# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 18:15:22 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}-4-methoxyphenyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1ccc(OC)c(Nc2ncc(Cl)c(n2)c3c[nH]c4ccccc34)c1
#
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
 1WY  1WY  N-(3-{[5-chloro-4-(1H-indol-3-yl)pyrimidin-2-yl]amino}-4-methoxyphenyl)propanamide  ligand  50  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1WY
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
 1WY  C2   C   CR6   0   0.608   0.2809   0.3591  -0.2252
 1WY  C3   C   CR6   0   0.340   2.4450   1.1411  -0.2518
 1WY  C5   C   CR6   0  -0.221   1.9206   2.4443  -0.1497
 1WY  C6   C   CR16  0   0.042   0.5492   2.5842  -0.1092
 1WY  C8   C   CR6   0   0.299  -1.8567  -0.9487  -0.1563
 1WY  C11  C   CR6   0   0.395  -4.1699  -0.2128  -0.0731
 1WY  C12  C   CR16  0  -0.368  -3.6489  -2.5530   0.0314
 1WY  C15  C   CH3   0  -0.431  -1.6906  -4.5846   0.0016
 1WY  C17  C   C     0   0.546  -6.3693   0.9638   0.0187
 1WY  C19  C   CH2   0  -0.585  -6.9206   2.3681  -0.1264
 1WY  C23  C   CR15  0  -0.040   4.9184   1.5733  -0.6853
 1WY  C24  C   CR56  0   0.067   4.4044  -0.5091   0.0145
 1WY  C27  C   CR16  0  -0.368   3.8838  -1.7261   0.4723
 1WY  C30  C   CR16  0  -0.282   6.1279  -2.6569   0.4853
 1WY  CL1  CL  CL    0  -0.124   2.8905   3.8662  -0.0225
 1WY  C22  C   CR5   0  -0.065   3.8502   0.7884  -0.2997
 1WY  C28  C   CR16  0  -0.258   4.7475  -2.7802   0.7018
 1WY  C29  C   CR16  0  -0.298   6.6716  -1.4694   0.0369
 1WY  C26  C   CR56  0   0.352   5.7951  -0.4124  -0.1911
 1WY  N25  N   NR15  0  -0.675   6.0596   0.8594  -0.6235
 1WY  N1   N   N     0  -0.509   1.5900   0.1247  -0.2837
 1WY  N4   N   N     0  -0.470  -0.2863   1.5583  -0.1526
 1WY  N7   N   NH1   0  -0.771  -0.4831  -0.7658  -0.2456
 1WY  C10  C   CR6   0   0.307  -2.2972  -2.2874  -0.0586
 1WY  C13  C   CR16  0  -0.335  -4.5950  -1.5293   0.0278
 1WY  C9   C   CR16  0  -0.446  -2.8010   0.0656  -0.1645
 1WY  N16  N   NH1   0  -0.750  -5.0190   0.9014  -0.1001
 1WY  O18  O   O     0  -0.475  -7.0798  -0.0080   0.2079
 1WY  C20  C   CH3   0  -0.657  -8.3791   2.4904   0.2748
 1WY  H1   H   HCR6  0   0.291   0.1082   3.5718  -0.0312
 1WY  H2   H   HCR6  0   0.282  -4.0030  -3.5721   0.1108
 1WY  H3   H   HCH3  0   0.262  -0.7670  -5.1571  -0.0283
 1WY  H4   H   HCH3  0   0.230  -2.2213  -4.8190   0.9281
 1WY  H5   H   HCH3  0   0.230  -2.3148  -4.8756  -0.8473
 1WY  H6   H   HCH2  0   0.263  -6.3071   3.0598   0.4568
 1WY  H7   H   HCH2  0   0.275  -6.7892   2.6690  -1.1708
 1WY  H8   H   HCR5  0   0.293   4.9461   2.5901  -1.0354
 1WY  H9   H   HCR6  0   0.252   2.8233  -1.8434   0.6373
 1WY  H10  H   HCR6  0   0.254   6.7763  -3.5025   0.6741
 1WY  H11  H   HCR6  0   0.250   4.3508  -3.7234   1.0542
 1WY  H12  H   HCR6  0   0.265   7.7359  -1.3624  -0.1289
 1WY  H13  H   HNR5  0   0.421   6.9689   1.2199  -0.8633
 1WY  H14  H   HNH1  0   0.410   0.0627  -1.6127  -0.2949
 1WY  H15  H   HCR6  0   0.277  -5.6386  -1.7823   0.1048
 1WY  H16  H   HCR6  0   0.298  -2.4689   1.0899  -0.2414
 1WY  H17  H   HNH1  0   0.414  -4.5499   1.7835  -0.2401
 1WY  H18  H   HCH3  0   0.229  -8.5309   2.2299   1.3219
 1WY  H19  H   HCH3  0   0.235  -8.7156   3.5175   0.1371
 1WY  H20  H   HCH3  0   0.229  -9.0194   1.8484  -0.3279
 1WY  O14  O   O2    0  -0.488  -1.3214  -3.2225  -0.0613

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
 1WY  CL1  C5   single    1.726  0.020  1.726
 1WY  N25  C23  aromatic  1.348  0.020  1.348
 1WY  N25  C26  aromatic  1.369  0.020  1.369
 1WY  C23  C22  aromatic  1.381  0.020  1.381
 1WY  C26  C29  aromatic  1.392  0.020  1.392
 1WY  C26  C24  aromatic  1.409  0.020  1.409
 1WY  C29  C30  aromatic  1.381  0.020  1.381
 1WY  C5   C3   aromatic  1.408  0.020  1.408
 1WY  C5   C6   aromatic  1.379  0.020  1.379
 1WY  C22  C24  aromatic  1.445  0.020  1.445
 1WY  C22  C3   single    1.450  0.020  1.450
 1WY  C24  C27  aromatic  1.401  0.020  1.401
 1WY  C3   N1   aromatic  1.329  0.020  1.329
 1WY  C6   N4   aromatic  1.324  0.020  1.324
 1WY  C30  C28  aromatic  1.403  0.020  1.403
 1WY  C27  C28  aromatic  1.382  0.020  1.382
 1WY  N1   C2   aromatic  1.331  0.020  1.331
 1WY  N4   C2   aromatic  1.329  0.020  1.329
 1WY  C2   N7   single    1.360  0.020  1.360
 1WY  O18  C17  double    1.219  0.020  1.219
 1WY  N7   C8   single    1.389  0.020  1.389
 1WY  C19  C20  single    1.518  0.020  1.518
 1WY  C19  C17  single    1.516  0.020  1.516
 1WY  C17  N16  single    1.357  0.020  1.357
 1WY  C9   C8   aromatic  1.386  0.020  1.386
 1WY  C9   C11  aromatic  1.400  0.020  1.400
 1WY  C8   C10  aromatic  1.413  0.020  1.413
 1WY  N16  C11  single    1.401  0.020  1.401
 1WY  C11  C13  aromatic  1.387  0.020  1.387
 1WY  C10  O14  single    1.352  0.020  1.352
 1WY  C10  C12  aromatic  1.380  0.020  1.380
 1WY  O14  C15  single    1.413  0.020  1.413
 1WY  C13  C12  aromatic  1.394  0.020  1.394
 1WY  C6   H1   single    0.930  0.020  1.080
 1WY  C12  H2   single    0.930  0.020  1.080
 1WY  C15  H3   single    0.970  0.020  1.090
 1WY  C15  H4   single    0.970  0.020  1.090
 1WY  C15  H5   single    0.970  0.020  1.090
 1WY  C19  H6   single    0.970  0.020  1.090
 1WY  C19  H7   single    0.970  0.020  1.090
 1WY  C23  H8   single    0.930  0.020  1.080
 1WY  C27  H9   single    0.930  0.020  1.080
 1WY  C30  H10  single    0.930  0.020  1.080
 1WY  C28  H11  single    0.930  0.020  1.080
 1WY  C29  H12  single    0.930  0.020  1.080
 1WY  N25  H13  single    0.860  0.020  1.020
 1WY  N7   H14  single    0.860  0.020  1.020
 1WY  C13  H15  single    0.930  0.020  1.080
 1WY  C9   H16  single    0.930  0.020  1.080
 1WY  N16  H17  single    0.860  0.020  1.020
 1WY  C20  H18  single    0.970  0.020  1.090
 1WY  C20  H19  single    0.970  0.020  1.090
 1WY  C20  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
 1WY  N7   C2   N4   120.50  3.000
 1WY  N7   C2   N1   113.97  3.000
 1WY  N4   C2   N1   125.53  3.000
 1WY  N1   C3   C22  115.91  3.000
 1WY  N1   C3   C5   118.04  3.000
 1WY  C22  C3   C5   126.04  3.000
 1WY  CL1  C5   C6   118.24  3.000
 1WY  C6   C5   C3   117.79  3.000
 1WY  CL1  C5   C3   123.95  3.000
 1WY  H1   C6   N4   116.84  3.000
 1WY  H1   C6   C5   119.92  3.000
 1WY  N4   C6   C5   123.23  3.000
 1WY  C9   C8   C10  118.79  3.000
 1WY  C10  C8   N7   115.96  3.000
 1WY  C9   C8   N7   125.25  3.000
 1WY  N16  C11  C9   115.67  3.000
 1WY  N16  C11  C13  124.78  3.000
 1WY  C9   C11  C13  119.56  3.000
 1WY  H2   C12  C13  118.02  3.000
 1WY  H2   C12  C10  120.44  3.000
 1WY  C13  C12  C10  121.54  3.000
 1WY  H5   C15  H4   108.90  3.000
 1WY  H5   C15  H3   108.88  3.000
 1WY  H4   C15  H3   108.84  3.000
 1WY  H5   C15  O14  111.80  3.000
 1WY  H4   C15  O14  111.80  3.000
 1WY  H3   C15  O14  106.53  3.000
 1WY  O18  C17  N16  123.85  3.000
 1WY  N16  C17  C19  113.34  3.000
 1WY  O18  C17  C19  122.80  3.000
 1WY  H7   C19  H6   105.52  3.000
 1WY  H7   C19  C20  110.21  3.000
 1WY  H6   C19  C20  110.33  3.000
 1WY  H7   C19  C17  107.60  3.000
 1WY  H6   C19  C17  109.34  3.000
 1WY  C20  C19  C17  113.51  3.000
 1WY  H8   C23  N25  119.60  3.000
 1WY  H8   C23  C22  130.41  3.000
 1WY  N25  C23  C22  109.95  3.000
 1WY  C26  C24  C22  106.56  3.000
 1WY  C22  C24  C27  135.11  3.000
 1WY  C26  C24  C27  118.30  3.000
 1WY  H9   C27  C28  120.38  3.000
 1WY  H9   C27  C24  120.63  3.000
 1WY  C28  C27  C24  118.99  3.000
 1WY  H10  C30  C29  119.52  3.000
 1WY  H10  C30  C28  119.60  3.000
 1WY  C29  C30  C28  120.88  3.000
 1WY  C24  C22  C23  105.93  3.000
 1WY  C24  C22  C3   125.65  3.000
 1WY  C23  C22  C3   128.39  3.000
 1WY  H11  C28  C30  119.18  3.000
 1WY  H11  C28  C27  119.32  3.000
 1WY  C30  C28  C27  121.49  3.000
 1WY  H12  C29  C26  121.26  3.000
 1WY  H12  C29  C30  121.46  3.000
 1WY  C26  C29  C30  117.28  3.000
 1WY  N25  C26  C29  129.45  3.000
 1WY  C29  C26  C24  123.06  3.000
 1WY  N25  C26  C24  107.49  3.000
 1WY  H13  N25  C26  125.61  3.000
 1WY  H13  N25  C23  124.33  3.000
 1WY  C26  N25  C23  110.06  3.000
 1WY  C3   N1   C2   119.81  3.000
 1WY  C6   N4   C2   115.58  3.000
 1WY  H14  N7   C8   115.32  3.000
 1WY  H14  N7   C2   113.03  3.000
 1WY  C8   N7   C2   131.59  3.000
 1WY  O14  C10  C12  125.03  3.000
 1WY  C12  C10  C8   119.48  3.000
 1WY  O14  C10  C8   115.49  3.000
 1WY  H15  C13  C12  119.02  3.000
 1WY  H15  C13  C11  121.69  3.000
 1WY  C12  C13  C11  119.28  3.000
 1WY  H16  C9   C11  119.62  3.000
 1WY  H16  C9   C8   119.03  3.000
 1WY  C11  C9   C8   121.35  3.000
 1WY  H17  N16  C17  115.76  3.000
 1WY  H17  N16  C11  114.60  3.000
 1WY  C17  N16  C11  129.63  3.000
 1WY  H20  C20  H19  107.72  3.000
 1WY  H20  C20  H18  108.01  3.000
 1WY  H19  C20  H18  107.69  3.000
 1WY  H20  C20  C19  111.80  3.000
 1WY  H19  C20  C19  109.84  3.000
 1WY  H18  C20  C19  111.63  3.000
 1WY  C10  O14  C15  118.58  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
 1WY  CONST_01  C5   C3   N1   C2      0.00   0.0  0
 1WY  CONST_02  C22  C3   N1   C2    180.00   0.0  0
 1WY  CONST_03  C5   C6   N4   C2      0.00   0.0  0
 1WY  CONST_04  N4   C6   C5   C3      0.00   0.0  0
 1WY  CONST_05  N25  C23  C22  C3    180.00   0.0  0
 1WY  CONST_06  C26  C24  C22  C3    180.00   0.0  0
 1WY  CONST_07  C27  C24  C22  C3      0.00   0.0  0
 1WY  CONST_08  N4   C2   N1   C3      0.00   0.0  0
 1WY  CONST_11  C22  C3   C5   C6    180.00   0.0  0
 1WY  CONST_12  N1   C3   C5   C6      0.00   0.0  0
 1WY  CONST_13  N1   C2   N4   C6      0.00   0.0  0
 1WY  CONST_14  C13  C11  C9   C8      0.00   0.0  0
 1WY  CONST_15  C13  C12  C10  C8      0.00   0.0  0
 1WY  CONST_16  C10  C8   C9   C11     0.00   0.0  0
 1WY  CONST_17  C10  C12  C13  C11     0.00   0.0  0
 1WY  CONST_18  C9   C8   C10  C12     0.00   0.0  0
 1WY  CONST_19  C9   C11  C13  C12     0.00   0.0  0
 1WY  CONST_20  C29  C26  N25  C23   180.00   0.0  0
 1WY  CONST_21  C24  C26  N25  C23     0.00   0.0  0
 1WY  CONST_22  C26  C24  C22  C23     0.00   0.0  0
 1WY  CONST_23  C27  C24  C22  C23   180.00   0.0  0
 1WY  CONST_25  C30  C29  C26  C24     0.00   0.0  0
 1WY  CONST_26  N25  C23  C22  C24     0.00   0.0  0
 1WY  CONST_28  C30  C28  C27  C24     0.00   0.0  0
 1WY  CONST_29  N25  C26  C24  C27   180.00   0.0  0
 1WY  CONST_30  C29  C26  C24  C27     0.00   0.0  0
 1WY  CONST_31  C29  C30  C28  C27     0.00   0.0  0
 1WY  CONST_32  N25  C26  C29  C30   180.00   0.0  0
 1WY  CONST_33  C26  N25  C23  C22     0.00   0.0  0
 1WY  CONST_34  N25  C26  C24  C22     0.00   0.0  0
 1WY  CONST_35  C29  C26  C24  C22   180.00   0.0  0
 1WY  CONST_36  C28  C27  C24  C22   180.00   0.0  0
 1WY  CONST_37  C26  C29  C30  C28     0.00   0.0  0
 1WY  CONST_38  C26  C24  C27  C28     0.00   0.0  0
 1WY  CONST_39  N7   C2   N1   C3    180.00   0.0  0
 1WY  CONST_40  N7   C2   N4   C6    180.00   0.0  0
 1WY  CONST_41  N16  C11  C9   C8    180.00   0.0  0
 1WY  CONST_42  N7   C8   C9   C11   180.00   0.0  0
 1WY  CONST_43  N7   C8   C10  C12   180.00   0.0  0
 1WY  CONST_44  N16  C11  C13  C12   180.00   0.0  0
 1WY  CONST_45  C9   C8   C10  O14   180.00   0.0  0
 1WY  CONST_46  C13  C12  C10  O14   180.00   0.0  0
 1WY  CONST_47  C22  C3   C5   CL1     0.00   0.0  0
 1WY  CONST_48  N1   C3   C5   CL1   180.00   0.0  0
 1WY  CONST_49  N4   C6   C5   CL1   180.00   0.0  0
 1WY  CONST_50  H1   C6   N4   C2    180.00   0.0  0
 1WY  CONST_51  H8   C23  C22  C3      0.00   0.0  0
 1WY  CONST_52  H2   C12  C10  C8    180.00   0.0  0
 1WY  CONST_53  H13  N25  C26  C24   180.00   0.0  0
 1WY  CONST_54  H12  C29  C26  C24   180.00   0.0  0
 1WY  CONST_55  H11  C28  C27  C24   180.00   0.0  0
 1WY  CONST_56  H10  C30  C28  C27   180.00   0.0  0
 1WY  CONST_57  H9   C27  C28  C30   180.00   0.0  0
 1WY  CONST_58  H16  C9   C8   C10   180.00   0.0  0
 1WY  CONST_59  H15  C13  C12  C10   180.00   0.0  0
 1WY  CONST_60  C9   C11  N16  C17   180.00   0.0  0
 1WY  CONST_61  C13  C11  N16  C17     0.00   0.0  0
 1WY  CONST_62  H17  N16  C11  C13   180.00   0.0  0
 1WY  CONST_63  O18  C17  N16  C11     0.00   0.0  0
 1WY  CONST_64  C19  C17  N16  C11   180.00   0.0  0
 1WY  Var_01    C9   C8   N7   C2      7.46  30.0  2
 1WY  Var_02    N1   C2   N7   C8    177.44  30.0  2
 1WY  Var_03    H3   C15  O14  C10   179.12  30.0  3
 1WY  Var_04    C20  C19  C17  N16  -168.53  30.0  1
 1WY  Var_05    H18  C20  C19  C17    61.26  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
 1WY  plan-1  C2   0.020
 1WY  plan-1  C3   0.020
 1WY  plan-1  C5   0.020
 1WY  plan-1  C6   0.020
 1WY  plan-1  CL1  0.020
 1WY  plan-1  C22  0.020
 1WY  plan-1  N1   0.020
 1WY  plan-1  N4   0.020
 1WY  plan-1  N7   0.020
 1WY  plan-1  H1   0.020
 1WY  plan-2  C8   0.020
 1WY  plan-2  C11  0.020
 1WY  plan-2  C12  0.020
 1WY  plan-2  N7   0.020
 1WY  plan-2  C10  0.020
 1WY  plan-2  C13  0.020
 1WY  plan-2  C9   0.020
 1WY  plan-2  N16  0.020
 1WY  plan-2  H2   0.020
 1WY  plan-2  H15  0.020
 1WY  plan-2  H16  0.020
 1WY  plan-2  O14  0.020
 1WY  plan-3  C3   0.020
 1WY  plan-3  C23  0.020
 1WY  plan-3  C24  0.020
 1WY  plan-3  C27  0.020
 1WY  plan-3  C30  0.020
 1WY  plan-3  C22  0.020
 1WY  plan-3  C28  0.020
 1WY  plan-3  C29  0.020
 1WY  plan-3  C26  0.020
 1WY  plan-3  N25  0.020
 1WY  plan-3  H8   0.020
 1WY  plan-3  H9   0.020
 1WY  plan-3  H10  0.020
 1WY  plan-3  H11  0.020
 1WY  plan-3  H12  0.020
 1WY  plan-3  H13  0.020
 1WY  plan-4  C11  0.020
 1WY  plan-4  C17  0.020
 1WY  plan-4  C19  0.020
 1WY  plan-4  N16  0.020
 1WY  plan-4  O18  0.020
 1WY  plan-4  H17  0.020

