# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 18:00:46 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 3-{4-[(tridec-2-yn-1-yloxy)methyl]phenyl}propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCC#CCOCc1ccc(CCC(O)=O)cc1
#
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
 OYP  OYP  '3-{4-[(tridec-2-yn-1-yloxy)methyl]phenyl}propanoic acid'  ligand  60  26  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OYP
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
 OYP  C1    C  CR16  0  -0.284  -5.4468   1.9505   0.4132
 OYP  O1    O  OH1   0  -0.596  -6.5632  -4.6650   1.3646
 OYP  C2    C  CR6   0   0.070  -4.5628   2.0491  -0.6554
 OYP  O2    O  O     0  -0.445  -8.3938  -3.8505   0.3868
 OYP  C3    C  CR16  0  -0.274  -4.5441   1.0244  -1.5980
 OYP  O3    O  O2    0  -0.483  -2.3545   2.7945  -0.2862
 OYP  C4    C  CR16  0  -0.293  -5.3872  -0.0687  -1.4723
 OYP  C5    C  CR6   0   0.116  -6.2741  -0.1706  -0.4020
 OYP  C6    C  CR16  0  -0.294  -6.2921   0.8561   0.5374
 OYP  C7    C  CH2   0  -0.512  -7.1508  -1.3815  -0.2416
 OYP  C8    C  CH2   0  -0.575  -6.4249  -2.4708   0.5417
 OYP  C9    C  C     0   0.552  -7.2490  -3.7131   0.7395
 OYP  C10   C  CH2   0  -0.215  -3.6175   3.2059  -0.7720
 OYP  C11   C  CH2   0  -0.333  -1.3992   3.8257  -0.3713
 OYP  C12   C  CSP   0  -0.017  -0.1370   3.3628   0.1904
 OYP  C13   C  CSP   0   0.145   0.9130   2.9995   0.6526
 OYP  C14   C  CH2   0  -0.616   2.1863   2.5582   1.2066
 OYP  C15   C  CH2   0  -0.420   3.0241   1.7289   0.2306
 OYP  C16   C  CH2   0  -0.419   4.3472   1.2990   0.8499
 OYP  C17   C  CH2   0  -0.414   5.2122   0.4701  -0.0899
 OYP  C18   C  CH2   0  -0.412   6.5417   0.0640   0.5343
 OYP  C19   C  CH2   0  -0.412   7.4192  -0.7713  -0.3884
 OYP  C20   C  CH2   0  -0.411   8.7465  -1.1658   0.2480
 OYP  C21   C  CH2   0  -0.407   9.6307  -2.0091  -0.6607
 OYP  C22   C  CH2   0  -0.418  10.9579  -2.3944  -0.0178
 OYP  C23   C  CH3   0  -0.664  11.8331  -3.2474  -0.9249
 OYP  H1    H  HCR6  0   0.251  -5.4809   2.7374   1.1575
 OYP  HO1   H  HOH1  0   0.479  -7.1182  -5.4504   1.4813
 OYP  H3    H  HCR6  0   0.250  -3.8693   1.0825  -2.4442
 OYP  H4    H  HCR6  0   0.249  -5.3594  -0.8520  -2.2209
 OYP  H6    H  HCR6  0   0.249  -6.9764   0.8053   1.3763
 OYP  H7    H  HCH2  0   0.255  -8.0724  -1.1074   0.2745
 OYP  H7A   H  HCH2  0   0.255  -7.4381  -1.7644  -1.2225
 OYP  H8    H  HCH2  0   0.286  -5.4930  -2.7474   0.0400
 OYP  H8A   H  HCH2  0   0.289  -6.1286  -2.0975   1.5271
 OYP  H10   H  HCH2  0   0.218  -3.5370   3.5307  -1.8179
 OYP  H10A  H  HCH2  0   0.222  -3.9898   4.0641  -0.1971
 OYP  H11   H  HCH2  0   0.238  -1.2462   4.1367  -1.4145
 OYP  H11A  H  HCH2  0   0.237  -1.7352   4.7204   0.1717
 OYP  H14   H  HCH2  0   0.264   2.7550   3.4373   1.5243
 OYP  H14A  H  HCH2  0   0.264   1.9983   1.9777   2.1147
 OYP  H15   H  HCH2  0   0.227   2.4546   0.8482  -0.0790
 OYP  H15A  H  HCH2  0   0.226   3.2102   2.3129  -0.6748
 OYP  H16   H  HCH2  0   0.213   4.9031   2.1883   1.1670
 OYP  H16A  H  HCH2  0   0.214   4.1503   0.7255   1.7623
 OYP  H17   H  HCH2  0   0.209   4.6638  -0.4279  -0.3951
 OYP  H17A  H  HCH2  0   0.209   5.3995   1.0362  -1.0088
 OYP  H18   H  HCH2  0   0.207   7.0876   0.9646   0.8370
 OYP  H18A  H  HCH2  0   0.207   6.3516  -0.4954   1.4572
 OYP  H19   H  HCH2  0   0.207   6.8772  -1.6752  -0.6885
 OYP  H19A  H  HCH2  0   0.206   7.6108  -0.2148  -1.3125
 OYP  H20   H  HCH2  0   0.206   9.2882  -0.2601   0.5432
 OYP  H20A  H  HCH2  0   0.206   8.5528  -1.7148   1.1764
 OYP  H21   H  HCH2  0   0.205   9.0928  -2.9180  -0.9532
 OYP  H21A  H  HCH2  0   0.205   9.8244  -1.4627  -1.5907
 OYP  H22   H  HCH2  0   0.210  11.4977  -1.4855   0.2662
 OYP  H22A  H  HCH2  0   0.210  10.7632  -2.9320   0.9154
 OYP  H23   H  HCH3  0   0.216  11.3318  -4.1793  -1.1929
 OYP  H23A  H  HCH3  0   0.216  12.0681  -2.7237  -1.8534
 OYP  H23B  H  HCH3  0   0.226  12.7771  -3.5066  -0.4443

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
 OYP  C6   C1    aromatic  1.388  0.020  1.388
 OYP  C1   C2    aromatic  1.390  0.020  1.390
 OYP  C1   H1    single    0.930  0.020  1.080
 OYP  O1   C9    single    1.329  0.020  1.329
 OYP  O1   HO1   single    0.850  0.020  0.980
 OYP  C10  C2    single    1.498  0.020  1.498
 OYP  C2   C3    aromatic  1.392  0.020  1.392
 OYP  O2   C9    double    1.206  0.020  1.206
 OYP  C4   C3    aromatic  1.386  0.020  1.386
 OYP  C3   H3    single    0.930  0.020  1.080
 OYP  C10  O3    single    1.414  0.020  1.414
 OYP  O3   C11   single    1.408  0.020  1.408
 OYP  C5   C4    aromatic  1.394  0.020  1.394
 OYP  C4   H4    single    0.930  0.020  1.080
 OYP  C6   C5    aromatic  1.392  0.020  1.392
 OYP  C5   C7    single    1.504  0.020  1.504
 OYP  C6   H6    single    0.930  0.020  1.080
 OYP  C8   C7    single    1.525  0.020  1.525
 OYP  C7   H7    single    0.970  0.020  1.090
 OYP  C7   H7A   single    0.970  0.020  1.090
 OYP  C9   C8    single    1.504  0.020  1.504
 OYP  C8   H8    single    0.970  0.020  1.090
 OYP  C8   H8A   single    0.970  0.020  1.090
 OYP  C10  H10   single    0.970  0.020  1.090
 OYP  C10  H10A  single    0.970  0.020  1.090
 OYP  C11  C12   single    1.457  0.020  1.457
 OYP  C11  H11   single    0.970  0.020  1.090
 OYP  C11  H11A  single    0.970  0.020  1.090
 OYP  C12  C13   triple    1.203  0.020  1.203
 OYP  C13  C14   single    1.457  0.020  1.457
 OYP  C15  C14   single    1.530  0.020  1.530
 OYP  C14  H14   single    0.970  0.020  1.090
 OYP  C14  H14A  single    0.970  0.020  1.090
 OYP  C16  C15   single    1.523  0.020  1.523
 OYP  C15  H15   single    0.970  0.020  1.090
 OYP  C15  H15A  single    0.970  0.020  1.090
 OYP  C17  C16   single    1.523  0.020  1.523
 OYP  C16  H16   single    0.970  0.020  1.090
 OYP  C16  H16A  single    0.970  0.020  1.090
 OYP  C18  C17   single    1.524  0.020  1.524
 OYP  C17  H17   single    0.970  0.020  1.090
 OYP  C17  H17A  single    0.970  0.020  1.090
 OYP  C19  C18   single    1.523  0.020  1.523
 OYP  C18  H18   single    0.970  0.020  1.090
 OYP  C18  H18A  single    0.970  0.020  1.090
 OYP  C20  C19   single    1.524  0.020  1.524
 OYP  C19  H19   single    0.970  0.020  1.090
 OYP  C19  H19A  single    0.970  0.020  1.090
 OYP  C21  C20   single    1.523  0.020  1.523
 OYP  C20  H20   single    0.970  0.020  1.090
 OYP  C20  H20A  single    0.970  0.020  1.090
 OYP  C21  C22   single    1.524  0.020  1.524
 OYP  C21  H21   single    0.970  0.020  1.090
 OYP  C21  H21A  single    0.970  0.020  1.090
 OYP  C23  C22   single    1.522  0.020  1.522
 OYP  C22  H22   single    0.970  0.020  1.090
 OYP  C22  H22A  single    0.970  0.020  1.090
 OYP  C23  H23   single    0.970  0.020  1.090
 OYP  C23  H23A  single    0.970  0.020  1.090
 OYP  C23  H23B  single    0.970  0.020  1.090

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
 OYP  H1    C1   C6    119.46  3.000
 OYP  H1    C1   C2    119.76  3.000
 OYP  C6    C1   C2    120.78  3.000
 OYP  HO1   O1   C9    109.97  3.000
 OYP  C10   C2   C3    120.47  3.000
 OYP  C3    C2   C1    118.46  3.000
 OYP  C10   C2   C1    121.04  3.000
 OYP  H3    C3   C4    119.45  3.000
 OYP  H3    C3   C2    119.83  3.000
 OYP  C4    C3   C2    120.72  3.000
 OYP  C11   O3   C10   111.84  3.000
 OYP  H4    C4   C5    119.60  3.000
 OYP  H4    C4   C3    119.44  3.000
 OYP  C5    C4   C3    120.95  3.000
 OYP  C7    C5   C6    120.97  3.000
 OYP  C7    C5   C4    120.79  3.000
 OYP  C6    C5   C4    118.20  3.000
 OYP  H6    C6   C5    119.74  3.000
 OYP  H6    C6   C1    119.38  3.000
 OYP  C5    C6   C1    120.88  3.000
 OYP  H7A   C7   H7    106.91  3.000
 OYP  H7A   C7   C8    109.65  3.000
 OYP  H7    C7   C8    109.78  3.000
 OYP  H7A   C7   C5    109.88  3.000
 OYP  H7    C7   C5    109.92  3.000
 OYP  C8    C7   C5    110.64  3.000
 OYP  H8A   C8   H8    105.58  3.000
 OYP  H8A   C8   C9    108.16  3.000
 OYP  H8    C8   C9    108.56  3.000
 OYP  H8A   C8   C7    110.34  3.000
 OYP  H8    C8   C7    110.51  3.000
 OYP  C9    C8   C7    113.37  3.000
 OYP  C8    C9   O2    125.17  3.000
 OYP  C8    C9   O1    111.75  3.000
 OYP  O2    C9   O1    123.08  3.000
 OYP  H10A  C10  H10   107.00  3.000
 OYP  H10A  C10  O3    110.50  3.000
 OYP  H10   C10  O3    110.35  3.000
 OYP  H10A  C10  C2    110.41  3.000
 OYP  H10   C10  C2    110.41  3.000
 OYP  O3    C10  C2    108.19  3.000
 OYP  H11A  C11  H11   106.33  3.000
 OYP  H11A  C11  C12   109.45  3.000
 OYP  H11   C11  C12   109.58  3.000
 OYP  H11A  C11  O3    111.02  3.000
 OYP  H11   C11  O3    111.04  3.000
 OYP  C12   C11  O3    109.37  3.000
 OYP  C13   C12  C11   180.00  3.000
 OYP  C14   C13  C12   180.00  3.000
 OYP  H14A  C14  H14   105.93  3.000
 OYP  H14A  C14  C15   109.63  3.000
 OYP  H14   C14  C15   109.64  3.000
 OYP  H14A  C14  C13   109.03  3.000
 OYP  H14   C14  C13   108.73  3.000
 OYP  C15   C14  C13   113.58  3.000
 OYP  H15A  C15  H15   106.53  3.000
 OYP  H15A  C15  C16   109.86  3.000
 OYP  H15   C15  C16   109.89  3.000
 OYP  H15A  C15  C14   109.38  3.000
 OYP  H15   C15  C14   109.38  3.000
 OYP  C16   C15  C14   111.67  3.000
 OYP  H16A  C16  H16   105.96  3.000
 OYP  H16A  C16  C17   109.34  3.000
 OYP  H16   C16  C17   109.40  3.000
 OYP  H16A  C16  C15   109.29  3.000
 OYP  H16   C16  C15   109.23  3.000
 OYP  C17   C16  C15   113.34  3.000
 OYP  H17A  C17  H17   105.99  3.000
 OYP  H17A  C17  C18   109.40  3.000
 OYP  H17   C17  C18   109.41  3.000
 OYP  H17A  C17  C16   109.49  3.000
 OYP  H17   C17  C16   109.50  3.000
 OYP  C18   C17  C16   112.82  3.000
 OYP  H18A  C18  H18   105.87  3.000
 OYP  H18A  C18  C19   109.29  3.000
 OYP  H18   C18  C19   109.34  3.000
 OYP  H18A  C18  C17   109.25  3.000
 OYP  H18   C18  C17   109.19  3.000
 OYP  C19   C18  C17   113.62  3.000
 OYP  H19A  C19  H19   105.93  3.000
 OYP  H19A  C19  C20   109.35  3.000
 OYP  H19   C19  C20   109.37  3.000
 OYP  H19A  C19  C18   109.46  3.000
 OYP  H19   C19  C18   109.48  3.000
 OYP  C20   C19  C18   113.01  3.000
 OYP  H20A  C20  H20   105.85  3.000
 OYP  H20A  C20  C21   109.32  3.000
 OYP  H20   C20  C21   109.36  3.000
 OYP  H20A  C20  C19   109.24  3.000
 OYP  H20   C20  C19   109.21  3.000
 OYP  C21   C20  C19   113.57  3.000
 OYP  H21A  C21  H21   105.89  3.000
 OYP  H21A  C21  C22   109.27  3.000
 OYP  H21   C21  C22   109.28  3.000
 OYP  H21A  C21  C20   109.45  3.000
 OYP  H21   C21  C20   109.48  3.000
 OYP  C22   C21  C20   113.20  3.000
 OYP  H22A  C22  H22   105.92  3.000
 OYP  H22A  C22  C23   109.58  3.000
 OYP  H22   C22  C23   109.66  3.000
 OYP  H22A  C22  C21   109.20  3.000
 OYP  H22   C22  C21   109.20  3.000
 OYP  C23   C22  C21   113.02  3.000
 OYP  H23B  C23  H23A  107.61  3.000
 OYP  H23B  C23  H23   107.63  3.000
 OYP  H23A  C23  H23   107.43  3.000
 OYP  H23B  C23  C22   111.61  3.000
 OYP  H23A  C23  C22   111.21  3.000
 OYP  H23   C23  C22   111.15  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
 OYP  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 OYP  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 OYP  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 OYP  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 OYP  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 OYP  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 OYP  CONST_07  C7   C5   C6   C1   180.00   0.0  0
 OYP  CONST_08  C7   C5   C4   C3   180.00   0.0  0
 OYP  CONST_09  C10  C2   C3   C4   180.00   0.0  0
 OYP  CONST_10  C10  C2   C1   C6   180.00   0.0  0
 OYP  CONST_11  H3   C3   C2   C1   180.00   0.0  0
 OYP  CONST_12  H6   C6   C1   C2   180.00   0.0  0
 OYP  CONST_13  H4   C4   C3   C2   180.00   0.0  0
 OYP  CONST_14  H1   C1   C2   C3   180.00   0.0  0
 OYP  CONST_15  HO1  O1   C9   O2     0.00   0.0  0
 OYP  Var_01    O3   C10  C2   C1    98.63  30.0  3
 OYP  Var_02    C8   C7   C5   C4    87.39  30.0  2
 OYP  Var_03    C9   C8   C7   C5   179.95  30.0  1
 OYP  Var_04    C7   C8   C9   O1   176.78  30.0  3
 OYP  Var_05    C12  C11  O3   C10  177.75  30.0  3
 OYP  Var_06    C15  C14  C13  C12  -13.69  30.0  3
 OYP  Var_07    C16  C15  C14  C13  179.62  30.0  2
 OYP  Var_08    C17  C16  C15  C14  179.99  30.0  1
 OYP  Var_09    C18  C17  C16  C15  179.14  30.0  1
 OYP  Var_10    C19  C18  C17  C16  179.75  30.0  1
 OYP  Var_11    C20  C19  C18  C17  179.82  30.0  1
 OYP  Var_12    C21  C20  C19  C18  179.64  30.0  1
 OYP  Var_13    C22  C21  C20  C19  179.79  30.0  2
 OYP  Var_14    C23  C22  C21  C20  179.49  30.0  3
 OYP  Var_15    H23  C23  C22  C21  -60.04  30.0  3

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
 OYP  plan-1  C1   0.020
 OYP  plan-1  C2   0.020
 OYP  plan-1  C3   0.020
 OYP  plan-1  C4   0.020
 OYP  plan-1  C5   0.020
 OYP  plan-1  C6   0.020
 OYP  plan-1  C7   0.020
 OYP  plan-1  C10  0.020
 OYP  plan-1  H1   0.020
 OYP  plan-1  H3   0.020
 OYP  plan-1  H4   0.020
 OYP  plan-1  H6   0.020
 OYP  plan-2  O1   0.020
 OYP  plan-2  O2   0.020
 OYP  plan-2  C8   0.020
 OYP  plan-2  C9   0.020
 OYP  plan-2  HO1  0.020

