1   C11  116.86  3.000
 XL5  N3   C12  N2   118.14  3.000
 XL5  N3   C12  N1   116.27  3.000
 XL5  N2   C12  N1   125.56  3.000
 XL5  C13  N2   C12  117.36  3.000
 XL5  H11  C13  N2   115.97  3.000
 XL5  H11  C13  C10  122.11  3.000
 XL5  N2   C13  C10  121.92  3.000
 XL5  H12  N3   C14  117.50  3.000
 XL5  H12  N3   C12  115.10  3.000
 XL5  C14  N3   C12  121.16  3.000
 XL5  C19  C14  C15  118.90  3.000
 XL5  C19  C14  N3   120.86  3.000
 XL5  C15  C14  N3   120.24  3.000
 XL5  N4   C15  C16  124.84  3.000
 XL5  C16  C15  C14  119.08  3.000
 XL5  N4   C15  C14  116.08  3.000
 XL5  H13  C16  C17  119.41  3.000
 XL5  H13  C16  C15  120.79  3.000
 XL5  C17  C16  C15  119.81  3.000
 XL5  H14  C17  C18  119.22  3.000
 XL5  H14  C17  C16  118.84  3.000
 XL5  C18  C17  C16  121.95  3.000
 XL5  H15  C18  C19  120.86  3.000
 XL5  H15  C18  C17  121.84  3.000
 XL5  C19  C18  C17  117.29  3.000
 XL5  F1   C19  C18  119.42  3.000
 XL5  F1   C19  C14  117.60  3.000
 XL5  C18  C19  C14  122.97  3.000
 XL5  H16  N4   C20  116.54  3.000
 XL5  H16  N4   C15  113.80  3.000
 XL5  C20  N4   C15  129.65  3.000
 XL5  O4   C20  C21  123.09  3.000
 XL5  O4   C20  N4   123.81  3.000
 XL5  C21  C20  N4   113.09  3.000
 XL5  H18  C21  H17  105.51  3.000
 XL5  H18  C21  C22  110.33  3.000
 XL5  H17  C21  C22  110.47  3.000
 XL5  H18  C21  C20  108.03  3.000
 XL5  H17  C21  C20  108.57  3.000
 XL5  C22  C21  C20  113.57  3.000
 XL5  H21  C22  H20  108.06  3.000
 XL5  H21  C22  H19  107.68  3.000
 XL5  H20  C22  H19  107.73  3.000
 XL5  H21  C22  C21  111.75  3.000
 XL5  H20  C22  C21  111.75  3.000
 XL5  H19  C22  C21  109.72  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
 XL5  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 XL5  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 XL5  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 XL5  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 XL5  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 XL5  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 XL5  CONST_07  C12  N2   C13  C10     0.00   0.0  0
 XL5  CONST_08  C12  N1   C11  C10     0.00   0.0  0
 XL5  CONST_09  N2   C13  C10  C11     0.00   0.0  0
 XL5  CONST_10  N2   C12  N1   C11     0.00   0.0  0
 XL5  CONST_11  C13  N2   C12  N1      0.00   0.0  0
 XL5  CONST_12  C13  C10  C11  N1      0.00   0.0  0
 XL5  CONST_13  C17  C16  C15  C14     0.00   0.0  0
 XL5  CONST_14  C17  C18  C19  C14     0.00   0.0  0
 XL5  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 XL5  CONST_16  C18  C19  C14  C15     0.00   0.0  0
 XL5  CONST_17  C19  C14  C15  C16     0.00   0.0  0
 XL5  CONST_18  C19  C18  C17  C16     0.00   0.0  0
 XL5  CONST_19  C9   C3   C2   C1    180.00   0.0  0
 XL5  CONST_20  O2   C5   C6   C1    180.00   0.0  0
 XL5  CONST_21  CL2  C4   C3   C2    180.00   0.0  0
 XL5  CONST_22  O1   C1   C2   C3    180.00   0.0  0
 XL5  CONST_23  O2   C5   C4   C3    180.00   0.0  0
 XL5  CONST_24  CL1  C2   C3   C4    180.00   0.0  0
 XL5  CONST_25  O1   C1   C6   C5    180.00   0.0  0
 XL5  CONST_26  C9   C3   C4   C5    180.00   0.0  0
 XL5  CONST_27  CL1  C2   C1   C6    180.00   0.0  0
 XL5  CONST_28  CL2  C4   C5   C6    180.00   0.0  0
 XL5  CONST_29  N2   C13  C10  O3    180.00   0.0  0
 XL5  CONST_30  N1   C11  C10  O3    180.00   0.0  0
 XL5  CONST_31  N3   C12  N1   C11   180.00   0.0  0
 XL5  CONST_32  N3   C12  N2   C13   180.00   0.0  0
 XL5  CONST_33  C16  C15  C14  N3    180.00   0.0  0
 XL5  CONST_34  C18  C19  C14  N3    180.00   0.0  0
 XL5  CONST_35  F1   C19  C14  C15   180.00   0.0  0
 XL5  CONST_36  N4   C15  C16  C17   180.00   0.0  0
 XL5  CONST_37  F1   C19  C18  C17   180.00   0.0  0
 XL5  CONST_38  N4   C15  C14  C19   180.00   0.0  0
 XL5  CONST_39  H1   C6   C1   C2    180.00   0.0  0
 XL5  CONST_40  H11  C13  C10  C11   180.00   0.0  0
 XL5  CONST_41  H10  C11  N1   C12   180.00   0.0  0
 XL5  CONST_42  H13  C16  C15  C14   180.00   0.0  0
 XL5  CONST_43  H15  C18  C19  C14   180.00   0.0  0
 XL5  CONST_44  H14  C17  C16  C15   180.00   0.0  0
 XL5  CONST_45  C20  N4   C15  C14   180.00   0.0  0
 XL5  CONST_46  C20  N4   C15  C16     0.00   0.0  0
 XL5  CONST_47  H16  N4   C15  C14     0.00   0.0  0
 XL5  CONST_48  C21  C20  N4   C15   180.00   0.0  0
 XL5  CONST_49  O4   C20  N4   C15     0.00   0.0  0
 XL5  Var_01    C14  N3   C12  N1   -164.10  30.0  2
 XL5  Var_02    C15  C14  N3   C12  -103.66  30.0  2
 XL5  Var_03    O3   C9   C3   C2     97.16  30.0  2
 XL5  Var_04    C13  C10  O3   C9      7.11  30.0  2
 XL5  Var_05    H2   C7   O1   C1    179.69  30.0  3
 XL5  Var_06    H5   C8   O2   C5   -179.04  30.0  3
 XL5  Var_07    C22  C21  C20  N4   -177.77  30.0  1
 XL5  Var_08    H19  C22  C21  C20  -178.97  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
 XL5  plan-1  C1   0.020
 XL5  plan-1  C2   0.020
 XL5  plan-1  C3   0.020
 XL5  plan-1  C4   0.020
 XL5  plan-1  C5   0.020
 XL5  plan-1  C6   0.020
 XL5  plan-1  O1   0.020
 XL5  plan-1  O2   0.020
 XL5  plan-1  CL1  0.020
 XL5  plan-1  CL2  0.020
 XL5  plan-1  C9   0.020
 XL5  plan-1  H1   0.020
 XL5  plan-2  O3   0.020
 XL5  plan-2  C10  0.020
 XL5  plan-2  C11  0.020
 XL5  plan-2  N1   0.020
 XL5  plan-2  C12  0.020
 XL5  plan-2  N2   0.020
 XL5  plan-2  C13  0.020
 XL5  plan-2  N3   0.020
 XL5  plan-2  H10  0.020
 XL5  plan-2  H11  0.020
 XL5  plan-3  N3   0.020
 XL5  plan-3  C14  0.020
 XL5  plan-3  C15  0.020
 XL5  plan-3  C16  0.020
 XL5  plan-3  C17  0.020
 XL5  plan-3  C18  0.020
 XL5  plan-3  C19  0.020
 XL5  plan-3  N4   0.020
 XL5  plan-3  F1   0.020
 XL5  plan-3  H13  0.020
 XL5  plan-3  H14  0.020
 XL5  plan-3  H15  0.020
 XL5  plan-4  C15  0.020
 XL5  plan-4  N4   0.020
 XL5  plan-4  C20  0.020
 XL5  plan-4  C21  0.020
 XL5  plan-4  O4   0.020
 XL5  plan-4  H16  0.020

