# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 15:55:48 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 1-(3,4,5-trihydroxyphenyl)decan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCC(=O)c1cc(O)c(O)c(O)c1
#
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
 3MX  3MX  1-(3,4,5-trihydroxyphenyl)decan-1-one  ligand  44  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3MX
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
 3MX  C1   C  C     0   0.377    1.4097  -1.1125  -0.0092
 3MX  C3   C  CR6   0  -0.007    2.7806  -0.5380  -0.0790
 3MX  C4   C  CR16  0  -0.396    3.8676  -1.4089  -0.0527
 3MX  C5   C  CR6   0   0.322    5.1610  -0.9183  -0.1137
 3MX  C6   C  CR6   0   0.189    5.3803   0.4579  -0.2024
 3MX  C7   C  CR6   0   0.313    4.2913   1.3303  -0.2299
 3MX  C8   C  CR16  0  -0.460    2.9984   0.8371  -0.1678
 3MX  O9   O  OH1   0  -0.634    6.1901  -1.7880  -0.0857
 3MX  O10  O  OH1   0  -0.632    6.6588   0.8795  -0.2588
 3MX  O11  O  OH1   0  -0.643    4.5993   2.6420  -0.3175
 3MX  O12  O  O     0  -0.406    1.2526  -2.3142   0.0737
 3MX  C13  C  CH2   0  -0.587    0.2288  -0.1727  -0.0436
 3MX  C14  C  CH2   0  -0.410   -1.1214  -0.8686   0.0236
 3MX  C15  C  CH2   0  -0.416   -2.2813   0.1194  -0.0004
 3MX  C16  C  CH2   0  -0.413   -3.6381  -0.5730   0.0312
 3MX  C17  C  CH2   0  -0.412   -4.8147   0.3947   0.0145
 3MX  C18  C  CH2   0  -0.412   -6.1658  -0.3101   0.0194
 3MX  C19  C  CH2   0  -0.406   -7.3491   0.6495   0.0064
 3MX  C20  C  CH2   0  -0.419   -8.6985  -0.0591  -0.0016
 3MX  C21  C  CH3   0  -0.663   -9.8737   0.9088  -0.0152
 3MX  H1   H  HCR6  0   0.264    3.7144  -2.4778   0.0169
 3MX  H2   H  HCR6  0   0.279    2.1732   1.5374  -0.1897
 3MX  H3   H  HOH1  0   0.475    7.0345  -1.3228  -0.1165
 3MX  H4   H  HOH1  0   0.485    6.7103   1.8427  -0.2826
 3MX  H5   H  HOH1  0   0.485    3.8044   3.1866  -0.3081
 3MX  H6   H  HCH2  0   0.267    0.3302   0.5410   0.7818
 3MX  H7   H  HCH2  0   0.266    0.2938   0.4339  -0.9539
 3MX  H8   H  HCH2  0   0.221   -1.2216  -1.5615  -0.8161
 3MX  H9   H  HCH2  0   0.222   -1.1828  -1.4756   0.9307
 3MX  H10  H  HCH2  0   0.211   -2.1985   0.8025   0.8520
 3MX  H11  H  HCH2  0   0.210   -2.2132   0.7447  -0.8976
 3MX  H12  H  HCH2  0   0.208   -3.7172  -1.2514  -0.8257
 3MX  H13  H  HCH2  0   0.208   -3.7024  -1.2060   0.9234
 3MX  H14  H  HCH2  0   0.207   -4.7482   1.0633   0.8801
 3MX  H15  H  HCH2  0   0.207   -4.7437   1.0376  -0.8701
 3MX  H16  H  HCH2  0   0.206   -6.2300  -0.9751  -0.8492
 3MX  H17  H  HCH2  0   0.206   -7.2914   1.3096   0.8793
 3MX  H18  H  HCH2  0   0.210   -8.7554  -0.7187  -0.8733
 3MX  H19  H  HCH2  0   0.210   -8.7693  -0.7111   0.8748
 3MX  H20  H  HCH3  0   0.216   -9.8587   1.5570   0.8629
 3MX  H21  H  HCH3  0   0.216   -9.8442   1.5498  -0.8983
 3MX  H22  H  HCH3  0   0.225  -10.8291   0.3829  -0.0209
 3MX  H23  H  HCH2  0   0.206   -6.2345  -0.9580   0.9006
 3MX  H24  H  HCH2  0   0.205   -7.2776   1.3027  -0.8708

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
 3MX  O11  C7   single    1.350  0.020  1.350
 3MX  O12  C1   double    1.215  0.020  1.215
 3MX  C8   C7   aromatic  1.385  0.020  1.385
 3MX  C8   C3   aromatic  1.395  0.020  1.395
 3MX  C14  C15  single    1.524  0.020  1.524
 3MX  C14  C13  single    1.520  0.020  1.520
 3MX  C7   C6   aromatic  1.396  0.020  1.396
 3MX  C1   C13  single    1.510  0.020  1.510
 3MX  C1   C3   single    1.488  0.020  1.488
 3MX  C15  C16  single    1.524  0.020  1.524
 3MX  C16  C17  single    1.523  0.020  1.523
 3MX  C21  C20  single    1.523  0.020  1.523
 3MX  C3   C4   aromatic  1.393  0.020  1.393
 3MX  C20  C19  single    1.524  0.020  1.524
 3MX  C6   O10  single    1.347  0.020  1.347
 3MX  C6   C5   aromatic  1.396  0.020  1.396
 3MX  C17  C18  single    1.524  0.020  1.524
 3MX  C4   C5   aromatic  1.385  0.020  1.385
 3MX  C19  C18  single    1.523  0.020  1.523
 3MX  C5   O9   single    1.348  0.020  1.348
 3MX  C4   H1   single    0.930  0.020  1.080
 3MX  C8   H2   single    0.930  0.020  1.080
 3MX  O9   H3   single    0.850  0.020  0.980
 3MX  O10  H4   single    0.850  0.020  0.980
 3MX  O11  H5   single    0.850  0.020  0.980
 3MX  C13  H6   single    0.970  0.020  1.090
 3MX  C13  H7   single    0.970  0.020  1.090
 3MX  C14  H8   single    0.970  0.020  1.090
 3MX  C14  H9   single    0.970  0.020  1.090
 3MX  C15  H10  single    0.970  0.020  1.090
 3MX  C15  H11  single    0.970  0.020  1.090
 3MX  C16  H12  single    0.970  0.020  1.090
 3MX  C16  H13  single    0.970  0.020  1.090
 3MX  C17  H14  single    0.970  0.020  1.090
 3MX  C17  H15  single    0.970  0.020  1.090
 3MX  C18  H16  single    0.970  0.020  1.090
 3MX  C19  H17  single    0.970  0.020  1.090
 3MX  C20  H18  single    0.970  0.020  1.090
 3MX  C20  H19  single    0.970  0.020  1.090
 3MX  C21  H20  single    0.970  0.020  1.090
 3MX  C21  H21  single    0.970  0.020  1.090
 3MX  C21  H22  single    0.970  0.020  1.090
 3MX  C18  H23  single    0.970  0.020  1.090
 3MX  C19  H24  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
 3MX  C13  C1   O12  121.08  3.000
 3MX  C13  C1   C3   118.64  3.000
 3MX  O12  C1   C3   120.28  3.000
 3MX  C8   C3   C4   119.71  3.000
 3MX  C4   C3   C1   118.47  3.000
 3MX  C8   C3   C1   121.83  3.000
 3MX  H1   C4   C5   119.02  3.000
 3MX  H1   C4   C3   120.55  3.000
 3MX  C5   C4   C3   120.43  3.000
 3MX  O9   C5   C6   121.16  3.000
 3MX  O9   C5   C4   118.93  3.000
 3MX  C6   C5   C4   119.92  3.000
 3MX  O10  C6   C7   122.96  3.000
 3MX  O10  C6   C5   117.39  3.000
 3MX  C7   C6   C5   119.65  3.000
 3MX  O11  C7   C8   124.17  3.000
 3MX  C8   C7   C6   120.33  3.000
 3MX  O11  C7   C6   115.50  3.000
 3MX  H2   C8   C7   118.70  3.000
 3MX  H2   C8   C3   121.33  3.000
 3MX  C7   C8   C3   119.97  3.000
 3MX  H3   O9   C5   110.89  3.000
 3MX  H4   O10  C6   111.34  3.000
 3MX  H5   O11  C7   111.12  3.000
 3MX  H7   C13  H6   105.05  3.000
 3MX  H7   C13  C14  110.05  3.000
 3MX  H6   C13  C14  110.30  3.000
 3MX  H7   C13  C1   108.49  3.000
 3MX  H6   C13  C1   108.42  3.000
 3MX  C14  C13  C1   114.12  3.000
 3MX  H9   C14  H8   106.28  3.000
 3MX  H9   C14  C15  109.29  3.000
 3MX  H8   C14  C15  109.21  3.000
 3MX  H9   C14  C13  109.92  3.000
 3MX  H8   C14  C13  109.73  3.000
 3MX  C15  C14  C13  112.24  3.000
 3MX  H11  C15  H10  106.06  3.000
 3MX  H11  C15  C16  109.37  3.000
 3MX  H10  C15  C16  109.54  3.000
 3MX  H11  C15  C14  109.61  3.000
 3MX  H10  C15  C14  109.54  3.000
 3MX  C16  C15  C14  112.51  3.000
 3MX  H13  C16  H12  105.95  3.000
 3MX  H13  C16  C17  109.30  3.000
 3MX  H12  C16  C17  109.21  3.000
 3MX  H13  C16  C15  109.37  3.000
 3MX  H12  C16  C15  109.23  3.000
 3MX  C17  C16  C15  113.51  3.000
 3MX  H15  C17  H14  106.00  3.000
 3MX  H15  C17  C18  109.35  3.000
 3MX  H14  C17  C18  109.48  3.000
 3MX  H15  C17  C16  109.35  3.000
 3MX  H14  C17  C16  109.40  3.000
 3MX  C18  C17  C16  113.01  3.000
 3MX  H23  C18  H16  105.95  3.000
 3MX  H23  C18  C19  109.30  3.000
 3MX  H16  C18  C19  109.26  3.000
 3MX  H23  C18  C17  109.37  3.000
 3MX  H16  C18  C17  109.28  3.000
 3MX  C19  C18  C17  113.41  3.000
 3MX  H24  C19  H17  105.96  3.000
 3MX  H24  C19  C20  109.31  3.000
 3MX  H17  C19  C20  109.32  3.000
 3MX  H24  C19  C18  109.36  3.000
 3MX  H17  C19  C18  109.37  3.000
 3MX  C20  C19  C18  113.26  3.000
 3MX  H19  C20  H18  105.98  3.000
 3MX  H19  C20  C21  109.63  3.000
 3MX  H18  C20  C21  109.62  3.000
 3MX  H19  C20  C19  109.27  3.000
 3MX  H18  C20  C19  109.29  3.000
 3MX  C21  C20  C19  112.82  3.000
 3MX  H22  C21  H21  107.62  3.000
 3MX  H22  C21  H20  107.62  3.000
 3MX  H21  C21  H20  107.56  3.000
 3MX  H22  C21  C20  111.69  3.000
 3MX  H21  C21  C20  111.08  3.000
 3MX  H20  C21  C20  111.08  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
 3MX  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 3MX  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 3MX  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 3MX  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 3MX  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 3MX  CONST_06  C8   C3   C4   C5      0.00   0.0  0
 3MX  CONST_07  C7   C8   C3   C1    180.00   0.0  0
 3MX  CONST_08  C5   C4   C3   C1    180.00   0.0  0
 3MX  CONST_09  O11  C7   C8   C3    180.00   0.0  0
 3MX  CONST_10  O9   C5   C4   C3    180.00   0.0  0
 3MX  CONST_11  O10  C6   C5   C4    180.00   0.0  0
 3MX  CONST_12  O11  C7   C6   C5    180.00   0.0  0
 3MX  CONST_13  O9   C5   C6   C7    180.00   0.0  0
 3MX  CONST_14  O10  C6   C7   C8    180.00   0.0  0
 3MX  CONST_15  H2   C8   C3   C4    180.00   0.0  0
 3MX  CONST_16  H1   C4   C5   C6    180.00   0.0  0
 3MX  Var_01    O12  C1   C3   C4      0.28  30.0  2
 3MX  Var_02    C14  C13  C1   C3    179.59  30.0  3
 3MX  Var_03    C15  C14  C13  C1    179.44  30.0  2
 3MX  Var_04    C16  C15  C14  C13   178.55  30.0  3
 3MX  Var_05    C17  C16  C15  C14   179.73  30.0  3
 3MX  Var_06    C18  C17  C16  C15   178.90  30.0  3
 3MX  Var_07    C19  C18  C17  C16   179.85  30.0  3
 3MX  Var_08    C20  C19  C18  C17   179.47  30.0  2
 3MX  Var_09    C21  C20  C19  C18  -179.97  30.0  2
 3MX  Var_10    H20  C21  C20  C19   -59.85  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
 3MX  plan-1  C1   0.020
 3MX  plan-1  C3   0.020
 3MX  plan-1  C4   0.020
 3MX  plan-1  C5   0.020
 3MX  plan-1  C6   0.020
 3MX  plan-1  C7   0.020
 3MX  plan-1  C8   0.020
 3MX  plan-1  O9   0.020
 3MX  plan-1  O10  0.020
 3MX  plan-1  O11  0.020
 3MX  plan-1  H1   0.020
 3MX  plan-1  H2   0.020
 3MX  plan-2  C1   0.020
 3MX  plan-2  C3   0.020
 3MX  plan-2  O12  0.020
 3MX  plan-2  C13  0.020

