# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:27:01 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-methylphenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(C)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
 XL6  XL6  N-[2-({5-[(2,6-dichloro-3,5-dimethoxyphenyl)methoxy]pyrimidin-2-yl}amino)-3-methylphenyl]propanamide  ligand  57  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_XL6
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
 XL6  C1   C   CR6   0   0.533  -5.3608   0.2086   0.5819
 XL6  C2   C   CR6   0  -0.291  -4.0405  -0.2096   0.7680
 XL6  C3   C   CR6   0   0.266  -2.9698   0.6121   0.4340
 XL6  C4   C   CR6   0  -0.276  -3.2415   1.8572  -0.1248
 XL6  C5   C   CR6   0   0.530  -4.5515   2.2971  -0.3202
 XL6  C6   C   CR16  0  -0.569  -5.6061   1.4647   0.0393
 XL6  O1   O   O2    0  -0.453  -6.3184  -0.6484   0.9420
 XL6  O2   O   O2    0  -0.453  -4.7068   3.5105  -0.8541
 XL6  C7   C   CH3   0  -0.444  -7.6745  -0.2801   0.7566
 XL6  C8   C   CH3   0  -0.444  -6.0187   3.9970  -1.0820
 XL6  CL1  CL  CL    0  -0.102  -3.7857  -1.7905   1.4211
 XL6  CL2  CL  CL    0  -0.100  -1.9554   2.9089  -0.6022
 XL6  C9   C   CH2   0  -0.261  -1.5503   0.1680   0.6197
 XL6  O3   O   O2    0  -0.460  -1.1097  -0.3244  -0.6345
 XL6  C10  C   CR6   0   0.259   0.1766  -0.7172  -0.7295
 XL6  C11  C   CR16  0  -0.097   0.6226  -1.1849  -1.9653
 XL6  N1   N   N     0  -0.430   1.8615  -1.5804  -2.1680
 XL6  C12  C   CR6   0   0.553   2.6929  -1.5236  -1.1239
 XL6  N2   N   N     0  -0.419   2.3664  -1.1214   0.0931
 XL6  C13  C   CR16  0  -0.126   1.1166  -0.7160   0.2890
 XL6  N3   N   NH1   0  -0.757   3.9838  -1.9064  -1.3676
 XL6  C14  C   CR6   0   0.221   4.9837  -1.9842  -0.3827
 XL6  C15  C   CR6   0   0.343   5.4385  -0.8111   0.2327
 XL6  C16  C   CR16  0  -0.324   6.4229  -0.8833   1.2125
 XL6  C17  C   CR16  0  -0.248   6.9654  -2.1123   1.5503
 XL6  C18  C   CR16  0  -0.326   6.5390  -3.2688   0.9142
 XL6  C19  C   CR6   0   0.073   5.5415  -3.2230  -0.0542
 XL6  C20  C   CH3   0  -0.736   5.0549  -4.4749  -0.7221
 XL6  N4   N   NH1   0  -0.731   4.9109   0.4128  -0.1950
 XL6  C21  C   C     0   0.542   4.4318   1.3907   0.6168
 XL6  C22  C   CH2   0  -0.577   3.6912   2.4948  -0.1037
 XL6  C23  C   CH3   0  -0.660   4.0694   3.8792   0.4044
 XL6  O4   O   O     0  -0.475   4.5771   1.3846   1.8259
 XL6  H1   H   HCR6  0   0.323  -6.6243   1.7927  -0.1101
 XL6  H2   H   HCH3  0   0.237  -7.9028  -0.0917  -0.2948
 XL6  H3   H   HCH3  0   0.269  -8.2673  -1.1235   1.0996
 XL6  H4   H   HCH3  0   0.238  -7.9395   0.6009   1.3457
 XL6  H5   H   HCH3  0   0.238  -6.5837   4.0888  -0.1517
 XL6  H6   H   HCH3  0   0.269  -5.9039   4.9834  -1.5224
 XL6  H7   H   HCH3  0   0.237  -6.5708   3.3606  -1.7773
 XL6  H8   H   HCH2  0   0.252  -0.9339   1.0108   0.9459
 XL6  H9   H   HCH2  0   0.259  -1.4761  -0.6046   1.3879
 XL6  H10  H   HCR6  0   0.282  -0.0606  -1.2327  -2.8078
 XL6  H11  H   HCR6  0   0.290   0.8760  -0.3924   1.2956
 XL6  H12  H   HNH1  0   0.399   4.1315  -2.3965  -2.2364
 XL6  H13  H   HCR6  0   0.264   6.7849   0.0171   1.6865
 XL6  H14  H   HCR6  0   0.257   7.7374  -2.1645   2.3065
 XL6  H15  H   HCR6  0   0.251   6.9767  -4.2233   1.1795
 XL6  H16  H   HCH3  0   0.251   3.9741  -4.5870  -0.6214
 XL6  H17  H   HCH3  0   0.248   5.2790  -4.4829  -1.7909
 XL6  H18  H   HCH3  0   0.254   5.5249  -5.3541  -0.2853
 XL6  H19  H   HNH1  0   0.404   4.6505   0.4594  -1.1691
 XL6  H20  H   HCH2  0   0.252   3.8468   2.4299  -1.1820
 XL6  H21  H   HCH2  0   0.265   2.6229   2.3208   0.0613
 XL6  H22  H   HCH3  0   0.232   3.8762   3.9777   1.4713
 XL6  H23  H   HCH3  0   0.232   5.1249   4.0895   0.2301
 XL6  H24  H   HCH3  0   0.239   3.4880   4.6417  -0.1124

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
 XL6  C20  C19  single    1.500  0.020  1.500
 XL6  C18  C19  aromatic  1.391  0.020  1.391
 XL6  C18  C17  aromatic  1.387  0.020  1.387
 XL6  CL2  C4   single    1.729  0.020  1.729
 XL6  C19  C14  aromatic  1.398  0.020  1.398
 XL6  O2   C8   single    1.418  0.020  1.418
 XL6  O2   C5   single    1.335  0.020  1.335
 XL6  C17  C16  aromatic  1.385  0.020  1.385
 XL6  C5   C4   aromatic  1.396  0.020  1.396
 XL6  C5   C6   aromatic  1.391  0.020  1.391
 XL6  C4   C3   aromatic  1.391  0.020  1.391
 XL6  C14  N3   single    1.406  0.020  1.406
 XL6  C14  C15  aromatic  1.401  0.020  1.401
 XL6  N2   C13  aromatic  1.328  0.020  1.328
 XL6  N2   C12  aromatic  1.323  0.020  1.323
 XL6  C6   C1   aromatic  1.390  0.020  1.390
 XL6  C9   C3   single    1.499  0.020  1.499
 XL6  C9   O3   single    1.418  0.020  1.418
 XL6  C3   C2   aromatic  1.390  0.020  1.390
 XL6  N3   C12  single    1.368  0.020  1.368
 XL6  C16  C15  aromatic  1.391  0.020  1.391
 XL6  C13  C10  aromatic  1.386  0.020  1.386
 XL6  C12  N1   aromatic  1.336  0.020  1.336
 XL6  C15  N4   single    1.400  0.020  1.400
 XL6  C10  O3   single    1.348  0.020  1.348
 XL6  C10  C11  aromatic  1.395  0.020  1.395
 XL6  N1   C11  aromatic  1.316  0.020  1.316
 XL6  C2   C1   aromatic  1.397  0.020  1.397
 XL6  C2   CL1  single    1.729  0.020  1.729
 XL6  C1   O1   single    1.335  0.020  1.335
 XL6  O1   C7   single    1.417  0.020  1.417
 XL6  N4   C21  single    1.358  0.020  1.358
 XL6  O4   C21  double    1.218  0.020  1.218
 XL6  C21  C22  single    1.512  0.020  1.512
 XL6  C22  C23  single    1.523  0.020  1.523
 XL6  C6   H1   single    0.930  0.020  1.080
 XL6  C7   H2   single    0.970  0.020  1.090
 XL6  C7   H3   single    0.970  0.020  1.090
 XL6  C7   H4   single    0.970  0.020  1.090
 XL6  C8   H5   single    0.970  0.020  1.090
 XL6  C8   H6   single    0.970  0.020  1.090
 XL6  C8   H7   single    0.970  0.020  1.090
 XL6  C9   H8   single    0.970  0.020  1.090
 XL6  C9   H9   single    0.970  0.020  1.090
 XL6  C11  H10  single    0.930  0.020  1.080
 XL6  C13  H11  single    0.930  0.020  1.080
 XL6  N3   H12  single    0.860  0.020  1.020
 XL6  C16  H13  single    0.930  0.020  1.080
 XL6  C17  H14  single    0.930  0.020  1.080
 XL6  C18  H15  single    0.930  0.020  1.080
 XL6  C20  H16  single    0.970  0.020  1.090
 XL6  C20  H17  single    0.970  0.020  1.090
 XL6  C20  H18  single    0.970  0.020  1.090
 XL6  N4   H19  single    0.860  0.020  1.020
 XL6  C22  H20  single    0.970  0.020  1.090
 XL6  C22  H21  single    0.970  0.020  1.090
 XL6  C23  H22  single    0.970  0.020  1.090
 XL6  C23  H23  single    0.970  0.020  1.090
 XL6  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
 XL6  O1   C1   C6   123.98  3.000
 XL6  O1   C1   C2   116.73  3.000
 XL6  C6   C1   C2   119.29  3.000
 XL6  CL1  C2   C3   121.16  3.000
 XL6  CL1  C2   C1   117.59  3.000
 XL6  C3   C2   C1   121.25  3.000
 XL6  C9   C3   C4   119.98  3.000
 XL6  C9   C3   C2   121.63  3.000
 XL6  C4   C3   C2   118.35  3.000
 XL6  CL2  C4   C5   117.90  3.000
 XL6  C5   C4   C3   121.44  3.000
 XL6  CL2  C4   C3   120.67  3.000
 XL6  O2   C5   C6   124.01  3.000
 XL6  C6   C5   C4   119.13  3.000
 XL6  O2   C5   C4   116.86  3.000
 XL6  H1   C6   C5   119.82  3.000
 XL6  H1   C6   C1   119.66  3.000
 XL6  C5   C6   C1   120.52  3.000
 XL6  C7   O1   C1   118.97  3.000
 XL6  C8   O2   C5   118.94  3.000
 XL6  H4   C7   H3   108.88  3.000
 XL6  H4   C7   H2   109.22  3.000
 XL6  H3   C7   H2   108.89  3.000
 XL6  H4   C7   O1   111.79  3.000
 XL6  H3   C7   O1   106.20  3.000
 XL6  H2   C7   O1   111.76  3.000
 XL6  H7   C8   H6   108.93  3.000
 XL6  H7   C8   H5   109.25  3.000
 XL6  H6   C8   H5   108.88  3.000
 XL6  H7   C8   O2   111.73  3.000
 XL6  H6   C8   O2   106.20  3.000
 XL6  H5   C8   O2   111.75  3.000
 XL6  H9   C9   H8   107.28  3.000
 XL6  H9   C9   O3   110.82  3.000
 XL6  H8   C9   O3   110.87  3.000
 XL6  H9   C9   C3   111.17  3.000
 XL6  H8   C9   C3   110.02  3.000
 XL6  O3   C9   C3   106.72  3.000
 XL6  C10  O3   C9   117.39  3.000
 XL6  C13  C10  C11  115.76  3.000
 XL6  C11  C10  O3   117.73  3.000
 XL6  C13  C10  O3   126.51  3.000
 XL6  H10  C11  N1   117.36  3.000
 XL6  H10  C11  C10  120.07  3.000
 XL6  N1   C11  C10  122.57  3.000
 XL6  C12  N1   C11  116.92  3.000
 XL6  N3   C12  N2   118.81  3.000
 XL6  N3   C12  N1   115.85  3.000
 XL6  N2   C12  N1   125.34  3.000
 XL6  C13  N2   C12  117.44  3.000
 XL6  H11  C13  N2   115.90  3.000
 XL6  H11  C13  C10  122.13  3.000
 XL6  N2   C13  C10  121.97  3.000
 XL6  H12  N3   C14  118.21  3.000
 XL6  H12  N3   C12  115.31  3.000
 XL6  C14  N3   C12  124.18  3.000
 XL6  C19  C14  C15  120.63  3.000
 XL6  C15  C14  N3   119.51  3.000
 XL6  C19  C14  N3   119.84  3.000
 XL6  N4   C15  C16  121.83  3.000
 XL6  N4   C15  C14  118.40  3.000
 XL6  C16  C15  C14  119.73  3.000
 XL6  H13  C16  C17  120.09  3.000
 XL6  H13  C16  C15  120.21  3.000
 XL6  C17  C16  C15  119.67  3.000
 XL6  H14  C17  C18  119.98  3.000
 XL6  H14  C17  C16  119.52  3.000
 XL6  C18  C17  C16  120.50  3.000
 XL6  H15  C18  C19  119.30  3.000
 XL6  H15  C18  C17  119.88  3.000
 XL6  C19  C18  C17  120.81  3.000
 XL6  C20  C19  C18  121.01  3.000
 XL6  C18  C19  C14  118.62  3.000
 XL6  C20  C19  C14  120.37  3.000
 XL6  H18  C20  H17  107.35  3.000
 XL6  H18  C20  H16  107.91  3.000
 XL6  H17  C20  H16  107.03  3.000
 XL6  H18  C20  C19  110.82  3.000
 XL6  H17  C20  C19  112.05  3.000
 XL6  H16  C20  C19  111.47  3.000
 XL6  H19  N4   C21  116.91  3.000
 XL6  H19  N4   C15  115.63  3.000
 XL6  C21  N4   C15  125.44  3.000
 XL6  O4   C21  C22  122.35  3.000
 XL6  C22  C21  N4   114.43  3.000
 XL6  O4   C21  N4   123.22  3.000
 XL6  H21  C22  H20  106.18  3.000
 XL6  H21  C22  C23  109.67  3.000
 XL6  H20  C22  C23  110.38  3.000
 XL6  H21  C22  C21  106.86  3.000
 XL6  H20  C22  C21  110.95  3.000
 XL6  C23  C22  C21  112.53  3.000
 XL6  H24  C23  H23  107.81  3.000
 XL6  H24  C23  H22  107.87  3.000
 XL6  H23  C23  H22  108.12  3.000
 XL6  H24  C23  C22  110.22  3.000
 XL6  H23  C23  C22  111.26  3.000
 XL6  H22  C23  C22  111.42  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
 XL6  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 XL6  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 XL6  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 XL6  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 XL6  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 XL6  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 XL6  CONST_07  C12  N2   C13  C10     0.00   0.0  0
 XL6  CONST_08  C12  N1   C11  C10     0.00   0.0  0
 XL6  CONST_09  N2   C13  C10  C11     0.00   0.0  0
 XL6  CONST_10  N2   C12  N1   C11     0.00   0.0  0
 XL6  CONST_11  C13  N2   C12  N1      0.00   0.0  0
 XL6  CONST_12  C13  C10  C11  N1      0.00   0.0  0
 XL6  CONST_13  C17  C18  C19  C14     0.00   0.0  0
 XL6  CONST_14  C17  C16  C15  C14     0.00   0.0  0
 XL6  CONST_15  C18  C19  C14  C15     0.00   0.0  0
 XL6  CONST_16  C18  C17  C16  C15     0.00   0.0  0
 XL6  CONST_17  C19  C18  C17  C16     0.00   0.0  0
 XL6  CONST_18  C19  C14  C15  C16     0.00   0.0  0
 XL6  CONST_19  O2   C5   C6   C1    180.00   0.0  0
 XL6  CONST_20  C9   C3   C2   C1    180.00   0.0  0
 XL6  CONST_21  CL2  C4   C3   C2    180.00   0.0  0
 XL6  CONST_22  O2   C5   C4   C3    180.00   0.0  0
 XL6  CONST_23  O1   C1   C2   C3    180.00   0.0  0
 XL6  CONST_24  CL1  C2   C3   C4    180.00   0.0  0
 XL6  CONST_25  C9   C3   C4   C5    180.00   0.0  0
 XL6  CONST_26  O1   C1   C6   C5    180.00   0.0  0
 XL6  CONST_27  CL2  C4   C5   C6    180.00   0.0  0
 XL6  CONST_28  CL1  C2   C1   C6    180.00   0.0  0
 XL6  CONST_29  N2   C13  C10  O3    180.00   0.0  0
 XL6  CONST_30  N1   C11  C10  O3    180.00   0.0  0
 XL6  CONST_31  N3   C12  N1   C11   180.00   0.0  0
 XL6  CONST_32  N3   C12  N2   C13   180.00   0.0  0
 XL6  CONST_33  C18  C19  C14  N3    180.00   0.0  0
 XL6  CONST_34  C16  C15  C14  N3    180.00   0.0  0
 XL6  CONST_35  C20  C19  C14  C15   180.00   0.0  0
 XL6  CONST_36  C20  C19  C18  C17   180.00   0.0  0
 XL6  CONST_37  N4   C15  C16  C17   180.00   0.0  0
 XL6  CONST_38  N4   C15  C14  C19   180.00   0.0  0
 XL6  CONST_39  H1   C6   C1   C2    180.00   0.0  0
 XL6  CONST_40  H11  C13  C10  C11   180.00   0.0  0
 XL6  CONST_41  H10  C11  N1   C12   180.00   0.0  0
 XL6  CONST_42  H15  C18  C19  C14   180.00   0.0  0
 XL6  CONST_43  H13  C16  C15  C14   180.00   0.0  0
 XL6  CONST_44  H14  C17  C16  C15   180.00   0.0  0
 XL6  CONST_48  O4   C21  N4   C15     0.00   0.0  0
 XL6  CONST_49  C22  C21  N4   C15   180.00   0.0  0
 XL6  Var_01    C14  N3   C12  N1   -176.39  30.0  3
 XL6  Var_02    C19  C14  N3   C12   114.98  30.0  2
 XL6  Var_03    O3   C9   C3   C2     96.74  30.0  2
 XL6  Var_04    C13  C10  O3   C9      1.45  30.0  3
 XL6  Var_05    H16  C20  C19  C14   -54.39  30.0  2
 XL6  Var_06    H2   C7   O1   C1     60.51  30.0  3
 XL6  Var_07    H5   C8   O2   C5     61.85  30.0  3
 XL6  Var_08    C23  C22  C21  N4   -136.30  30.0  3
 XL6  Var_09    H22  C23  C22  C21   -58.14  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
 XL6  plan-1  C1   0.020
 XL6  plan-1  C2   0.020
 XL6  plan-1  C3   0.020
 XL6  plan-1  C4   0.020
 XL6  plan-1  C5   0.020
 XL6  plan-1  C6   0.020
 XL6  plan-1  O1   0.020
 XL6  plan-1  O2   0.020
 XL6  plan-1  CL1  0.020
 XL6  plan-1  CL2  0.020
 XL6  plan-1  C9   0.020
 XL6  plan-1  H1   0.020
 XL6  plan-2  O3   0.020
 XL6  plan-2  C10  0.020
 XL6  plan-2  C11  0.020
 XL6  plan-2  N1   0.020
 XL6  plan-2  C12  0.020
 XL6  plan-2  N2   0.020
 XL6  plan-2  C13  0.020
 XL6  plan-2  N3   0.020
 XL6  plan-2  H10  0.020
 XL6  plan-2  H11  0.020
 XL6  plan-3  N3   0.020
 XL6  plan-3  C14  0.020
 XL6  plan-3  C15  0.020
 XL6  plan-3  C16  0.020
 XL6  plan-3  C17  0.020
 XL6  plan-3  C18  0.020
 XL6  plan-3  C19  0.020
 XL6  plan-3  C20  0.020
 XL6  plan-3  N4   0.020
 XL6  plan-3  H13  0.020
 XL6  plan-3  H14  0.020
 XL6  plan-3  H15  0.020
 XL6  plan-4  C15  0.020
 XL6  plan-4  N4   0.020
 XL6  plan-4  C21  0.020
 XL6  plan-4  C22  0.020
 XL6  plan-4  O4   0.020
 XL6  plan-4  H19  0.020

