# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:48:30 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 2-{(3R,4S)-3-[(5-{[benzyl(methyl)amino]methyl}-1,2-oxazol-3-yl)methyl]piperidin-4-yl}-N-(1,3-thiazol-2-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1onc(C[C@H]2CNCC[C@H]2CC(=O)Nc3sccn3)c1)Cc4ccccc4
#
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
 D9S  D9S  2-{(3R,4S)-3-[(5-{[benzyl(methyl)amino]methyl}-1,2-oxazol-3-yl)methyl]piperidin-4-yl}-N-(1,3-thiazol-2-yl)acetamide  ligand  60  31  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D9S
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
 D9S  C4   C  CR16  0  -0.241  -13.5276   3.5334   1.6059
 D9S  C5   C  CR16  0  -0.270  -13.6021   4.9159   1.7365
 D9S  C6   C  CR16  0  -0.241  -12.5657   5.7060   1.2603
 D9S  N1   N  N     0  -0.187   -8.0726  -0.0569   4.3204
 D9S  C7   C  CR16  0  -0.310  -11.4611   5.1151   0.6575
 D9S  C8   C  CH2   0  -0.379   -9.0875   2.3072   1.7979
 D9S  N2   N  NH1   0  -0.576  -12.6014  -2.8620   6.9295
 D9S  C9   C  CR5   0   0.449   -9.0145   1.1419   2.7224
 D9S  C10  C  CR15  0  -0.515   -9.8514   0.1061   2.9640
 D9S  C11  C  CR5   0   0.290   -9.1990  -0.6239   3.9920
 D9S  C12  C  CH2   0  -0.539   -9.6666  -1.8577   4.6822
 D9S  N3   N  NH1   0  -0.696   -9.1791   0.3910   9.6011
 D9S  C13  C  CH1   0  -0.243  -10.9505  -1.6422   5.4897
 D9S  C14  C  CH2   0  -0.298  -11.3670  -2.9499   6.1706
 D9S  C15  C  CH2   0  -0.321  -12.5779  -1.7640   7.8828
 D9S  N4   N  N     0  -0.422   -8.5561   1.0507  11.7465
 D9S  O1   O  O     0  -0.455   -9.7138   1.7846   7.9256
 D9S  C19  C  C     0   0.582   -9.5455   0.6428   8.3135
 D9S  C20  C  CR5   0   0.295   -8.9327   1.3569  10.5468
 D9S  S    S  S2    0   0.225   -9.0997   3.0498  10.2307
 D9S  C22  C  CR15  0  -0.515   -8.6191   3.3515  11.8586
 D9S  C21  C  CR15  0  -0.022   -8.3762   2.1813  12.4936
 D9S  C17  C  CH1   0  -0.249  -10.8875  -0.4784   6.4922
 D9S  C16  C  CH2   0  -0.447  -12.2156  -0.4196   7.2580
 D9S  O    O  O     0  -0.348   -7.9529   1.0475   3.5257
 D9S  N    N  NT    0  -0.412   -9.7046   1.9363   0.5434
 D9S  C    C  CH3   0  -0.530   -8.8160   1.1372  -0.2760
 D9S  C2   C  CR6   0   0.077  -11.3813   3.7339   0.5163
 D9S  C3   C  CR16  0  -0.279  -12.4259   2.9477   1.0002
 D9S  H1   H  HCR6  0   0.253  -14.3320   2.9116   1.9780
 D9S  H2   H  HCR6  0   0.254  -14.4619   5.3722   2.2096
 D9S  H3   H  HCR6  0   0.254  -12.6112   6.7826   1.3638
 D9S  H4   H  HCR6  0   0.249  -10.6495   5.7360   0.2953
 D9S  H5   H  HCH2  0   0.242   -8.0832   2.7420   1.6683
 D9S  H6   H  HCH2  0   0.283   -9.6970   3.0787   2.2774
 D9S  H7   H  HNH1  0   0.339  -13.3707  -2.7196   6.2847
 D9S  H9   H  HCR5  0   0.271  -10.7914  -0.1140   2.4878
 D9S  H10  H  HCH2  0   0.271   -9.8579  -2.6289   3.9309
 D9S  H11  H  HCH2  0   0.254   -8.8641  -2.2433   5.3156
 D9S  H12  H  HNH1  0   0.426   -9.0332  -0.5611   9.9047
 D9S  H13  H  HCH1  0   0.239  -11.7472  -1.3918   4.7770
 D9S  H14  H  HCH2  0   0.240  -11.4804  -3.7308   5.4139
 D9S  H15  H  HCH2  0   0.217  -10.5704  -3.2932   6.8407
 D9S  H16  H  HCH2  0   0.241  -13.5548  -1.7002   8.3660
 D9S  H17  H  HCH2  0   0.216  -11.8636  -2.0161   8.6740
 D9S  H18  H  HCR5  0   0.301   -8.5415   4.3545  12.2461
 D9S  H19  H  HCR5  0   0.271   -8.0588   2.0895  13.5224
 D9S  H20  H  HCH2  0   0.261   -9.6999  -1.4802   8.0364
 D9S  H21  H  HCH2  0   0.297   -8.7566  -0.6135   6.8507
 D9S  H22  H  HCH1  0   0.252  -10.7819   0.4498   5.9225
 D9S  H23  H  HCH2  0   0.234  -12.1905   0.3570   8.0275
 D9S  H24  H  HCH2  0   0.232  -13.0078  -0.1280   6.5608
 D9S  H26  H  HCH3  0   0.242   -8.5355   0.2235   0.2482
 D9S  H27  H  HCH3  0   0.241   -9.3252   0.8460  -1.1947
 D9S  H28  H  HCH3  0   0.203   -7.8910   1.6646  -0.5515
 D9S  H29  H  HCH2  0   0.258  -10.5129   2.7581  -1.1655
 D9S  H30  H  HCH2  0   0.220   -9.4198   3.8548  -0.3386
 D9S  H31  H  HCR6  0   0.246  -12.3662   1.8703   0.9071
 D9S  C1   C  CH2   0  -0.326  -10.2023   3.0966  -0.1729
 D9S  C18  C  CH2   0  -0.602   -9.6819  -0.5706   7.4330

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
 D9S  C4   C3   aromatic  1.387  0.020  1.387
 D9S  C4   C5   aromatic  1.391  0.020  1.391
 D9S  C3   C2   aromatic  1.394  0.020  1.394
 D9S  C5   C6   aromatic  1.387  0.020  1.387
 D9S  C2   C1   single    1.507  0.020  1.507
 D9S  C2   C7   aromatic  1.391  0.020  1.391
 D9S  C1   N    single    1.452  0.020  1.452
 D9S  C6   C7   aromatic  1.390  0.020  1.390
 D9S  N    C    single    1.449  0.020  1.449
 D9S  N    C8   single    1.446  0.020  1.446
 D9S  C8   C9   single    1.489  0.020  1.489
 D9S  C9   C10  aromatic  1.353  0.020  1.353
 D9S  C9   O    aromatic  1.335  0.020  1.335
 D9S  C10  C11  aromatic  1.420  0.020  1.420
 D9S  O    N1   aromatic  1.366  0.020  1.366
 D9S  C11  N1   aromatic  1.303  0.020  1.303
 D9S  C11  C12  single    1.489  0.020  1.489
 D9S  C12  C13  single    1.532  0.020  1.532
 D9S  C13  C14  single    1.532  0.020  1.532
 D9S  C13  C17  single    1.537  0.020  1.537
 D9S  C14  N2   single    1.452  0.020  1.452
 D9S  C17  C18  single    1.532  0.020  1.532
 D9S  C17  C16  single    1.534  0.020  1.534
 D9S  N2   C15  single    1.454  0.020  1.454
 D9S  C18  C19  single    1.505  0.020  1.505
 D9S  C16  C15  single    1.526  0.020  1.526
 D9S  O1   C19  double    1.218  0.020  1.218
 D9S  C19  N3   single    1.362  0.020  1.362
 D9S  N3   C20  single    1.374  0.020  1.374
 D9S  S    C20  aromatic  1.730  0.020  1.730
 D9S  S    C22  aromatic  1.724  0.020  1.724
 D9S  C20  N4   aromatic  1.294  0.020  1.294
 D9S  C22  C21  aromatic  1.353  0.020  1.353
 D9S  N4   C21  aromatic  1.367  0.020  1.367
 D9S  C4   H1   single    0.930  0.020  1.080
 D9S  C5   H2   single    0.930  0.020  1.080
 D9S  C6   H3   single    0.930  0.020  1.080
 D9S  C7   H4   single    0.930  0.020  1.080
 D9S  C8   H5   single    0.970  0.020  1.090
 D9S  C8   H6   single    0.970  0.020  1.090
 D9S  N2   H7   single    0.890  0.020  1.040
 D9S  C10  H9   single    0.930  0.020  1.080
 D9S  C12  H10  single    0.970  0.020  1.090
 D9S  C12  H11  single    0.970  0.020  1.090
 D9S  N3   H12  single    0.860  0.020  1.020
 D9S  C13  H13  single    0.970  0.020  1.090
 D9S  C14  H14  single    0.970  0.020  1.090
 D9S  C14  H15  single    0.970  0.020  1.090
 D9S  C15  H16  single    0.970  0.020  1.090
 D9S  C15  H17  single    0.970  0.020  1.090
 D9S  C22  H18  single    0.930  0.020  1.080
 D9S  C21  H19  single    0.930  0.020  1.080
 D9S  C18  H20  single    0.970  0.020  1.090
 D9S  C18  H21  single    0.970  0.020  1.090
 D9S  C17  H22  single    0.970  0.020  1.090
 D9S  C16  H23  single    0.970  0.020  1.090
 D9S  C16  H24  single    0.970  0.020  1.090
 D9S  C    H26  single    0.970  0.020  1.090
 D9S  C    H27  single    0.970  0.020  1.090
 D9S  C    H28  single    0.970  0.020  1.090
 D9S  C1   H29  single    0.970  0.020  1.090
 D9S  C1   H30  single    0.970  0.020  1.090
 D9S  C3   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
 D9S  H1   C4   C3   119.85  3.000
 D9S  H1   C4   C5   119.93  3.000
 D9S  C3   C4   C5   120.22  3.000
 D9S  H2   C5   C6   120.22  3.000
 D9S  H2   C5   C4   120.18  3.000
 D9S  C6   C5   C4   119.59  3.000
 D9S  H3   C6   C7   119.84  3.000
 D9S  H3   C6   C5   120.14  3.000
 D9S  C7   C6   C5   120.02  3.000
 D9S  O    N1   C11  106.31  3.000
 D9S  H4   C7   C2   119.47  3.000
 D9S  H4   C7   C6   119.75  3.000
 D9S  C2   C7   C6   120.78  3.000
 D9S  H6   C8   H5   106.32  3.000
 D9S  H6   C8   N    108.86  3.000
 D9S  H5   C8   N    112.83  3.000
 D9S  H6   C8   C9   107.88  3.000
 D9S  H5   C8   C9   109.70  3.000
 D9S  N    C8   C9   111.02  3.000
 D9S  H7   N2   C15  108.85  3.000
 D9S  H7   N2   C14  108.74  3.000
 D9S  C15  N2   C14  112.00  3.000
 D9S  O    C9   C10  109.28  3.000
 D9S  O    C9   C8   117.90  3.000
 D9S  C10  C9   C8   132.80  3.000
 D9S  H9   C10  C11  128.06  3.000
 D9S  H9   C10  C9   128.13  3.000
 D9S  C11  C10  C9   103.81  3.000
 D9S  C12  C11  C10  128.13  3.000
 D9S  C12  C11  N1   121.00  3.000
 D9S  C10  C11  N1   110.86  3.000
 D9S  H11  C12  H10  106.13  3.000
 D9S  H11  C12  C13  111.08  3.000
 D9S  H10  C12  C13  108.34  3.000
 D9S  H11  C12  C11  109.30  3.000
 D9S  H10  C12  C11  108.71  3.000
 D9S  C13  C12  C11  113.01  3.000
 D9S  H12  N3   C20  115.46  3.000
 D9S  H12  N3   C19  119.82  3.000
 D9S  C20  N3   C19  124.67  3.000
 D9S  H13  C13  C17  106.28  3.000
 D9S  H13  C13  C14  106.61  3.000
 D9S  C17  C13  C14  111.56  3.000
 D9S  H13  C13  C12  107.34  3.000
 D9S  C17  C13  C12  114.57  3.000
 D9S  C14  C13  C12  110.01  3.000
 D9S  H15  C14  H14  105.94  3.000
 D9S  H15  C14  C13  109.97  3.000
 D9S  H14  C14  C13  109.28  3.000
 D9S  H15  C14  N2   108.51  3.000
 D9S  H14  C14  N2   108.47  3.000
 D9S  C13  C14  N2   114.32  3.000
 D9S  H17  C15  H16  106.09  3.000
 D9S  H17  C15  C16  110.10  3.000
 D9S  H16  C15  C16  110.01  3.000
 D9S  H17  C15  N2   108.08  3.000
 D9S  H16  C15  N2   108.65  3.000
 D9S  C16  C15  N2   113.62  3.000
 D9S  C21  N4   C20  110.44  3.000
 D9S  C18  C19  O1   123.85  3.000
 D9S  O1   C19  N3   120.78  3.000
 D9S  C18  C19  N3   115.36  3.000
 D9S  S    C20  N4   115.40  3.000
 D9S  N4   C20  N3   121.60  3.000
 D9S  S    C20  N3   123.00  3.000
 D9S  C22  S    C20   88.38  3.000
 D9S  H18  C22  C21  128.53  3.000
 D9S  H18  C22  S    121.48  3.000
 D9S  C21  C22  S    109.99  3.000
 D9S  H19  C21  C22  124.96  3.000
 D9S  H19  C21  N4   119.25  3.000
 D9S  C22  C21  N4   115.79  3.000
 D9S  H22  C17  C16  108.12  3.000
 D9S  H22  C17  C18  107.15  3.000
 D9S  C16  C17  C18  112.15  3.000
 D9S  H22  C17  C13  107.85  3.000
 D9S  C16  C17  C13  108.61  3.000
 D9S  C18  C17  C13  112.77  3.000
 D9S  H24  C16  H23  105.99  3.000
 D9S  H24  C16  C17  108.59  3.000
 D9S  H23  C16  C17  111.02  3.000
 D9S  H24  C16  C15  108.88  3.000
 D9S  H23  C16  C15  110.06  3.000
 D9S  C17  C16  C15  112.09  3.000
 D9S  C9   O    N1   109.74  3.000
 D9S  C1   N    C    111.84  3.000
 D9S  C    N    C8   111.73  3.000
 D9S  C1   N    C8   111.67  3.000
 D9S  H28  C    H27  108.05  3.000
 D9S  H28  C    H26  107.81  3.000
 D9S  H27  C    H26  107.55  3.000
 D9S  H28  C    N    113.15  3.000
 D9S  H27  C    N    109.73  3.000
 D9S  H26  C    N    110.37  3.000
 D9S  C3   C2   C1   120.43  3.000
 D9S  C1   C2   C7   120.75  3.000
 D9S  C3   C2   C7   118.80  3.000
 D9S  H31  C3   C2   119.33  3.000
 D9S  H31  C3   C4   120.10  3.000
 D9S  C2   C3   C4   120.58  3.000
 D9S  H30  C1   H29  106.15  3.000
 D9S  H30  C1   C2   109.47  3.000
 D9S  H29  C1   C2   108.89  3.000
 D9S  H30  C1   N    112.37  3.000
 D9S  H29  C1   N    107.33  3.000
 D9S  C2   C1   N    112.37  3.000
 D9S  H21  C18  H20  105.99  3.000
 D9S  H21  C18  C17  109.94  3.000
 D9S  H20  C18  C17  112.12  3.000
 D9S  H21  C18  C19  105.44  3.000
 D9S  H20  C18  C19  110.48  3.000
 D9S  C17  C18  C19  112.46  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
 D9S  CONST_01  C7   C2   C3   C4     0.00   0.0  0
 D9S  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 D9S  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 D9S  CONST_04  C2   C7   C6   C5     0.00   0.0  0
 D9S  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 D9S  CONST_06  C3   C2   C7   C6     0.00   0.0  0
 D9S  CONST_07  C10  C9   O    N1     0.00   0.0  0
 D9S  CONST_08  C9   C10  C11  N1     0.00   0.0  0
 D9S  CONST_09  C11  N1   O    C9     0.00   0.0  0
 D9S  CONST_10  O    N1   C11  C10    0.00   0.0  0
 D9S  CONST_11  O    C9   C10  C11    0.00   0.0  0
 D9S  CONST_12  C22  S    C20  N4     0.00   0.0  0
 D9S  CONST_13  S    C22  C21  N4     0.00   0.0  0
 D9S  CONST_14  C21  C22  S    C20    0.00   0.0  0
 D9S  CONST_15  C22  C21  N4   C20    0.00   0.0  0
 D9S  CONST_16  C21  N4   C20  S      0.00   0.0  0
 D9S  CONST_17  C1   C2   C3   C4   180.00   0.0  0
 D9S  CONST_18  C1   C2   C7   C6   180.00   0.0  0
 D9S  CONST_19  C8   C9   O    N1   180.00   0.0  0
 D9S  CONST_20  C11  C10  C9   C8   180.00   0.0  0
 D9S  CONST_21  C12  C11  C10  C9   180.00   0.0  0
 D9S  CONST_22  O    N1   C11  C12  180.00   0.0  0
 D9S  CONST_23  C22  S    C20  N3   180.00   0.0  0
 D9S  CONST_24  C21  N4   C20  N3   180.00   0.0  0
 D9S  CONST_25  H3   C6   C5   C4   180.00   0.0  0
 D9S  CONST_26  H31  C3   C4   C5   180.00   0.0  0
 D9S  CONST_27  H4   C7   C6   C5   180.00   0.0  0
 D9S  CONST_28  H1   C4   C5   C6   180.00   0.0  0
 D9S  CONST_29  H9   C10  C11  N1   180.00   0.0  0
 D9S  CONST_30  H2   C5   C6   C7   180.00   0.0  0
 D9S  CONST_31  H18  C22  C21  N4   180.00   0.0  0
 D9S  CONST_32  H19  C21  N4   C20  180.00   0.0  0
 D9S  CONST_33  C19  N3   C20  N4   180.00   0.0  0
 D9S  CONST_34  S    C20  N3   C19    0.00   0.0  0
 D9S  CONST_35  H12  N3   C20  N4     0.00   0.0  0
 D9S  CONST_36  C20  N3   C19  O1     0.00   0.0  0
 D9S  CONST_37  C18  C19  N3   C20  180.00   0.0  0
 D9S  Var_01    C17  C16  C15  N2   -54.52  30.0  1
 D9S  Var_02    C15  N2   C14  C13  -52.72  30.0  1
 D9S  Var_03    C16  C15  N2   C14   52.89  30.0  1
 D9S  Var_04    C13  C12  C11  N1   114.65  30.0  2
 D9S  Var_05    N    C1   C2   C7   135.71  30.0  2
 D9S  Var_06    N    C8   C9   C10  -36.74  30.0  1
 D9S  Var_07    C2   C1   N    C8   -68.73  30.0  1
 D9S  Var_08    C1   N    C8   C9   160.18  30.0  1
 D9S  Var_09    C17  C18  C19  N3   139.99  30.0  1
 D9S  Var_10    H26  C    N    C8    59.59  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
 D9S  chir_01  C13  C12  C14  C17  negativ
 D9S  chir_02  C17  C16  C18  C13  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
 D9S  plan-1  N1   0.020
 D9S  plan-1  C8   0.020
 D9S  plan-1  C9   0.020
 D9S  plan-1  C10  0.020
 D9S  plan-1  C11  0.020
 D9S  plan-1  C12  0.020
 D9S  plan-1  O    0.020
 D9S  plan-1  H9   0.020
 D9S  plan-2  N3   0.020
 D9S  plan-2  N4   0.020
 D9S  plan-2  C20  0.020
 D9S  plan-2  S    0.020
 D9S  plan-2  C22  0.020
 D9S  plan-2  C21  0.020
 D9S  plan-2  H18  0.020
 D9S  plan-2  H19  0.020
 D9S  plan-3  C4   0.020
 D9S  plan-3  C5   0.020
 D9S  plan-3  C6   0.020
 D9S  plan-3  C7   0.020
 D9S  plan-3  C2   0.020
 D9S  plan-3  C3   0.020
 D9S  plan-3  H1   0.020
 D9S  plan-3  H2   0.020
 D9S  plan-3  H3   0.020
 D9S  plan-3  H4   0.020
 D9S  plan-3  H31  0.020
 D9S  plan-3  C1   0.020
 D9S  plan-4  N3   0.020
 D9S  plan-4  O1   0.020
 D9S  plan-4  C19  0.020
 D9S  plan-4  C20  0.020
 D9S  plan-4  H12  0.020
 D9S  plan-4  C18  0.020

