# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 04:31:13 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3-(cyclohexylmethyl)-6,8-bis(oxidanyl)isochromen-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)OC(=Cc2c1)CC3CCCCC3
#
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
 D5O  D5O  3-(cyclohexylmethyl)-6,8-bis(oxidanyl)isochromen-1-one  ligand  38  20  .  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_D5O
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
 D5O  C1   C  CR6   0   0.397   3.3144   0.7874   0.5383
 D5O  C10  C  CH2   0  -0.511  -1.9470   0.0107  -1.3847
 D5O  C11  C  CH1   0  -0.238  -3.0003   0.1280  -0.2754
 D5O  C12  C  CH2   0  -0.429  -3.9649  -0.9094   1.8202
 D5O  C13  C  CH2   0  -0.429  -5.3539  -0.9184   1.1914
 D5O  C14  C  CH2   0  -0.434  -5.4927   0.1945   0.1586
 D5O  C15  C  CH2   0  -0.418  -4.3965   0.1162  -0.8973
 D5O  C17  C  CH2   0  -0.416  -2.8677  -0.9841   0.7632
 D5O  C2   C  CR16  0  -0.455   4.2837  -0.1948   0.4346
 D5O  C3   C  CR6   0   0.415   3.9682  -1.4248  -0.1454
 D5O  C4   C  CR16  0  -0.509   2.6885  -1.6899  -0.6299
 D5O  C5   C  CR66  0   0.304   1.7118  -0.7108  -0.5317
 D5O  C6   C  CR16  0  -0.482   0.3734  -0.9092  -1.0168
 D5O  C7   C  CR6   0   0.419  -0.5387   0.0653  -0.9119
 D5O  C8   C  CR6   0   0.606   0.9928   1.5437   0.1567
 D5O  C9   C  CR66  0  -0.392   2.0089   0.5355   0.0536
 D5O  O1   O  OH1   0  -0.620   3.6452   1.9494   1.0938
 D5O  O2   O  OH1   0  -0.614   4.9505  -2.3276  -0.2106
 D5O  O3   O  O     0  -0.450  -0.2274   1.2576  -0.3328
 D5O  O4   O  O     0  -0.479   1.1426   2.6488   0.6529
 D5O  H1   H  HCH2  0   0.257  -2.0851  -0.9310  -1.9209
 D5O  H2   H  HCH2  0   0.269  -2.1038   0.8130  -2.1139
 D5O  H3   H  HCH1  0   0.225  -2.8682   1.0921   0.2308
 D5O  H4   H  HCH2  0   0.210  -3.8422   0.0072   2.4078
 D5O  H5   H  HCH2  0   0.227  -3.8607  -1.7402   2.5223
 D5O  H6   H  HCH2  0   0.208  -5.5299  -1.8873   0.7114
 D5O  H7   H  HCH2  0   0.226  -6.1191  -0.8136   1.9646
 D5O  H8   H  HCH2  0   0.227  -6.4744   0.1518  -0.3198
 D5O  H9   H  HCH2  0   0.210  -5.4374   1.1648   0.6647
 D5O  H10  H  HCH2  0   0.229  -4.4937   0.9463  -1.6032
 D5O  H11  H  HCH2  0   0.209  -4.5161  -0.8029  -1.4840
 D5O  H12  H  HCH2  0   0.209  -2.9161  -1.9540   0.2526
 D5O  H13  H  HCH2  0   0.231  -1.8870  -0.9420   1.2453
 D5O  H14  H  HCR6  0   0.282   5.2848  -0.0091   0.8030
 D5O  H15  H  HCR6  0   0.277   2.4544  -2.6478  -1.0795
 D5O  H16  H  HCR6  0   0.277   0.0942  -1.8469  -1.4760
 D5O  H17  H  HOH1  0   0.479   2.8550   2.5287   1.0983
 D5O  H18  H  HOH1  0   0.483   4.6429  -3.1396  -0.6309

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
 D5O  O2   C3   single    1.336  0.020  1.336
 D5O  C3   C4   aromatic  1.394  0.020  1.394
 D5O  C3   C2   aromatic  1.396  0.020  1.396
 D5O  C4   C5   aromatic  1.386  0.020  1.386
 D5O  C2   C1   aromatic  1.384  0.020  1.384
 D5O  C5   C6   single    1.437  0.020  1.437
 D5O  C5   C9   aromatic  1.409  0.020  1.409
 D5O  C1   C9   aromatic  1.415  0.020  1.415
 D5O  C1   O1   single    1.330  0.020  1.330
 D5O  C6   C7   double    1.339  0.020  1.339
 D5O  C9   C8   single    1.435  0.020  1.435
 D5O  C7   C10  single    1.487  0.020  1.487
 D5O  C7   O3   single    1.362  0.020  1.362
 D5O  C8   O3   single    1.345  0.020  1.345
 D5O  C8   O4   double    1.221  0.020  1.221
 D5O  C10  C11  single    1.534  0.020  1.534
 D5O  C17  C11  single    1.527  0.020  1.527
 D5O  C17  C12  single    1.525  0.020  1.525
 D5O  C11  C15  single    1.528  0.020  1.528
 D5O  C12  C13  single    1.525  0.020  1.525
 D5O  C15  C14  single    1.524  0.020  1.524
 D5O  C13  C14  single    1.525  0.020  1.525
 D5O  C10  H1   single    0.970  0.020  1.090
 D5O  C10  H2   single    0.970  0.020  1.090
 D5O  C11  H3   single    0.970  0.020  1.090
 D5O  C12  H4   single    0.970  0.020  1.090
 D5O  C12  H5   single    0.970  0.020  1.090
 D5O  C13  H6   single    0.970  0.020  1.090
 D5O  C13  H7   single    0.970  0.020  1.090
 D5O  C14  H8   single    0.970  0.020  1.090
 D5O  C14  H9   single    0.970  0.020  1.090
 D5O  C15  H10  single    0.970  0.020  1.090
 D5O  C15  H11  single    0.970  0.020  1.090
 D5O  C17  H12  single    0.970  0.020  1.090
 D5O  C17  H13  single    0.970  0.020  1.090
 D5O  C2   H14  single    0.930  0.020  1.080
 D5O  C4   H15  single    0.930  0.020  1.080
 D5O  C6   H16  single    0.930  0.020  1.080
 D5O  O1   H17  single    0.850  0.020  0.980
 D5O  O2   H18  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
 D5O  O1   C1   C9   121.88  3.000
 D5O  O1   C1   C2   118.51  3.000
 D5O  C9   C1   C2   119.61  3.000
 D5O  H2   C10  H1   106.65  3.000
 D5O  H2   C10  C7   108.69  3.000
 D5O  H1   C10  C7   107.91  3.000
 D5O  H2   C10  C11  109.09  3.000
 D5O  H1   C10  C11  109.51  3.000
 D5O  C7   C10  C11  114.69  3.000
 D5O  H3   C11  C17  108.40  3.000
 D5O  H3   C11  C15  107.73  3.000
 D5O  C17  C11  C15  110.51  3.000
 D5O  H3   C11  C10  108.55  3.000
 D5O  C15  C11  C10  109.41  3.000
 D5O  C17  C11  C10  112.11  3.000
 D5O  H5   C12  H4   106.31  3.000
 D5O  H5   C12  C17  109.85  3.000
 D5O  H4   C12  C17  109.40  3.000
 D5O  H5   C12  C13  110.33  3.000
 D5O  H4   C12  C13  109.15  3.000
 D5O  C17  C12  C13  111.66  3.000
 D5O  H7   C13  H6   106.39  3.000
 D5O  H7   C13  C14  110.22  3.000
 D5O  H6   C13  C14  109.52  3.000
 D5O  H7   C13  C12  110.21  3.000
 D5O  H6   C13  C12  109.40  3.000
 D5O  C14  C13  C12  110.98  3.000
 D5O  H9   C14  H8   106.39  3.000
 D5O  H9   C14  C15  109.22  3.000
 D5O  H8   C14  C15  109.93  3.000
 D5O  H9   C14  C13  109.20  3.000
 D5O  H8   C14  C13  110.47  3.000
 D5O  C15  C14  C13  111.49  3.000
 D5O  H11  C15  H10  106.32  3.000
 D5O  H11  C15  C14  109.58  3.000
 D5O  H10  C15  C14  110.13  3.000
 D5O  H11  C15  C11  108.89  3.000
 D5O  H10  C15  C11  109.75  3.000
 D5O  C14  C15  C11  112.01  3.000
 D5O  H13  C17  H12  106.19  3.000
 D5O  H13  C17  C12  109.73  3.000
 D5O  H12  C17  C12  109.52  3.000
 D5O  H13  C17  C11  110.46  3.000
 D5O  H12  C17  C11  108.87  3.000
 D5O  C12  C17  C11  111.91  3.000
 D5O  H14  C2   C3   120.09  3.000
 D5O  H14  C2   C1   120.03  3.000
 D5O  C3   C2   C1   119.88  3.000
 D5O  O2   C3   C4   121.98  3.000
 D5O  C4   C3   C2   121.30  3.000
 D5O  O2   C3   C2   116.72  3.000
 D5O  H15  C4   C5   120.10  3.000
 D5O  H15  C4   C3   120.71  3.000
 D5O  C5   C4   C3   119.20  3.000
 D5O  C9   C5   C6   117.31  3.000
 D5O  C9   C5   C4   120.38  3.000
 D5O  C6   C5   C4   122.31  3.000
 D5O  H16  C6   C7   119.25  3.000
 D5O  H16  C6   C5   120.25  3.000
 D5O  C7   C6   C5   120.50  3.000
 D5O  O3   C7   C6   120.99  3.000
 D5O  O3   C7   C10  112.58  3.000
 D5O  C6   C7   C10  126.43  3.000
 D5O  O4   C8   O3   116.85  3.000
 D5O  O4   C8   C9   125.33  3.000
 D5O  O3   C8   C9   117.82  3.000
 D5O  C8   C9   C5   120.14  3.000
 D5O  C8   C9   C1   120.23  3.000
 D5O  C5   C9   C1   119.63  3.000
 D5O  H17  O1   C1   108.54  3.000
 D5O  H18  O2   C3   110.83  3.000
 D5O  C8   O3   C7   123.25  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
 D5O  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 D5O  CONST_02  C4   C5   C9   C1      0.00   0.0  0
 D5O  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 D5O  CONST_04  C5   C9   C1   C2      0.00   0.0  0
 D5O  CONST_05  C9   C5   C4   C3      0.00   0.0  0
 D5O  CONST_06  C9   C1   C2   C3      0.00   0.0  0
 D5O  CONST_07  O2   C3   C2   C1    180.00   0.0  0
 D5O  CONST_08  O1   C1   C2   C3    180.00   0.0  0
 D5O  CONST_09  O2   C3   C4   C5    180.00   0.0  0
 D5O  CONST_10  O1   C1   C9   C5    180.00   0.0  0
 D5O  CONST_11  O1   C1   C9   C8      0.00   0.0  0
 D5O  CONST_12  H15  C4   C3   C2    180.00   0.0  0
 D5O  CONST_13  H14  C2   C3   C4    180.00   0.0  0
 D5O  Var_01    O3   C8   C9   C1    179.29  30.0  1
 D5O  Var_02    C13  C12  C17  C11    55.13  30.0  1
 D5O  Var_03    C13  C14  C15  C11   -55.35  30.0  1
 D5O  Var_04    C15  C14  C13  C12    54.83  30.0  1
 D5O  Var_05    C17  C12  C13  C14   -54.78  30.0  1
 D5O  Var_06    C7   C6   C5   C4   -179.51  30.0  1
 D5O  Var_07    O3   C7   C6   C5     -0.72  30.0  1
 D5O  Var_08    C9   C8   O3   C7      0.20  30.0  1
 D5O  Var_09    C6   C7   C10  C11   117.01  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
 D5O  chir_01  C11  C10  C17  C15  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
 D5O  plan-1  C8   0.020
 D5O  plan-1  C9   0.020
 D5O  plan-1  O3   0.020
 D5O  plan-1  O4   0.020
 D5O  plan-2  C1   0.020
 D5O  plan-2  C2   0.020
 D5O  plan-2  C3   0.020
 D5O  plan-2  C4   0.020
 D5O  plan-2  C5   0.020
 D5O  plan-2  C6   0.020
 D5O  plan-2  C8   0.020
 D5O  plan-2  C9   0.020
 D5O  plan-2  O1   0.020
 D5O  plan-2  O2   0.020
 D5O  plan-2  H14  0.020
 D5O  plan-2  H15  0.020

