# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:45:27 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: octyl 3,4,5-trihydroxybenzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCOC(=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
 65D  65D  'octyl 3,4,5-trihydroxybenzoate'  ligand  42  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_65D
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
 65D  O3   O  OH1   0  -0.634    6.1655  -1.4782   0.0907
 65D  C4   C  CH2   0  -0.400   -4.6037  -0.2869   0.0465
 65D  C5   C  CH2   0  -0.414   -3.4978   0.7596   0.0183
 65D  C6   C  CH2   0  -0.450   -2.1022   0.1513   0.0939
 65D  C7   C  CH2   0  -0.142   -1.0420   1.2287   0.0702
 65D  C8   C  C     0   0.631    1.3177   1.3579   0.0937
 65D  C9   C  CR6   0  -0.062    2.5828   0.5774   0.1186
 65D  C10  C  CR16  0  -0.361    3.7759   1.2865   0.0900
 65D  C11  C  CR6   0   0.367    4.9822   0.5992   0.0942
 65D  C12  C  CR6   0   0.084    4.9812  -0.7934   0.1327
 65D  C13  C  CR6   0   0.347    3.7792  -1.4971   0.1346
 65D  C14  C  CR16  0  -0.429    2.5723  -0.8154   0.1369
 65D  O1   O  O     0  -0.477    1.2807   2.5665   0.0456
 65D  O2   O  OH1   0  -0.631    3.7738  -2.8452   0.1243
 65D  O    O  O2    0  -0.458    0.2453   0.5949   0.1232
 65D  C3   C  CH2   0  -0.403   -5.9966   0.3226  -0.0433
 65D  C2   C  CH2   0  -0.394   -7.1136  -0.7118  -0.0077
 65D  C1   C  CH2   0  -0.410   -8.5048  -0.0981  -0.1051
 65D  C    C  CH3   0  -0.642   -9.6153  -1.1378  -0.0664
 65D  H1   H  HOH1  0   0.465    6.4875  -1.6636   0.9805
 65D  H2   H  HCH2  0   0.207   -4.4614  -0.9902  -0.7805
 65D  H3   H  HCH2  0   0.207   -4.5227  -0.8783   0.9646
 65D  H4   H  HCH2  0   0.210   -3.5870   1.3563  -0.8956
 65D  H5   H  HCH2  0   0.212   -3.6390   1.4571   0.8502
 65D  H6   H  HOH1  0   0.451    6.8683   0.6734  -0.0508
 65D  H7   H  HCH2  0   0.228   -2.0065  -0.4409   1.0082
 65D  H8   H  HCH2  0   0.226   -1.9525  -0.5310  -0.7473
 65D  H9   H  HCH2  0   0.223   -1.1158   1.8261  -0.8417
 65D  H10  H  HCH2  0   0.226   -1.1527   1.9031   0.9222
 65D  H11  H  HCR6  0   0.258    3.7828   2.3667   0.0607
 65D  H12  H  HCR6  0   0.261    1.6458  -1.3730   0.1423
 65D  H13  H  HOH1  0   0.456    4.6794  -3.1638   0.0204
 65D  H14  H  HCH2  0   0.198   -6.1350   1.0340   0.7783
 65D  H15  H  HCH2  0   0.200   -6.9744  -1.4254  -0.8271
 65D  H16  H  HCH2  0   0.205   -8.6426   0.6173   0.7114
 65D  H17  H  HCH2  0   0.205   -8.5786   0.4845  -1.0287
 65D  H18  H  HCH3  0   0.210   -9.5229  -1.8444  -0.8926
 65D  H19  H  HCH3  0   0.210   -9.5860  -1.7126   0.8608
 65D  H20  H  HCH3  0   0.221  -10.6008  -0.6770  -0.1354
 65D  H21  H  HCH2  0   0.202   -6.0752   0.9092  -0.9654
 65D  H22  H  HCH2  0   0.202   -7.0393  -1.2980   0.9149
 65D  O4   O  OH1   0  -0.602    6.1313   1.2870   0.0529

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
 65D  O3   C12  single    1.369  0.020  1.369
 65D  O4   C11  single    1.340  0.020  1.340
 65D  C12  C11  aromatic  1.393  0.020  1.393
 65D  C12  C13  aromatic  1.393  0.020  1.393
 65D  O2   C13  single    1.348  0.020  1.348
 65D  C11  C10  aromatic  1.388  0.020  1.388
 65D  C13  C14  aromatic  1.386  0.020  1.386
 65D  C10  C9   aromatic  1.388  0.020  1.388
 65D  C14  C9   aromatic  1.393  0.020  1.393
 65D  C9   C8   single    1.487  0.020  1.487
 65D  C8   O    single    1.316  0.020  1.316
 65D  C8   O1   double    1.210  0.020  1.210
 65D  C4   C5   single    1.523  0.020  1.523
 65D  C4   C3   single    1.523  0.020  1.523
 65D  O    C7   single    1.436  0.020  1.436
 65D  C5   C6   single    1.524  0.020  1.524
 65D  C3   C2   single    1.523  0.020  1.523
 65D  C7   C6   single    1.512  0.020  1.512
 65D  C2   C1   single    1.524  0.020  1.524
 65D  C1   C    single    1.522  0.020  1.522
 65D  O3   H1   single    0.850  0.020  0.980
 65D  C4   H2   single    0.970  0.020  1.090
 65D  C4   H3   single    0.970  0.020  1.090
 65D  C5   H4   single    0.970  0.020  1.090
 65D  C5   H5   single    0.970  0.020  1.090
 65D  O4   H6   single    0.850  0.020  0.980
 65D  C6   H7   single    0.970  0.020  1.090
 65D  C6   H8   single    0.970  0.020  1.090
 65D  C7   H9   single    0.970  0.020  1.090
 65D  C7   H10  single    0.970  0.020  1.090
 65D  C10  H11  single    0.930  0.020  1.080
 65D  C14  H12  single    0.930  0.020  1.080
 65D  O2   H13  single    0.850  0.020  0.980
 65D  C3   H14  single    0.970  0.020  1.090
 65D  C2   H15  single    0.970  0.020  1.090
 65D  C1   H16  single    0.970  0.020  1.090
 65D  C1   H17  single    0.970  0.020  1.090
 65D  C    H18  single    0.970  0.020  1.090
 65D  C    H19  single    0.970  0.020  1.090
 65D  C    H20  single    0.970  0.020  1.090
 65D  C3   H21  single    0.970  0.020  1.090
 65D  C2   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
 65D  H1   O3   C12  110.91  3.000
 65D  H3   C4   H2   106.06  3.000
 65D  H3   C4   C3   109.46  3.000
 65D  H2   C4   C3   109.35  3.000
 65D  H3   C4   C5   109.45  3.000
 65D  H2   C4   C5   109.46  3.000
 65D  C3   C4   C5   112.84  3.000
 65D  H5   C5   H4   106.05  3.000
 65D  H5   C5   C6   109.55  3.000
 65D  H4   C5   C6   109.48  3.000
 65D  H5   C5   C4   109.27  3.000
 65D  H4   C5   C4   109.32  3.000
 65D  C6   C5   C4   112.94  3.000
 65D  H8   C6   H7   107.06  3.000
 65D  H8   C6   C7   109.67  3.000
 65D  H7   C6   C7   109.74  3.000
 65D  H8   C6   C5   109.64  3.000
 65D  H7   C6   C5   109.74  3.000
 65D  C7   C6   C5   110.91  3.000
 65D  H10  C7   H9   107.85  3.000
 65D  H10  C7   O    109.55  3.000
 65D  H9   C7   O    109.43  3.000
 65D  H10  C7   C6   110.90  3.000
 65D  H9   C7   C6   110.82  3.000
 65D  O    C7   C6   108.28  3.000
 65D  O    C8   O1   123.70  3.000
 65D  O1   C8   C9   123.43  3.000
 65D  O    C8   C9   112.86  3.000
 65D  C14  C9   C10  121.16  3.000
 65D  C14  C9   C8   121.25  3.000
 65D  C10  C9   C8   117.57  3.000
 65D  H11  C10  C11  119.30  3.000
 65D  H11  C10  C9   121.11  3.000
 65D  C11  C10  C9   119.59  3.000
 65D  C12  C11  C10  119.63  3.000
 65D  C10  C11  O4   119.40  3.000
 65D  C12  C11  O4   120.97  3.000
 65D  C13  C12  C11  120.38  3.000
 65D  C13  C12  O3   119.60  3.000
 65D  C11  C12  O3   119.91  3.000
 65D  O2   C13  C14  119.23  3.000
 65D  C14  C13  C12  120.19  3.000
 65D  O2   C13  C12  120.58  3.000
 65D  H12  C14  C13  119.49  3.000
 65D  H12  C14  C9   121.48  3.000
 65D  C13  C14  C9   119.02  3.000
 65D  H13  O2   C13  109.09  3.000
 65D  C8   O    C7   118.28  3.000
 65D  H21  C3   H14  105.93  3.000
 65D  H21  C3   C2   109.31  3.000
 65D  H14  C3   C2   109.32  3.000
 65D  H21  C3   C4   109.24  3.000
 65D  H14  C3   C4   109.34  3.000
 65D  C2   C3   C4   113.43  3.000
 65D  H22  C2   H15  105.83  3.000
 65D  H22  C2   C1   109.34  3.000
 65D  H15  C2   C1   109.30  3.000
 65D  H22  C2   C3   109.48  3.000
 65D  H15  C2   C3   109.38  3.000
 65D  C1   C2   C3   113.25  3.000
 65D  H17  C1   H16  105.85  3.000
 65D  H17  C1   C    109.64  3.000
 65D  H16  C1   C    109.62  3.000
 65D  H17  C1   C2   109.26  3.000
 65D  H16  C1   C2   109.30  3.000
 65D  C    C1   C2   112.92  3.000
 65D  H20  C    H19  107.50  3.000
 65D  H20  C    H18  107.60  3.000
 65D  H19  C    H18  107.46  3.000
 65D  H20  C    C1   111.67  3.000
 65D  H19  C    C1   111.22  3.000
 65D  H18  C    C1   111.19  3.000
 65D  H6   O4   C11  109.39  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
 65D  CONST_01  C12  C11  C10  C9      0.00   0.0  0
 65D  CONST_02  C12  C13  C14  C9      0.00   0.0  0
 65D  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 65D  CONST_04  C13  C14  C9   C10     0.00   0.0  0
 65D  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 65D  CONST_06  C14  C9   C10  C11     0.00   0.0  0
 65D  CONST_07  C10  C11  C12  O3    180.00   0.0  0
 65D  CONST_08  C14  C13  C12  O3    180.00   0.0  0
 65D  CONST_09  C13  C12  C11  O4    180.00   0.0  0
 65D  CONST_10  C9   C10  C11  O4    180.00   0.0  0
 65D  CONST_11  C11  C10  C9   C8    180.00   0.0  0
 65D  CONST_12  C13  C14  C9   C8    180.00   0.0  0
 65D  CONST_13  O2   C13  C14  C9    180.00   0.0  0
 65D  CONST_14  O2   C13  C12  C11   180.00   0.0  0
 65D  CONST_15  H12  C14  C9   C10   180.00   0.0  0
 65D  CONST_16  H11  C10  C11  C12   180.00   0.0  0
 65D  Var_01    O    C8   C9   C10   179.97  30.0  2
 65D  Var_02    C9   C8   O    C7   -178.49  30.0  1
 65D  Var_03    C7   C6   C5   C4   -179.69  30.0  3
 65D  Var_04    C1   C2   C3   C4   -179.70  30.0  3
 65D  Var_05    C2   C3   C4   C5   -179.65  30.0  3
 65D  Var_06    O    C7   C6   C5   -179.14  30.0  1
 65D  Var_07    C3   C4   C5   C6   -179.42  30.0  2
 65D  Var_08    C    C1   C2   C3   -179.90  30.0  3
 65D  Var_09    H18  C    C1   C2    -59.92  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
 65D  plan-1  O3   0.020
 65D  plan-1  C8   0.020
 65D  plan-1  C9   0.020
 65D  plan-1  C10  0.020
 65D  plan-1  C11  0.020
 65D  plan-1  C12  0.020
 65D  plan-1  C13  0.020
 65D  plan-1  C14  0.020
 65D  plan-1  O2   0.020
 65D  plan-1  H11  0.020
 65D  plan-1  H12  0.020
 65D  plan-1  O4   0.020
 65D  plan-2  C8   0.020
 65D  plan-2  C9   0.020
 65D  plan-2  O1   0.020
 65D  plan-2  O    0.020

