# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 05:29:16 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N-(2-{[6-(2,6-dichloro-3,5-dimethoxyphenyl)quinazolin-2-yl]amino}-3-methylphenyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(C)c1Nc2ncc3cc(ccc3n2)c4c(Cl)c(OC)cc(OC)c4Cl
#
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
 40M  40M  N-(2-{[6-(2,6-dichloro-3,5-dimethoxyphenyl)quinazolin-2-yl]amino}-3-methylphenyl)propanamide  ligand  59  35  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_40M
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
 40M  O    O   O     0  -0.468  -6.1263  -1.8015   2.0340
 40M  C6   C   C     0   0.548  -5.5385  -1.8925   0.9725
 40M  C7   C   CH2   0  -0.589  -4.8664  -3.1686   0.5111
 40M  C8   C   CH3   0  -0.659  -5.4101  -4.4143   1.1880
 40M  N    N   NH1   0  -0.738  -5.3950  -0.8622   0.0957
 40M  C4   C   CR6   0   0.357  -5.7742   0.4704   0.2485
 40M  C5   C   CR16  0  -0.343  -6.8126   0.8846   1.0812
 40M  C3   C   CR16  0  -0.235  -7.1486   2.2278   1.1361
 40M  C1   C   CR16  0  -0.339  -6.4707   3.1678   0.3767
 40M  C    C   CR6   0   0.098  -5.4266   2.7772  -0.4560
 40M  C25  C   CH3   0  -0.731  -4.6716   3.7842  -1.2716
 40M  C2   C   CR6   0   0.182  -5.0865   1.4263  -0.5133
 40M  N1   N   NH1   0  -0.755  -4.0458   0.9996  -1.3722
 40M  C12  C   CR6   0   0.546  -2.7640   0.7999  -0.9580
 40M  N3   N   N     0  -0.426  -2.5682   0.7874   0.3845
 40M  C11  C   CR16  0  -0.015  -1.3508   0.5800   0.7926
 40M  C9   C   CR66  0   0.001  -0.2673   0.3768  -0.0891
 40M  C13  C   CR16  0  -0.314   1.0551   0.1659   0.3407
 40M  N2   N   N     0  -0.491  -1.8502   0.6219  -1.8827
 40M  C10  C   CR66  0   0.276  -0.5870   0.4084  -1.4639
 40M  C15  C   CR16  0  -0.313   0.4554   0.2172  -2.3973
 40M  C16  C   CR16  0  -0.247   1.7350   0.0105  -1.9581
 40M  C14  C   CR6   0   0.035   2.0530  -0.0150  -0.5801
 40M  C22  C   CR6   0   0.248   3.4527  -0.2275  -0.1488
 40M  C21  C   CR6   0  -0.294   4.2125   0.8248   0.3502
 40M  CL1  CL  CL    0  -0.102   3.5455   2.4147   0.4560
 40M  C20  C   CR6   0  -0.293   4.0374  -1.4858  -0.2377
 40M  CL   CL  CL    0  -0.101   3.1270  -2.8261  -0.8361
 40M  C18  C   CR6   0   0.531   5.3565  -1.7030   0.1646
 40M  O1   O   O2    0  -0.454   5.8258  -2.9468   0.0423
 40M  C23  C   CH3   0  -0.444   7.1507  -3.2267   0.4617
 40M  C17  C   CR16  0  -0.572   6.0964  -0.6371   0.6663
 40M  C19  C   CR6   0   0.532   5.5323   0.6308   0.7638
 40M  O2   O   O2    0  -0.454   6.1789   1.7004   1.2334
 40M  C24  C   CH3   0  -0.444   7.5228   1.5568   1.6600
 40M  H1   H   HCH2  0   0.261  -4.9516  -3.2553  -0.5748
 40M  H2   H   HCH2  0   0.276  -3.7957  -3.0666   0.7171
 40M  H3   H   HCH3  0   0.237  -4.8871  -5.2956   0.8190
 40M  H4   H   HCH3  0   0.231  -5.2763  -4.3769   2.2678
 40M  H5   H   HCH3  0   0.230  -6.4725  -4.5482   0.9846
 40M  H6   H   HNH1  0   0.411  -4.8387  -1.0481  -0.7265
 40M  H7   H   HCR6  0   0.273  -7.3639   0.1720   1.6721
 40M  H8   H   HCR6  0   0.258  -7.9605   2.5411   1.7798
 40M  H9   H   HCR6  0   0.251  -6.7472   4.2131   0.4341
 40M  H10  H   HCH3  0   0.249  -3.5980   3.7301  -1.0856
 40M  H11  H   HCH3  0   0.250  -4.8182   3.6305  -2.3425
 40M  H12  H   HCH3  0   0.253  -4.9994   4.7956  -1.0381
 40M  H13  H   HNH1  0   0.400  -4.1617   1.1409  -2.3652
 40M  H14  H   HCR6  0   0.280  -1.1823   0.5695   1.8660
 40M  H15  H   HCR6  0   0.266   1.2708   0.1488   1.4026
 40M  H16  H   HCR6  0   0.265   0.2288   0.2412  -3.4552
 40M  H17  H   HCR6  0   0.267   2.5289  -0.1267  -2.6816
 40M  H18  H   HCH3  0   0.269   7.3108  -4.2846   0.2737
 40M  H19  H   HCH3  0   0.237   7.8866  -2.6513  -0.1043
 40M  H20  H   HCH3  0   0.238   7.2868  -3.0325   1.5280
 40M  H21  H   HCR6  0   0.321   7.1166  -0.7947   0.9836
 40M  H22  H   HCH3  0   0.237   8.1747   1.2392   0.8432
 40M  H23  H   HCH3  0   0.269   7.8394   2.5383   2.0017
 40M  H24  H   HCH3  0   0.237   7.6123   0.8480   2.4862

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
 40M  O    C6   double    1.217  0.020  1.217
 40M  C7   C6   single    1.514  0.020  1.514
 40M  C7   C8   single    1.518  0.020  1.518
 40M  C6   N    single    1.360  0.020  1.360
 40M  N    C4   single    1.394  0.020  1.394
 40M  C5   C4   aromatic  1.394  0.020  1.394
 40M  C5   C3   aromatic  1.386  0.020  1.386
 40M  C4   C2   aromatic  1.402  0.020  1.402
 40M  C3   C1   aromatic  1.386  0.020  1.386
 40M  C2   N1   single    1.415  0.020  1.415
 40M  C2   C    aromatic  1.394  0.020  1.394
 40M  N1   C12  single    1.362  0.020  1.362
 40M  C1   C    aromatic  1.391  0.020  1.391
 40M  C    C25  single    1.500  0.020  1.500
 40M  C12  N3   aromatic  1.357  0.020  1.357
 40M  C12  N2   aromatic  1.312  0.020  1.312
 40M  N3   C11  aromatic  1.301  0.020  1.301
 40M  N2   C10  aromatic  1.348  0.020  1.348
 40M  C11  C9   aromatic  1.412  0.020  1.412
 40M  C10  C9   aromatic  1.412  0.020  1.412
 40M  C10  C15  aromatic  1.412  0.020  1.412
 40M  C9   C13  aromatic  1.406  0.020  1.406
 40M  C15  C16  aromatic  1.369  0.020  1.369
 40M  C13  C14  aromatic  1.370  0.020  1.370
 40M  CL   C20  single    1.727  0.020  1.727
 40M  C16  C14  aromatic  1.414  0.020  1.414
 40M  C14  C22  single    1.480  0.020  1.480
 40M  C22  C20  aromatic  1.390  0.020  1.390
 40M  C22  C21  aromatic  1.391  0.020  1.391
 40M  C20  C18  aromatic  1.396  0.020  1.396
 40M  O1   C18  single    1.335  0.020  1.335
 40M  O1   C23  single    1.418  0.020  1.418
 40M  C18  C17  aromatic  1.391  0.020  1.391
 40M  C21  CL1  single    1.727  0.020  1.727
 40M  C21  C19  aromatic  1.397  0.020  1.397
 40M  C17  C19  aromatic  1.391  0.020  1.391
 40M  C19  O2   single    1.335  0.020  1.335
 40M  O2   C24  single    1.417  0.020  1.417
 40M  C7   H1   single    0.970  0.020  1.090
 40M  C7   H2   single    0.970  0.020  1.090
 40M  C8   H3   single    0.970  0.020  1.090
 40M  C8   H4   single    0.970  0.020  1.090
 40M  C8   H5   single    0.970  0.020  1.090
 40M  N    H6   single    0.860  0.020  1.020
 40M  C5   H7   single    0.930  0.020  1.080
 40M  C3   H8   single    0.930  0.020  1.080
 40M  C1   H9   single    0.930  0.020  1.080
 40M  C25  H10  single    0.970  0.020  1.090
 40M  C25  H11  single    0.970  0.020  1.090
 40M  C25  H12  single    0.970  0.020  1.090
 40M  N1   H13  single    0.890  0.020  1.040
 40M  C11  H14  single    0.930  0.020  1.080
 40M  C13  H15  single    0.930  0.020  1.080
 40M  C15  H16  single    0.930  0.020  1.080
 40M  C16  H17  single    0.930  0.020  1.080
 40M  C23  H18  single    0.970  0.020  1.090
 40M  C23  H19  single    0.970  0.020  1.090
 40M  C23  H20  single    0.970  0.020  1.090
 40M  C17  H21  single    0.930  0.020  1.080
 40M  C24  H22  single    0.970  0.020  1.090
 40M  C24  H23  single    0.970  0.020  1.090
 40M  C24  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
 40M  N    C6   C7   113.27  3.000
 40M  N    C6   O    123.82  3.000
 40M  C7   C6   O    122.90  3.000
 40M  H2   C7   H1   105.69  3.000
 40M  H2   C7   C8   110.04  3.000
 40M  H1   C7   C8   110.49  3.000
 40M  H2   C7   C6   107.35  3.000
 40M  H1   C7   C6   109.58  3.000
 40M  C8   C7   C6   113.37  3.000
 40M  H5   C8   H4   108.00  3.000
 40M  H5   C8   H3   107.79  3.000
 40M  H4   C8   H3   107.74  3.000
 40M  H5   C8   C7   111.51  3.000
 40M  H4   C8   C7   111.71  3.000
 40M  H3   C8   C7   109.93  3.000
 40M  H6   N    C4   114.53  3.000
 40M  H6   N    C6   116.32  3.000
 40M  C4   N    C6   128.65  3.000
 40M  C2   C4   C5   119.16  3.000
 40M  C2   C4   N    117.30  3.000
 40M  C5   C4   N    123.52  3.000
 40M  H7   C5   C3   119.69  3.000
 40M  H7   C5   C4   120.81  3.000
 40M  C3   C5   C4   119.49  3.000
 40M  H8   C3   C1   119.78  3.000
 40M  H8   C3   C5   119.07  3.000
 40M  C1   C3   C5   121.15  3.000
 40M  H9   C1   C    119.63  3.000
 40M  H9   C1   C3   120.06  3.000
 40M  C    C1   C3   120.31  3.000
 40M  C2   C    C25  120.36  3.000
 40M  C25  C    C1   120.98  3.000
 40M  C2   C    C1   118.66  3.000
 40M  H12  C25  H11  107.51  3.000
 40M  H12  C25  H10  107.81  3.000
 40M  H11  C25  H10  107.00  3.000
 40M  H12  C25  C    110.83  3.000
 40M  H11  C25  C    111.80  3.000
 40M  H10  C25  C    111.67  3.000
 40M  N1   C2   C    119.76  3.000
 40M  C    C2   C4   121.23  3.000
 40M  N1   C2   C4   119.00  3.000
 40M  H13  N1   C12  115.32  3.000
 40M  H13  N1   C2   118.05  3.000
 40M  C12  N1   C2   123.49  3.000
 40M  N2   C12  N3   126.55  3.000
 40M  N2   C12  N1   117.46  3.000
 40M  N3   C12  N1   115.99  3.000
 40M  C11  N3   C12  116.55  3.000
 40M  H14  C11  C9   119.77  3.000
 40M  H14  C11  N3   117.17  3.000
 40M  C9   C11  N3   123.06  3.000
 40M  C10  C9   C13  120.92  3.000
 40M  C13  C9   C11  123.54  3.000
 40M  C10  C9   C11  115.54  3.000
 40M  H15  C13  C14  120.77  3.000
 40M  H15  C13  C9   119.27  3.000
 40M  C14  C13  C9   119.96  3.000
 40M  C10  N2   C12  117.08  3.000
 40M  C15  C10  N2   120.52  3.000
 40M  C15  C10  C9   118.26  3.000
 40M  N2   C10  C9   121.22  3.000
 40M  H16  C15  C16  120.85  3.000
 40M  H16  C15  C10  119.25  3.000
 40M  C16  C15  C10  119.90  3.000
 40M  H17  C16  C14  118.94  3.000
 40M  H17  C16  C15  119.35  3.000
 40M  C14  C16  C15  121.70  3.000
 40M  C22  C14  C16  119.94  3.000
 40M  C22  C14  C13  120.80  3.000
 40M  C16  C14  C13  119.26  3.000
 40M  C20  C22  C21  118.56  3.000
 40M  C21  C22  C14  120.84  3.000
 40M  C20  C22  C14  120.60  3.000
 40M  C19  C21  CL1  118.33  3.000
 40M  C19  C21  C22  121.16  3.000
 40M  CL1  C21  C22  120.50  3.000
 40M  C18  C20  CL   118.50  3.000
 40M  C18  C20  C22  121.32  3.000
 40M  CL   C20  C22  120.18  3.000
 40M  C17  C18  O1   124.05  3.000
 40M  C17  C18  C20  119.16  3.000
 40M  O1   C18  C20  116.79  3.000
 40M  C23  O1   C18  119.04  3.000
 40M  H20  C23  H19  109.16  3.000
 40M  H20  C23  H18  108.89  3.000
 40M  H19  C23  H18  108.91  3.000
 40M  H20  C23  O1   111.73  3.000
 40M  H19  C23  O1   111.86  3.000
 40M  H18  C23  O1   106.19  3.000
 40M  H21  C17  C19  119.70  3.000
 40M  H21  C17  C18  119.77  3.000
 40M  C19  C17  C18  120.53  3.000
 40M  O2   C19  C17  123.95  3.000
 40M  O2   C19  C21  116.77  3.000
 40M  C17  C19  C21  119.28  3.000
 40M  C24  O2   C19  118.94  3.000
 40M  H24  C24  H23  108.93  3.000
 40M  H24  C24  H22  109.15  3.000
 40M  H23  C24  H22  108.90  3.000
 40M  H24  C24  O2   111.78  3.000
 40M  H23  C24  O2   106.23  3.000
 40M  H22  C24  O2   111.74  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
 40M  CONST_01  C1   C3   C5   C4      0.00   0.0  0
 40M  CONST_02  C1   C    C2   C4      0.00   0.0  0
 40M  CONST_03  C    C2   C4   C5      0.00   0.0  0
 40M  CONST_04  C    C1   C3   C5      0.00   0.0  0
 40M  CONST_05  C2   C4   C5   C3      0.00   0.0  0
 40M  CONST_06  C2   C    C1   C3      0.00   0.0  0
 40M  CONST_07  C9   C11  N3   C12     0.00   0.0  0
 40M  CONST_08  C9   C10  N2   C12     0.00   0.0  0
 40M  CONST_09  C15  C10  N2   C12   180.00   0.0  0
 40M  CONST_10  C10  N2   C12  N3      0.00   0.0  0
 40M  CONST_11  C10  C9   C11  N3      0.00   0.0  0
 40M  CONST_12  C13  C9   C11  N3    180.00   0.0  0
 40M  CONST_13  N2   C12  N3   C11     0.00   0.0  0
 40M  CONST_14  N2   C10  C9   C11     0.00   0.0  0
 40M  CONST_15  C15  C10  C9   C11   180.00   0.0  0
 40M  CONST_16  C14  C13  C9   C11   180.00   0.0  0
 40M  CONST_17  C16  C15  C10  C9      0.00   0.0  0
 40M  CONST_18  C16  C14  C13  C9      0.00   0.0  0
 40M  CONST_19  C22  C14  C13  C9    180.00   0.0  0
 40M  CONST_20  N2   C10  C9   C13   180.00   0.0  0
 40M  CONST_21  C15  C10  C9   C13     0.00   0.0  0
 40M  CONST_22  C15  C16  C14  C13     0.00   0.0  0
 40M  CONST_25  C16  C15  C10  N2    180.00   0.0  0
 40M  CONST_26  C14  C13  C9   C10     0.00   0.0  0
 40M  CONST_27  C14  C16  C15  C10     0.00   0.0  0
 40M  CONST_28  C22  C14  C16  C15   180.00   0.0  0
 40M  CONST_31  C18  C20  C22  C14   180.00   0.0  0
 40M  CONST_32  C19  C21  C22  C14   180.00   0.0  0
 40M  CONST_33  C17  C18  C20  C22     0.00   0.0  0
 40M  CONST_34  C17  C19  C21  C22     0.00   0.0  0
 40M  CONST_35  C18  C20  C22  C21     0.00   0.0  0
 40M  CONST_36  C18  C17  C19  C21     0.00   0.0  0
 40M  CONST_37  C19  C21  C22  C20     0.00   0.0  0
 40M  CONST_38  C19  C17  C18  C20     0.00   0.0  0
 40M  CONST_39  C3   C5   C4   N     180.00   0.0  0
 40M  CONST_40  C    C2   C4   N     180.00   0.0  0
 40M  CONST_41  C25  C    C2   C4    180.00   0.0  0
 40M  CONST_42  N1   C2   C4   C5    180.00   0.0  0
 40M  CONST_43  C25  C    C1   C3    180.00   0.0  0
 40M  CONST_44  N1   C2   C    C1    180.00   0.0  0
 40M  CONST_45  C11  N3   C12  N1    180.00   0.0  0
 40M  CONST_46  C10  N2   C12  N1    180.00   0.0  0
 40M  CONST_47  CL   C20  C22  C14     0.00   0.0  0
 40M  CONST_48  CL1  C21  C22  C14     0.00   0.0  0
 40M  CONST_49  O1   C18  C20  C22   180.00   0.0  0
 40M  CONST_50  O2   C19  C21  C22   180.00   0.0  0
 40M  CONST_51  CL   C20  C22  C21   180.00   0.0  0
 40M  CONST_52  C20  C22  C21  CL1   180.00   0.0  0
 40M  CONST_53  C17  C19  C21  CL1   180.00   0.0  0
 40M  CONST_54  C17  C18  C20  CL    180.00   0.0  0
 40M  CONST_55  O2   C19  C17  C18   180.00   0.0  0
 40M  CONST_56  C19  C17  C18  O1    180.00   0.0  0
 40M  CONST_57  H8   C3   C5   C4    180.00   0.0  0
 40M  CONST_58  H9   C1   C3   C5    180.00   0.0  0
 40M  CONST_59  H7   C5   C3   C1    180.00   0.0  0
 40M  CONST_60  H14  C11  N3   C12   180.00   0.0  0
 40M  CONST_61  H15  C13  C9   C11     0.00   0.0  0
 40M  CONST_62  H16  C15  C10  C9    180.00   0.0  0
 40M  CONST_63  H17  C16  C14  C13   180.00   0.0  0
 40M  CONST_64  H21  C17  C19  C21   180.00   0.0  0
 40M  CONST_68  C4   N    C6   O       0.00   0.0  0
 40M  CONST_69  C4   N    C6   C7    180.00   0.0  0
 40M  Var_01    C12  N1   C2   C4    -84.41  30.0  2
 40M  Var_02    N3   C12  N1   C2     11.96  30.0  2
 40M  Var_03    C17  C18  O1   C23     0.99  30.0  2
 40M  Var_04    H10  C25  C    C1    125.28  30.0  2
 40M  Var_05    H18  C23  O1   C18   179.82  30.0  3
 40M  Var_06    H22  C24  O2   C19    61.64  30.0  3
 40M  Var_07    C8   C7   C6   O      21.73  30.0  2
 40M  Var_08    H3   C8   C7   C6   -179.80  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
 40M  plan-1  N    0.020
 40M  plan-1  C4   0.020
 40M  plan-1  C5   0.020
 40M  plan-1  C3   0.020
 40M  plan-1  C1   0.020
 40M  plan-1  C    0.020
 40M  plan-1  C25  0.020
 40M  plan-1  C2   0.020
 40M  plan-1  N1   0.020
 40M  plan-1  H7   0.020
 40M  plan-1  H8   0.020
 40M  plan-1  H9   0.020
 40M  plan-2  C14  0.020
 40M  plan-2  C22  0.020
 40M  plan-2  C21  0.020
 40M  plan-2  CL1  0.020
 40M  plan-2  C20  0.020
 40M  plan-2  CL   0.020
 40M  plan-2  C18  0.020
 40M  plan-2  O1   0.020
 40M  plan-2  C17  0.020
 40M  plan-2  C19  0.020
 40M  plan-2  O2   0.020
 40M  plan-2  H21  0.020
 40M  plan-3  N1   0.020
 40M  plan-3  C12  0.020
 40M  plan-3  N3   0.020
 40M  plan-3  C11  0.020
 40M  plan-3  C9   0.020
 40M  plan-3  C13  0.020
 40M  plan-3  N2   0.020
 40M  plan-3  C10  0.020
 40M  plan-3  C15  0.020
 40M  plan-3  C16  0.020
 40M  plan-3  C14  0.020
 40M  plan-3  C22  0.020
 40M  plan-3  H14  0.020
 40M  plan-3  H15  0.020
 40M  plan-3  H16  0.020
 40M  plan-3  H17  0.020
 40M  plan-4  O    0.020
 40M  plan-4  C6   0.020
 40M  plan-4  C7   0.020
 40M  plan-4  N    0.020
 40M  plan-4  C4   0.020
 40M  plan-4  H6   0.020

