# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:54:23 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-(3,4,5-trihydroxyphenyl)dodecan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC(=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
 3MJ  3MJ  1-(3,4,5-trihydroxyphenyl)dodecan-1-one  ligand  50  22  .  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_3MJ
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
 3MJ  C7   C  CR16  0  -0.429  -5.0224  -1.1222   0.0939
 3MJ  C5   C  CR6   0   0.189  -6.3677   0.8722  -0.0755
 3MJ  C6   C  CR6   0   0.294  -6.2638  -0.5178   0.0251
 3MJ  C4   C  CR6   0   0.335  -5.2107   1.6498  -0.1045
 3MJ  C3   C  CR16  0  -0.423  -3.9659   1.0412  -0.0358
 3MJ  C2   C  CR6   0  -0.008  -3.8645  -0.3438   0.0633
 3MJ  C1   C  C     0   0.377  -2.5441  -1.0267   0.1347
 3MJ  C11  C  CH2   0  -0.587  -1.2981  -0.1767   0.0917
 3MJ  C12  C  CH2   0  -0.411   0.0073  -0.9541   0.1397
 3MJ  C13  C  CH2   0  -0.415   1.2125  -0.0209   0.1113
 3MJ  C14  C  CH2   0  -0.414   2.5448  -0.7594   0.1123
 3MJ  C15  C  CH2   0  -0.412   3.7440   0.1807   0.0955
 3MJ  C16  C  CH2   0  -0.412   5.0831  -0.5448   0.0613
 3MJ  C17  C  CH2   0  -0.411   6.2764   0.4030   0.0475
 3MJ  O8   O  OH1   0  -0.633  -5.2713   2.9930  -0.1998
 3MJ  O9   O  OH1   0  -0.632  -7.5505   1.5137  -0.1498
 3MJ  O10  O  OH1   0  -0.642  -7.4365  -1.1867   0.0474
 3MJ  C18  C  CH2   0  -0.412   7.6190  -0.3153  -0.0053
 3MJ  C19  C  CH2   0  -0.406   8.8086   0.6368  -0.0178
 3MJ  C20  C  CH2   0  -0.419  10.1543  -0.0763  -0.0729
 3MJ  C21  C  CH3   0  -0.662  11.3322   0.8886  -0.0836
 3MJ  O22  O  O     0  -0.407  -2.4813  -2.2365   0.2250
 3MJ  H1   H  HCR6  0   0.274  -4.9524  -2.2006   0.1685
 3MJ  H2   H  HCR6  0   0.270  -3.0892   1.6741  -0.0619
 3MJ  H3   H  HCH2  0   0.266  -1.3307   0.4390  -0.8137
 3MJ  H4   H  HCH2  0   0.267  -1.3419   0.5365   0.9227
 3MJ  H5   H  HCH2  0   0.222   0.0456  -1.5705   1.0418
 3MJ  H6   H  HCH2  0   0.222   0.0617  -1.6430  -0.7077
 3MJ  H7   H  HCH2  0   0.210   1.1564   0.6194  -0.7762
 3MJ  H8   H  HCH2  0   0.211   1.1696   0.6541   0.9734
 3MJ  H9   H  HCH2  0   0.208   2.6032  -1.4086   0.9931
 3MJ  H10  H  HCH2  0   0.208   2.5920  -1.4239  -0.7576
 3MJ  H11  H  HCH2  0   0.207   3.6701   0.8441  -0.7737
 3MJ  H12  H  HCH2  0   0.207   3.7052   0.8322   0.9759
 3MJ  H13  H  HCH2  0   0.207   5.1592  -1.2118   0.9274
 3MJ  H14  H  HCH2  0   0.206   5.1234  -1.1915  -0.8225
 3MJ  H15  H  HCH2  0   0.206   6.1921   1.0774  -0.8121
 3MJ  H16  H  HCH2  0   0.206   6.2409   1.0424   0.9368
 3MJ  H17  H  HOH1  0   0.475  -6.1863   3.2936  -0.2504
 3MJ  H18  H  HOH1  0   0.485  -8.2876   0.8926  -0.1087
 3MJ  H19  H  HOH1  0   0.485  -7.2891  -2.1366   0.1156
 3MJ  H20  H  HCH2  0   0.206   7.7043  -0.9909   0.8533
 3MJ  H21  H  HCH2  0   0.206   7.6554  -0.9529  -0.8959
 3MJ  H22  H  HCH2  0   0.205   8.7221   1.3136  -0.8754
 3MJ  H23  H  HCH2  0   0.205   8.7727   1.2739   0.8734
 3MJ  H24  H  HCH2  0   0.210  10.2405  -0.7522   0.7838
 3MJ  H25  H  HCH2  0   0.210  10.1911  -0.7116  -0.9635
 3MJ  H26  H  HCH3  0   0.216  11.2886   1.5515  -0.9496
 3MJ  H27  H  HCH3  0   0.215  11.3344   1.5148   0.8106
 3MJ  H28  H  HCH3  0   0.225  12.2860   0.3607  -0.1191

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
 3MJ  C16  C17  single    1.524  0.020  1.524
 3MJ  C16  C15  single    1.523  0.020  1.523
 3MJ  C17  C18  single    1.524  0.020  1.524
 3MJ  O10  C6   single    1.350  0.020  1.350
 3MJ  O22  C1   double    1.215  0.020  1.215
 3MJ  C18  C19  single    1.524  0.020  1.524
 3MJ  C7   C6   aromatic  1.382  0.020  1.382
 3MJ  C7   C2   aromatic  1.396  0.020  1.396
 3MJ  C6   C5   aromatic  1.398  0.020  1.398
 3MJ  C15  C14  single    1.524  0.020  1.524
 3MJ  C1   C2   single    1.488  0.020  1.488
 3MJ  C1   C11  single    1.509  0.020  1.509
 3MJ  C14  C13  single    1.523  0.020  1.523
 3MJ  C2   C3   aromatic  1.392  0.020  1.392
 3MJ  C19  C20  single    1.524  0.020  1.524
 3MJ  C5   O9   single    1.348  0.020  1.348
 3MJ  C5   C4   aromatic  1.394  0.020  1.394
 3MJ  C3   C4   aromatic  1.387  0.020  1.387
 3MJ  C11  C12  single    1.520  0.020  1.520
 3MJ  C4   O8   single    1.348  0.020  1.348
 3MJ  C13  C12  single    1.524  0.020  1.524
 3MJ  C20  C21  single    1.523  0.020  1.523
 3MJ  C7   H1   single    0.930  0.020  1.080
 3MJ  C3   H2   single    0.930  0.020  1.080
 3MJ  C11  H3   single    0.970  0.020  1.090
 3MJ  C11  H4   single    0.970  0.020  1.090
 3MJ  C12  H5   single    0.970  0.020  1.090
 3MJ  C12  H6   single    0.970  0.020  1.090
 3MJ  C13  H7   single    0.970  0.020  1.090
 3MJ  C13  H8   single    0.970  0.020  1.090
 3MJ  C14  H9   single    0.970  0.020  1.090
 3MJ  C14  H10  single    0.970  0.020  1.090
 3MJ  C15  H11  single    0.970  0.020  1.090
 3MJ  C15  H12  single    0.970  0.020  1.090
 3MJ  C16  H13  single    0.970  0.020  1.090
 3MJ  C16  H14  single    0.970  0.020  1.090
 3MJ  C17  H15  single    0.970  0.020  1.090
 3MJ  C17  H16  single    0.970  0.020  1.090
 3MJ  O8   H17  single    0.850  0.020  0.980
 3MJ  O9   H18  single    0.850  0.020  0.980
 3MJ  O10  H19  single    0.850  0.020  0.980
 3MJ  C18  H20  single    0.970  0.020  1.090
 3MJ  C18  H21  single    0.970  0.020  1.090
 3MJ  C19  H22  single    0.970  0.020  1.090
 3MJ  C19  H23  single    0.970  0.020  1.090
 3MJ  C20  H24  single    0.970  0.020  1.090
 3MJ  C20  H25  single    0.970  0.020  1.090
 3MJ  C21  H26  single    0.970  0.020  1.090
 3MJ  C21  H27  single    0.970  0.020  1.090
 3MJ  C21  H28  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
 3MJ  H1   C7   C2   120.21  3.000
 3MJ  H1   C7   C6   119.78  3.000
 3MJ  C2   C7   C6   120.01  3.000
 3MJ  O9   C5   C4   117.50  3.000
 3MJ  C4   C5   C6   119.64  3.000
 3MJ  O9   C5   C6   122.86  3.000
 3MJ  O10  C6   C5   115.43  3.000
 3MJ  C5   C6   C7   120.34  3.000
 3MJ  O10  C6   C7   124.23  3.000
 3MJ  O8   C4   C3   118.75  3.000
 3MJ  O8   C4   C5   121.32  3.000
 3MJ  C3   C4   C5   119.93  3.000
 3MJ  H2   C3   C2   121.65  3.000
 3MJ  H2   C3   C4   117.99  3.000
 3MJ  C2   C3   C4   120.35  3.000
 3MJ  C1   C2   C3   121.63  3.000
 3MJ  C3   C2   C7   119.73  3.000
 3MJ  C1   C2   C7   118.63  3.000
 3MJ  O22  C1   C11  121.36  3.000
 3MJ  C11  C1   C2   118.22  3.000
 3MJ  O22  C1   C2   120.42  3.000
 3MJ  H4   C11  H3   105.06  3.000
 3MJ  H4   C11  C12  110.07  3.000
 3MJ  H3   C11  C12  109.82  3.000
 3MJ  H4   C11  C1   108.18  3.000
 3MJ  H3   C11  C1   108.40  3.000
 3MJ  C12  C11  C1   114.84  3.000
 3MJ  H6   C12  H5   106.41  3.000
 3MJ  H6   C12  C13  109.39  3.000
 3MJ  H5   C12  C13  109.44  3.000
 3MJ  H6   C12  C11  109.91  3.000
 3MJ  H5   C12  C11  110.15  3.000
 3MJ  C13  C12  C11  111.42  3.000
 3MJ  H8   C13  H7   105.97  3.000
 3MJ  H8   C13  C14  109.41  3.000
 3MJ  H7   C13  C14  109.18  3.000
 3MJ  H8   C13  C12  109.36  3.000
 3MJ  H7   C13  C12  109.41  3.000
 3MJ  C14  C13  C12  113.24  3.000
 3MJ  H10  C14  H9   106.06  3.000
 3MJ  H10  C14  C15  109.35  3.000
 3MJ  H9   C14  C15  109.42  3.000
 3MJ  H10  C14  C13  109.34  3.000
 3MJ  H9   C14  C13  109.54  3.000
 3MJ  C15  C14  C13  112.90  3.000
 3MJ  H12  C15  H11  105.96  3.000
 3MJ  H12  C15  C16  109.40  3.000
 3MJ  H11  C15  C16  109.26  3.000
 3MJ  H12  C15  C14  109.27  3.000
 3MJ  H11  C15  C14  109.22  3.000
 3MJ  C16  C15  C14  113.46  3.000
 3MJ  H14  C16  H13  106.00  3.000
 3MJ  H14  C16  C17  109.33  3.000
 3MJ  H13  C16  C17  109.35  3.000
 3MJ  H14  C16  C15  109.35  3.000
 3MJ  H13  C16  C15  109.46  3.000
 3MJ  C17  C16  C15  113.10  3.000
 3MJ  H16  C17  H15  105.96  3.000
 3MJ  H16  C17  C18  109.37  3.000
 3MJ  H15  C17  C18  109.31  3.000
 3MJ  H16  C17  C16  109.28  3.000
 3MJ  H15  C17  C16  109.25  3.000
 3MJ  C18  C17  C16  113.40  3.000
 3MJ  H17  O8   C4   110.91  3.000
 3MJ  H18  O9   C5   111.21  3.000
 3MJ  H19  O10  C6   110.90  3.000
 3MJ  H21  C18  H20  105.99  3.000
 3MJ  H21  C18  C19  109.33  3.000
 3MJ  H20  C18  C19  109.32  3.000
 3MJ  H21  C18  C17  109.37  3.000
 3MJ  H20  C18  C17  109.40  3.000
 3MJ  C19  C18  C17  113.18  3.000
 3MJ  H23  C19  H22  105.95  3.000
 3MJ  H23  C19  C20  109.28  3.000
 3MJ  H22  C19  C20  109.29  3.000
 3MJ  H23  C19  C18  109.33  3.000
 3MJ  H22  C19  C18  109.31  3.000
 3MJ  C20  C19  C18  113.41  3.000
 3MJ  H25  C20  H24  106.00  3.000
 3MJ  H25  C20  C21  109.63  3.000
 3MJ  H24  C20  C21  109.63  3.000
 3MJ  H25  C20  C19  109.31  3.000
 3MJ  H24  C20  C19  109.28  3.000
 3MJ  C21  C20  C19  112.76  3.000
 3MJ  H28  C21  H27  107.60  3.000
 3MJ  H28  C21  H26  107.64  3.000
 3MJ  H27  C21  H26  107.55  3.000
 3MJ  H28  C21  C20  111.72  3.000
 3MJ  H27  C21  C20  111.06  3.000
 3MJ  H26  C21  C20  111.07  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
 3MJ  CONST_01  C4   C5   C6   C7      0.00   0.0  0
 3MJ  CONST_02  C4   C3   C2   C7      0.00   0.0  0
 3MJ  CONST_03  C2   C7   C6   C5      0.00   0.0  0
 3MJ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 3MJ  CONST_05  C3   C2   C7   C6      0.00   0.0  0
 3MJ  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 3MJ  CONST_07  O9   C5   C6   C7    180.00   0.0  0
 3MJ  CONST_08  C1   C2   C7   C6    180.00   0.0  0
 3MJ  CONST_09  O8   C4   C5   C6    180.00   0.0  0
 3MJ  CONST_10  O10  C6   C5   C4    180.00   0.0  0
 3MJ  CONST_11  C1   C2   C3   C4    180.00   0.0  0
 3MJ  CONST_12  O9   C5   C4   C3    180.00   0.0  0
 3MJ  CONST_13  O10  C6   C7   C2    180.00   0.0  0
 3MJ  CONST_14  O8   C4   C3   C2    180.00   0.0  0
 3MJ  CONST_15  H2   C3   C2   C7    180.00   0.0  0
 3MJ  CONST_16  H1   C7   C6   C5    180.00   0.0  0
 3MJ  Var_01    O22  C1   C2   C7     -0.39  30.0  2
 3MJ  Var_02    C12  C11  C1   C2   -178.75  30.0  3
 3MJ  Var_03    C13  C12  C11  C1   -179.21  30.0  3
 3MJ  Var_04    C14  C13  C12  C11  -178.14  30.0  1
 3MJ  Var_05    C15  C14  C13  C12  -179.53  30.0  1
 3MJ  Var_06    C16  C15  C14  C13  -178.57  30.0  1
 3MJ  Var_07    C17  C16  C15  C14  -179.88  30.0  1
 3MJ  Var_08    C18  C17  C16  C15  -179.24  30.0  3
 3MJ  Var_09    C19  C18  C17  C16  -179.95  30.0  3
 3MJ  Var_10    C20  C19  C18  C17  -179.90  30.0  3
 3MJ  Var_11    C21  C20  C19  C18  -179.96  30.0  3
 3MJ  Var_12    H26  C21  C20  C19   -60.03  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
 3MJ  plan-1  C7   0.020
 3MJ  plan-1  C5   0.020
 3MJ  plan-1  C6   0.020
 3MJ  plan-1  C4   0.020
 3MJ  plan-1  C3   0.020
 3MJ  plan-1  C2   0.020
 3MJ  plan-1  C1   0.020
 3MJ  plan-1  O8   0.020
 3MJ  plan-1  O9   0.020
 3MJ  plan-1  O10  0.020
 3MJ  plan-1  H1   0.020
 3MJ  plan-1  H2   0.020
 3MJ  plan-2  C2   0.020
 3MJ  plan-2  C1   0.020
 3MJ  plan-2  C11  0.020
 3MJ  plan-2  O22  0.020

