# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:38:22 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 3-{(2R,5R)-5-cyclohexyl-2-[(2R)-2-hydroxypropyl]-3-oxomorpholin-4-yl}-5-(3,3-dimethylbut-1-yn-1-yl)thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)C[C@H]1OC[C@@H](C2CCCCC2)N(C1=O)c3cc(sc3C(O)=O)C#CC(C)(C)C
#
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
 33H  33H  '3-{(2R,5R)-5-cyclohexyl-2-[(2R)-2-hydroxypropyl]-3-oxomorpholin-4-yl}-5-(3,3-dimethylbut-1-yn-1-yl)thiophene-2-carboxylic acid'  ligand  64  31  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_33H
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
 33H  C1   C  CR5   0   0.460   0.3692  -0.8641  -0.2805
 33H  C2   C  CR6   0   0.508  -1.6458  -0.9878   0.9359
 33H  C3   C  CR16  0  -0.058  -3.1540  -0.7693   1.0236
 33H  O1   O  O     0  -0.470  -3.6877  -0.0782  -0.0732
 33H  O2   O  O     0  -0.480  -1.0403  -1.4820   1.8729
 33H  O3   O  O     0  -0.419  -0.9166  -3.2840  -1.4825
 33H  C11  C  CH2   0  -0.425  -1.8180   2.3043  -0.6261
 33H  C12  C  CH2   0  -0.495  -3.5047  -0.0164   2.3025
 33H  C13  C  CR15  0  -0.225   1.3138   0.0487   0.2304
 33H  C14  C  CR5   0  -0.475   2.6066  -0.3685   0.0364
 33H  C15  C  CR5   0  -0.393   0.9506  -1.9702  -0.8546
 33H  C16  C  C     0   0.531   0.2798  -3.1403  -1.4245
 33H  C17  C  CSP   0   0.140   3.7999   0.2748   0.4175
 33H  C18  C  CSP   0   0.284   4.8348   0.7989   0.7492
 33H  C19  C  CT    0  -0.311   6.0993   1.4152   1.1533
 33H  C20  C  CH3   0  -0.633   7.1955   0.3418   1.1321
 33H  C21  C  CH3   0  -0.635   6.4507   2.5419   0.1732
 33H  C22  C  CH3   0  -0.634   5.9501   1.9794   2.5720
 33H  C23  C  CH1   0   0.029  -4.9495  -0.1832   2.7676
 33H  C24  C  CH3   0  -0.680  -5.1878   0.6125   4.0446
 33H  N1   N  NR6   0  -0.590  -1.0205  -0.6442  -0.2132
 33H  C4   C  C     0  -0.233  -3.1633  -0.5205  -1.2984
 33H  C5   C  CR16  0  -0.096  -1.6966  -0.1600  -1.4220
 33H  C6   C  CH1   0  -0.230  -1.3654   1.3134  -1.6974
 33H  C7   C  CH2   0  -0.428  -1.8732   1.7467  -3.0727
 33H  C8   C  CH2   0  -0.429  -1.4084   3.1596  -3.4144
 33H  C9   C  CH2   0  -0.430  -1.8218   4.1557  -2.3363
 33H  C10  C  CH2   0  -0.429  -1.3355   3.7139  -0.9603
 33H  S1   S  S2    0   0.307   2.6630  -1.8844  -0.7774
 33H  O4   O  OH1   0  -0.600   1.1605  -4.0303  -1.8637
 33H  O5   O  OH1   0  -0.663  -5.9002   0.1391   1.7737
 33H  H1   H  HCR6  0   0.258  -3.5788  -1.7868   1.0777
 33H  H2   H  HCH2  0   0.223  -2.9082   2.3078  -0.5512
 33H  H3   H  HCH2  0   0.221  -1.4417   2.0065   0.3566
 33H  H4   H  HCH2  0   0.258  -2.8611  -0.3731   3.1072
 33H  H5   H  HCH2  0   0.242  -3.2694   1.0453   2.1620
 33H  H6   H  HCR5  0   0.282   1.0500   0.9742   0.7213
 33H  H7   H  HCH3  0   0.237   7.3131  -0.0850   0.1357
 33H  H8   H  HCH3  0   0.238   8.1488   0.7833   1.4263
 33H  H9   H  HCH3  0   0.237   6.9683  -0.4672   1.8266
 33H  H10  H  HCH3  0   0.238   5.6819   3.3148   0.1632
 33H  H11  H  HCH3  0   0.238   7.3938   3.0044   0.4692
 33H  H12  H  HCH3  0   0.237   6.5657   2.1607  -0.8418
 33H  H13  H  HCH3  0   0.237   5.6941   1.1937   3.2837
 33H  H14  H  HCH3  0   0.238   6.8921   2.4293   2.8894
 33H  H15  H  HCH3  0   0.238   5.1767   2.7467   2.6168
 33H  H16  H  HCH1  0   0.222  -5.1123  -1.2447   2.9829
 33H  H17  H  HCH3  0   0.220  -5.0110   1.6785   3.8802
 33H  H18  H  HCH3  0   0.235  -6.2129   0.4880   4.3947
 33H  H19  H  HCH3  0   0.224  -4.5205   0.2852   4.8429
 33H  H20  H  H     0   0.238  -3.2753  -1.6078  -1.4040
 33H  H21  H  H     0   0.258  -3.7437  -0.0554  -2.0955
 33H  H22  H  HCR6  0   0.266  -1.3055  -0.7390  -2.2650
 33H  H23  H  HCH1  0   0.227  -0.2682   1.3663  -1.7413
 33H  H24  H  HCH2  0   0.230  -1.5320   1.0434  -3.8380
 33H  H25  H  HCH2  0   0.215  -2.9684   1.7217  -3.0898
 33H  H26  H  HCH2  0   0.211  -0.3182   3.1675  -3.5190
 33H  H27  H  HCH2  0   0.228  -1.8144   3.4601  -4.3830
 33H  H28  H  HCH2  0   0.227  -1.4372   5.1507  -2.5740
 33H  H29  H  HCH2  0   0.208  -2.9141   4.2402  -2.3227
 33H  H30  H  HCH2  0   0.227  -1.6786   4.4148  -0.1952
 33H  H31  H  HCH2  0   0.208  -0.2401   3.7398  -0.9367
 33H  H32  H  HOH1  0   0.495   0.7070  -4.8011  -2.2369
 33H  H33  H  HOH1  0   0.438  -5.6948   1.0139   1.4287

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
 33H  O3   C16  double    1.206  0.020  1.206
 33H  O4   C16  single    1.327  0.020  1.327
 33H  C16  C15  single    1.464  0.020  1.464
 33H  C15  S1   aromatic  1.716  0.020  1.716
 33H  C15  C1   aromatic  1.375  0.020  1.375
 33H  O2   C2   double    1.220  0.020  1.220
 33H  C3   C2   single    1.526  0.020  1.526
 33H  C3   C12  single    1.525  0.020  1.525
 33H  C3   O1   single    1.402  0.020  1.402
 33H  S1   C14  aromatic  1.721  0.020  1.721
 33H  C2   N1   single    1.353  0.020  1.353
 33H  C4   O1   single    1.404  0.020  1.404
 33H  C4   C5   single    1.515  0.020  1.515
 33H  N1   C1   single    1.409  0.020  1.409
 33H  N1   C5   single    1.467  0.020  1.467
 33H  C1   C13  aromatic  1.410  0.020  1.410
 33H  C12  C23  single    1.527  0.020  1.527
 33H  C5   C6   single    1.535  0.020  1.535
 33H  C14  C13  aromatic  1.372  0.020  1.372
 33H  C14  C17  single    1.408  0.020  1.408
 33H  C23  O5   single    1.413  0.020  1.413
 33H  C23  C24  single    1.523  0.020  1.523
 33H  C6   C7   single    1.529  0.020  1.529
 33H  C6   C11  single    1.528  0.020  1.528
 33H  C17  C18  triple    1.207  0.020  1.207
 33H  C7   C8   single    1.526  0.020  1.526
 33H  C18  C19  single    1.464  0.020  1.464
 33H  C11  C10  single    1.527  0.020  1.527
 33H  C22  C19  single    1.534  0.020  1.534
 33H  C8   C9   single    1.525  0.020  1.525
 33H  C19  C20  single    1.534  0.020  1.534
 33H  C19  C21  single    1.534  0.020  1.534
 33H  C10  C9   single    1.525  0.020  1.525
 33H  C3   H1   single    0.970  0.020  1.090
 33H  C11  H2   single    0.970  0.020  1.090
 33H  C11  H3   single    0.970  0.020  1.090
 33H  C12  H4   single    0.970  0.020  1.090
 33H  C12  H5   single    0.970  0.020  1.090
 33H  C13  H6   single    0.930  0.020  1.080
 33H  C20  H7   single    0.970  0.020  1.090
 33H  C20  H8   single    0.970  0.020  1.090
 33H  C20  H9   single    0.970  0.020  1.090
 33H  C21  H10  single    0.970  0.020  1.090
 33H  C21  H11  single    0.970  0.020  1.090
 33H  C21  H12  single    0.970  0.020  1.090
 33H  C22  H13  single    0.970  0.020  1.090
 33H  C22  H14  single    0.970  0.020  1.090
 33H  C22  H15  single    0.970  0.020  1.090
 33H  C23  H16  single    0.970  0.020  1.090
 33H  C24  H17  single    0.970  0.020  1.090
 33H  C24  H18  single    0.970  0.020  1.090
 33H  C24  H19  single    0.970  0.020  1.090
 33H  C4   H20  single    0.970  0.020  1.090
 33H  C4   H21  single    0.970  0.020  1.090
 33H  C5   H22  single    0.970  0.020  1.090
 33H  C6   H23  single    0.970  0.020  1.090
 33H  C7   H24  single    0.970  0.020  1.090
 33H  C7   H25  single    0.970  0.020  1.090
 33H  C8   H26  single    0.970  0.020  1.090
 33H  C8   H27  single    0.970  0.020  1.090
 33H  C9   H28  single    0.970  0.020  1.090
 33H  C9   H29  single    0.970  0.020  1.090
 33H  C10  H30  single    0.970  0.020  1.090
 33H  C10  H31  single    0.970  0.020  1.090
 33H  O4   H32  single    0.850  0.020  0.980
 33H  O5   H33  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
 33H  N1   C1   C15  124.24  3.000
 33H  N1   C1   C13  122.87  3.000
 33H  C15  C1   C13  112.88  3.000
 33H  N1   C2   O2   121.72  3.000
 33H  N1   C2   C3   117.98  3.000
 33H  O2   C2   C3   120.28  3.000
 33H  H1   C3   C12  108.99  3.000
 33H  H1   C3   O1   110.26  3.000
 33H  C12  C3   O1   108.97  3.000
 33H  H1   C3   C2   104.54  3.000
 33H  O1   C3   C2   113.69  3.000
 33H  C12  C3   C2   110.25  3.000
 33H  C4   O1   C3   112.65  3.000
 33H  H3   C11  H2   106.41  3.000
 33H  H3   C11  C10  109.84  3.000
 33H  H2   C11  C10  109.10  3.000
 33H  H3   C11  C6   110.58  3.000
 33H  H2   C11  C6   110.22  3.000
 33H  C10  C11  C6   110.59  3.000
 33H  H5   C12  H4   106.54  3.000
 33H  H5   C12  C23  110.36  3.000
 33H  H4   C12  C23  107.33  3.000
 33H  H5   C12  C3   108.74  3.000
 33H  H4   C12  C3   108.76  3.000
 33H  C23  C12  C3   114.78  3.000
 33H  H6   C13  C14  123.70  3.000
 33H  H6   C13  C1   123.77  3.000
 33H  C14  C13  C1   112.54  3.000
 33H  S1   C14  C17  120.17  3.000
 33H  C17  C14  C13  128.40  3.000
 33H  S1   C14  C13  111.43  3.000
 33H  S1   C15  C16  120.96  3.000
 33H  S1   C15  C1   111.28  3.000
 33H  C16  C15  C1   127.70  3.000
 33H  O4   C16  C15  111.15  3.000
 33H  C15  C16  O3   124.62  3.000
 33H  O4   C16  O3   124.23  3.000
 33H  C18  C17  C14  180.00  3.000
 33H  C19  C18  C17  180.00  3.000
 33H  C22  C19  C21  110.06  3.000
 33H  C21  C19  C20  109.96  3.000
 33H  C22  C19  C20  109.85  3.000
 33H  C21  C19  C18  109.31  3.000
 33H  C20  C19  C18  108.60  3.000
 33H  C22  C19  C18  109.03  3.000
 33H  H9   C20  H8   108.09  3.000
 33H  H9   C20  H7   108.31  3.000
 33H  H8   C20  H7   108.10  3.000
 33H  H9   C20  C19  111.19  3.000
 33H  H8   C20  C19  109.72  3.000
 33H  H7   C20  C19  111.32  3.000
 33H  H12  C21  H11  108.03  3.000
 33H  H12  C21  H10  108.28  3.000
 33H  H11  C21  H10  108.14  3.000
 33H  H12  C21  C19  111.23  3.000
 33H  H11  C21  C19  109.63  3.000
 33H  H10  C21  C19  111.41  3.000
 33H  H15  C22  H14  108.08  3.000
 33H  H15  C22  H13  108.28  3.000
 33H  H14  C22  H13  108.06  3.000
 33H  H15  C22  C19  111.45  3.000
 33H  H14  C22  C19  109.67  3.000
 33H  H13  C22  C19  111.18  3.000
 33H  H16  C23  O5   105.03  3.000
 33H  H16  C23  C24  108.55  3.000
 33H  O5   C23  C24  111.42  3.000
 33H  H16  C23  C12  107.85  3.000
 33H  C24  C23  C12  110.26  3.000
 33H  O5   C23  C12  113.42  3.000
 33H  H19  C24  H18  107.81  3.000
 33H  H19  C24  H17  107.68  3.000
 33H  H18  C24  H17  108.16  3.000
 33H  H19  C24  C23  111.17  3.000
 33H  H18  C24  C23  110.89  3.000
 33H  H17  C24  C23  110.98  3.000
 33H  C5   N1   C2   124.80  3.000
 33H  C5   N1   C1   117.82  3.000
 33H  C2   N1   C1   117.20  3.000
 33H  H21  C4   H20  107.33  3.000
 33H  H21  C4   C5   110.74  3.000
 33H  H20  C4   C5   109.05  3.000
 33H  H21  C4   O1   107.74  3.000
 33H  H20  C4   O1   110.96  3.000
 33H  C5   C4   O1   110.96  3.000
 33H  H22  C5   C6   107.00  3.000
 33H  H22  C5   C4   106.42  3.000
 33H  C6   C5   C4   116.86  3.000
 33H  H22  C5   N1   107.17  3.000
 33H  C6   C5   N1   111.42  3.000
 33H  C4   C5   N1   107.48  3.000
 33H  H23  C6   C7   106.38  3.000
 33H  H23  C6   C5   105.58  3.000
 33H  C7   C6   C5   111.21  3.000
 33H  H23  C6   C11  107.00  3.000
 33H  C7   C6   C11  110.40  3.000
 33H  C5   C6   C11  115.64  3.000
 33H  H25  C7   H24  106.63  3.000
 33H  H25  C7   C8   108.79  3.000
 33H  H24  C7   C8   110.09  3.000
 33H  H25  C7   C6   109.85  3.000
 33H  H24  C7   C6   110.09  3.000
 33H  C8   C7   C6   111.26  3.000
 33H  H27  C8   H26  106.45  3.000
 33H  H27  C8   C9   110.27  3.000
 33H  H26  C8   C9   109.43  3.000
 33H  H27  C8   C7   109.88  3.000
 33H  H26  C8   C7   109.35  3.000
 33H  C9   C8   C7   111.34  3.000
 33H  H29  C9   H28  106.46  3.000
 33H  H29  C9   C10  109.22  3.000
 33H  H28  C9   C10  110.35  3.000
 33H  H29  C9   C8   109.23  3.000
 33H  H28  C9   C8   110.22  3.000
 33H  C10  C9   C8   111.24  3.000
 33H  H31  C10  H30  106.48  3.000
 33H  H31  C10  C9   109.35  3.000
 33H  H30  C10  C9   110.23  3.000
 33H  H31  C10  C11  109.44  3.000
 33H  H30  C10  C11  109.85  3.000
 33H  C9   C10  C11  111.36  3.000
 33H  C15  S1   C14   91.87  3.000
 33H  H32  O4   C16  110.51  3.000
 33H  H33  O5   C23  108.41  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
 33H  CONST_01  C14  S1   C15  C1      0.00   0.0  0
 33H  CONST_02  S1   C14  C13  C1      0.00   0.0  0
 33H  CONST_03  S1   C15  C1   C13     0.00   0.0  0
 33H  CONST_04  C15  S1   C14  C13     0.00   0.0  0
 33H  CONST_05  C15  C1   C13  C14     0.00   0.0  0
 33H  CONST_06  N1   C1   C13  C14   180.00   0.0  0
 33H  CONST_07  S1   C15  C1   N1    180.00   0.0  0
 33H  CONST_08  C3   C2   N1   C1    180.00   0.0  0
 33H  CONST_09  C5   N1   C2   C3      0.00   0.0  0
 33H  CONST_10  C17  C14  C13  C1    180.00   0.0  0
 33H  CONST_11  C16  C15  C1   C13   180.00   0.0  0
 33H  CONST_12  C16  C15  S1   C14   180.00   0.0  0
 33H  CONST_13  C17  C14  S1   C15   180.00   0.0  0
 33H  CONST_14  N1   C1   C15  C16     0.00   0.0  0
 33H  CONST_15  O2   C2   N1   C1      0.00   0.0  0
 33H  CONST_16  C5   N1   C2   O2    180.00   0.0  0
 33H  CONST_17  H6   C13  C1   C15   180.00   0.0  0
 33H  CONST_18  H32  O4   C16  C15   180.00   0.0  0
 33H  Var_01    C15  C1   N1   C2     96.92  30.0  2
 33H  Var_02    C5   C4   O1   C3    -67.83  30.0  1
 33H  Var_03    C8   C9   C10  C11   -55.26  30.0  1
 33H  Var_04    C9   C8   C7   C6    -55.41  30.0  1
 33H  Var_05    C9   C10  C11  C6     56.72  30.0  1
 33H  Var_06    C10  C9   C8   C7     54.43  30.0  1
 33H  Var_07    O3   C16  C15  C1      1.05  30.0  2
 33H  Var_08    C22  C19  C18  C17  -108.62  30.0  3
 33H  Var_09    H13  C22  C19  C18    59.77  30.0  3
 33H  Var_10    H7   C20  C19  C18    60.12  30.0  3
 33H  Var_11    H10  C21  C19  C18    60.40  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
 33H  chir_01  C3   C2   C12  O1   negativ
 33H  chir_02  C23  O5   C24  C12  positiv
 33H  chir_03  C5   N1   C4   C6   negativ
 33H  chir_04  C6   C11  C7   C5   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
 33H  plan-1  C1   0.020
 33H  plan-1  C13  0.020
 33H  plan-1  C14  0.020
 33H  plan-1  C15  0.020
 33H  plan-1  C16  0.020
 33H  plan-1  C17  0.020
 33H  plan-1  C18  0.020
 33H  plan-1  N1   0.020
 33H  plan-1  S1   0.020
 33H  plan-1  H6   0.020
 33H  plan-2  C1   0.020
 33H  plan-2  C2   0.020
 33H  plan-2  C3   0.020
 33H  plan-2  O2   0.020
 33H  plan-2  N1   0.020
 33H  plan-2  C5   0.020
 33H  plan-3  O3   0.020
 33H  plan-3  C15  0.020
 33H  plan-3  C16  0.020
 33H  plan-3  O4   0.020
 33H  plan-3  H32  0.020

