# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 01:27:09 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: (1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyladamantane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@]12C[C@@H]3C[C@](C1)(C[C@@](C3)(C2)c4ccccc4)C(=O)N[C@H]5CC[C@H](N)CC5
#
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
 YOD  YOD  "(1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyladamantane-1-carboxamide"
  ligand  65  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YOD
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
 YOD  C21  C  CH1   0  -0.051  -42.7236  18.0655   -7.7360
 YOD  C22  C  CH2   0  -0.434  -43.5906  18.9895   -6.8799
 YOD  C23  C  CH2   0  -0.438  -43.1252  20.4369   -6.9790
 YOD  C24  C  CH1   0  -0.050  -41.6594  20.5789   -6.5867
 YOD  C26  C  CH2   0  -0.437  -40.8042  19.6708   -7.4629
 YOD  C27  C  CH2   0  -0.451  -41.2502  18.2162   -7.3695
 YOD  C11  C  CR6   0   0.222  -46.9237  12.1202   -9.4431
 YOD  C13  C  CR16  0  -0.240  -47.3347  11.3913  -11.7243
 YOD  C14  C  CR16  0  -0.275  -48.6480  11.0662  -11.4069
 YOD  C29  C  CH2   0  -0.382  -45.1889  14.7868   -6.4825
 YOD  C15  C  CR16  0  -0.233  -49.0971  11.2689  -10.1120
 YOD  C12  C  CR16  0  -0.321  -46.4895  11.9102  -10.7557
 YOD  C03  C  CH2   0  -0.562  -46.3245  13.5854   -4.6504
 YOD  C04  C  CT    0  -0.076  -45.6348  13.4001   -6.0020
 YOD  C05  C  CH2   0  -0.397  -44.4057  12.4954   -5.9065
 YOD  C06  C  CR16  0  -0.246  -43.7433  12.3770   -7.2767
 YOD  C07  C  C     0  -0.407  -43.2945  13.7567   -7.7548
 YOD  C08  C  CH2   0  -0.399  -46.6116  12.8199   -7.0259
 YOD  C09  C  CR6   0  -0.183  -45.9650  12.6907   -8.4093
 YOD  C16  C  CR16  0  -0.349  -48.2441  11.7895   -9.1444
 YOD  C17  C  C     0  -0.371  -45.5067  14.0905   -8.8568
 YOD  C18  C  CR6   0  -0.278  -44.5099  14.6919   -7.8603
 YOD  N20  N  NH1   0  -0.650  -43.1283  16.6801   -7.5943
 YOD  N25  N  NH2   0  -0.804  -41.2352  21.9629   -6.7425
 YOD  O28  O  O     0  -0.485  -44.6480  16.6626   -9.2548
 YOD  S02  S  S2    0  -0.040  -46.9368  12.0779   -3.8362
 YOD  H1   H  HCH1  0   0.235  -42.8474  18.3428   -8.7861
 YOD  H2   H  HCH2  0   0.237  -44.6353  18.9034   -7.1874
 YOD  H3   H  HCH2  0   0.214  -43.5381  18.6531   -5.8385
 YOD  H4   H  HCH2  0   0.230  -43.7481  21.0726   -6.3430
 YOD  H5   H  HCH2  0   0.213  -43.2499  20.7996   -8.0055
 YOD  H6   H  HCH1  0   0.186  -41.5591  20.2236   -5.5465
 YOD  H7   H  HCH2  0   0.232  -39.7522  19.7537   -7.1749
 YOD  H8   H  HCH2  0   0.214  -40.8761  20.0161   -8.5000
 YOD  H9   H  HCH2  0   0.241  -40.6403  17.5896   -8.0242
 YOD  H10  H  HCH2  0   0.218  -41.0935  17.8526   -6.3468
 YOD  H11  H  HCR6  0   0.249  -46.9658  11.2402  -12.7310
 YOD  H12  H  HCR6  0   0.249  -49.3100  10.6601  -12.1609
 YOD  H13  H  HCH2  0   0.235  -44.5100  15.2233   -5.7421
 YOD  H14  H  HCH2  0   0.238  -46.0575  15.4521   -6.5464
 YOD  H15  H  HCR6  0   0.249  -50.1171  11.0216   -9.8456
 YOD  H18  H  HCR6  0   0.245  -45.4713  12.1539  -11.0353
 YOD  H19  H  HCH3  0   0.270  -45.8929  10.8450   -2.1008
 YOD  H20  H  HCH3  0   0.261  -44.6777  11.3485   -3.2810
 YOD  H21  H  HCH3  0   0.260  -45.3096  12.5138   -2.0981
 YOD  H22  H  HCH2  0   0.271  -45.6579  14.0923   -3.9470
 YOD  H23  H  HCH2  0   0.270  -47.1977  14.2309   -4.7785
 YOD  H24  H  HCH2  0   0.230  -44.7005  11.5026   -5.5539
 YOD  H25  H  HCH2  0   0.224  -43.6987  12.9026   -5.1755
 YOD  H26  H  HCR6  0   0.233  -42.8680  11.7254   -7.2045
 YOD  H27  H  H     0   0.238  -42.8018  13.6787   -8.7291
 YOD  H28  H  H     0   0.232  -42.5513  14.1504   -7.0554
 YOD  H29  H  HCH2  0   0.229  -47.4928  13.4698   -7.0784
 YOD  H30  H  HCH2  0   0.234  -46.9567  11.8411   -6.6772
 YOD  H31  H  HCR6  0   0.250  -48.6316  11.9327   -8.1452
 YOD  H32  H  H     0   0.235  -45.0437  14.0344   -9.8453
 YOD  H33  H  H     0   0.234  -46.3808  14.7398   -8.9514
 YOD  H34  H  HNH1  0   0.392  -42.7817  16.1976   -6.7798
 YOD  H35  H  HNH2  0   0.339  -41.7759  22.5519   -6.1201
 YOD  H36  H  HNH2  0   0.339  -40.2736  22.0574   -6.4372
 YOD  C19  C  C     0   0.610  -44.1077  16.0986   -8.3126
 YOD  C10  C  C     0  -0.397  -44.7314  11.7805   -8.2754
 YOD  H16  H  H     0   0.230  -45.0461  10.7840   -7.9496
 YOD  C01  C  CH3   0  -0.766  -45.5626  11.6667   -2.7342
 YOD  H17  H  H     0   0.233  -44.2410  11.6578   -9.2449

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
 YOD  C13  C14  aromatic  1.390  0.020  1.390
 YOD  C13  C12  aromatic  1.386  0.020  1.386
 YOD  C14  C15  aromatic  1.386  0.020  1.386
 YOD  C12  C11  aromatic  1.398  0.020  1.398
 YOD  C15  C16  aromatic  1.391  0.020  1.391
 YOD  C11  C16  aromatic  1.394  0.020  1.394
 YOD  C11  C09  single    1.521  0.020  1.521
 YOD  O28  C19  double    1.224  0.020  1.224
 YOD  C17  C09  single    1.539  0.020  1.539
 YOD  C17  C18  single    1.532  0.020  1.532
 YOD  C09  C10  single    1.539  0.020  1.539
 YOD  C09  C08  single    1.533  0.020  1.533
 YOD  C10  C06  single    1.526  0.020  1.526
 YOD  C26  C27  single    1.524  0.020  1.524
 YOD  C26  C24  single    1.524  0.020  1.524
 YOD  C19  C18  single    1.531  0.020  1.531
 YOD  C19  N20  single    1.347  0.020  1.347
 YOD  C27  C21  single    1.526  0.020  1.526
 YOD  C21  N20  single    1.450  0.020  1.450
 YOD  C21  C22  single    1.529  0.020  1.529
 YOD  C18  C07  single    1.537  0.020  1.537
 YOD  C18  C29  single    1.539  0.020  1.539
 YOD  C07  C06  single    1.528  0.020  1.528
 YOD  N25  C24  single    1.456  0.020  1.456
 YOD  C06  C05  single    1.526  0.020  1.526
 YOD  C08  C04  single    1.529  0.020  1.529
 YOD  C24  C23  single    1.524  0.020  1.524
 YOD  C23  C22  single    1.524  0.020  1.524
 YOD  C29  C04  single    1.534  0.020  1.534
 YOD  C04  C05  single    1.529  0.020  1.529
 YOD  C04  C03  single    1.529  0.020  1.529
 YOD  C03  S02  single    1.819  0.020  1.819
 YOD  S02  C01  single    1.809  0.020  1.809
 YOD  C21  H1   single    0.970  0.020  1.090
 YOD  C22  H2   single    0.970  0.020  1.090
 YOD  C22  H3   single    0.970  0.020  1.090
 YOD  C23  H4   single    0.970  0.020  1.090
 YOD  C23  H5   single    0.970  0.020  1.090
 YOD  C24  H6   single    0.970  0.020  1.090
 YOD  C26  H7   single    0.970  0.020  1.090
 YOD  C26  H8   single    0.970  0.020  1.090
 YOD  C27  H9   single    0.970  0.020  1.090
 YOD  C27  H10  single    0.970  0.020  1.090
 YOD  C13  H11  single    0.930  0.020  1.080
 YOD  C14  H12  single    0.930  0.020  1.080
 YOD  C29  H13  single    0.970  0.020  1.090
 YOD  C29  H14  single    0.970  0.020  1.090
 YOD  C15  H15  single    0.930  0.020  1.080
 YOD  C10  H16  single    0.970  0.020  1.090
 YOD  C10  H17  single    0.970  0.020  1.090
 YOD  C12  H18  single    0.930  0.020  1.080
 YOD  C01  H19  single    0.970  0.020  1.090
 YOD  C01  H20  single    0.970  0.020  1.090
 YOD  C01  H21  single    0.970  0.020  1.090
 YOD  C03  H22  single    0.970  0.020  1.090
 YOD  C03  H23  single    0.970  0.020  1.090
 YOD  C05  H24  single    0.970  0.020  1.090
 YOD  C05  H25  single    0.970  0.020  1.090
 YOD  C06  H26  single    0.970  0.020  1.090
 YOD  C07  H27  single    0.970  0.020  1.090
 YOD  C07  H28  single    0.970  0.020  1.090
 YOD  C08  H29  single    0.970  0.020  1.090
 YOD  C08  H30  single    0.970  0.020  1.090
 YOD  C16  H31  single    0.930  0.020  1.080
 YOD  C17  H32  single    0.970  0.020  1.090
 YOD  C17  H33  single    0.970  0.020  1.090
 YOD  N20  H34  single    0.860  0.020  1.020
 YOD  N25  H35  single    0.890  0.020  1.040
 YOD  N25  H36  single    0.890  0.020  1.040

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
 YOD  H1   C21  N20  107.73  3.000
 YOD  H1   C21  C27  108.36  3.000
 YOD  N20  C21  C27  109.90  3.000
 YOD  H1   C21  C22  108.69  3.000
 YOD  N20  C21  C22  111.37  3.000
 YOD  C27  C21  C22  110.69  3.000
 YOD  H3   C22  H2   106.81  3.000
 YOD  H3   C22  C23  109.81  3.000
 YOD  H2   C22  C23  110.41  3.000
 YOD  H3   C22  C21  108.63  3.000
 YOD  H2   C22  C21  109.69  3.000
 YOD  C23  C22  C21  111.37  3.000
 YOD  H5   C23  H4   106.71  3.000
 YOD  H5   C23  C24  108.65  3.000
 YOD  H4   C23  C24  110.11  3.000
 YOD  H5   C23  C22  109.91  3.000
 YOD  H4   C23  C22  109.90  3.000
 YOD  C24  C23  C22  111.44  3.000
 YOD  H6   C24  N25  112.35  3.000
 YOD  H6   C24  C26  107.40  3.000
 YOD  N25  C24  C26  109.96  3.000
 YOD  H6   C24  C23  107.46  3.000
 YOD  N25  C24  C23  109.95  3.000
 YOD  C26  C24  C23  109.65  3.000
 YOD  H8   C26  H7   106.77  3.000
 YOD  H8   C26  C27  109.85  3.000
 YOD  H7   C26  C27  109.73  3.000
 YOD  H8   C26  C24  108.64  3.000
 YOD  H7   C26  C24  110.07  3.000
 YOD  C27  C26  C24  111.66  3.000
 YOD  H10  C27  H9   106.80  3.000
 YOD  H10  C27  C26  109.37  3.000
 YOD  H9   C27  C26  110.32  3.000
 YOD  H10  C27  C21  109.22  3.000
 YOD  H9   C27  C21  109.79  3.000
 YOD  C26  C27  C21  111.23  3.000
 YOD  C16  C11  C09  122.72  3.000
 YOD  C09  C11  C12  119.91  3.000
 YOD  C16  C11  C12  117.37  3.000
 YOD  H11  C13  C12  119.61  3.000
 YOD  H11  C13  C14  120.11  3.000
 YOD  C12  C13  C14  120.28  3.000
 YOD  H12  C14  C15  120.51  3.000
 YOD  H12  C14  C13  120.44  3.000
 YOD  C15  C14  C13  119.05  3.000
 YOD  H14  C29  H13  106.78  3.000
 YOD  H14  C29  C18  109.57  3.000
 YOD  H13  C29  C18  110.87  3.000
 YOD  H14  C29  C04  109.68  3.000
 YOD  H13  C29  C04  109.19  3.000
 YOD  C18  C29  C04  110.67  3.000
 YOD  H15  C15  C16  119.47  3.000
 YOD  H15  C15  C14  120.12  3.000
 YOD  C16  C15  C14  120.41  3.000
 YOD  H18  C12  C13  118.47  3.000
 YOD  H18  C12  C11  120.01  3.000
 YOD  C13  C12  C11  121.52  3.000
 YOD  H23  C03  H22  106.77  3.000
 YOD  H23  C03  S02  105.83  3.000
 YOD  H22  C03  S02  107.54  3.000
 YOD  H23  C03  C04  109.16  3.000
 YOD  H22  C03  C04  110.48  3.000
 YOD  S02  C03  C04  116.56  3.000
 YOD  C08  C04  C05  109.31  3.000
 YOD  C05  C04  C03  112.28  3.000
 YOD  C08  C04  C03  110.47  3.000
 YOD  C03  C04  C29  107.38  3.000
 YOD  C05  C04  C29  108.71  3.000
 YOD  C08  C04  C29  108.60  3.000
 YOD  H25  C05  H24  107.23  3.000
 YOD  H25  C05  C06  110.35  3.000
 YOD  H24  C05  C06  109.63  3.000
 YOD  H25  C05  C04  109.91  3.000
 YOD  H24  C05  C04  109.90  3.000
 YOD  C06  C05  C04  109.79  3.000
 YOD  H26  C06  C07  108.88  3.000
 YOD  H26  C06  C05  109.53  3.000
 YOD  C07  C06  C05  109.78  3.000
 YOD  H26  C06  C10  109.17  3.000
 YOD  C05  C06  C10  109.68  3.000
 YOD  C07  C06  C10  109.78  3.000
 YOD  H28  C07  H27  106.79  3.000
 YOD  H28  C07  C18  111.24  3.000
 YOD  H27  C07  C18  109.77  3.000
 YOD  H28  C07  C06  108.94  3.000
 YOD  H27  C07  C06  110.27  3.000
 YOD  C18  C07  C06  109.80  3.000
 YOD  H30  C08  H29  106.98  3.000
 YOD  H30  C08  C09  110.19  3.000
 YOD  H29  C08  C09  110.24  3.000
 YOD  H30  C08  C04  109.10  3.000
 YOD  H29  C08  C04  108.70  3.000
 YOD  C09  C08  C04  111.52  3.000
 YOD  C17  C09  C08  108.14  3.000
 YOD  C08  C09  C10  108.03  3.000
 YOD  C17  C09  C10  108.94  3.000
 YOD  C08  C09  C11  112.28  3.000
 YOD  C10  C09  C11  110.03  3.000
 YOD  C17  C09  C11  109.34  3.000
 YOD  H31  C16  C15  118.21  3.000
 YOD  H31  C16  C11  120.41  3.000
 YOD  C15  C16  C11  121.38  3.000
 YOD  H33  C17  H32  106.91  3.000
 YOD  H33  C17  C18  110.08  3.000
 YOD  H32  C17  C18  109.43  3.000
 YOD  H33  C17  C09  109.11  3.000
 YOD  H32  C17  C09  110.02  3.000
 YOD  C18  C17  C09  111.20  3.000
 YOD  C19  C18  C17  109.84  3.000
 YOD  C19  C18  C07  111.80  3.000
 YOD  C17  C18  C07  108.67  3.000
 YOD  C07  C18  C29  108.96  3.000
 YOD  C19  C18  C29  108.89  3.000
 YOD  C17  C18  C29  108.62  3.000
 YOD  H34  N20  C19  118.32  3.000
 YOD  H34  N20  C21  116.12  3.000
 YOD  C19  N20  C21  124.29  3.000
 YOD  H36  N25  H35  105.49  3.000
 YOD  H36  N25  C24  109.45  3.000
 YOD  H35  N25  C24  109.36  3.000
 YOD  C03  S02  C01  101.85  3.000
 YOD  O28  C19  N20  122.19  3.000
 YOD  N20  C19  C18  115.48  3.000
 YOD  O28  C19  C18  122.33  3.000
 YOD  H17  C10  H16  106.90  3.000
 YOD  H17  C10  C09  110.41  3.000
 YOD  H16  C10  C09  109.51  3.000
 YOD  H17  C10  C06  109.49  3.000
 YOD  H16  C10  C06  110.32  3.000
 YOD  C09  C10  C06  110.16  3.000
 YOD  H21  C01  H20  109.40  3.000
 YOD  H21  C01  H19  108.52  3.000
 YOD  H20  C01  H19  108.57  3.000
 YOD  H21  C01  S02  110.82  3.000
 YOD  H20  C01  S02  112.23  3.000
 YOD  H19  C01  S02  107.19  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
 YOD  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 YOD  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 YOD  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 YOD  CONST_04  C16  C11  C12  C13     0.00   0.0  0
 YOD  CONST_05  C12  C13  C14  C15     0.00   0.0  0
 YOD  CONST_06  C12  C11  C16  C15     0.00   0.0  0
 YOD  CONST_07  C09  C11  C12  C13   180.00   0.0  0
 YOD  CONST_08  C09  C11  C16  C15   180.00   0.0  0
 YOD  CONST_09  H11  C13  C12  C11   180.00   0.0  0
 YOD  CONST_10  H15  C15  C16  C11   180.00   0.0  0
 YOD  CONST_11  H15  C15  C14  C13   180.00   0.0  0
 YOD  CONST_12  H18  C12  C13  C14   180.00   0.0  0
 YOD  CONST_13  H31  C16  C15  C14   180.00   0.0  0
 YOD  CONST_14  H11  C13  C14  C15   180.00   0.0  0
 YOD  CONST_15  H12  C14  C13  C12   180.00   0.0  0
 YOD  CONST_16  H31  C16  C11  C12   180.00   0.0  0
 YOD  CONST_17  H18  C12  C11  C09     0.00   0.0  0
 YOD  CONST_18  H31  C16  C11  C09     0.00   0.0  0
 YOD  CONST_19  H12  C14  C15  C16   180.00   0.0  0
 YOD  CONST_20  H18  C12  C11  C16   180.00   0.0  0
 YOD  CONST_21  C18  C19  N20  C21   180.00   0.0  0
 YOD  CONST_22  O28  C19  N20  C21     0.00   0.0  0
 YOD  CONST_23  H34  N20  C19  C18     0.00   0.0  0
 YOD  CONST_24  H34  N20  C19  O28   180.00   0.0  0
 YOD  Var_01    C24  C26  C27  C21    56.47  30.0  1
 YOD  Var_02    C24  C23  C22  C21   -56.52  30.0  1
 YOD  Var_03    H7   C26  C27  C21   178.79  30.0  1
 YOD  Var_04    H8   C26  C27  C21   -64.12  30.0  1
 YOD  Var_05    H4   C23  C22  C21  -178.87  30.0  1
 YOD  Var_06    H5   C23  C22  C21    63.98  30.0  1
 YOD  Var_07    H9   C27  C26  C24   178.55  30.0  1
 YOD  Var_08    H10  C27  C26  C24   -64.26  30.0  1
 YOD  Var_09    H2   C22  C23  C24  -178.64  30.0  1
 YOD  Var_10    H3   C22  C23  C24    63.85  30.0  1
 YOD  Var_11    C04  C03  S02  C01    95.02  30.0  1
 YOD  Var_12    H22  C03  S02  C01   -29.60  30.0  1
 YOD  Var_13    H23  C03  S02  C01  -143.44  30.0  1
 YOD  Var_14    H19  C01  S02  C03   172.52  30.0  3
 YOD  Var_15    H20  C01  S02  C03   -68.37  30.0  3
 YOD  Var_16    H21  C01  S02  C03    54.27  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
 YOD  chir_01  C21  C27  N20  C22  negativ
 YOD  chir_02  C24  N25  C23  C26  negativ
 YOD  chir_03  C04  C29  C08  C03  positiv
 YOD  chir_04  C06  C05  C07  C10  positiv
 YOD  chir_05  C09  C17  C11  C08  positiv
 YOD  chir_06  C18  C17  C07  C29  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
 YOD  plan-1  C11  0.020
 YOD  plan-1  C13  0.020
 YOD  plan-1  C14  0.020
 YOD  plan-1  C15  0.020
 YOD  plan-1  C12  0.020
 YOD  plan-1  C09  0.020
 YOD  plan-1  C16  0.020
 YOD  plan-1  H11  0.020
 YOD  plan-1  H12  0.020
 YOD  plan-1  H15  0.020
 YOD  plan-1  H18  0.020
 YOD  plan-1  H31  0.020
 YOD  plan-2  C21  0.020
 YOD  plan-2  C18  0.020
 YOD  plan-2  N20  0.020
 YOD  plan-2  O28  0.020
 YOD  plan-2  H34  0.020
 YOD  plan-2  C19  0.020

