# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:18:24 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-(3,4,5-trihydroxyphenyl)octan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=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
 3NB  3NB  1-(3,4,5-trihydroxyphenyl)octan-1-one  ligand  38  18  .  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_3NB
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
 3NB  C16  C  CH2   0  -0.407  -5.8419  -0.6011   0.0254
 3NB  C18  C  CH3   0  -0.663  -8.3566  -0.9477   0.0529
 3NB  C17  C  CH2   0  -0.419  -7.2150   0.0595   0.0599
 3NB  C14  C  CH2   0  -0.415  -3.3190  -0.2528  -0.0130
 3NB  C13  C  CH2   0  -0.410  -2.1863   0.7662   0.0020
 3NB  C15  C  CH2   0  -0.413  -4.6946   0.4008   0.0336
 3NB  C12  C  CH2   0  -0.587  -0.8182   0.1063  -0.0663
 3NB  C1   C  C     0   0.377   0.3373   1.0778  -0.0465
 3NB  C2   C  CR6   0  -0.007   1.7229   0.5386  -0.1011
 3NB  C3   C  CR16  0  -0.460   1.9775  -0.8312  -0.1702
 3NB  C4   C  CR6   0   0.314   3.2828  -1.2918  -0.2181
 3NB  C5   C  CR6   0   0.189   4.3486  -0.3915  -0.1942
 3NB  C6   C  CR6   0   0.322   4.0927   0.9798  -0.1256
 3NB  C7   C  CR16  0  -0.396   2.7869   1.4376  -0.0796
 3NB  O8   O  OH1   0  -0.634   5.0993   1.8759  -0.1034
 3NB  O9   O  OH1   0  -0.632   5.6380  -0.7807  -0.2350
 3NB  O10  O  OH1   0  -0.643   3.6244  -2.5966  -0.2860
 3NB  O11  O  O     0  -0.406   0.1485   2.2762   0.0136
 3NB  H1   H  HCH2  0   0.206  -5.7420  -1.2758   0.8831
 3NB  H2   H  HCH2  0   0.206  -5.7665  -1.2338  -0.8663
 3NB  H3   H  HCH3  0   0.225  -9.3289  -0.4541   0.0741
 3NB  H4   H  HCH3  0   0.216  -8.3232  -1.5730  -0.8413
 3NB  H5   H  HCH3  0   0.216  -8.3023  -1.6091   0.9193
 3NB  H6   H  HCH2  0   0.210  -7.2887   0.6933   0.9493
 3NB  H7   H  HCH2  0   0.210  -7.3130   0.7322  -0.7981
 3NB  H8   H  HCH2  0   0.210  -3.2422  -0.8746  -0.9119
 3NB  H9   H  HCH2  0   0.211  -3.2098  -0.9351   0.8372
 3NB  H10  H  HCH2  0   0.221  -2.3075   1.4525  -0.8402
 3NB  H11  H  HCH2  0   0.222  -2.2603   1.3758   0.9065
 3NB  H12  H  HCH2  0   0.208  -4.8008   1.0797  -0.8198
 3NB  H13  H  HCH2  0   0.208  -4.7679   1.0286   0.9287
 3NB  H14  H  HCH2  0   0.266  -0.6942  -0.5985   0.7635
 3NB  H15  H  HCH2  0   0.267  -0.7408  -0.5050  -0.9726
 3NB  H16  H  HCR6  0   0.279   1.1711  -1.5529  -0.1889
 3NB  H17  H  HCR6  0   0.264   2.6061   2.5031  -0.0256
 3NB  H18  H  HOH1  0   0.475   5.9552   1.4318  -0.1254
 3NB  H19  H  HOH1  0   0.485   5.7130  -1.7421  -0.2658
 3NB  H20  H  HOH1  0   0.485   2.8424  -3.1597  -0.2963

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
 3NB  C18  C17  single    1.522  0.020  1.522
 3NB  O10  C4   single    1.350  0.020  1.350
 3NB  O11  C1   double    1.215  0.020  1.215
 3NB  C16  C17  single    1.524  0.020  1.524
 3NB  C16  C15  single    1.523  0.020  1.523
 3NB  C4   C3   aromatic  1.385  0.020  1.385
 3NB  C4   C5   aromatic  1.395  0.020  1.395
 3NB  C3   C2   aromatic  1.395  0.020  1.395
 3NB  O9   C5   single    1.347  0.020  1.347
 3NB  C5   C6   aromatic  1.397  0.020  1.397
 3NB  C1   C2   single    1.488  0.020  1.488
 3NB  C1   C12  single    1.510  0.020  1.510
 3NB  C2   C7   aromatic  1.393  0.020  1.393
 3NB  C15  C14  single    1.524  0.020  1.524
 3NB  C14  C13  single    1.524  0.020  1.524
 3NB  C6   C7   aromatic  1.384  0.020  1.384
 3NB  C6   O8   single    1.348  0.020  1.348
 3NB  C13  C12  single    1.521  0.020  1.521
 3NB  C16  H1   single    0.970  0.020  1.090
 3NB  C16  H2   single    0.970  0.020  1.090
 3NB  C18  H3   single    0.970  0.020  1.090
 3NB  C18  H4   single    0.970  0.020  1.090
 3NB  C18  H5   single    0.970  0.020  1.090
 3NB  C17  H6   single    0.970  0.020  1.090
 3NB  C17  H7   single    0.970  0.020  1.090
 3NB  C14  H8   single    0.970  0.020  1.090
 3NB  C14  H9   single    0.970  0.020  1.090
 3NB  C13  H10  single    0.970  0.020  1.090
 3NB  C13  H11  single    0.970  0.020  1.090
 3NB  C15  H12  single    0.970  0.020  1.090
 3NB  C15  H13  single    0.970  0.020  1.090
 3NB  C12  H14  single    0.970  0.020  1.090
 3NB  C12  H15  single    0.970  0.020  1.090
 3NB  C3   H16  single    0.930  0.020  1.080
 3NB  C7   H17  single    0.930  0.020  1.080
 3NB  O8   H18  single    0.850  0.020  0.980
 3NB  O9   H19  single    0.850  0.020  0.980
 3NB  O10  H20  single    0.850  0.020  0.980

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
 3NB  H2   C16  H1   105.97  3.000
 3NB  H2   C16  C15  109.41  3.000
 3NB  H1   C16  C15  109.40  3.000
 3NB  H2   C16  C17  109.30  3.000
 3NB  H1   C16  C17  109.34  3.000
 3NB  C15  C16  C17  113.16  3.000
 3NB  H5   C18  H4   107.56  3.000
 3NB  H5   C18  H3   107.65  3.000
 3NB  H4   C18  H3   107.60  3.000
 3NB  H5   C18  C17  111.10  3.000
 3NB  H4   C18  C17  111.09  3.000
 3NB  H3   C18  C17  111.66  3.000
 3NB  H7   C17  H6   105.96  3.000
 3NB  H7   C17  C18  109.62  3.000
 3NB  H6   C17  C18  109.65  3.000
 3NB  H7   C17  C16  109.23  3.000
 3NB  H6   C17  C16  109.27  3.000
 3NB  C18  C17  C16  112.87  3.000
 3NB  H9   C14  H8   106.03  3.000
 3NB  H9   C14  C15  109.47  3.000
 3NB  H8   C14  C15  109.38  3.000
 3NB  H9   C14  C13  109.56  3.000
 3NB  H8   C14  C13  109.60  3.000
 3NB  C15  C14  C13  112.58  3.000
 3NB  H11  C13  H10  106.26  3.000
 3NB  H11  C13  C12  109.88  3.000
 3NB  H10  C13  C12  109.73  3.000
 3NB  H11  C13  C14  109.31  3.000
 3NB  H10  C13  C14  109.26  3.000
 3NB  C12  C13  C14  112.22  3.000
 3NB  H13  C15  H12  105.94  3.000
 3NB  H13  C15  C14  109.34  3.000
 3NB  H12  C15  C14  109.24  3.000
 3NB  H13  C15  C16  109.32  3.000
 3NB  H12  C15  C16  109.29  3.000
 3NB  C14  C15  C16  113.44  3.000
 3NB  H15  C12  H14  105.04  3.000
 3NB  H15  C12  C1   108.40  3.000
 3NB  H14  C12  C1   108.50  3.000
 3NB  H15  C12  C13  110.05  3.000
 3NB  H14  C12  C13  110.30  3.000
 3NB  C1   C12  C13  114.13  3.000
 3NB  O11  C1   C2   120.27  3.000
 3NB  C2   C1   C12  118.62  3.000
 3NB  O11  C1   C12  121.10  3.000
 3NB  C7   C2   C3   119.67  3.000
 3NB  C7   C2   C1   118.48  3.000
 3NB  C3   C2   C1   121.85  3.000
 3NB  H16  C3   C4   118.67  3.000
 3NB  H16  C3   C2   121.31  3.000
 3NB  C4   C3   C2   120.02  3.000
 3NB  O10  C4   C5   115.54  3.000
 3NB  C5   C4   C3   120.31  3.000
 3NB  O10  C4   C3   124.15  3.000
 3NB  O9   C5   C6   117.41  3.000
 3NB  C6   C5   C4   119.63  3.000
 3NB  O9   C5   C4   122.96  3.000
 3NB  O8   C6   C7   118.94  3.000
 3NB  O8   C6   C5   121.11  3.000
 3NB  C7   C6   C5   119.94  3.000
 3NB  H17  C7   C6   119.00  3.000
 3NB  H17  C7   C2   120.57  3.000
 3NB  C6   C7   C2   120.43  3.000
 3NB  H18  O8   C6   110.87  3.000
 3NB  H19  O9   C5   111.30  3.000
 3NB  H20  O10  C4   111.09  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
 3NB  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 3NB  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 3NB  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 3NB  CONST_04  C6   C7   C2   C3      0.00   0.0  0
 3NB  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 3NB  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 3NB  CONST_07  C4   C3   C2   C1    180.00   0.0  0
 3NB  CONST_08  C6   C7   C2   C1    180.00   0.0  0
 3NB  CONST_09  O10  C4   C3   C2    180.00   0.0  0
 3NB  CONST_10  O8   C6   C7   C2    180.00   0.0  0
 3NB  CONST_11  O9   C5   C4   C3    180.00   0.0  0
 3NB  CONST_12  O8   C6   C5   C4    180.00   0.0  0
 3NB  CONST_13  O10  C4   C5   C6    180.00   0.0  0
 3NB  CONST_14  O9   C5   C6   C7    180.00   0.0  0
 3NB  CONST_15  H17  C7   C2   C3    180.00   0.0  0
 3NB  CONST_16  H16  C3   C4   C5    180.00   0.0  0
 3NB  Var_01    C3   C2   C1   C12     0.03  30.0  2
 3NB  Var_02    C2   C1   C12  C13   179.65  30.0  1
 3NB  Var_03    C13  C14  C15  C16  -179.76  30.0  3
 3NB  Var_04    C15  C16  C17  C18  -179.94  30.0  1
 3NB  Var_05    C14  C15  C16  C17  -179.50  30.0  3
 3NB  Var_06    C1   C12  C13  C14  -179.68  30.0  3
 3NB  Var_07    C12  C13  C14  C15  -179.12  30.0  3
 3NB  Var_08    H3   C18  C17  C16  -179.79  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
 3NB  plan-1  C1   0.020
 3NB  plan-1  C2   0.020
 3NB  plan-1  C3   0.020
 3NB  plan-1  C4   0.020
 3NB  plan-1  C5   0.020
 3NB  plan-1  C6   0.020
 3NB  plan-1  C7   0.020
 3NB  plan-1  O8   0.020
 3NB  plan-1  O9   0.020
 3NB  plan-1  O10  0.020
 3NB  plan-1  H16  0.020
 3NB  plan-1  H17  0.020
 3NB  plan-2  C12  0.020
 3NB  plan-2  C1   0.020
 3NB  plan-2  C2   0.020
 3NB  plan-2  O11  0.020

