# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 19:54:35 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  59  26  .  2021-08-17  2021-08-17  
;
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  C1     0  -0.285  -5.4465   1.9680   0.3824
 OYP  O1    O  OC    -1  -0.629  -6.5690  -4.6801   1.4025
 OYP  C2    C  C      0   0.067  -4.5546   2.0642  -0.6802
 OYP  O2    O  O      0  -0.606  -8.3853  -3.7723   0.4865
 OYP  C3    C  C1     0  -0.275  -4.5193   1.0275  -1.6093
 OYP  O3    O  O2     0  -0.483  -2.3564   2.8304  -0.2919
 OYP  C4    C  C1     0  -0.300  -5.3519  -0.0732  -1.4759
 OYP  C5    C  C      0   0.126  -6.2472  -0.1753  -0.4115
 OYP  C6    C  C1     0  -0.300  -6.2814   0.8665   0.5126
 OYP  C7    C  CH2    0  -0.500  -7.1042  -1.3967  -0.2351
 OYP  C8    C  CH2    0  -0.576  -6.3807  -2.4724   0.5714
 OYP  C9    C  C      0   0.413  -7.1895  -3.7554   0.8373
 OYP  C10   C  CH2    0  -0.215  -3.6165   3.2261  -0.7997
 OYP  C11   C  CH2    0  -0.333  -1.4077   3.8674  -0.3754
 OYP  C12   C  CSP    0  -0.016  -0.1448   3.4119   0.1912
 OYP  C13   C  CSP    0   0.143   0.9009   3.0501   0.6643
 OYP  C14   C  CH2    0  -0.616   2.1700   2.6049   1.2246
 OYP  C15   C  CH2    0  -0.420   3.0127   1.7806   0.2487
 OYP  C16   C  CH2    0  -0.419   4.3327   1.3466   0.8719
 OYP  C17   C  CH2    0  -0.414   5.1949   0.5106  -0.0641
 OYP  C18   C  CH2    0  -0.412   6.5183   0.0923   0.5650
 OYP  C19   C  CH2    0  -0.412   7.3915  -0.7481  -0.3571
 OYP  C20   C  CH2    0  -0.411   8.7139  -1.1565   0.2806
 OYP  C21   C  CH2    0  -0.407   9.5943  -1.9988  -0.6330
 OYP  C22   C  CH2    0  -0.418  10.9174  -2.3992   0.0090
 OYP  C23   C  CH3    0  -0.663  11.7896  -3.2479  -0.9050
 OYP  H1    H  H      0   0.248  -5.4948   2.7636   1.1171
 OYP  H3    H  H      0   0.247  -3.8385   1.0816  -2.4513
 OYP  H4    H  H      0   0.244  -5.3073  -0.8659  -2.2139
 OYP  H6    H  H      0   0.244  -6.9715   0.8188   1.3472
 OYP  H7    H  HCH2   0   0.230  -8.0348  -1.1279   0.2674
 OYP  H7A   H  HCH2   0   0.229  -7.3827  -1.7972  -1.2123
 OYP  H8    H  HCH2   0   0.227  -5.4457  -2.7422   0.0691
 OYP  H8A   H  HCH2   0   0.231  -6.0745  -2.0562   1.5382
 OYP  H10   H  HCH2   0   0.217  -3.5229   3.5384  -1.8484
 OYP  H10A  H  HCH2   0   0.220  -4.0019   4.0889  -0.2404
 OYP  H11   H  HCH2   0   0.237  -1.2530   4.1782  -1.4183
 OYP  H11A  H  HCH2   0   0.237  -1.7508   4.7606   0.1657
 OYP  H14   H  HCH2   0   0.264   2.7377   3.4809   1.5522
 OYP  H14A  H  HCH2   0   0.264   1.9754   2.0189   2.1278
 OYP  H15   H  HCH2   0   0.227   2.4444   0.9018  -0.0685
 OYP  H15A  H  HCH2   0   0.226   3.2033   2.3693  -0.6526
 OYP  H16   H  HCH2   0   0.214   4.8922   2.2344   1.1866
 OYP  H16A  H  HCH2   0   0.214   4.1315   0.7775   1.7862
 OYP  H17   H  HCH2   0   0.209   4.6401  -0.3825  -0.3723
 OYP  H17A  H  HCH2   0   0.209   5.3914   1.0756  -0.9820
 OYP  H18   H  HCH2   0   0.207   7.0706   0.9879   0.8717
 OYP  H18A  H  HCH2   0   0.207   6.3199  -0.4673   1.4859
 OYP  H19   H  HCH2   0   0.207   6.8427  -1.6464  -0.6614
 OYP  H19A  H  HCH2   0   0.206   7.5903  -0.1907  -1.2791
 OYP  H20   H  HCH2   0   0.206   9.2612  -0.2570   0.5843
 OYP  H20A  H  HCH2   0   0.206   8.5136  -1.7115   1.2038
 OYP  H21   H  HCH2   0   0.206   9.0505  -2.9013  -0.9341
 OYP  H21A  H  HCH2   0   0.205   9.7939  -1.4464  -1.5581
 OYP  H22   H  HCH2   0   0.210  11.4623  -1.4972   0.3048
 OYP  H22A  H  HCH2   0   0.210  10.7167  -2.9457   0.9358
 OYP  H23   H  HCH3   0   0.216  11.2844  -4.1750  -1.1823
 OYP  H23A  H  HCH3   0   0.215  12.0280  -2.7167  -1.8284
 OYP  H23B  H  HCH3   0   0.226  12.7322  -3.5157  -0.4262

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  1.391  0.020  1.391
 OYP  C1   H1    single    0.930  0.020  1.080
 OYP  O1   C9    deloc     1.249  0.020  1.249
 OYP  C10  C2    single    1.498  0.020  1.498
 OYP  C2   C3    aromatic  1.393  0.020  1.393
 OYP  O2   C9    deloc     1.246  0.020  1.246
 OYP  C4   C3    aromatic  1.387  0.020  1.387
 OYP  C3   H3    single    0.930  0.020  1.080
 OYP  C10  O3    single    1.415  0.020  1.415
 OYP  O3   C11   single    1.408  0.020  1.408
 OYP  C5   C4    aromatic  1.395  0.020  1.395
 OYP  C4   H4    single    0.930  0.020  1.080
 OYP  C6   C5    aromatic  1.393  0.020  1.393
 OYP  C5   C7    single    1.503  0.020  1.503
 OYP  C6   H6    single    0.930  0.020  1.080
 OYP  C8   C7    single    1.527  0.020  1.527
 OYP  C7   H7    single    0.970  0.020  1.090
 OYP  C7   H7A   single    0.970  0.020  1.090
 OYP  C9   C8    single    1.540  0.020  1.540
 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    119.47  3.000
 OYP  H1    C1   C2    119.71  3.000
 OYP  C6    C1   C2    120.81  3.000
 OYP  C10   C2   C3    120.55  3.000
 OYP  C3    C2   C1    118.33  3.000
 OYP  C10   C2   C1    121.08  3.000
 OYP  H3    C3   C4    119.43  3.000
 OYP  H3    C3   C2    119.80  3.000
 OYP  C4    C3   C2    120.77  3.000
 OYP  C11   O3   C10   111.89  3.000
 OYP  H4    C4   C5    119.51  3.000
 OYP  H4    C4   C3    119.36  3.000
 OYP  C5    C4   C3    121.13  3.000
 OYP  C7    C5   C6    121.07  3.000
 OYP  C7    C5   C4    121.02  3.000
 OYP  C6    C5   C4    117.86  3.000
 OYP  H6    C6   C5    119.57  3.000
 OYP  H6    C6   C1    119.34  3.000
 OYP  C5    C6   C1    121.09  3.000
 OYP  H7A   C7   H7    106.55  3.000
 OYP  H7A   C7   C8    109.58  3.000
 OYP  H7    C7   C8    109.54  3.000
 OYP  H7A   C7   C5    109.79  3.000
 OYP  H7    C7   C5    109.89  3.000
 OYP  C8    C7   C5    111.38  3.000
 OYP  H8A   C8   H8    105.05  3.000
 OYP  H8A   C8   C9    108.11  3.000
 OYP  H8    C8   C9    108.81  3.000
 OYP  H8A   C8   C7    109.32  3.000
 OYP  H8    C8   C7    109.62  3.000
 OYP  C9    C8   C7    115.43  3.000
 OYP  C8    C9   O2    117.82  3.000
 OYP  C8    C9   O1    115.73  3.000
 OYP  O2    C9   O1    126.45  3.000
 OYP  H10A  C10  H10   107.03  3.000
 OYP  H10A  C10  O3    110.46  3.000
 OYP  H10   C10  O3    110.26  3.000
 OYP  H10A  C10  C2    110.43  3.000
 OYP  H10   C10  C2    110.49  3.000
 OYP  O3    C10  C2    108.19  3.000
 OYP  H11A  C11  H11   106.33  3.000
 OYP  H11A  C11  C12   109.46  3.000
 OYP  H11   C11  C12   109.59  3.000
 OYP  H11A  C11  O3    111.04  3.000
 OYP  H11   C11  O3    111.06  3.000
 OYP  C12   C11  O3    109.31  3.000
 OYP  C13   C12  C11   180.00  3.000
 OYP  C14   C13  C12   180.00  3.000
 OYP  H14A  C14  H14   105.90  3.000
 OYP  H14A  C14  C15   109.63  3.000
 OYP  H14   C14  C15   109.66  3.000
 OYP  H14A  C14  C13   109.04  3.000
 OYP  H14   C14  C13   108.81  3.000
 OYP  C15   C14  C13   113.51  3.000
 OYP  H15A  C15  H15   106.52  3.000
 OYP  H15A  C15  C16   109.86  3.000
 OYP  H15   C15  C16   109.89  3.000
 OYP  H15A  C15  C14   109.37  3.000
 OYP  H15   C15  C14   109.36  3.000
 OYP  C16   C15  C14   111.71  3.000
 OYP  H16A  C16  H16   105.96  3.000
 OYP  H16A  C16  C17   109.38  3.000
 OYP  H16   C16  C17   109.41  3.000
 OYP  H16A  C16  C15   109.29  3.000
 OYP  H16   C16  C15   109.22  3.000
 OYP  C17   C16  C15   113.31  3.000
 OYP  H17A  C17  H17   105.99  3.000
 OYP  H17A  C17  C18   109.37  3.000
 OYP  H17   C17  C18   109.40  3.000
 OYP  H17A  C17  C16   109.48  3.000
 OYP  H17   C17  C16   109.49  3.000
 OYP  C18   C17  C16   112.87  3.000
 OYP  H18A  C18  H18   105.86  3.000
 OYP  H18A  C18  C19   109.32  3.000
 OYP  H18   C18  C19   109.36  3.000
 OYP  H18A  C18  C17   109.26  3.000
 OYP  H18   C18  C17   109.20  3.000
 OYP  C19   C18  C17   113.55  3.000
 OYP  H19A  C19  H19   105.91  3.000
 OYP  H19A  C19  C20   109.33  3.000
 OYP  H19   C19  C20   109.34  3.000
 OYP  H19A  C19  C18   109.45  3.000
 OYP  H19   C19  C18   109.48  3.000
 OYP  C20   C19  C18   113.09  3.000
 OYP  H20A  C20  H20   105.87  3.000
 OYP  H20A  C20  C21   109.33  3.000
 OYP  H20   C20  C21   109.36  3.000
 OYP  H20A  C20  C19   109.25  3.000
 OYP  H20   C20  C19   109.23  3.000
 OYP  C21   C20  C19   113.51  3.000
 OYP  H21A  C21  H21   105.87  3.000
 OYP  H21A  C21  C22   109.26  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   113.23  3.000
 OYP  H22A  C22  H22   105.90  3.000
 OYP  H22A  C22  C23   109.59  3.000
 OYP  H22   C22  C23   109.67  3.000
 OYP  H22A  C22  C21   109.19  3.000
 OYP  H22   C22  C21   109.23  3.000
 OYP  C23   C22  C21   113.02  3.000
 OYP  H23B  C23  H23A  107.58  3.000
 OYP  H23B  C23  H23   107.64  3.000
 OYP  H23A  C23  H23   107.43  3.000
 OYP  H23B  C23  C22   111.63  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  Var_01    O3   C10  C2   C1    98.23  30.0  3
 OYP  Var_02    C8   C7   C5   C4    87.32  30.0  2
 OYP  Var_03    C9   C8   C7   C5   178.60  30.0  1
 OYP  Var_04    C7   C8   C9   O1   174.49  30.0  3
 OYP  Var_05    C12  C11  O3   C10  178.59  30.0  3
 OYP  Var_06    C15  C14  C13  C12    2.03  30.0  3
 OYP  Var_07    C16  C15  C14  C13  179.55  30.0  1
 OYP  Var_08    C17  C16  C15  C14  179.40  30.0  1
 OYP  Var_09    C18  C17  C16  C15  179.49  30.0  1
 OYP  Var_10    C19  C18  C17  C16  179.84  30.0  2
 OYP  Var_11    C20  C19  C18  C17  179.80  30.0  1
 OYP  Var_12    C21  C20  C19  C18  179.94  30.0  1
 OYP  Var_13    C22  C21  C20  C19  179.78  30.0  1
 OYP  Var_14    C23  C22  C21  C20  179.65  30.0  3
 OYP  Var_15    H23  C23  C22  C21  -60.19  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

