# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 04:02:34 2022
#   Inital geometry file: a 139 line input string
#   Ligand name: N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}-1-methylazetidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](NC(=O)C1CN(C)C1)c2[nH]c(cn2)c3cc4ccccc4nc3OC
#
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
 YEM  YEM  N-{(1S)-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]pentyl}-1-methylazetidine-3-carboxamide  ligand  59  30  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YEM
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
 YEM  O1   O  O     0  -0.472  76.3482  32.8549  -1.1325
 YEM  C18  C  C     0   0.575  76.1970  31.8788  -0.4162
 YEM  C19  C  C     0  -0.463  77.3346  31.0302   0.1018
 YEM  C21  C  C     0  -0.253  78.7251  31.4266  -0.4017
 YEM  N4   N  N     0  -0.393  78.6193  30.4094  -1.4497
 YEM  C22  C  CH3   0  -0.522  79.7957  29.6491  -1.7744
 YEM  C20  C  C     0  -0.259  77.5504  29.7349  -0.7147
 YEM  N3   N  NH1   0  -0.661  74.9775  31.4577  -0.0240
 YEM  C13  C  CH1   0  -0.134  73.7481  32.0692  -0.4867
 YEM  C14  C  CH2   0  -0.461  72.5683  31.2222   0.0021
 YEM  C15  C  CH2   0  -0.417  71.2122  31.7204  -0.4754
 YEM  C16  C  CH2   0  -0.418  70.0800  30.7893  -0.0594
 YEM  C17  C  CH3   0  -0.660  68.7159  31.2837  -0.5181
 YEM  C11  C  CR5   0   0.466  73.6455  33.4906  -0.0268
 YEM  N1   N  NR15  0  -0.665  73.9742  33.8820   1.2176
 YEM  N2   N  N     0  -0.444  73.1927  34.4963  -0.7335
 YEM  C12  C  CR15  0  -0.254  73.2438  35.5816   0.0879
 YEM  C10  C  CR5   0   0.321  73.7353  35.2323   1.3248
 YEM  C7   C  CR6   0  -0.090  73.9596  35.9608   2.5630
 YEM  C6   C  CR16  0  -0.258  74.0459  35.3308   3.7761
 YEM  C4   C  CR66  0   0.094  74.2848  36.0559   4.9654
 YEM  C5   C  CR16  0  -0.318  74.3800  35.4413   6.2310
 YEM  C    C  CR16  0  -0.259  74.6113  36.1979   7.3505
 YEM  C8   C  CR6   0   0.454  74.1152  37.3912   2.5879
 YEM  O    O  O2    0  -0.461  74.0277  38.0023   1.4116
 YEM  C9   C  CH3   0  -0.416  74.1779  39.4148   1.3719
 YEM  N    N  N     0  -0.494  74.3318  38.0845   3.6583
 YEM  C3   C  CR66  0   0.205  74.4237  37.4561   4.8571
 YEM  C2   C  CR16  0  -0.289  74.6605  38.2144   6.0201
 YEM  C1   C  CR16  0  -0.261  74.7528  37.5941   7.2411
 YEM  H1   H  H     0   0.289  77.2344  30.8851   1.1782
 YEM  H2   H  H     0   0.214  79.4953  31.1985   0.3474
 YEM  H3   H  H     0   0.229  78.8698  32.4499  -0.7528
 YEM  H5   H  HCH3  0   0.232  79.5503  28.8662  -2.4938
 YEM  H6   H  HCH3  0   0.232  80.5441  30.2961  -2.2348
 YEM  H7   H  HCH3  0   0.191  80.2560  29.1706  -0.8963
 YEM  H8   H  H     0   0.233  76.7192  29.3649  -1.3208
 YEM  H9   H  H     0   0.218  77.9066  28.9174  -0.0740
 YEM  H10  H  HNH1  0   0.409  74.9059  30.6273   0.5438
 YEM  H11  H  HCH1  0   0.267  73.7281  32.0917  -1.5810
 YEM  H12  H  HCH2  0   0.246  72.7227  30.1992  -0.3553
 YEM  H13  H  HCH2  0   0.234  72.5846  31.1791   1.0962
 YEM  H14  H  HCH2  0   0.225  71.0176  32.7208  -0.0789
 YEM  H15  H  HCH2  0   0.217  71.2211  31.8195  -1.5658
 YEM  H16  H  HCH2  0   0.214  70.2631  29.7900  -0.4655
 YEM  H17  H  HCH2  0   0.214  70.0843  30.6801   1.0293
 YEM  H18  H  HCH3  0   0.226  67.9197  30.6083  -0.2038
 YEM  H19  H  HCH3  0   0.217  68.4948  32.2699  -0.1062
 YEM  H20  H  HCH3  0   0.216  68.6707  31.3637  -1.6057
 YEM  H21  H  HNR5  0   0.418  74.3925  33.2873   1.9172
 YEM  H23  H  HCR5  0   0.255  72.9158  36.5504  -0.2482
 YEM  H24  H  HCR6  0   0.264  73.9167  34.2578   3.8570
 YEM  H25  H  HCR6  0   0.259  74.2692  34.3659   6.3054
 YEM  H26  H  HCR6  0   0.258  74.6854  35.7253   8.3209
 YEM  H27  H  HCH3  0   0.248  74.0730  39.6936   0.3268
 YEM  H28  H  HCH3  0   0.232  73.4104  39.9177   1.9608
 YEM  H29  H  HCH3  0   0.232  75.1581  39.7254   1.7346
 YEM  H30  H  HCR6  0   0.257  74.7667  39.2880   5.9293
 YEM  H31  H  HCR6  0   0.260  74.9356  38.1830   8.1306

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
 YEM  O1   C18  double    1.220  0.020  1.220
 YEM  N4   C21  single    1.464  0.020  1.464
 YEM  N4   C22  single    1.438  0.020  1.438
 YEM  N4   C20  single    1.462  0.020  1.462
 YEM  C21  C19  single    1.531  0.020  1.531
 YEM  C18  C19  single    1.511  0.020  1.511
 YEM  C18  N3   single    1.348  0.020  1.348
 YEM  N2   C11  aromatic  1.310  0.020  1.310
 YEM  N2   C12  aromatic  1.362  0.020  1.362
 YEM  C13  N3   single    1.449  0.020  1.449
 YEM  C13  C14  single    1.532  0.020  1.532
 YEM  C13  C11  single    1.497  0.020  1.497
 YEM  C15  C14  single    1.522  0.020  1.522
 YEM  C15  C16  single    1.524  0.020  1.524
 YEM  C17  C16  single    1.522  0.020  1.522
 YEM  C20  C19  single    1.546  0.020  1.546
 YEM  C11  N1   aromatic  1.345  0.020  1.345
 YEM  C12  C10  aromatic  1.376  0.020  1.376
 YEM  N1   C10  aromatic  1.375  0.020  1.375
 YEM  C10  C7   single    1.454  0.020  1.454
 YEM  O    C9   single    1.421  0.020  1.421
 YEM  O    C8   single    1.328  0.020  1.328
 YEM  C7   C8   aromatic  1.439  0.020  1.439
 YEM  C7   C6   aromatic  1.370  0.020  1.370
 YEM  C8   N    aromatic  1.294  0.020  1.294
 YEM  C6   C4   aromatic  1.413  0.020  1.413
 YEM  N    C3   aromatic  1.357  0.020  1.357
 YEM  C4   C3   aromatic  1.411  0.020  1.411
 YEM  C4   C5   aromatic  1.410  0.020  1.410
 YEM  C3   C2   aromatic  1.408  0.020  1.408
 YEM  C5   C    aromatic  1.371  0.020  1.371
 YEM  C2   C1   aromatic  1.373  0.020  1.373
 YEM  C    C1   aromatic  1.408  0.020  1.408
 YEM  C19  H1   single    0.970  0.020  1.090
 YEM  C21  H2   single    0.970  0.020  1.090
 YEM  C21  H3   single    0.970  0.020  1.090
 YEM  C22  H5   single    0.970  0.020  1.090
 YEM  C22  H6   single    0.970  0.020  1.090
 YEM  C22  H7   single    0.970  0.020  1.090
 YEM  C20  H8   single    0.970  0.020  1.090
 YEM  C20  H9   single    0.970  0.020  1.090
 YEM  N3   H10  single    0.860  0.020  1.020
 YEM  C13  H11  single    0.970  0.020  1.090
 YEM  C14  H12  single    0.970  0.020  1.090
 YEM  C14  H13  single    0.970  0.020  1.090
 YEM  C15  H14  single    0.970  0.020  1.090
 YEM  C15  H15  single    0.970  0.020  1.090
 YEM  C16  H16  single    0.970  0.020  1.090
 YEM  C16  H17  single    0.970  0.020  1.090
 YEM  C17  H18  single    0.970  0.020  1.090
 YEM  C17  H19  single    0.970  0.020  1.090
 YEM  C17  H20  single    0.970  0.020  1.090
 YEM  N1   H21  single    0.860  0.020  1.020
 YEM  C12  H23  single    0.930  0.020  1.080
 YEM  C6   H24  single    0.930  0.020  1.080
 YEM  C5   H25  single    0.930  0.020  1.080
 YEM  C    H26  single    0.930  0.020  1.080
 YEM  C9   H27  single    0.970  0.020  1.090
 YEM  C9   H28  single    0.970  0.020  1.090
 YEM  C9   H29  single    0.970  0.020  1.090
 YEM  C2   H30  single    0.930  0.020  1.080
 YEM  C1   H31  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
 YEM  N3   C18  C19  113.94  3.000
 YEM  N3   C18  O1   122.18  3.000
 YEM  C19  C18  O1   123.87  3.000
 YEM  H1   C19  C20  114.99  3.000
 YEM  H1   C19  C21  116.27  3.000
 YEM  C20  C19  C21   85.21  3.000
 YEM  H1   C19  C18  110.11  3.000
 YEM  C20  C19  C18  113.24  3.000
 YEM  C21  C19  C18  115.19  3.000
 YEM  H3   C21  H2   108.73  3.000
 YEM  H3   C21  N4   115.51  3.000
 YEM  H2   C21  N4   113.24  3.000
 YEM  H3   C21  C19  117.96  3.000
 YEM  H2   C21  C19  111.03  3.000
 YEM  N4   C21  C19   89.43  3.000
 YEM  C20  N4   C22  117.88  3.000
 YEM  C20  N4   C21   90.77  3.000
 YEM  C22  N4   C21  118.02  3.000
 YEM  H7   C22  H6   107.91  3.000
 YEM  H7   C22  H5   107.94  3.000
 YEM  H6   C22  H5   107.55  3.000
 YEM  H7   C22  N4   113.07  3.000
 YEM  H6   C22  N4   110.05  3.000
 YEM  H5   C22  N4   110.14  3.000
 YEM  H9   C20  H8   108.55  3.000
 YEM  H9   C20  N4   113.56  3.000
 YEM  H8   C20  N4   115.67  3.000
 YEM  H9   C20  C19  111.15  3.000
 YEM  H8   C20  C19  118.05  3.000
 YEM  N4   C20  C19   88.91  3.000
 YEM  H10  N3   C13  117.84  3.000
 YEM  H10  N3   C18  119.02  3.000
 YEM  C13  N3   C18  122.87  3.000
 YEM  H11  C13  C11  106.63  3.000
 YEM  H11  C13  C14  108.43  3.000
 YEM  C11  C13  C14  111.95  3.000
 YEM  H11  C13  N3   110.08  3.000
 YEM  C11  C13  N3   111.14  3.000
 YEM  C14  C13  N3   108.55  3.000
 YEM  H13  C14  H12  106.70  3.000
 YEM  H13  C14  C15  109.86  3.000
 YEM  H12  C14  C15  109.23  3.000
 YEM  H13  C14  C13  109.21  3.000
 YEM  H12  C14  C13  107.68  3.000
 YEM  C15  C14  C13  113.90  3.000
 YEM  H15  C15  H14  106.25  3.000
 YEM  H15  C15  C16  109.47  3.000
 YEM  H14  C15  C16  109.13  3.000
 YEM  H15  C15  C14  109.57  3.000
 YEM  H14  C15  C14  110.14  3.000
 YEM  C16  C15  C14  112.12  3.000
 YEM  H17  C16  H16  106.11  3.000
 YEM  H17  C16  C17  109.63  3.000
 YEM  H16  C16  C17  109.57  3.000
 YEM  H17  C16  C15  109.25  3.000
 YEM  H16  C16  C15  109.41  3.000
 YEM  C17  C16  C15  112.66  3.000
 YEM  H20  C17  H19  107.54  3.000
 YEM  H20  C17  H18  107.60  3.000
 YEM  H19  C17  H18  107.64  3.000
 YEM  H20  C17  C16  111.18  3.000
 YEM  H19  C17  C16  111.19  3.000
 YEM  H18  C17  C16  111.50  3.000
 YEM  N2   C11  N1   111.10  3.000
 YEM  N1   C11  C13  122.93  3.000
 YEM  N2   C11  C13  125.93  3.000
 YEM  H21  N1   C10  126.63  3.000
 YEM  H21  N1   C11  124.83  3.000
 YEM  C10  N1   C11  108.38  3.000
 YEM  C12  N2   C11  105.87  3.000
 YEM  H23  C12  C10  128.16  3.000
 YEM  H23  C12  N2   121.15  3.000
 YEM  C10  C12  N2   110.69  3.000
 YEM  C7   C10  C12  133.90  3.000
 YEM  C7   C10  N1   122.10  3.000
 YEM  C12  C10  N1   103.96  3.000
 YEM  C8   C7   C6   115.79  3.000
 YEM  C6   C7   C10  122.24  3.000
 YEM  C8   C7   C10  121.97  3.000
 YEM  H24  C6   C4   117.73  3.000
 YEM  H24  C6   C7   120.94  3.000
 YEM  C4   C6   C7   121.33  3.000
 YEM  C3   C4   C5   119.65  3.000
 YEM  C5   C4   C6   122.89  3.000
 YEM  C3   C4   C6   117.46  3.000
 YEM  H25  C5   C    120.59  3.000
 YEM  H25  C5   C4   119.16  3.000
 YEM  C    C5   C4   120.25  3.000
 YEM  H26  C    C1   119.75  3.000
 YEM  H26  C    C5   120.20  3.000
 YEM  C1   C    C5   120.06  3.000
 YEM  N    C8   O    119.82  3.000
 YEM  N    C8   C7   124.41  3.000
 YEM  O    C8   C7   115.77  3.000
 YEM  C9   O    C8   118.36  3.000
 YEM  H29  C9   H28  108.77  3.000
 YEM  H29  C9   H27  109.49  3.000
 YEM  H28  C9   H27  109.46  3.000
 YEM  H29  C9   O    111.64  3.000
 YEM  H28  C9   O    111.65  3.000
 YEM  H27  C9   O    105.76  3.000
 YEM  C3   N    C8   119.62  3.000
 YEM  C2   C3   N    119.45  3.000
 YEM  C2   C3   C4   119.17  3.000
 YEM  N    C3   C4   121.38  3.000
 YEM  H30  C2   C1   121.07  3.000
 YEM  H30  C2   C3   118.76  3.000
 YEM  C1   C2   C3   120.17  3.000
 YEM  H31  C1   C2   119.77  3.000
 YEM  H31  C1   C    119.52  3.000
 YEM  C2   C1   C    120.71  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
 YEM  CONST_01  C10  C12  N2   C11     0.00   0.0  0
 YEM  CONST_02  C12  C10  N1   C11     0.00   0.0  0
 YEM  CONST_03  C7   C10  N1   C11   180.00   0.0  0
 YEM  CONST_04  C12  N2   C11  N1      0.00   0.0  0
 YEM  CONST_05  N2   C12  C10  N1      0.00   0.0  0
 YEM  CONST_08  C10  N1   C11  N2      0.00   0.0  0
 YEM  CONST_09  C7   C10  C12  N2    180.00   0.0  0
 YEM  CONST_12  N    C8   C7   C10   180.00   0.0  0
 YEM  CONST_13  C4   C6   C7   C10   180.00   0.0  0
 YEM  CONST_14  C3   N    C8   C7      0.00   0.0  0
 YEM  CONST_15  C3   C4   C6   C7      0.00   0.0  0
 YEM  CONST_16  C5   C4   C6   C7    180.00   0.0  0
 YEM  CONST_17  N    C8   C7   C6      0.00   0.0  0
 YEM  CONST_18  N    C3   C4   C6      0.00   0.0  0
 YEM  CONST_19  C2   C3   C4   C6    180.00   0.0  0
 YEM  CONST_20  C    C5   C4   C6    180.00   0.0  0
 YEM  CONST_21  C8   C7   C6   C4      0.00   0.0  0
 YEM  CONST_22  C8   N    C3   C4      0.00   0.0  0
 YEM  CONST_23  C1   C2   C3   C4      0.00   0.0  0
 YEM  CONST_24  C1   C    C5   C4      0.00   0.0  0
 YEM  CONST_25  N    C3   C4   C5    180.00   0.0  0
 YEM  CONST_26  C2   C3   C4   C5      0.00   0.0  0
 YEM  CONST_27  C2   C1   C    C5      0.00   0.0  0
 YEM  CONST_28  C3   C4   C5   C       0.00   0.0  0
 YEM  CONST_29  C3   C2   C1   C       0.00   0.0  0
 YEM  CONST_30  C2   C3   N    C8    180.00   0.0  0
 YEM  CONST_31  C1   C2   C3   N     180.00   0.0  0
 YEM  CONST_32  C12  N2   C11  C13   180.00   0.0  0
 YEM  CONST_33  C10  N1   C11  C13   180.00   0.0  0
 YEM  CONST_34  O    C8   C7   C10     0.00   0.0  0
 YEM  CONST_35  O    C8   C7   C6    180.00   0.0  0
 YEM  CONST_36  C3   N    C8   O     180.00   0.0  0
 YEM  CONST_37  H23  C12  N2   C11   180.00   0.0  0
 YEM  CONST_38  H21  N1   C11  N2    180.00   0.0  0
 YEM  CONST_39  H24  C6   C7   C10     0.00   0.0  0
 YEM  CONST_40  H25  C5   C4   C6      0.00   0.0  0
 YEM  CONST_41  H30  C2   C3   C4    180.00   0.0  0
 YEM  CONST_42  H26  C    C5   C4    180.00   0.0  0
 YEM  CONST_43  H31  C1   C    C5    180.00   0.0  0
 YEM  CONST_44  C13  N3   C18  C19   180.00   0.0  0
 YEM  CONST_45  H10  N3   C18  C19     0.00   0.0  0
 YEM  CONST_46  C13  N3   C18  O1      0.00   0.0  0
 YEM  Var_01    C20  N4   C21  C19   -18.43  30.0  1
 YEM  Var_02    N    C8   O    C9      0.02  30.0  2
 YEM  Var_03    H5   C22  N4   C21   174.33  30.0  3
 YEM  Var_04    H27  C9   O    C8    179.90  30.0  3
 YEM  Var_05    C16  C15  C14  C13   175.48  30.0  1
 YEM  Var_06    C17  C16  C15  C14   179.39  30.0  3
 YEM  Var_07    H18  C17  C16  C15  -179.54  30.0  3

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
 YEM  chir_01  C19  C21  C18  C20  negativ
 YEM  chir_02  C13  N3   C11  C14  positiv

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
 YEM  plan-1  C13  0.020
 YEM  plan-1  C11  0.020
 YEM  plan-1  N1   0.020
 YEM  plan-1  N2   0.020
 YEM  plan-1  C12  0.020
 YEM  plan-1  C10  0.020
 YEM  plan-1  C7   0.020
 YEM  plan-1  H21  0.020
 YEM  plan-1  H23  0.020
 YEM  plan-2  C10  0.020
 YEM  plan-2  C7   0.020
 YEM  plan-2  C6   0.020
 YEM  plan-2  C4   0.020
 YEM  plan-2  C5   0.020
 YEM  plan-2  C    0.020
 YEM  plan-2  C8   0.020
 YEM  plan-2  O    0.020
 YEM  plan-2  N    0.020
 YEM  plan-2  C3   0.020
 YEM  plan-2  C2   0.020
 YEM  plan-2  C1   0.020
 YEM  plan-2  H24  0.020
 YEM  plan-2  H25  0.020
 YEM  plan-2  H26  0.020
 YEM  plan-2  H30  0.020
 YEM  plan-2  H31  0.020
 YEM  plan-3  O1   0.020
 YEM  plan-3  C18  0.020
 YEM  plan-3  C19  0.020
 YEM  plan-3  N3   0.020
 YEM  plan-3  C13  0.020
 YEM  plan-3  H10  0.020

