# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 14:50:34 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-(3-{[2-amino-3-(4-phenoxyphenyl)pyridin-4-yl]oxy}phenyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(Oc2ccnc(N)c2c3ccc(Oc4ccccc4)cc3)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
 KHD  KHD  N-(3-{[2-amino-3-(4-phenoxyphenyl)pyridin-4-yl]oxy}phenyl)propanamide  ligand  55  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KHD
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
 KHD  N3   N  N     0  -0.463   1.1233  -4.6803   0.5638
 KHD  C4   C  CR6   0   0.422   0.0312  -4.0008   0.2114
 KHD  C5   C  CR6   0  -0.187  -0.0655  -2.5998   0.3219
 KHD  C6   C  CR6   0   0.444   1.0406  -1.9229   0.8196
 KHD  C8   C  CR6   0   0.051  -1.2941  -1.8779  -0.0768
 KHD  C10  C  CR16  0  -0.297  -2.4611  -0.3929  -1.5882
 KHD  C13  C  CR16  0  -0.280  -2.4706  -2.0223   0.6572
 KHD  C15  C  CR6   0   0.364  -5.1924   1.1960  -0.6559
 KHD  C17  C  CR16  0  -0.246  -6.9448   2.8267  -0.4633
 KHD  C20  C  CR16  0  -0.342  -4.4308   1.8952   0.2732
 KHD  C22  C  CR6   0   0.335   2.0031   0.1564   1.3475
 KHD  C24  C  CR16  0  -0.243   3.2098   1.2459   3.0778
 KHD  C26  C  CR6   0   0.382   3.9977   1.3635   0.7969
 KHD  O31  O  O     0  -0.466   4.2285   1.1791  -2.1109
 KHD  C29  C  C     0   0.554   5.0697   1.7275  -1.4239
 KHD  C30  C  CH2   0  -0.584   6.3370   2.3216  -1.9996
 KHD  C32  C  CH3   0  -0.659   6.2315   2.6334  -3.4823
 KHD  N28  N  NH1   0  -0.749   4.9783   1.8444  -0.0699
 KHD  C27  C  CR16  0  -0.382   2.9115   0.5871   0.3928
 KHD  C23  C  CR16  0  -0.327   2.1260   0.4693   2.6885
 KHD  C25  C  CR16  0  -0.348   4.1364   1.6860   2.1510
 KHD  O21  O  O2    0  -0.503   0.9206  -0.5827   0.9268
 KHD  N7   N  NH2   0  -0.830  -1.0216  -4.7398  -0.2405
 KHD  C2   C  CR16  0  -0.063   2.1548  -3.9966   1.0378
 KHD  C1   C  CR16  0  -0.439   2.1871  -2.6252   1.1911
 KHD  C9   C  CR16  0  -0.272  -1.3065  -1.0576  -1.2028
 KHD  C11  C  CR6   0   0.298  -3.6203  -0.5568  -0.8463
 KHD  C12  C  CR16  0  -0.286  -3.6325  -1.3666   0.2798
 KHD  O14  O  O2    0  -0.514  -4.7756   0.0507  -1.2667
 KHD  C16  C  CR16  0  -0.329  -6.4511   1.6613  -1.0264
 KHD  C18  C  CR16  0  -0.273  -6.1961   3.5343   0.4704
 KHD  C19  C  CR16  0  -0.246  -4.9432   3.0617   0.8300
 KHD  H1   H  HCR6  0   0.273  -2.4623   0.2406  -2.4662
 KHD  H2   H  HCR6  0   0.263  -2.4810  -2.6562   1.5350
 KHD  H3   H  HCR6  0   0.260  -7.9248   3.1809  -0.7557
 KHD  H4   H  HCR6  0   0.277  -3.4471   1.5529   0.5663
 KHD  H5   H  HCR6  0   0.269   3.3351   1.5093   4.1195
 KHD  H6   H  HCH2  0   0.262   6.6172   3.2169  -1.4396
 KHD  H7   H  HCH2  0   0.280   7.1401   1.5976  -1.8258
 KHD  H8   H  HCH3  0   0.231   5.4648   3.3821  -3.6805
 KHD  H9   H  HCH3  0   0.238   7.1798   3.0242  -3.8482
 KHD  H10  H  HCH3  0   0.231   5.9925   1.7449  -4.0642
 KHD  H11  H  HNH1  0   0.417   5.7351   2.3353   0.3820
 KHD  H12  H  HCR6  0   0.296   2.7649   0.3171  -0.6405
 KHD  H13  H  HCR6  0   0.273   1.3984   0.1186   3.4084
 KHD  H14  H  HCR6  0   0.275   4.9771   2.2867   2.4766
 KHD  H15  H  HNH2  0   0.385  -0.7994  -5.6767  -0.5354
 KHD  H16  H  HNH2  0   0.391  -1.7191  -4.2841  -0.8049
 KHD  H17  H  HCR6  0   0.262   3.0255  -4.5802   1.3173
 KHD  H18  H  HCR6  0   0.281   3.0685  -2.1416   1.5852
 KHD  H19  H  HCR6  0   0.256  -0.4063  -0.9412  -1.7925
 KHD  H20  H  HCR6  0   0.275  -4.5420  -1.4899   0.8540
 KHD  H21  H  HCR6  0   0.268  -7.0353   1.1097  -1.7523
 KHD  H22  H  HCR6  0   0.255  -6.5852   4.4428   0.9098
 KHD  H23  H  HCR6  0   0.262  -4.3459   3.6025   1.5530

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
 KHD  C2   N3   aromatic  1.325  0.020  1.325
 KHD  C2   C1   aromatic  1.380  0.020  1.380
 KHD  O31  C29  double    1.217  0.020  1.217
 KHD  C32  C30  single    1.519  0.020  1.519
 KHD  N3   C4   aromatic  1.334  0.020  1.334
 KHD  C1   C6   aromatic  1.395  0.020  1.395
 KHD  C29  C30  single    1.513  0.020  1.513
 KHD  C29  N28  single    1.362  0.020  1.362
 KHD  C24  C25  aromatic  1.382  0.020  1.382
 KHD  C24  C23  aromatic  1.389  0.020  1.389
 KHD  C25  C26  aromatic  1.399  0.020  1.399
 KHD  C23  C22  aromatic  1.382  0.020  1.382
 KHD  C26  N28  single    1.394  0.020  1.394
 KHD  C26  C27  aromatic  1.395  0.020  1.395
 KHD  C4   N7   single    1.363  0.020  1.363
 KHD  C4   C5   aromatic  1.409  0.020  1.409
 KHD  C6   O21  single    1.350  0.020  1.350
 KHD  C6   C5   aromatic  1.389  0.020  1.389
 KHD  C22  C27  aromatic  1.386  0.020  1.386
 KHD  C22  O21  single    1.377  0.020  1.377
 KHD  C5   C8   single    1.480  0.020  1.480
 KHD  C8   C13  aromatic  1.394  0.020  1.394
 KHD  C8   C9   aromatic  1.393  0.020  1.393
 KHD  C13  C12  aromatic  1.386  0.020  1.386
 KHD  C9   C10  aromatic  1.387  0.020  1.387
 KHD  C12  C11  aromatic  1.387  0.020  1.387
 KHD  C10  C11  aromatic  1.386  0.020  1.386
 KHD  C11  O14  single    1.371  0.020  1.371
 KHD  C16  C17  aromatic  1.385  0.020  1.385
 KHD  C16  C15  aromatic  1.392  0.020  1.392
 KHD  O14  C15  single    1.363  0.020  1.363
 KHD  C17  C18  aromatic  1.390  0.020  1.390
 KHD  C15  C20  aromatic  1.390  0.020  1.390
 KHD  C18  C19  aromatic  1.387  0.020  1.387
 KHD  C20  C19  aromatic  1.390  0.020  1.390
 KHD  C10  H1   single    0.930  0.020  1.080
 KHD  C13  H2   single    0.930  0.020  1.080
 KHD  C17  H3   single    0.930  0.020  1.080
 KHD  C20  H4   single    0.930  0.020  1.080
 KHD  C24  H5   single    0.930  0.020  1.080
 KHD  C30  H6   single    0.970  0.020  1.090
 KHD  C30  H7   single    0.970  0.020  1.090
 KHD  C32  H8   single    0.970  0.020  1.090
 KHD  C32  H9   single    0.970  0.020  1.090
 KHD  C32  H10  single    0.970  0.020  1.090
 KHD  N28  H11  single    0.860  0.020  1.020
 KHD  C27  H12  single    0.930  0.020  1.080
 KHD  C23  H13  single    0.930  0.020  1.080
 KHD  C25  H14  single    0.930  0.020  1.080
 KHD  N7   H15  single    0.890  0.020  1.040
 KHD  N7   H16  single    0.890  0.020  1.040
 KHD  C2   H17  single    0.930  0.020  1.080
 KHD  C1   H18  single    0.930  0.020  1.080
 KHD  C9   H19  single    0.930  0.020  1.080
 KHD  C12  H20  single    0.930  0.020  1.080
 KHD  C16  H21  single    0.930  0.020  1.080
 KHD  C18  H22  single    0.930  0.020  1.080
 KHD  C19  H23  single    0.930  0.020  1.080

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
 KHD  C2   N3   C4   117.98  3.000
 KHD  N7   C4   C5   120.80  3.000
 KHD  C5   C4   N3   122.84  3.000
 KHD  N7   C4   N3   116.34  3.000
 KHD  C8   C5   C6   121.34  3.000
 KHD  C8   C5   C4   121.40  3.000
 KHD  C6   C5   C4   117.26  3.000
 KHD  C1   C6   O21  123.49  3.000
 KHD  O21  C6   C5   116.20  3.000
 KHD  C1   C6   C5   120.31  3.000
 KHD  C9   C8   C13  118.62  3.000
 KHD  C9   C8   C5   120.83  3.000
 KHD  C13  C8   C5   120.55  3.000
 KHD  H1   C10  C11  120.15  3.000
 KHD  H1   C10  C9   120.45  3.000
 KHD  C11  C10  C9   119.40  3.000
 KHD  H2   C13  C12  119.31  3.000
 KHD  H2   C13  C8   119.70  3.000
 KHD  C12  C13  C8   120.99  3.000
 KHD  C16  C15  O14  115.98  3.000
 KHD  O14  C15  C20  123.68  3.000
 KHD  C16  C15  C20  120.34  3.000
 KHD  H3   C17  C18  120.17  3.000
 KHD  H3   C17  C16  119.22  3.000
 KHD  C18  C17  C16  120.61  3.000
 KHD  H4   C20  C19  119.47  3.000
 KHD  H4   C20  C15  121.34  3.000
 KHD  C19  C20  C15  119.19  3.000
 KHD  O21  C22  C23  119.20  3.000
 KHD  O21  C22  C27  118.14  3.000
 KHD  C23  C22  C27  122.64  3.000
 KHD  H5   C24  C25  119.36  3.000
 KHD  H5   C24  C23  119.76  3.000
 KHD  C25  C24  C23  120.87  3.000
 KHD  C25  C26  C27  119.07  3.000
 KHD  C27  C26  N28  124.02  3.000
 KHD  C25  C26  N28  116.90  3.000
 KHD  N28  C29  C30  113.62  3.000
 KHD  N28  C29  O31  123.61  3.000
 KHD  C30  C29  O31  122.75  3.000
 KHD  H7   C30  H6   105.80  3.000
 KHD  H7   C30  C32  109.98  3.000
 KHD  H6   C30  C32  110.49  3.000
 KHD  H7   C30  C29  107.11  3.000
 KHD  H6   C30  C29  109.96  3.000
 KHD  C32  C30  C29  113.19  3.000
 KHD  H10  C32  H9   107.73  3.000
 KHD  H10  C32  H8   108.00  3.000
 KHD  H9   C32  H8   107.75  3.000
 KHD  H10  C32  C30  111.69  3.000
 KHD  H9   C32  C30  109.95  3.000
 KHD  H8   C32  C30  111.56  3.000
 KHD  H11  N28  C29  115.89  3.000
 KHD  H11  N28  C26  114.64  3.000
 KHD  C29  N28  C26  129.46  3.000
 KHD  H12  C27  C26  121.53  3.000
 KHD  H12  C27  C22  119.54  3.000
 KHD  C26  C27  C22  118.92  3.000
 KHD  H13  C23  C24  121.30  3.000
 KHD  H13  C23  C22  120.81  3.000
 KHD  C24  C23  C22  117.89  3.000
 KHD  H14  C25  C26  119.72  3.000
 KHD  H14  C25  C24  119.68  3.000
 KHD  C26  C25  C24  120.60  3.000
 KHD  C22  O21  C6   119.17  3.000
 KHD  H16  N7   H15  114.20  3.000
 KHD  H16  N7   C4   118.40  3.000
 KHD  H15  N7   C4   115.54  3.000
 KHD  H17  C2   C1   119.15  3.000
 KHD  H17  C2   N3   116.07  3.000
 KHD  C1   C2   N3   124.79  3.000
 KHD  H18  C1   C2   120.30  3.000
 KHD  H18  C1   C6   122.86  3.000
 KHD  C2   C1   C6   116.83  3.000
 KHD  H19  C9   C10  119.30  3.000
 KHD  H19  C9   C8   119.75  3.000
 KHD  C10  C9   C8   120.95  3.000
 KHD  O14  C11  C12  120.01  3.000
 KHD  O14  C11  C10  119.22  3.000
 KHD  C12  C11  C10  120.73  3.000
 KHD  H20  C12  C11  120.29  3.000
 KHD  H20  C12  C13  120.38  3.000
 KHD  C11  C12  C13  119.32  3.000
 KHD  C11  O14  C15  119.49  3.000
 KHD  H21  C16  C17  120.58  3.000
 KHD  H21  C16  C15  119.73  3.000
 KHD  C17  C16  C15  119.69  3.000
 KHD  H22  C18  C19  120.40  3.000
 KHD  H22  C18  C17  120.44  3.000
 KHD  C19  C18  C17  119.16  3.000
 KHD  H23  C19  C18  120.10  3.000
 KHD  H23  C19  C20  118.89  3.000
 KHD  C18  C19  C20  121.00  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
 KHD  CONST_01  C6   C1   C2   N3      0.00   0.0  0
 KHD  CONST_02  C6   C5   C4   N3      0.00   0.0  0
 KHD  CONST_03  C8   C5   C4   N3    180.00   0.0  0
 KHD  CONST_04  C1   C2   N3   C4      0.00   0.0  0
 KHD  CONST_05  C1   C6   C5   C4      0.00   0.0  0
 KHD  CONST_08  C2   N3   C4   C5      0.00   0.0  0
 KHD  CONST_09  C2   C1   C6   C5      0.00   0.0  0
 KHD  CONST_10  C12  C13  C8   C5    180.00   0.0  0
 KHD  CONST_11  C10  C9   C8   C5    180.00   0.0  0
 KHD  CONST_14  C1   C6   C5   C8    180.00   0.0  0
 KHD  CONST_15  C11  C12  C13  C8      0.00   0.0  0
 KHD  CONST_16  C11  C10  C9   C8      0.00   0.0  0
 KHD  CONST_17  C13  C8   C9   C10     0.00   0.0  0
 KHD  CONST_18  C13  C12  C11  C10     0.00   0.0  0
 KHD  CONST_19  C18  C17  C16  C15     0.00   0.0  0
 KHD  CONST_20  C18  C19  C20  C15     0.00   0.0  0
 KHD  CONST_21  C20  C15  C16  C17     0.00   0.0  0
 KHD  CONST_22  C20  C19  C18  C17     0.00   0.0  0
 KHD  CONST_23  C25  C24  C23  C22     0.00   0.0  0
 KHD  CONST_24  C25  C26  C27  C22     0.00   0.0  0
 KHD  CONST_25  C27  C26  C25  C24     0.00   0.0  0
 KHD  CONST_26  C27  C22  C23  C24     0.00   0.0  0
 KHD  CONST_27  C23  C24  C25  C26     0.00   0.0  0
 KHD  CONST_28  C23  C22  C27  C26     0.00   0.0  0
 KHD  CONST_29  C12  C13  C8   C9      0.00   0.0  0
 KHD  CONST_30  C12  C11  C10  C9      0.00   0.0  0
 KHD  CONST_31  C19  C18  C17  C16     0.00   0.0  0
 KHD  CONST_32  C19  C20  C15  C16     0.00   0.0  0
 KHD  CONST_33  O21  C6   C5   C4    180.00   0.0  0
 KHD  CONST_34  N7   C4   C5   C6    180.00   0.0  0
 KHD  CONST_35  N7   C4   C5   C8      0.00   0.0  0
 KHD  CONST_36  O21  C6   C5   C8      0.00   0.0  0
 KHD  CONST_37  O14  C11  C12  C13   180.00   0.0  0
 KHD  CONST_38  O14  C15  C16  C17   180.00   0.0  0
 KHD  CONST_39  N28  C26  C27  C22   180.00   0.0  0
 KHD  CONST_40  N28  C26  C25  C24   180.00   0.0  0
 KHD  CONST_41  O21  C22  C23  C24   180.00   0.0  0
 KHD  CONST_42  O21  C22  C27  C26   180.00   0.0  0
 KHD  CONST_43  C2   C1   C6   O21   180.00   0.0  0
 KHD  CONST_44  C2   N3   C4   N7    180.00   0.0  0
 KHD  CONST_45  O14  C11  C10  C9    180.00   0.0  0
 KHD  CONST_46  C19  C20  C15  O14   180.00   0.0  0
 KHD  CONST_47  H18  C1   C2   N3    180.00   0.0  0
 KHD  CONST_48  H17  C2   N3   C4    180.00   0.0  0
 KHD  CONST_49  H2   C13  C8   C5      0.00   0.0  0
 KHD  CONST_50  H19  C9   C8   C5      0.00   0.0  0
 KHD  CONST_51  H20  C12  C13  C8    180.00   0.0  0
 KHD  CONST_52  H1   C10  C9   C8    180.00   0.0  0
 KHD  CONST_53  H3   C17  C16  C15   180.00   0.0  0
 KHD  CONST_54  H23  C19  C20  C15   180.00   0.0  0
 KHD  CONST_55  H21  C16  C15  C20   180.00   0.0  0
 KHD  CONST_56  H22  C18  C19  C20   180.00   0.0  0
 KHD  CONST_57  H5   C24  C23  C22   180.00   0.0  0
 KHD  CONST_58  H14  C25  C26  C27   180.00   0.0  0
 KHD  CONST_59  H13  C23  C22  C27   180.00   0.0  0
 KHD  CONST_60  H12  C27  C22  C23   180.00   0.0  0
 KHD  CONST_61  H4   C20  C15  C16   180.00   0.0  0
 KHD  CONST_62  C25  C26  N28  C29   180.00   0.0  0
 KHD  CONST_63  C27  C26  N28  C29     0.00   0.0  0
 KHD  CONST_66  H11  N28  C26  C27   180.00   0.0  0
 KHD  CONST_67  O31  C29  N28  C26     0.00   0.0  0
 KHD  CONST_68  C30  C29  N28  C26   180.00   0.0  0
 KHD  Var_01    C23  C22  O21  C6    -94.22  30.0  3
 KHD  Var_02    C12  C11  O14  C15    80.67  30.0  2
 KHD  Var_03    C1   C6   O21  C22     4.05  30.0  1
 KHD  Var_04    C16  C15  O14  C11  -172.47  30.0  2
 KHD  Var_05    C32  C30  C29  O31    21.39  30.0  3
 KHD  Var_06    H8   C32  C30  C29    62.49  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
 KHD  plan-1  C5   0.020
 KHD  plan-1  C8   0.020
 KHD  plan-1  C10  0.020
 KHD  plan-1  C13  0.020
 KHD  plan-1  C9   0.020
 KHD  plan-1  C11  0.020
 KHD  plan-1  C12  0.020
 KHD  plan-1  O14  0.020
 KHD  plan-1  H1   0.020
 KHD  plan-1  H2   0.020
 KHD  plan-1  H19  0.020
 KHD  plan-1  H20  0.020
 KHD  plan-2  C22  0.020
 KHD  plan-2  C24  0.020
 KHD  plan-2  C26  0.020
 KHD  plan-2  N28  0.020
 KHD  plan-2  C27  0.020
 KHD  plan-2  C23  0.020
 KHD  plan-2  C25  0.020
 KHD  plan-2  O21  0.020
 KHD  plan-2  H5   0.020
 KHD  plan-2  H12  0.020
 KHD  plan-2  H13  0.020
 KHD  plan-2  H14  0.020
 KHD  plan-3  N3   0.020
 KHD  plan-3  C4   0.020
 KHD  plan-3  C5   0.020
 KHD  plan-3  C6   0.020
 KHD  plan-3  C8   0.020
 KHD  plan-3  O21  0.020
 KHD  plan-3  N7   0.020
 KHD  plan-3  C2   0.020
 KHD  plan-3  C1   0.020
 KHD  plan-3  H17  0.020
 KHD  plan-3  H18  0.020
 KHD  plan-4  C15  0.020
 KHD  plan-4  C17  0.020
 KHD  plan-4  C20  0.020
 KHD  plan-4  O14  0.020
 KHD  plan-4  C16  0.020
 KHD  plan-4  C18  0.020
 KHD  plan-4  C19  0.020
 KHD  plan-4  H3   0.020
 KHD  plan-4  H4   0.020
 KHD  plan-4  H21  0.020
 KHD  plan-4  H22  0.020
 KHD  plan-4  H23  0.020
 KHD  plan-5  C26  0.020
 KHD  plan-5  O31  0.020
 KHD  plan-5  C29  0.020
 KHD  plan-5  C30  0.020
 KHD  plan-5  N28  0.020
 KHD  plan-5  H11  0.020
 KHD  plan-6  C4   0.020
 KHD  plan-6  N7   0.020
 KHD  plan-6  H15  0.020
 KHD  plan-6  H16  0.020

