# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 03:33:08 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)isochromen-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCC[C@@H](C1)CC2=Cc3cc(O)cc(O)c3C(=O)O2
#
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
 D5F  D5F  3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)isochromen-1-one  ligand  41  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D5F
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
 D5F  C11  C  CH1   0  -0.237  -2.6593   0.4242   0.3016
 D5F  C12  C  CH1   0  -0.240  -5.1292   0.7474  -0.2746
 D5F  C13  C  CH2   0  -0.422  -5.1389  -0.6520  -0.8958
 D5F  C1   C  CR6   0   0.399   3.6072  -0.9313  -0.0139
 D5F  C10  C  CH2   0  -0.517  -1.6537   0.5436   1.4581
 D5F  C2   C  CR16  0  -0.498   4.5163  -0.0012  -0.4915
 D5F  C3   C  CR6   0   0.416   4.1450   1.3391  -0.6090
 D5F  C4   C  CR16  0  -0.461   2.8671   1.7700  -0.2550
 D5F  C5   C  CR66  0   0.301   1.9518   0.8465   0.2223
 D5F  C6   C  CR16  0  -0.479   0.6171   1.2140   0.6076
 D5F  C7   C  CR6   0   0.415  -0.2396   0.2917   1.0641
 D5F  C8   C  CR6   0   0.609   1.3550  -1.4632   0.8471
 D5F  C9   C  CR66  0  -0.391   2.3071  -0.5120   0.3498
 D5F  C14  C  CH2   0  -0.439  -3.7649  -1.0704  -1.4075
 D5F  C15  C  CH2   0  -0.419  -2.7030  -0.9728  -0.3157
 D5F  C16  C  CH3   0  -0.665  -4.9842   1.8493  -1.3211
 D5F  C17  C  CH2   0  -0.413  -4.0462   0.8279   0.8038
 D5F  O2   O  OH1   0  -0.616   4.9952   2.2635  -1.0637
 D5F  O3   O  O     0  -0.448   0.1318  -1.0131   1.1823
 D5F  O4   O  O     0  -0.480   1.5621  -2.6573   0.9961
 D5F  H1   H  HCH1  0   0.231  -2.3481   1.1324  -0.4763
 D5F  H2   H  HCH1  0   0.224  -6.0949   0.8987   0.2194
 D5F  H3   H  HCH2  0   0.215  -5.4666  -1.3696  -0.1357
 D5F  H4   H  HCH2  0   0.223  -5.8750  -0.6996  -1.7036
 D5F  H5   H  HCH2  0   0.268  -1.7119   1.5560   1.8640
 D5F  H6   H  HCH2  0   0.259  -1.9396  -0.1379   2.2648
 D5F  H7   H  HCR6  0   0.288   5.5116  -0.3260  -0.7723
 D5F  H8   H  HCR6  0   0.268   2.5976   2.8136  -0.3528
 D5F  H9   H  HCR6  0   0.275   0.2923   2.2427   0.5332
 D5F  H10  H  HCH2  0   0.229  -3.8064  -2.0926  -1.7916
 D5F  H11  H  HCH2  0   0.214  -3.4690  -0.4429  -2.2547
 D5F  H12  H  HCH2  0   0.230  -1.7294  -1.2403  -0.7337
 D5F  H13  H  HCH2  0   0.208  -2.9146  -1.7074   0.4710
 D5F  H14  H  HCH3  0   0.225  -5.7923   1.7978  -2.0527
 D5F  H15  H  HCH3  0   0.224  -5.0218   2.8353  -0.8541
 D5F  H16  H  HCH3  0   0.219  -4.0430   1.7888  -1.8699
 D5F  H17  H  HCH2  0   0.218  -4.3229   0.1677   1.6349
 D5F  H18  H  HCH2  0   0.225  -4.0079   1.8412   1.2168
 D5F  H19  H  HOH1  0   0.479   3.2418  -2.7253   0.4351
 D5F  H20  H  HOH1  0   0.483   5.8462   1.8714  -1.2927
 D5F  O1   O  OH1   0  -0.619   3.9919  -2.1997   0.0860

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
 D5F  O2   C3   single    1.336  0.020  1.336
 D5F  C3   C4   aromatic  1.394  0.020  1.394
 D5F  C3   C2   aromatic  1.396  0.020  1.396
 D5F  C4   C5   aromatic  1.385  0.020  1.385
 D5F  C2   C1   aromatic  1.386  0.020  1.386
 D5F  C5   C6   single    1.437  0.020  1.437
 D5F  C5   C9   aromatic  1.410  0.020  1.410
 D5F  C1   C9   aromatic  1.414  0.020  1.414
 D5F  C1   O1   single    1.329  0.020  1.329
 D5F  C6   C7   double    1.339  0.020  1.339
 D5F  C9   C8   single    1.435  0.020  1.435
 D5F  C7   C10  single    1.489  0.020  1.489
 D5F  C7   O3   single    1.362  0.020  1.362
 D5F  C8   O3   single    1.346  0.020  1.346
 D5F  C8   O4   double    1.221  0.020  1.221
 D5F  C10  C11  single    1.537  0.020  1.537
 D5F  C16  C12  single    1.527  0.020  1.527
 D5F  C17  C12  single    1.530  0.020  1.530
 D5F  C17  C11  single    1.529  0.020  1.529
 D5F  C12  C13  single    1.531  0.020  1.531
 D5F  C11  C15  single    1.528  0.020  1.528
 D5F  C15  C14  single    1.526  0.020  1.526
 D5F  C13  C14  single    1.525  0.020  1.525
 D5F  C11  H1   single    0.970  0.020  1.090
 D5F  C12  H2   single    0.970  0.020  1.090
 D5F  C13  H3   single    0.970  0.020  1.090
 D5F  C13  H4   single    0.970  0.020  1.090
 D5F  C10  H5   single    0.970  0.020  1.090
 D5F  C10  H6   single    0.970  0.020  1.090
 D5F  C2   H7   single    0.930  0.020  1.080
 D5F  C4   H8   single    0.930  0.020  1.080
 D5F  C6   H9   single    0.930  0.020  1.080
 D5F  C14  H10  single    0.970  0.020  1.090
 D5F  C14  H11  single    0.970  0.020  1.090
 D5F  C15  H12  single    0.970  0.020  1.090
 D5F  C15  H13  single    0.970  0.020  1.090
 D5F  C16  H14  single    0.970  0.020  1.090
 D5F  C16  H15  single    0.970  0.020  1.090
 D5F  C16  H16  single    0.970  0.020  1.090
 D5F  C17  H17  single    0.970  0.020  1.090
 D5F  C17  H18  single    0.970  0.020  1.090
 D5F  O1   H19  single    0.850  0.020  0.980
 D5F  O2   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
 D5F  H1   C11  C17  108.65  3.000
 D5F  H1   C11  C15  108.18  3.000
 D5F  C17  C11  C15  110.37  3.000
 D5F  H1   C11  C10  107.32  3.000
 D5F  C15  C11  C10  113.18  3.000
 D5F  C17  C11  C10  109.01  3.000
 D5F  H2   C12  C17  107.39  3.000
 D5F  H2   C12  C16  107.05  3.000
 D5F  C17  C12  C16  112.20  3.000
 D5F  H2   C12  C13  107.68  3.000
 D5F  C17  C12  C13  109.78  3.000
 D5F  C16  C12  C13  112.47  3.000
 D5F  H4   C13  H3   106.41  3.000
 D5F  H4   C13  C14  110.28  3.000
 D5F  H3   C13  C14  108.83  3.000
 D5F  H4   C13  C12  110.10  3.000
 D5F  H3   C13  C12  108.61  3.000
 D5F  C14  C13  C12  112.41  3.000
 D5F  O1   C1   C9   122.00  3.000
 D5F  O1   C1   C2   118.46  3.000
 D5F  C9   C1   C2   119.54  3.000
 D5F  H6   C10  H5   106.83  3.000
 D5F  H6   C10  C7   109.74  3.000
 D5F  H5   C10  C7   107.79  3.000
 D5F  H6   C10  C11  109.60  3.000
 D5F  H5   C10  C11  108.46  3.000
 D5F  C7   C10  C11  114.14  3.000
 D5F  H7   C2   C3   120.68  3.000
 D5F  H7   C2   C1   119.38  3.000
 D5F  C3   C2   C1   119.94  3.000
 D5F  O2   C3   C4   117.13  3.000
 D5F  C4   C3   C2   121.28  3.000
 D5F  O2   C3   C2   121.60  3.000
 D5F  H8   C4   C5   120.63  3.000
 D5F  H8   C4   C3   120.22  3.000
 D5F  C5   C4   C3   119.15  3.000
 D5F  C9   C5   C6   117.14  3.000
 D5F  C9   C5   C4   120.47  3.000
 D5F  C6   C5   C4   122.39  3.000
 D5F  H9   C6   C7   119.12  3.000
 D5F  H9   C6   C5   120.25  3.000
 D5F  C7   C6   C5   120.63  3.000
 D5F  O3   C7   C6   121.01  3.000
 D5F  O3   C7   C10  113.45  3.000
 D5F  C6   C7   C10  125.53  3.000
 D5F  O4   C8   O3   116.80  3.000
 D5F  O4   C8   C9   125.31  3.000
 D5F  O3   C8   C9   117.89  3.000
 D5F  C8   C9   C5   120.19  3.000
 D5F  C8   C9   C1   120.19  3.000
 D5F  C5   C9   C1   119.62  3.000
 D5F  H11  C14  H10  105.92  3.000
 D5F  H11  C14  C15  109.20  3.000
 D5F  H10  C14  C15  109.73  3.000
 D5F  H11  C14  C13  110.24  3.000
 D5F  H10  C14  C13  109.90  3.000
 D5F  C15  C14  C13  111.68  3.000
 D5F  H13  C15  H12  106.40  3.000
 D5F  H13  C15  C14  109.64  3.000
 D5F  H12  C15  C14  109.31  3.000
 D5F  H13  C15  C11  109.15  3.000
 D5F  H12  C15  C11  110.66  3.000
 D5F  C14  C15  C11  111.55  3.000
 D5F  H16  C16  H15  107.15  3.000
 D5F  H16  C16  H14  107.39  3.000
 D5F  H15  C16  H14  107.69  3.000
 D5F  H16  C16  C12  112.75  3.000
 D5F  H15  C16  C12  110.82  3.000
 D5F  H14  C16  C12  110.81  3.000
 D5F  H18  C17  H17  106.26  3.000
 D5F  H18  C17  C12  109.83  3.000
 D5F  H17  C17  C12  108.89  3.000
 D5F  H18  C17  C11  109.66  3.000
 D5F  H17  C17  C11  108.58  3.000
 D5F  C12  C17  C11  113.36  3.000
 D5F  H20  O2   C3   111.16  3.000
 D5F  C8   O3   C7   123.14  3.000
 D5F  H19  O1   C1   108.48  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
 D5F  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 D5F  CONST_02  C4   C5   C9   C1     0.00   0.0  0
 D5F  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 D5F  CONST_04  C5   C9   C1   C2     0.00   0.0  0
 D5F  CONST_05  C9   C5   C4   C3     0.00   0.0  0
 D5F  CONST_06  C9   C1   C2   C3     0.00   0.0  0
 D5F  CONST_07  O2   C3   C2   C1   180.00   0.0  0
 D5F  CONST_08  O1   C1   C2   C3   180.00   0.0  0
 D5F  CONST_09  O2   C3   C4   C5   180.00   0.0  0
 D5F  CONST_10  O1   C1   C9   C5   180.00   0.0  0
 D5F  CONST_11  O1   C1   C9   C8     0.00   0.0  0
 D5F  CONST_12  H8   C4   C3   C2   180.00   0.0  0
 D5F  CONST_13  H7   C2   C3   C4   180.00   0.0  0
 D5F  Var_01    C13  C14  C15  C11  -54.95  30.0  1
 D5F  Var_02    C15  C14  C13  C12   54.91  30.0  1
 D5F  Var_03    O3   C8   C9   C1   179.85  30.0  1
 D5F  Var_04    C7   C6   C5   C4   179.97  30.0  1
 D5F  Var_05    O3   C7   C6   C5     0.37  30.0  1
 D5F  Var_06    C9   C8   O3   C7     0.37  30.0  1
 D5F  Var_07    C6   C7   C10  C11   88.29  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 D5F  chir_01  C11  C10  C17  C15  positiv
 D5F  chir_02  C12  C13  C17  C16  negativ

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
 D5F  plan-1  C8  0.020
 D5F  plan-1  C9  0.020
 D5F  plan-1  O3  0.020
 D5F  plan-1  O4  0.020
 D5F  plan-2  C1  0.020
 D5F  plan-2  C2  0.020
 D5F  plan-2  C3  0.020
 D5F  plan-2  C4  0.020
 D5F  plan-2  C5  0.020
 D5F  plan-2  C6  0.020
 D5F  plan-2  C8  0.020
 D5F  plan-2  C9  0.020
 D5F  plan-2  O2  0.020
 D5F  plan-2  H7  0.020
 D5F  plan-2  H8  0.020
 D5F  plan-2  O1  0.020

