# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 00:30:33 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCC[C@@H](C1)C[C@H]2Cc3cc(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
 D4O  D4O  (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one  ligand  43  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_D4O
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
 D4O  C15  C  CH2   0  -0.413  -4.0748  -1.2113  -1.0195
 D4O  C12  C  CH1   0  -0.236  -4.3648   0.4199   1.4368
 D4O  C13  C  CH2   0  -0.421  -5.5697  -0.2292   0.7508
 D4O  C16  C  CH3   0  -0.663  -4.2236   1.8998   1.0869
 D4O  C17  C  CH2   0  -0.418  -3.0884  -0.3672   1.1215
 D4O  C1   C  CR6   0   0.394   3.3379   1.2242  -0.0453
 D4O  C11  C  CH1   0  -0.240  -2.8514  -0.5568  -0.3778
 D4O  C14  C  CH2   0  -0.439  -5.3521  -0.4249  -0.7460
 D4O  C2   C  CR16  0  -0.497   4.4621   0.5456   0.4055
 D4O  C3   C  CR6   0   0.405   4.4450  -0.8391   0.5209
 D4O  C4   C  CR16  0  -0.491   3.2927  -1.5581   0.2033
 D4O  C5   C  CR6   0   0.174   2.1703  -0.8835  -0.2326
 D4O  C6   C  CH2   0  -0.525   0.9141  -1.6261  -0.5704
 D4O  C7   C  CH1   0   0.031  -0.2835  -0.7594  -0.2507
 D4O  C8   C  C     0   0.556   0.9798   1.1830  -0.9244
 D4O  C9   C  CR6   0  -0.292   2.1674   0.5121  -0.3768
 D4O  O2   O  OH1   0  -0.617   5.5621  -1.4323   0.9553
 D4O  O3   O  O2    0  -0.454  -0.1614   0.4894  -0.9507
 D4O  O4   O  O     0  -0.437   0.9628   2.2998  -1.3847
 D4O  H1   H  HCH2  0   0.224  -3.9191  -1.3103  -2.0978
 D4O  H2   H  HCH2  0   0.203  -4.1853  -2.2303  -0.6279
 D4O  H3   H  HCH1  0   0.222  -4.5265   0.3598   2.5186
 D4O  H4   H  HCH2  0   0.213  -5.7528  -1.2079   1.2087
 D4O  H5   H  HCH2  0   0.221  -6.4687   0.3678   0.9305
 D4O  H6   H  HCH3  0   0.218  -4.0329   2.0643   0.0257
 D4O  H7   H  HCH3  0   0.223  -5.1295   2.4511   1.3460
 D4O  H8   H  HCH3  0   0.224  -3.3939   2.3483   1.6368
 D4O  H9   H  HCH2  0   0.226  -2.2362   0.1363   1.5879
 D4O  H10  H  HCH2  0   0.212  -3.1562  -1.3573   1.5887
 D4O  H13  H  HCH1  0   0.222  -2.7224   0.4276  -0.8417
 D4O  H14  H  HCH2  0   0.212  -5.2968   0.5449  -1.2506
 D4O  H15  H  HCH2  0   0.226  -6.2099  -0.9430  -1.1819
 D4O  H16  H  HCR6  0   0.284   5.3591   1.0933   0.6718
 D4O  H17  H  HCR6  0   0.273   3.2720  -2.6372   0.3062
 D4O  H18  H  HCH2  0   0.270   0.9083  -1.8988  -1.6314
 D4O  H19  H  HCH2  0   0.274   0.8591  -2.5547  -0.0013
 D4O  H20  H  HCH1  0   0.249  -0.2860  -0.5463   0.8243
 D4O  H21  H  HOH1  0   0.481   4.1949   2.9047   0.1465
 D4O  H22  H  HOH1  0   0.482   5.4484  -2.3894   0.9923
 D4O  C10  C  CH2   0  -0.439  -1.5998  -1.3862  -0.6668
 D4O  O1   O  OH1   0  -0.601   3.3458   2.5555  -0.1505
 D4O  H11  H  HCH2  0   0.232  -1.6804  -2.3493  -0.1518
 D4O  H12  H  HCH2  0   0.234  -1.5511  -1.6139  -1.7371

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
 D4O  O2   C3   single    1.337  0.020  1.337
 D4O  C3   C4   aromatic  1.395  0.020  1.395
 D4O  C3   C2   aromatic  1.390  0.020  1.390
 D4O  C4   C5   aromatic  1.380  0.020  1.380
 D4O  C2   C1   aromatic  1.388  0.020  1.388
 D4O  C5   C9   aromatic  1.403  0.020  1.403
 D4O  C5   C6   single    1.498  0.020  1.498
 D4O  C1   C9   aromatic  1.410  0.020  1.410
 D4O  C1   O1   single    1.335  0.020  1.335
 D4O  C9   C8   single    1.470  0.020  1.470
 D4O  C6   C7   single    1.512  0.020  1.512
 D4O  C7   C10  single    1.516  0.020  1.516
 D4O  C7   O3   single    1.437  0.020  1.437
 D4O  C8   O4   double    1.208  0.020  1.208
 D4O  C8   O3   single    1.336  0.020  1.336
 D4O  C10  C11  single    1.529  0.020  1.529
 D4O  C11  C17  single    1.530  0.020  1.530
 D4O  C11  C15  single    1.529  0.020  1.529
 D4O  C12  C17  single    1.532  0.020  1.532
 D4O  C12  C16  single    1.527  0.020  1.527
 D4O  C12  C13  single    1.531  0.020  1.531
 D4O  C15  C14  single    1.525  0.020  1.525
 D4O  C13  C14  single    1.525  0.020  1.525
 D4O  C15  H1   single    0.970  0.020  1.090
 D4O  C15  H2   single    0.970  0.020  1.090
 D4O  C12  H3   single    0.970  0.020  1.090
 D4O  C13  H4   single    0.970  0.020  1.090
 D4O  C13  H5   single    0.970  0.020  1.090
 D4O  C16  H6   single    0.970  0.020  1.090
 D4O  C16  H7   single    0.970  0.020  1.090
 D4O  C16  H8   single    0.970  0.020  1.090
 D4O  C17  H9   single    0.970  0.020  1.090
 D4O  C17  H10  single    0.970  0.020  1.090
 D4O  C10  H11  single    0.970  0.020  1.090
 D4O  C10  H12  single    0.970  0.020  1.090
 D4O  C11  H13  single    0.970  0.020  1.090
 D4O  C14  H14  single    0.970  0.020  1.090
 D4O  C14  H15  single    0.970  0.020  1.090
 D4O  C2   H16  single    0.930  0.020  1.080
 D4O  C4   H17  single    0.930  0.020  1.080
 D4O  C6   H18  single    0.970  0.020  1.090
 D4O  C6   H19  single    0.970  0.020  1.090
 D4O  C7   H20  single    0.970  0.020  1.090
 D4O  O1   H21  single    0.850  0.020  0.980
 D4O  O2   H22  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
 D4O  H2   C15  H1   106.38  3.000
 D4O  H2   C15  C14  109.31  3.000
 D4O  H1   C15  C14  110.04  3.000
 D4O  H2   C15  C11  109.17  3.000
 D4O  H1   C15  C11  109.79  3.000
 D4O  C14  C15  C11  111.98  3.000
 D4O  H3   C12  C17  107.34  3.000
 D4O  H3   C12  C16  107.04  3.000
 D4O  C17  C12  C16  111.94  3.000
 D4O  H3   C12  C13  107.65  3.000
 D4O  C16  C12  C13  112.39  3.000
 D4O  C17  C12  C13  110.21  3.000
 D4O  H5   C13  H4   106.34  3.000
 D4O  H5   C13  C14  110.40  3.000
 D4O  H4   C13  C14  108.62  3.000
 D4O  H5   C13  C12  109.98  3.000
 D4O  H4   C13  C12  108.84  3.000
 D4O  C14  C13  C12  112.45  3.000
 D4O  H8   C16  H7   107.68  3.000
 D4O  H8   C16  H6   107.17  3.000
 D4O  H7   C16  H6   107.45  3.000
 D4O  H8   C16  C12  110.67  3.000
 D4O  H7   C16  C12  110.99  3.000
 D4O  H6   C16  C12  112.66  3.000
 D4O  H10  C17  H9   106.37  3.000
 D4O  H10  C17  C11  108.38  3.000
 D4O  H9   C17  C11  110.74  3.000
 D4O  H10  C17  C12  108.93  3.000
 D4O  H9   C17  C12  108.95  3.000
 D4O  C11  C17  C12  113.23  3.000
 D4O  O1   C1   C9   119.34  3.000
 D4O  O1   C1   C2   120.53  3.000
 D4O  C9   C1   C2   120.12  3.000
 D4O  H13  C11  C10  108.12  3.000
 D4O  H13  C11  C17  108.77  3.000
 D4O  C10  C11  C17  112.29  3.000
 D4O  H13  C11  C15  107.53  3.000
 D4O  C17  C11  C15  109.90  3.000
 D4O  C10  C11  C15  110.09  3.000
 D4O  H15  C14  H14  106.00  3.000
 D4O  H15  C14  C13  109.89  3.000
 D4O  H14  C14  C13  110.24  3.000
 D4O  H15  C14  C15  109.98  3.000
 D4O  H14  C14  C15  109.39  3.000
 D4O  C13  C14  C15  111.21  3.000
 D4O  H16  C2   C3   119.55  3.000
 D4O  H16  C2   C1   120.18  3.000
 D4O  C3   C2   C1   120.27  3.000
 D4O  O2   C3   C4   122.37  3.000
 D4O  C4   C3   C2   120.32  3.000
 D4O  O2   C3   C2   117.30  3.000
 D4O  H17  C4   C5   120.06  3.000
 D4O  H17  C4   C3   120.48  3.000
 D4O  C5   C4   C3   119.46  3.000
 D4O  C9   C5   C6   117.92  3.000
 D4O  C6   C5   C4   120.72  3.000
 D4O  C9   C5   C4   121.35  3.000
 D4O  H19  C6   H18  107.05  3.000
 D4O  H19  C6   C7   109.74  3.000
 D4O  H18  C6   C7   110.07  3.000
 D4O  H19  C6   C5   110.29  3.000
 D4O  H18  C6   C5   110.26  3.000
 D4O  C7   C6   C5   109.41  3.000
 D4O  H20  C7   O3   108.01  3.000
 D4O  H20  C7   C6   108.70  3.000
 D4O  O3   C7   C6   109.13  3.000
 D4O  H20  C7   C10  110.34  3.000
 D4O  O3   C7   C10  107.42  3.000
 D4O  C6   C7   C10  113.11  3.000
 D4O  O4   C8   O3   117.42  3.000
 D4O  O3   C8   C9   117.43  3.000
 D4O  O4   C8   C9   125.12  3.000
 D4O  C8   C9   C5   119.60  3.000
 D4O  C8   C9   C1   121.87  3.000
 D4O  C5   C9   C1   118.46  3.000
 D4O  H22  O2   C3   110.74  3.000
 D4O  C8   O3   C7   120.95  3.000
 D4O  H12  C10  H11  106.26  3.000
 D4O  H12  C10  C7   108.40  3.000
 D4O  H11  C10  C7   107.36  3.000
 D4O  H12  C10  C11  109.50  3.000
 D4O  H11  C10  C11  109.14  3.000
 D4O  C7   C10  C11  115.75  3.000
 D4O  H21  O1   C1   109.98  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
 D4O  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 D4O  CONST_02  C4   C5   C9   C1      0.00   0.0  0
 D4O  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 D4O  CONST_04  C5   C9   C1   C2      0.00   0.0  0
 D4O  CONST_05  C9   C5   C4   C3      0.00   0.0  0
 D4O  CONST_06  C9   C1   C2   C3      0.00   0.0  0
 D4O  CONST_07  O2   C3   C2   C1    180.00   0.0  0
 D4O  CONST_08  O1   C1   C2   C3    180.00   0.0  0
 D4O  CONST_09  O2   C3   C4   C5    180.00   0.0  0
 D4O  CONST_10  O1   C1   C9   C5    180.00   0.0  0
 D4O  CONST_11  O1   C1   C9   C8      0.00   0.0  0
 D4O  CONST_12  H17  C4   C3   C2    180.00   0.0  0
 D4O  CONST_13  H16  C2   C3   C4    180.00   0.0  0
 D4O  Var_01    C12  C13  C14  C15    54.66  30.0  1
 D4O  Var_02    C11  C15  C14  C13   -55.63  30.0  1
 D4O  Var_03    O3   C8   C9   C1   -166.57  30.0  1
 D4O  Var_04    C7   C6   C5   C4    147.99  30.0  1
 D4O  Var_05    C9   C8   O3   C7     11.28  30.0  1

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
 D4O  chir_01  C12  C17  C16  C13  negativ
 D4O  chir_02  C11  C15  C17  C10  negativ
 D4O  chir_03  C7   O3   C6   C10  positiv

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
 D4O  plan-1  C8   0.020
 D4O  plan-1  C9   0.020
 D4O  plan-1  O3   0.020
 D4O  plan-1  O4   0.020
 D4O  plan-2  C1   0.020
 D4O  plan-2  C2   0.020
 D4O  plan-2  C3   0.020
 D4O  plan-2  C4   0.020
 D4O  plan-2  C5   0.020
 D4O  plan-2  C6   0.020
 D4O  plan-2  C8   0.020
 D4O  plan-2  C9   0.020
 D4O  plan-2  O2   0.020
 D4O  plan-2  H16  0.020
 D4O  plan-2  H17  0.020
 D4O  plan-2  O1   0.020

