# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:30:11 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (3~{S})-3-(cyclohexylmethyl)-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)O[C@@H](CC3CCCCC3)Cc2c1
#
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
 D4U  D4U  (3~{S})-3-(cyclohexylmethyl)-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one  ligand  40  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_D4U
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
 D4U  C10  C  CH2   0  -0.443  -1.8813   1.0741   0.7234
 D4U  C11  C  CH1   0  -0.232  -3.0704   0.2215   0.2799
 D4U  C1   C  CR6   0   0.398   3.2642  -1.0280  -0.1047
 D4U  C12  C  CH2   0  -0.429  -4.4546  -0.6418  -1.6540
 D4U  C13  C  CH2   0  -0.428  -5.7252  -0.0992  -1.0089
 D4U  C14  C  CH2   0  -0.432  -5.5821  -0.0436   0.5081
 D4U  C15  C  CH2   0  -0.414  -4.3529   0.7606   0.9169
 D4U  C17  C  CH2   0  -0.427  -3.2261   0.1636  -1.2406
 D4U  C2   C  CR16  0  -0.495   4.3501  -0.2198  -0.4223
 D4U  C3   C  CR6   0   0.410   4.2159   1.1620  -0.3856
 D4U  C4   C  CR16  0  -0.449   3.0000   1.7596  -0.0271
 D4U  C5   C  CR6   0   0.173   1.9218   0.9618   0.2756
 D4U  C6   C  CH2   0  -0.528   0.6028   1.5303   0.6988
 D4U  C7   C  CH1   0   0.021  -0.5217   0.6364   0.2198
 D4U  C8   C  C     0   0.612   0.8837  -1.2780   0.5442
 D4U  C9   C  CR6   0  -0.342   2.0271  -0.4369   0.2251
 D4U  O2   O  OH1   0  -0.617   5.2296   1.9809  -0.6832
 D4U  O3   O  O2    0  -0.443  -0.3058  -0.7170   0.6775
 D4U  O4   O  O     0  -0.488   0.9682  -2.4880   0.7036
 D4U  H1   H  HCH2  0   0.235  -2.0303   2.1031   0.3798
 D4U  H2   H  HCH2  0   0.238  -1.8524   1.1178   1.8174
 D4U  H3   H  HCH1  0   0.217  -2.9234  -0.8029   0.6445
 D4U  H4   H  HCH2  0   0.209  -4.3166  -1.6867  -1.3550
 D4U  H5   H  HCH2  0   0.226  -4.5502  -0.6419  -2.7426
 D4U  H6   H  HCH2  0   0.207  -5.9250   0.9079  -1.3917
 D4U  H7   H  HCH2  0   0.225  -6.5846  -0.7140  -1.2885
 D4U  H8   H  HCH2  0   0.225  -6.4789   0.3857   0.9615
 D4U  H9   H  HCH2  0   0.208  -5.4939  -1.0634   0.8987
 D4U  H10  H  HCH2  0   0.225  -4.2508   0.7647   2.0060
 D4U  H11  H  HCH2  0   0.205  -4.4869   1.8062   0.6136
 D4U  H12  H  HCH2  0   0.206  -3.3145   1.1861  -1.6280
 D4U  H13  H  HCH2  0   0.230  -2.3361  -0.2687  -1.7054
 D4U  H14  H  HCR6  0   0.285   5.2947  -0.6798  -0.6891
 D4U  H15  H  HCR6  0   0.265   2.9171   2.8386   0.0057
 D4U  H16  H  HCH2  0   0.273   0.5716   1.6215   1.7900
 D4U  H17  H  HCH2  0   0.278   0.4634   2.5327   0.2920
 D4U  H18  H  HCH1  0   0.259  -0.5067   0.6170  -0.8750
 D4U  H19  H  HOH1  0   0.477   2.6017  -2.7635   0.1797
 D4U  H20  H  HOH1  0   0.482   6.0185   1.4800  -0.9220
 D4U  O1   O  OH1   0  -0.622   3.4353  -2.3461  -0.1291

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
 D4U  O2   C3   single    1.337  0.020  1.337
 D4U  C3   C4   aromatic  1.401  0.020  1.401
 D4U  C3   C2   aromatic  1.389  0.020  1.389
 D4U  C4   C5   aromatic  1.375  0.020  1.375
 D4U  C2   C1   aromatic  1.390  0.020  1.390
 D4U  C5   C6   single    1.497  0.020  1.497
 D4U  C5   C9   aromatic  1.404  0.020  1.404
 D4U  C1   C9   aromatic  1.410  0.020  1.410
 D4U  C1   O1   single    1.329  0.020  1.329
 D4U  C6   C7   single    1.514  0.020  1.514
 D4U  C9   C8   single    1.455  0.020  1.455
 D4U  C7   C10  single    1.514  0.020  1.514
 D4U  C7   O3   single    1.445  0.020  1.445
 D4U  C8   O3   single    1.322  0.020  1.322
 D4U  C8   O4   double    1.223  0.020  1.223
 D4U  C10  C11  single    1.529  0.020  1.529
 D4U  C17  C11  single    1.529  0.020  1.529
 D4U  C17  C12  single    1.526  0.020  1.526
 D4U  C11  C15  single    1.530  0.020  1.530
 D4U  C12  C13  single    1.525  0.020  1.525
 D4U  C15  C14  single    1.525  0.020  1.525
 D4U  C13  C14  single    1.525  0.020  1.525
 D4U  C10  H1   single    0.970  0.020  1.090
 D4U  C10  H2   single    0.970  0.020  1.090
 D4U  C11  H3   single    0.970  0.020  1.090
 D4U  C12  H4   single    0.970  0.020  1.090
 D4U  C12  H5   single    0.970  0.020  1.090
 D4U  C13  H6   single    0.970  0.020  1.090
 D4U  C13  H7   single    0.970  0.020  1.090
 D4U  C14  H8   single    0.970  0.020  1.090
 D4U  C14  H9   single    0.970  0.020  1.090
 D4U  C15  H10  single    0.970  0.020  1.090
 D4U  C15  H11  single    0.970  0.020  1.090
 D4U  C17  H12  single    0.970  0.020  1.090
 D4U  C17  H13  single    0.970  0.020  1.090
 D4U  C2   H14  single    0.930  0.020  1.080
 D4U  C4   H15  single    0.930  0.020  1.080
 D4U  C6   H16  single    0.970  0.020  1.090
 D4U  C6   H17  single    0.970  0.020  1.090
 D4U  C7   H18  single    0.970  0.020  1.090
 D4U  O1   H19  single    0.850  0.020  0.980
 D4U  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
 D4U  H2   C10  H1   106.22  3.000
 D4U  H2   C10  C7   108.67  3.000
 D4U  H1   C10  C7   106.83  3.000
 D4U  H2   C10  C11  109.42  3.000
 D4U  H1   C10  C11  109.09  3.000
 D4U  C7   C10  C11  116.14  3.000
 D4U  H3   C11  C17  107.98  3.000
 D4U  H3   C11  C15  107.63  3.000
 D4U  C17  C11  C15  109.99  3.000
 D4U  H3   C11  C10  108.66  3.000
 D4U  C15  C11  C10  109.56  3.000
 D4U  C17  C11  C10  112.87  3.000
 D4U  O1   C1   C9   122.19  3.000
 D4U  O1   C1   C2   118.14  3.000
 D4U  C9   C1   C2   119.67  3.000
 D4U  H5   C12  H4   106.43  3.000
 D4U  H5   C12  C17  109.89  3.000
 D4U  H4   C12  C17  109.15  3.000
 D4U  H5   C12  C13  110.40  3.000
 D4U  H4   C12  C13  109.20  3.000
 D4U  C17  C12  C13  111.62  3.000
 D4U  H7   C13  H6   106.51  3.000
 D4U  H7   C13  C14  110.41  3.000
 D4U  H6   C13  C14  109.34  3.000
 D4U  H7   C13  C12  110.29  3.000
 D4U  H6   C13  C12  109.34  3.000
 D4U  C14  C13  C12  110.84  3.000
 D4U  H9   C14  H8   106.49  3.000
 D4U  H9   C14  C15  109.29  3.000
 D4U  H8   C14  C15  110.07  3.000
 D4U  H9   C14  C13  109.17  3.000
 D4U  H8   C14  C13  110.49  3.000
 D4U  C15  C14  C13  111.20  3.000
 D4U  H11  C15  H10  106.44  3.000
 D4U  H11  C15  C14  109.28  3.000
 D4U  H10  C15  C14  110.13  3.000
 D4U  H11  C15  C11  108.85  3.000
 D4U  H10  C15  C11  109.73  3.000
 D4U  C14  C15  C11  112.23  3.000
 D4U  H13  C17  H12  106.50  3.000
 D4U  H13  C17  C12  109.36  3.000
 D4U  H12  C17  C12  109.35  3.000
 D4U  H13  C17  C11  110.78  3.000
 D4U  H12  C17  C11  108.90  3.000
 D4U  C12  C17  C11  111.79  3.000
 D4U  H14  C2   C3   120.87  3.000
 D4U  H14  C2   C1   119.35  3.000
 D4U  C3   C2   C1   119.79  3.000
 D4U  O2   C3   C4   116.98  3.000
 D4U  C4   C3   C2   120.99  3.000
 D4U  O2   C3   C2   122.03  3.000
 D4U  H15  C4   C5   120.77  3.000
 D4U  H15  C4   C3   119.95  3.000
 D4U  C5   C4   C3   119.29  3.000
 D4U  C9   C5   C6   117.04  3.000
 D4U  C9   C5   C4   120.76  3.000
 D4U  C6   C5   C4   122.18  3.000
 D4U  H17  C6   H16  106.94  3.000
 D4U  H17  C6   C7   109.24  3.000
 D4U  H16  C6   C7   110.06  3.000
 D4U  H17  C6   C5   110.86  3.000
 D4U  H16  C6   C5   109.77  3.000
 D4U  C7   C6   C5   109.91  3.000
 D4U  H18  C7   O3   107.34  3.000
 D4U  H18  C7   C6   108.45  3.000
 D4U  O3   C7   C6   109.98  3.000
 D4U  H18  C7   C10  110.48  3.000
 D4U  O3   C7   C10  107.43  3.000
 D4U  C6   C7   C10  113.01  3.000
 D4U  O4   C8   O3   117.95  3.000
 D4U  O4   C8   C9   123.10  3.000
 D4U  O3   C8   C9   118.95  3.000
 D4U  C8   C9   C5   120.61  3.000
 D4U  C8   C9   C1   119.90  3.000
 D4U  C5   C9   C1   119.47  3.000
 D4U  H20  O2   C3   110.93  3.000
 D4U  C8   O3   C7   120.00  3.000
 D4U  H19  O1   C1   107.84  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
 D4U  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 D4U  CONST_02  C4   C5   C9   C1      0.00   0.0  0
 D4U  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 D4U  CONST_04  C5   C9   C1   C2      0.00   0.0  0
 D4U  CONST_05  C9   C5   C4   C3      0.00   0.0  0
 D4U  CONST_06  C9   C1   C2   C3      0.00   0.0  0
 D4U  CONST_07  O2   C3   C2   C1    180.00   0.0  0
 D4U  CONST_08  O1   C1   C2   C3    180.00   0.0  0
 D4U  CONST_09  O2   C3   C4   C5    180.00   0.0  0
 D4U  CONST_10  O1   C1   C9   C5    180.00   0.0  0
 D4U  CONST_11  O1   C1   C9   C8      0.00   0.0  0
 D4U  CONST_12  H15  C4   C3   C2    180.00   0.0  0
 D4U  CONST_13  H14  C2   C3   C4    180.00   0.0  0
 D4U  Var_01    C13  C12  C17  C11    55.74  30.0  1
 D4U  Var_02    C13  C14  C15  C11   -55.79  30.0  1
 D4U  Var_03    O3   C8   C9   C1   -171.18  30.0  1
 D4U  Var_04    C15  C14  C13  C12    55.04  30.0  1
 D4U  Var_05    C17  C12  C13  C14   -55.25  30.0  1
 D4U  Var_06    C7   C6   C5   C4    147.86  30.0  1
 D4U  Var_07    C9   C8   O3   C7     13.94  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
 D4U  chir_01  C11  C10  C17  C15  positiv
 D4U  chir_02  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
 D4U  plan-1  C8   0.020
 D4U  plan-1  C9   0.020
 D4U  plan-1  O3   0.020
 D4U  plan-1  O4   0.020
 D4U  plan-2  C1   0.020
 D4U  plan-2  C2   0.020
 D4U  plan-2  C3   0.020
 D4U  plan-2  C4   0.020
 D4U  plan-2  C5   0.020
 D4U  plan-2  C6   0.020
 D4U  plan-2  C8   0.020
 D4U  plan-2  C9   0.020
 D4U  plan-2  O2   0.020
 D4U  plan-2  H14  0.020
 D4U  plan-2  H15  0.020
 D4U  plan-2  O1   0.020

