# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:39:27 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 1-(2,3,4-trihydroxyphenyl)nonan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC(=O)c1ccc(O)c(O)c1O
#
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
 3MZ  3MZ  1-(2,3,4-trihydroxyphenyl)nonan-1-one  ligand  41  19  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3MZ
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
 3MZ  C4   C  CR16  0  -0.387  -3.7122  -1.9013   0.0828
 3MZ  C13  C  CH2   0  -0.417   2.7743  -0.3823   0.0902
 3MZ  C15  C  CH2   0  -0.412   5.3108  -0.5815   0.0252
 3MZ  C17  C  CH2   0  -0.419   7.8501  -0.7702  -0.0538
 3MZ  C2   C  CR6   0  -0.170  -2.2909   0.0566   0.1428
 3MZ  C11  C  CH2   0  -0.579   0.2619  -0.1953   0.1376
 3MZ  C12  C  CH2   0  -0.411   1.5793   0.5639   0.1094
 3MZ  C16  C  CH2   0  -0.407   6.6410   0.1576  -0.0446
 3MZ  C18  C  CH3   0  -0.662   9.1698  -0.0150  -0.1343
 3MZ  C1   C  C     0   0.440  -0.9645   0.6786   0.1633
 3MZ  C3   C  CR16  0  -0.313  -2.4602  -1.3337   0.1029
 3MZ  C5   C  CR6   0   0.285  -4.8426  -1.0802   0.1010
 3MZ  C6   C  CR6   0   0.206  -4.7128   0.3041   0.1414
 3MZ  C7   C  CR6   0   0.289  -3.4400   0.8772   0.1631
 3MZ  O8   O  OH1   0  -0.623  -3.3806   2.2073   0.2035
 3MZ  O9   O  OH1   0  -0.629  -5.7751   1.1399   0.1603
 3MZ  O10  O  OH1   0  -0.631  -6.1003  -1.5519   0.0821
 3MZ  C14  C  CH2   0  -0.413   4.1073   0.3530   0.0388
 3MZ  O19  O  O     0  -0.468  -0.8502   1.9028   0.2030
 3MZ  H1   H  HCR6  0   0.280  -3.8262  -2.9778   0.0519
 3MZ  H2   H  HCH2  0   0.212   2.7458  -1.0250   0.9771
 3MZ  H3   H  HCH2  0   0.212   2.6960  -1.0529  -0.7727
 3MZ  H4   H  HCH2  0   0.207   5.2296  -1.2646  -0.8278
 3MZ  H5   H  HCH2  0   0.207   5.2906  -1.2125   0.9210
 3MZ  H6   H  HCH2  0   0.210   7.8356  -1.3921   0.8468
 3MZ  H7   H  HCH2  0   0.210   7.7692  -1.4601  -0.8994
 3MZ  H8   H  HCH2  0   0.270   0.1949  -0.8609  -0.7293
 3MZ  H9   H  HCH2  0   0.273   0.2279  -0.8565   1.0106
 3MZ  H10  H  HCH2  0   0.224   1.6526   1.2208   0.9798
 3MZ  H11  H  HCH2  0   0.224   1.6174   1.2117  -0.7706
 3MZ  H12  H  HCH2  0   0.206   6.6607   0.7855  -0.9429
 3MZ  H13  H  HCH2  0   0.206   6.7205   0.8451   0.8052
 3MZ  H14  H  HCH3  0   0.215   9.2237   0.5850  -1.0449
 3MZ  H15  H  HCH3  0   0.215   9.2867   0.6643   0.7127
 3MZ  H16  H  HCH3  0   0.226  10.0244  -0.6925  -0.1341
 3MZ  H17  H  HCR6  0   0.271  -1.5997  -1.9873   0.0886
 3MZ  H18  H  HOH1  0   0.477  -2.4241   2.4471   0.2171
 3MZ  H19  H  HOH1  0   0.474  -6.5969   0.6358   0.1586
 3MZ  H20  H  HOH1  0   0.488  -6.1122  -2.5157   0.0648
 3MZ  H21  H  HCH2  0   0.208   4.1346   0.9913  -0.8515
 3MZ  H22  H  HCH2  0   0.209   4.1835   1.0288   0.8979

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
 3MZ  O8   C7   single    1.332  0.020  1.332
 3MZ  C12  C11  single    1.521  0.020  1.521
 3MZ  C12  C13  single    1.524  0.020  1.524
 3MZ  O9   C6   single    1.352  0.020  1.352
 3MZ  C11  C1   single    1.506  0.020  1.506
 3MZ  C7   C6   aromatic  1.396  0.020  1.396
 3MZ  C7   C2   aromatic  1.412  0.020  1.412
 3MZ  C14  C13  single    1.523  0.020  1.523
 3MZ  C14  C15  single    1.524  0.020  1.524
 3MZ  C6   C5   aromatic  1.391  0.020  1.391
 3MZ  C1   C2   single    1.465  0.020  1.465
 3MZ  C1   O19  double    1.230  0.020  1.230
 3MZ  C2   C3   aromatic  1.401  0.020  1.401
 3MZ  C16  C15  single    1.523  0.020  1.523
 3MZ  C16  C17  single    1.524  0.020  1.524
 3MZ  C5   O10  single    1.343  0.020  1.343
 3MZ  C5   C4   aromatic  1.397  0.020  1.397
 3MZ  C17  C18  single    1.523  0.020  1.523
 3MZ  C3   C4   aromatic  1.375  0.020  1.375
 3MZ  C4   H1   single    0.930  0.020  1.080
 3MZ  C13  H2   single    0.970  0.020  1.090
 3MZ  C13  H3   single    0.970  0.020  1.090
 3MZ  C15  H4   single    0.970  0.020  1.090
 3MZ  C15  H5   single    0.970  0.020  1.090
 3MZ  C17  H6   single    0.970  0.020  1.090
 3MZ  C17  H7   single    0.970  0.020  1.090
 3MZ  C11  H8   single    0.970  0.020  1.090
 3MZ  C11  H9   single    0.970  0.020  1.090
 3MZ  C12  H10  single    0.970  0.020  1.090
 3MZ  C12  H11  single    0.970  0.020  1.090
 3MZ  C16  H12  single    0.970  0.020  1.090
 3MZ  C16  H13  single    0.970  0.020  1.090
 3MZ  C18  H14  single    0.970  0.020  1.090
 3MZ  C18  H15  single    0.970  0.020  1.090
 3MZ  C18  H16  single    0.970  0.020  1.090
 3MZ  C3   H17  single    0.930  0.020  1.080
 3MZ  O8   H18  single    0.850  0.020  0.980
 3MZ  O9   H19  single    0.850  0.020  0.980
 3MZ  O10  H20  single    0.850  0.020  0.980
 3MZ  C14  H21  single    0.970  0.020  1.090
 3MZ  C14  H22  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
 3MZ  H1   C4   C5   119.95  3.000
 3MZ  H1   C4   C3   120.45  3.000
 3MZ  C5   C4   C3   119.60  3.000
 3MZ  H3   C13  H2   106.06  3.000
 3MZ  H3   C13  C14  109.35  3.000
 3MZ  H2   C13  C14  109.46  3.000
 3MZ  H3   C13  C12  109.50  3.000
 3MZ  H2   C13  C12  109.49  3.000
 3MZ  C14  C13  C12  112.76  3.000
 3MZ  H5   C15  H4   106.02  3.000
 3MZ  H5   C15  C14  109.35  3.000
 3MZ  H4   C15  C14  109.32  3.000
 3MZ  H5   C15  C16  109.44  3.000
 3MZ  H4   C15  C16  109.36  3.000
 3MZ  C14  C15  C16  113.11  3.000
 3MZ  H7   C17  H6   106.05  3.000
 3MZ  H7   C17  C18  109.63  3.000
 3MZ  H6   C17  C18  109.68  3.000
 3MZ  H7   C17  C16  109.26  3.000
 3MZ  H6   C17  C16  109.29  3.000
 3MZ  C18  C17  C16  112.70  3.000
 3MZ  C7   C2   C3   118.60  3.000
 3MZ  C3   C2   C1   122.07  3.000
 3MZ  C7   C2   C1   119.33  3.000
 3MZ  H9   C11  H8   105.19  3.000
 3MZ  H9   C11  C1   108.14  3.000
 3MZ  H8   C11  C1   108.44  3.000
 3MZ  H9   C11  C12  110.06  3.000
 3MZ  H8   C11  C12  109.99  3.000
 3MZ  C1   C11  C12  114.58  3.000
 3MZ  H11  C12  H10  106.42  3.000
 3MZ  H11  C12  C11  109.93  3.000
 3MZ  H10  C12  C11  110.08  3.000
 3MZ  H11  C12  C13  109.29  3.000
 3MZ  H10  C12  C13  109.30  3.000
 3MZ  C11  C12  C13  111.68  3.000
 3MZ  H13  C16  H12  105.95  3.000
 3MZ  H13  C16  C17  109.21  3.000
 3MZ  H12  C16  C17  109.24  3.000
 3MZ  H13  C16  C15  109.40  3.000
 3MZ  H12  C16  C15  109.34  3.000
 3MZ  C17  C16  C15  113.43  3.000
 3MZ  H16  C18  H15  107.60  3.000
 3MZ  H16  C18  H14  107.62  3.000
 3MZ  H15  C18  H14  107.45  3.000
 3MZ  H16  C18  C17  111.78  3.000
 3MZ  H15  C18  C17  111.12  3.000
 3MZ  H14  C18  C17  111.07  3.000
 3MZ  O19  C1   C11  120.15  3.000
 3MZ  O19  C1   C2   120.47  3.000
 3MZ  C11  C1   C2   119.38  3.000
 3MZ  H17  C3   C2   120.29  3.000
 3MZ  H17  C3   C4   118.38  3.000
 3MZ  C2   C3   C4   121.34  3.000
 3MZ  O10  C5   C6   115.93  3.000
 3MZ  O10  C5   C4   123.43  3.000
 3MZ  C6   C5   C4   120.65  3.000
 3MZ  O9   C6   C7   117.55  3.000
 3MZ  C7   C6   C5   119.61  3.000
 3MZ  O9   C6   C5   122.85  3.000
 3MZ  O8   C7   C6   116.81  3.000
 3MZ  C6   C7   C2   120.21  3.000
 3MZ  O8   C7   C2   122.98  3.000
 3MZ  H18  O8   C7   106.65  3.000
 3MZ  H19  O9   C6   110.28  3.000
 3MZ  H20  O10  C5   111.28  3.000
 3MZ  H22  C14  H21  106.02  3.000
 3MZ  H22  C14  C15  109.29  3.000
 3MZ  H21  C14  C15  109.29  3.000
 3MZ  H22  C14  C13  109.40  3.000
 3MZ  H21  C14  C13  109.29  3.000
 3MZ  C15  C14  C13  113.30  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
 3MZ  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 3MZ  CONST_02  C7   C2   C3   C4      0.00   0.0  0
 3MZ  CONST_03  C5   C6   C7   C2      0.00   0.0  0
 3MZ  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 3MZ  CONST_05  C6   C7   C2   C3      0.00   0.0  0
 3MZ  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 3MZ  CONST_07  O9   C6   C5   C4    180.00   0.0  0
 3MZ  CONST_08  C1   C2   C3   C4    180.00   0.0  0
 3MZ  CONST_09  O9   C6   C7   C2    180.00   0.0  0
 3MZ  CONST_10  C6   C7   C2   C1    180.00   0.0  0
 3MZ  CONST_11  O8   C7   C2   C3    180.00   0.0  0
 3MZ  CONST_12  O10  C5   C4   C3    180.00   0.0  0
 3MZ  CONST_13  O8   C7   C6   C5    180.00   0.0  0
 3MZ  CONST_14  O10  C5   C6   C7    180.00   0.0  0
 3MZ  CONST_15  H1   C4   C3   C2    180.00   0.0  0
 3MZ  CONST_16  H17  C3   C4   C5    180.00   0.0  0
 3MZ  Var_01    C7   C2   C1   C11  -179.82  30.0  2
 3MZ  Var_02    C12  C11  C1   C2    177.81  30.0  1
 3MZ  Var_03    C1   C11  C12  C13   179.76  30.0  3
 3MZ  Var_04    C16  C15  C14  C13   179.25  30.0  3
 3MZ  Var_05    C12  C13  C14  C15   179.76  30.0  3
 3MZ  Var_06    C18  C17  C16  C15   179.57  30.0  3
 3MZ  Var_07    C14  C15  C16  C17   179.80  30.0  3
 3MZ  Var_08    C14  C13  C12  C11   179.06  30.0  3
 3MZ  Var_09    H14  C18  C17  C16   -60.11  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
 3MZ  plan-1  C4   0.020
 3MZ  plan-1  C2   0.020
 3MZ  plan-1  C1   0.020
 3MZ  plan-1  C3   0.020
 3MZ  plan-1  C5   0.020
 3MZ  plan-1  C6   0.020
 3MZ  plan-1  C7   0.020
 3MZ  plan-1  O8   0.020
 3MZ  plan-1  O9   0.020
 3MZ  plan-1  O10  0.020
 3MZ  plan-1  H1   0.020
 3MZ  plan-1  H17  0.020
 3MZ  plan-2  C2   0.020
 3MZ  plan-2  C11  0.020
 3MZ  plan-2  C1   0.020
 3MZ  plan-2  O19  0.020

