# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 01:24:57 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: ~{N}-[(1~{S})-2-[(4-methoxy-2,5-dimethyl-phenyl)methylamino]-1-[4-(3-oxidanylprop-1-ynyl)phenyl]ethyl]-5-methyl-1,2-oxazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(C)c(CNC[C@@H](NC(=O)c2cc(C)on2)c3ccc(cc3)C#CCO)cc1C
#
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
 5S6  5S6  ~{N}-[(1~{S})-2-[(4-methoxy-2,5-dimethyl-phenyl)methylamino]-1-[4-(3-oxidanylprop-1-ynyl)phenyl]ethyl]-5-methyl-1,2-oxazole-3-carboxamide  ligand  62  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5S6
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
 5S6  C8   C  CSP   0   0.228   6.4771  -1.6946  -0.1476
 5S6  C9   C  CSP   0  -0.054   7.6377  -2.0115  -0.0849
 5S6  C23  C  CR16  0  -0.273   4.2955  -1.7989  -1.2618
 5S6  C24  C  CR16  0  -0.270   4.5407  -0.4726   0.7309
 5S6  C21  C  CR16  0  -0.294   2.9630  -1.4311  -1.3329
 5S6  C20  C  CR16  0  -0.303   3.2055  -0.1141   0.6526
 5S6  C13  C  CR16  0  -0.336  -4.4138  -1.2025   1.4818
 5S6  C11  C  CR16  0  -0.434  -5.4526  -2.0472  -0.9114
 5S6  C4   C  CR15  0  -0.495   0.6317   4.7486  -0.8532
 5S6  C19  C  CR6   0  -0.113   5.1024  -1.3223  -0.2255
 5S6  C18  C  CR6   0   0.146   2.4013  -0.5875  -0.3795
 5S6  C12  C  CR6   0   0.056  -3.5718  -1.8379   0.5728
 5S6  C14  C  CR6   0   0.004  -5.7599  -0.9730   1.2361
 5S6  C15  C  CR6   0   0.080  -4.1017  -2.2641  -0.6463
 5S6  C10  C  CR6   0   0.353  -6.2770  -1.4088   0.0104
 5S6  C1   C  CR5   0   0.138   0.5471   3.4874  -0.2227
 5S6  C7   C  CR5   0   0.431   0.2749   5.6153   0.1260
 5S6  C32  C  CH3   0  -0.714  -6.6335  -0.2777   2.2375
 5S6  C30  C  CH3   0  -0.748  -3.2497  -2.9672  -1.6631
 5S6  C31  C  CH3   0  -0.747   0.1425   7.0870   0.1818
 5S6  C33  C  CH3   0  -0.435  -8.1730  -1.5718  -1.4154
 5S6  C27  C  CH2   0  -0.338   9.0443  -2.3887  -0.0170
 5S6  C26  C  CH2   0  -0.354  -2.1147  -2.0155   0.8976
 5S6  C28  C  CH2   0  -0.263   0.1124  -1.2240   0.3938
 5S6  C16  C  CH1   0  -0.171   0.9294  -0.2514  -0.4543
 5S6  N2   N  N     0  -0.169   0.1749   3.6001   1.0199
 5S6  N5   N  NH1   0  -0.666   0.6479   1.1051  -0.0341
 5S6  O17  O  O     0  -0.461   1.2134   2.0928  -1.9935
 5S6  O6   O  O     0  -0.323   0.0050   4.9208   1.2415
 5S6  O29  O  OH1   0  -0.665   9.2642  -3.1392   1.1555
 5S6  O25  O  O2    0  -0.468  -7.5893  -1.1694  -0.1942
 5S6  H1   H  HCR6  0   0.261   4.7176  -2.4523  -2.0139
 5S6  H2   H  HCR6  0   0.261   5.1541  -0.0924   1.5372
 5S6  H3   H  HCR6  0   0.259   2.3517  -1.8070  -2.1449
 5S6  H4   H  HCR6  0   0.253   2.7960   0.5497   1.4041
 5S6  H5   H  HCR6  0   0.237  -4.0008  -0.8681   2.4284
 5S6  H6   H  HCR6  0   0.266  -5.8489  -2.3922  -1.8581
 5S6  H7   H  HCR5  0   0.288   0.9062   4.9736  -1.8690
 5S6  H8   H  HCH3  0   0.240  -7.0277   0.6629   1.8478
 5S6  H9   H  HCH3  0   0.240  -7.4929  -0.8859   2.5251
 5S6  H10  H  HCH3  0   0.240  -6.0728  -0.0495   3.1429
 5S6  H11  H  HCH3  0   0.242  -2.9155  -3.9403  -1.2958
 5S6  H12  H  HCH3  0   0.245  -3.7969  -3.1382  -2.5891
 5S6  H13  H  HCH3  0   0.248  -2.3543  -2.3907  -1.8953
 5S6  H14  H  HCH3  0   0.273   0.8012   7.5135   0.9388
 5S6  H15  H  HCH3  0   0.271   0.4050   7.5159  -0.7818
 5S6  H16  H  HCH3  0   0.273  -0.8788   7.3829   0.4231
 5S6  H17  H  HCH3  0   0.226  -8.1178  -2.6539  -1.5600
 5S6  H18  H  HCH3  0   0.258  -9.2196  -1.2802  -1.3694
 5S6  H19  H  HCH3  0   0.226  -7.7087  -1.0792  -2.2738
 5S6  H20  H  HCH2  0   0.239   9.2960  -2.9553  -0.9221
 5S6  H21  H  HCH2  0   0.237   9.6537  -1.4765  -0.0410
 5S6  H22  H  HCH2  0   0.220  -1.9719  -1.9457   1.9863
 5S6  H23  H  HCH2  0   0.234  -1.7808  -3.0179   0.6126
 5S6  H24  H  HCH2  0   0.251   0.3895  -2.2382   0.0971
 5S6  H25  H  HCH2  0   0.209   0.4087  -1.1191   1.4517
 5S6  H26  H  HCH1  0   0.270   0.5983  -0.3592  -1.4901
 5S6  H27  H  HNH1  0   0.413   0.3959   1.2732   0.9293
 5S6  H28  H  HNH1  0   0.344  -1.5880  -0.1199   0.4465
 5S6  H30  H  HOH1  0   0.463  10.1879  -3.4100   1.1565
 5S6  N22  N  NH1   0  -0.582  -1.3049  -1.0520   0.1672
 5S6  C3   C  C     0   0.554   0.8377   2.1625  -0.8361

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
 5S6  C31  C7   single    1.479  0.020  1.479
 5S6  C7   O6   aromatic  1.341  0.020  1.341
 5S6  C7   C4   aromatic  1.356  0.020  1.356
 5S6  O6   N2   aromatic  1.350  0.020  1.350
 5S6  O29  C27  single    1.409  0.020  1.409
 5S6  C4   C1   aromatic  1.412  0.020  1.412
 5S6  N2   C1   aromatic  1.302  0.020  1.302
 5S6  C27  C9   single    1.458  0.020  1.458
 5S6  C1   C3   single    1.489  0.020  1.489
 5S6  C24  C20  aromatic  1.385  0.020  1.385
 5S6  C24  C19  aromatic  1.397  0.020  1.397
 5S6  C9   C8   triple    1.205  0.020  1.205
 5S6  C20  C18  aromatic  1.392  0.020  1.392
 5S6  C8   C19  single    1.426  0.020  1.426
 5S6  C3   N5   single    1.341  0.020  1.341
 5S6  C3   O17  double    1.219  0.020  1.219
 5S6  C19  C23  aromatic  1.397  0.020  1.397
 5S6  N5   C16  single    1.448  0.020  1.448
 5S6  C18  C16  single    1.512  0.020  1.512
 5S6  C18  C21  aromatic  1.391  0.020  1.391
 5S6  C16  C28  single    1.527  0.020  1.527
 5S6  C23  C21  aromatic  1.384  0.020  1.384
 5S6  C28  N22  single    1.446  0.020  1.446
 5S6  C30  C15  single    1.501  0.020  1.501
 5S6  C26  N22  single    1.455  0.020  1.455
 5S6  C26  C12  single    1.503  0.020  1.503
 5S6  C15  C12  aromatic  1.396  0.020  1.396
 5S6  C15  C11  aromatic  1.394  0.020  1.394
 5S6  C12  C13  aromatic  1.392  0.020  1.392
 5S6  C11  C10  aromatic  1.392  0.020  1.392
 5S6  C13  C14  aromatic  1.387  0.020  1.387
 5S6  C10  C14  aromatic  1.400  0.020  1.400
 5S6  C10  O25  single    1.350  0.020  1.350
 5S6  C14  C32  single    1.500  0.020  1.500
 5S6  C33  O25  single    1.412  0.020  1.412
 5S6  C23  H1   single    0.930  0.020  1.080
 5S6  C24  H2   single    0.930  0.020  1.080
 5S6  C21  H3   single    0.930  0.020  1.080
 5S6  C20  H4   single    0.930  0.020  1.080
 5S6  C13  H5   single    0.930  0.020  1.080
 5S6  C11  H6   single    0.930  0.020  1.080
 5S6  C4   H7   single    0.930  0.020  1.080
 5S6  C32  H8   single    0.970  0.020  1.090
 5S6  C32  H9   single    0.970  0.020  1.090
 5S6  C32  H10  single    0.970  0.020  1.090
 5S6  C30  H11  single    0.970  0.020  1.090
 5S6  C30  H12  single    0.970  0.020  1.090
 5S6  C30  H13  single    0.970  0.020  1.090
 5S6  C31  H14  single    0.970  0.020  1.090
 5S6  C31  H15  single    0.970  0.020  1.090
 5S6  C31  H16  single    0.970  0.020  1.090
 5S6  C33  H17  single    0.970  0.020  1.090
 5S6  C33  H18  single    0.970  0.020  1.090
 5S6  C33  H19  single    0.970  0.020  1.090
 5S6  C27  H20  single    0.970  0.020  1.090
 5S6  C27  H21  single    0.970  0.020  1.090
 5S6  C26  H22  single    0.970  0.020  1.090
 5S6  C26  H23  single    0.970  0.020  1.090
 5S6  C28  H24  single    0.970  0.020  1.090
 5S6  C28  H25  single    0.970  0.020  1.090
 5S6  C16  H26  single    0.970  0.020  1.090
 5S6  N5   H27  single    0.860  0.020  1.020
 5S6  N22  H28  single    0.890  0.020  1.040
 5S6  O29  H30  single    0.850  0.020  0.980

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
 5S6  C19  C8   C9   180.00  3.000
 5S6  C27  C9   C8   180.00  3.000
 5S6  H1   C23  C19  119.75  3.000
 5S6  H1   C23  C21  120.02  3.000
 5S6  C19  C23  C21  120.23  3.000
 5S6  H2   C24  C19  119.72  3.000
 5S6  H2   C24  C20  119.86  3.000
 5S6  C19  C24  C20  120.42  3.000
 5S6  H3   C21  C18  119.74  3.000
 5S6  H3   C21  C23  119.30  3.000
 5S6  C18  C21  C23  120.97  3.000
 5S6  H4   C20  C18  120.31  3.000
 5S6  H4   C20  C24  118.95  3.000
 5S6  C18  C20  C24  120.74  3.000
 5S6  H5   C13  C14  118.20  3.000
 5S6  H5   C13  C12  118.67  3.000
 5S6  C14  C13  C12  123.13  3.000
 5S6  H6   C11  C10  120.56  3.000
 5S6  H6   C11  C15  118.13  3.000
 5S6  C10  C11  C15  121.31  3.000
 5S6  H7   C4   C7   127.98  3.000
 5S6  H7   C4   C1   128.57  3.000
 5S6  C7   C4   C1   103.46  3.000
 5S6  C24  C19  C23  118.88  3.000
 5S6  C23  C19  C8   120.54  3.000
 5S6  C24  C19  C8   120.58  3.000
 5S6  C16  C18  C20  121.59  3.000
 5S6  C16  C18  C21  119.60  3.000
 5S6  C20  C18  C21  118.76  3.000
 5S6  C26  C12  C15  121.36  3.000
 5S6  C15  C12  C13  118.68  3.000
 5S6  C26  C12  C13  119.93  3.000
 5S6  C32  C14  C10  120.91  3.000
 5S6  C32  C14  C13  121.57  3.000
 5S6  C10  C14  C13  117.51  3.000
 5S6  C30  C15  C12  121.27  3.000
 5S6  C12  C15  C11  119.11  3.000
 5S6  C30  C15  C11  119.62  3.000
 5S6  O25  C10  C14  115.89  3.000
 5S6  O25  C10  C11  123.85  3.000
 5S6  C14  C10  C11  120.26  3.000
 5S6  N2   C1   C3   121.74  3.000
 5S6  C3   C1   C4   126.80  3.000
 5S6  N2   C1   C4   111.46  3.000
 5S6  O6   C7   C31  117.77  3.000
 5S6  O6   C7   C4   108.82  3.000
 5S6  C31  C7   C4   133.41  3.000
 5S6  H10  C32  H9   107.65  3.000
 5S6  H10  C32  H8   107.58  3.000
 5S6  H9   C32  H8   106.85  3.000
 5S6  H10  C32  C14  110.63  3.000
 5S6  H9   C32  C14  112.10  3.000
 5S6  H8   C32  C14  111.80  3.000
 5S6  H13  C30  H12  108.34  3.000
 5S6  H13  C30  H11  106.94  3.000
 5S6  H12  C30  H11  107.44  3.000
 5S6  H13  C30  C15  111.27  3.000
 5S6  H12  C30  C15  111.36  3.000
 5S6  H11  C30  C15  111.29  3.000
 5S6  H16  C31  H15  108.38  3.000
 5S6  H16  C31  H14  107.82  3.000
 5S6  H15  C31  H14  108.38  3.000
 5S6  H16  C31  C7   111.24  3.000
 5S6  H15  C31  C7   109.73  3.000
 5S6  H14  C31  C7   111.19  3.000
 5S6  H19  C33  H18  108.74  3.000
 5S6  H19  C33  H17  108.71  3.000
 5S6  H18  C33  H17  108.64  3.000
 5S6  H19  C33  O25  112.03  3.000
 5S6  H18  C33  O25  106.55  3.000
 5S6  H17  C33  O25  112.06  3.000
 5S6  H21  C27  H20  106.50  3.000
 5S6  H21  C27  O29  111.98  3.000
 5S6  H20  C27  O29  112.06  3.000
 5S6  H21  C27  C9   108.64  3.000
 5S6  H20  C27  C9   108.46  3.000
 5S6  O29  C27  C9   109.09  3.000
 5S6  H23  C26  H22  106.03  3.000
 5S6  H23  C26  N22  107.82  3.000
 5S6  H22  C26  N22  112.48  3.000
 5S6  H23  C26  C12  110.34  3.000
 5S6  H22  C26  C12  109.39  3.000
 5S6  N22  C26  C12  110.66  3.000
 5S6  H25  C28  H24  106.29  3.000
 5S6  H25  C28  N22  113.72  3.000
 5S6  H24  C28  N22  108.46  3.000
 5S6  H25  C28  C16  109.16  3.000
 5S6  H24  C28  C16  107.74  3.000
 5S6  N22  C28  C16  111.20  3.000
 5S6  H26  C16  N5   107.97  3.000
 5S6  H26  C16  C28  107.55  3.000
 5S6  N5   C16  C28  109.36  3.000
 5S6  H26  C16  C18  108.66  3.000
 5S6  C28  C16  C18  110.60  3.000
 5S6  N5   C16  C18  112.54  3.000
 5S6  O6   N2   C1   106.10  3.000
 5S6  H27  N5   C16  118.77  3.000
 5S6  H27  N5   C3   118.35  3.000
 5S6  C16  N5   C3   122.54  3.000
 5S6  N2   O6   C7   110.16  3.000
 5S6  H30  O29  C27  107.48  3.000
 5S6  C33  O25  C10  118.85  3.000
 5S6  H28  N22  C28  109.88  3.000
 5S6  H28  N22  C26  108.37  3.000
 5S6  C28  N22  C26  112.84  3.000
 5S6  O17  C3   N5   124.52  3.000
 5S6  O17  C3   C1   120.15  3.000
 5S6  N5   C3   C1   115.33  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
 5S6  CONST_01  C20  C24  C19  C23     0.00   0.0  0
 5S6  CONST_02  C20  C18  C21  C23     0.00   0.0  0
 5S6  CONST_03  C21  C18  C20  C24     0.00   0.0  0
 5S6  CONST_04  C21  C23  C19  C24     0.00   0.0  0
 5S6  CONST_05  C11  C15  C12  C13     0.00   0.0  0
 5S6  CONST_06  C11  C10  C14  C13     0.00   0.0  0
 5S6  CONST_07  N2   O6   C7   C4      0.00   0.0  0
 5S6  CONST_08  O6   N2   C1   C4      0.00   0.0  0
 5S6  CONST_09  C18  C20  C24  C19     0.00   0.0  0
 5S6  CONST_10  C18  C21  C23  C19     0.00   0.0  0
 5S6  CONST_11  C10  C11  C15  C12     0.00   0.0  0
 5S6  CONST_12  C10  C14  C13  C12     0.00   0.0  0
 5S6  CONST_13  C15  C12  C13  C14     0.00   0.0  0
 5S6  CONST_14  C15  C11  C10  C14     0.00   0.0  0
 5S6  CONST_15  O6   C7   C4   C1      0.00   0.0  0
 5S6  CONST_16  C7   O6   N2   C1      0.00   0.0  0
 5S6  CONST_17  N2   C1   C4   C7      0.00   0.0  0
 5S6  CONST_18  C20  C24  C19  C8    180.00   0.0  0
 5S6  CONST_19  C21  C23  C19  C8    180.00   0.0  0
 5S6  CONST_20  C16  C18  C21  C23   180.00   0.0  0
 5S6  CONST_21  C16  C18  C20  C24   180.00   0.0  0
 5S6  CONST_22  C30  C15  C12  C13   180.00   0.0  0
 5S6  CONST_23  O25  C10  C14  C13   180.00   0.0  0
 5S6  CONST_24  C26  C12  C15  C11   180.00   0.0  0
 5S6  CONST_25  C32  C14  C10  C11   180.00   0.0  0
 5S6  CONST_26  C32  C14  C13  C12   180.00   0.0  0
 5S6  CONST_27  C26  C12  C13  C14   180.00   0.0  0
 5S6  CONST_28  O25  C10  C11  C15   180.00   0.0  0
 5S6  CONST_29  C30  C15  C11  C10   180.00   0.0  0
 5S6  CONST_30  C31  C7   C4   C1    180.00   0.0  0
 5S6  CONST_31  C3   C1   C4   C7    180.00   0.0  0
 5S6  CONST_32  O6   N2   C1   C3    180.00   0.0  0
 5S6  CONST_33  N2   O6   C7   C31   180.00   0.0  0
 5S6  CONST_34  H2   C24  C19  C23   180.00   0.0  0
 5S6  CONST_35  H1   C23  C19  C24   180.00   0.0  0
 5S6  CONST_36  H4   C20  C18  C21   180.00   0.0  0
 5S6  CONST_37  H3   C21  C18  C20   180.00   0.0  0
 5S6  CONST_38  H6   C11  C15  C12   180.00   0.0  0
 5S6  CONST_39  H5   C13  C12  C15   180.00   0.0  0
 5S6  CONST_40  H7   C4   C1   N2    180.00   0.0  0
 5S6  CONST_41  C16  N5   C3   C1    180.00   0.0  0
 5S6  CONST_42  H27  N5   C3   C1      0.00   0.0  0
 5S6  CONST_43  O17  C3   N5   C16     0.00   0.0  0
 5S6  Var_01    N22  C26  C12  C13  -103.26  30.0  1
 5S6  Var_02    N5   C3   C1   C4   -178.31  30.0  2
 5S6  Var_03    H8   C32  C14  C13   117.20  30.0  2
 5S6  Var_04    H11  C30  C15  C11  -113.25  30.0  2
 5S6  Var_05    H14  C31  C7   C4   -120.55  30.0  2
 5S6  Var_06    C28  N22  C26  C12  -177.12  30.0  3
 5S6  Var_07    H17  C33  O25  C10    61.61  30.0  3
 5S6  Var_08    O29  C27  C9   C8    171.21  30.0  1
 5S6  Var_09    C16  C28  N22  C26   176.54  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5S6  chir_01  C16  N5  C18  C28  negativ

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
 5S6  plan-1  C4   0.020
 5S6  plan-1  C1   0.020
 5S6  plan-1  C7   0.020
 5S6  plan-1  C31  0.020
 5S6  plan-1  N2   0.020
 5S6  plan-1  O6   0.020
 5S6  plan-1  H7   0.020
 5S6  plan-1  C3   0.020
 5S6  plan-2  C8   0.020
 5S6  plan-2  C9   0.020
 5S6  plan-2  C23  0.020
 5S6  plan-2  C24  0.020
 5S6  plan-2  C21  0.020
 5S6  plan-2  C20  0.020
 5S6  plan-2  C19  0.020
 5S6  plan-2  C18  0.020
 5S6  plan-2  C16  0.020
 5S6  plan-2  H1   0.020
 5S6  plan-2  H2   0.020
 5S6  plan-2  H3   0.020
 5S6  plan-2  H4   0.020
 5S6  plan-3  C13  0.020
 5S6  plan-3  C11  0.020
 5S6  plan-3  C12  0.020
 5S6  plan-3  C14  0.020
 5S6  plan-3  C15  0.020
 5S6  plan-3  C10  0.020
 5S6  plan-3  C32  0.020
 5S6  plan-3  C30  0.020
 5S6  plan-3  C26  0.020
 5S6  plan-3  O25  0.020
 5S6  plan-3  H5   0.020
 5S6  plan-3  H6   0.020
 5S6  plan-4  C1   0.020
 5S6  plan-4  C16  0.020
 5S6  plan-4  N5   0.020
 5S6  plan-4  O17  0.020
 5S6  plan-4  H27  0.020
 5S6  plan-4  C3   0.020

