# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:26:08 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: (3~{R})-3-[[(3~{S})-3-ethylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H]1CCCN(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
 E5C  E5C  (3~{R})-3-[[(3~{S})-3-ethylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one  ligand  45  22  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E5C
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
 E5C  N    N  NT    0  -0.417  -5.5995  -24.2630  -48.3191
 E5C  C    C  CR6   0   0.400  -7.0274  -28.4289  -43.5152
 E5C  O    O  OH1   0  -0.619  -6.0681  -29.3410  -43.3972
 E5C  C1   C  CR16  0  -0.493  -7.9926  -28.3591  -42.5171
 E5C  C10  C  CH2   0  -0.431  -3.6886  -24.5510  -49.7928
 E5C  C11  C  CH2   0  -0.423  -2.9290  -23.4916  -49.0064
 E5C  C12  C  CH1   0  -0.227  -3.8825  -22.5073  -48.3349
 E5C  C13  C  CH2   0  -0.413  -3.1158  -21.4910  -47.4914
 E5C  C14  C  CH3   0  -0.669  -3.9695  -20.3613  -46.9292
 E5C  C15  C  CR66  0  -0.343  -7.0901  -27.5417  -44.6101
 E5C  C16  C  CR6   0   0.618  -6.0838  -27.6140  -45.6567
 E5C  C2   C  CR6   0   0.409  -9.0227  -27.4326  -42.6163
 E5C  C3   C  CR16  0  -0.443  -9.1092  -26.5658  -43.7141
 E5C  C4   C  CR66  0   0.173  -8.1510  -26.6269  -44.6989
 E5C  C5   C  C     0  -0.535  -8.2126  -25.7596  -45.9185
 E5C  C6   C  CR16  0   0.006  -6.8167  -25.4683  -46.4304
 E5C  C7   C  CH2   0  -0.320  -6.8410  -24.7459  -47.7734
 E5C  C8   C  CH2   0  -0.259  -4.9126  -23.2773  -47.5108
 E5C  C9   C  CH2   0  -0.272  -4.7046  -25.2455  -48.8988
 E5C  O2   O  O     0  -0.439  -6.0841  -26.6956  -46.6078
 E5C  O3   O  O     0  -0.483  -5.2375  -28.4951  -45.7108
 E5C  H2   H  HOH1  0   0.475  -5.5102  -29.2949  -44.2052
 E5C  H3   H  HCR6  0   0.282  -7.9363  -29.0376  -41.6732
 E5C  H4   H  HCH2  0   0.224  -3.0001  -25.2909  -50.2082
 E5C  H5   H  HCH2  0   0.210  -4.2078  -24.0859  -50.6360
 E5C  H6   H  HCH2  0   0.203  -2.3215  -23.9810  -48.2347
 E5C  H7   H  HCH2  0   0.227  -2.2318  -22.9557  -49.6562
 E5C  H8   H  HCH1  0   0.206  -4.4247  -21.9657  -49.1211
 E5C  H9   H  HCH2  0   0.208  -2.6091  -22.0139  -46.6731
 E5C  H10  H  HCH2  0   0.220  -2.3224  -21.0625  -48.1108
 E5C  H11  H  HCH3  0   0.228  -3.3538  -19.6254  -46.4109
 E5C  H12  H  HCH3  0   0.216  -4.5050  -19.8403  -47.7252
 E5C  H13  H  HCH3  0   0.221  -4.7107  -20.7208  -46.2148
 E5C  H14  H  HCR6  0   0.264  -9.9269  -25.8591  -43.7804
 E5C  H15  H  H     0   0.278  -8.7201  -24.8200  -45.6981
 E5C  H16  H  H     0   0.273  -8.7975  -26.2635  -46.6966
 E5C  H17  H  HCR6  0   0.259  -6.2785  -24.8701  -45.6864
 E5C  H18  H  HCH2  0   0.245  -7.5109  -23.8885  -47.6439
 E5C  H19  H  HCH2  0   0.245  -7.3193  -25.3997  -48.5103
 E5C  H20  H  HCH2  0   0.232  -5.6589  -22.5906  -47.1022
 E5C  H21  H  HCH2  0   0.182  -4.3925  -23.7285  -46.6455
 E5C  H22  H  HCH2  0   0.226  -5.2953  -25.9579  -49.4799
 E5C  H23  H  HCH2  0   0.189  -4.1600  -25.8275  -48.1388
 E5C  H24  H  HOH1  0   0.481  -9.8359  -27.9628  -40.9731
 E5C  O1   O  OH1   0  -0.614  -9.9753  -27.3261  -41.6848

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
 E5C  C10  C9   single    1.521  0.020  1.521
 E5C  C10  C11  single    1.522  0.020  1.522
 E5C  C9   N    single    1.450  0.020  1.450
 E5C  C11  C12  single    1.526  0.020  1.526
 E5C  N    C7   single    1.440  0.020  1.440
 E5C  N    C8   single    1.448  0.020  1.448
 E5C  C12  C8   single    1.527  0.020  1.527
 E5C  C12  C13  single    1.527  0.020  1.527
 E5C  C7   C6   single    1.525  0.020  1.525
 E5C  C13  C14  single    1.523  0.020  1.523
 E5C  C6   O2   single    1.440  0.020  1.440
 E5C  C6   C5   single    1.515  0.020  1.515
 E5C  O2   C16  single    1.322  0.020  1.322
 E5C  C5   C4   single    1.498  0.020  1.498
 E5C  C16  O3   double    1.223  0.020  1.223
 E5C  C16  C15  single    1.454  0.020  1.454
 E5C  C4   C15  aromatic  1.404  0.020  1.404
 E5C  C4   C3   aromatic  1.375  0.020  1.375
 E5C  C15  C    aromatic  1.411  0.020  1.411
 E5C  C3   C2   aromatic  1.401  0.020  1.401
 E5C  C    O    single    1.329  0.020  1.329
 E5C  C    C1   aromatic  1.390  0.020  1.390
 E5C  C2   C1   aromatic  1.389  0.020  1.389
 E5C  C2   O1   single    1.337  0.020  1.337
 E5C  O    H2   single    0.850  0.020  0.980
 E5C  C1   H3   single    0.930  0.020  1.080
 E5C  C10  H4   single    0.970  0.020  1.090
 E5C  C10  H5   single    0.970  0.020  1.090
 E5C  C11  H6   single    0.970  0.020  1.090
 E5C  C11  H7   single    0.970  0.020  1.090
 E5C  C12  H8   single    0.970  0.020  1.090
 E5C  C13  H9   single    0.970  0.020  1.090
 E5C  C13  H10  single    0.970  0.020  1.090
 E5C  C14  H11  single    0.970  0.020  1.090
 E5C  C14  H12  single    0.970  0.020  1.090
 E5C  C14  H13  single    0.970  0.020  1.090
 E5C  C3   H14  single    0.930  0.020  1.080
 E5C  C5   H15  single    0.970  0.020  1.090
 E5C  C5   H16  single    0.970  0.020  1.090
 E5C  C6   H17  single    0.970  0.020  1.090
 E5C  C7   H18  single    0.970  0.020  1.090
 E5C  C7   H19  single    0.970  0.020  1.090
 E5C  C8   H20  single    0.970  0.020  1.090
 E5C  C8   H21  single    0.970  0.020  1.090
 E5C  C9   H22  single    0.970  0.020  1.090
 E5C  C9   H23  single    0.970  0.020  1.090
 E5C  O1   H24  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
 E5C  C9   N    C8   113.06  3.000
 E5C  C8   N    C7   115.21  3.000
 E5C  C9   N    C7   117.16  3.000
 E5C  C15  C    C1   119.65  3.000
 E5C  C1   C    O    118.16  3.000
 E5C  C15  C    O    122.19  3.000
 E5C  H2   O    C    107.73  3.000
 E5C  H3   C1   C2   120.76  3.000
 E5C  H3   C1   C    119.42  3.000
 E5C  C2   C1   C    119.81  3.000
 E5C  H5   C10  H4   107.09  3.000
 E5C  H5   C10  C9   109.27  3.000
 E5C  H4   C10  C9   109.58  3.000
 E5C  H5   C10  C11  109.82  3.000
 E5C  H4   C10  C11  110.68  3.000
 E5C  C9   C10  C11  110.33  3.000
 E5C  H7   C11  H6   106.47  3.000
 E5C  H7   C11  C12  110.10  3.000
 E5C  H6   C11  C12  108.91  3.000
 E5C  H7   C11  C10  110.62  3.000
 E5C  H6   C11  C10  109.22  3.000
 E5C  C12  C11  C10  111.37  3.000
 E5C  H8   C12  C8   107.57  3.000
 E5C  H8   C12  C13  108.37  3.000
 E5C  C8   C12  C13  112.09  3.000
 E5C  H8   C12  C11  108.15  3.000
 E5C  C13  C12  C11  111.02  3.000
 E5C  C8   C12  C11  109.48  3.000
 E5C  H10  C13  H9   105.93  3.000
 E5C  H10  C13  C14  108.96  3.000
 E5C  H9   C13  C14  109.73  3.000
 E5C  H10  C13  C12  108.18  3.000
 E5C  H9   C13  C12  109.09  3.000
 E5C  C14  C13  C12  114.58  3.000
 E5C  H13  C14  H12  107.56  3.000
 E5C  H13  C14  H11  107.15  3.000
 E5C  H12  C14  H11  107.55  3.000
 E5C  H13  C14  C13  112.22  3.000
 E5C  H12  C14  C13  111.08  3.000
 E5C  H11  C14  C13  111.06  3.000
 E5C  C4   C15  C16  120.67  3.000
 E5C  C4   C15  C    119.51  3.000
 E5C  C16  C15  C    119.79  3.000
 E5C  O3   C16  O2   117.96  3.000
 E5C  O3   C16  C15  123.14  3.000
 E5C  O2   C16  C15  118.90  3.000
 E5C  O1   C2   C3   116.91  3.000
 E5C  O1   C2   C1   122.13  3.000
 E5C  C3   C2   C1   120.95  3.000
 E5C  H14  C3   C4   120.75  3.000
 E5C  H14  C3   C2   119.89  3.000
 E5C  C4   C3   C2   119.37  3.000
 E5C  C5   C4   C3   121.92  3.000
 E5C  C3   C4   C15  120.68  3.000
 E5C  C5   C4   C15  117.38  3.000
 E5C  H16  C5   H15  106.94  3.000
 E5C  H16  C5   C6   109.89  3.000
 E5C  H15  C5   C6   109.35  3.000
 E5C  H16  C5   C4   109.50  3.000
 E5C  H15  C5   C4   110.70  3.000
 E5C  C6   C5   C4   110.40  3.000
 E5C  H17  C6   O2   107.39  3.000
 E5C  H17  C6   C7   110.31  3.000
 E5C  O2   C6   C7   107.65  3.000
 E5C  H17  C6   C5   109.15  3.000
 E5C  O2   C6   C5   110.26  3.000
 E5C  C7   C6   C5   111.96  3.000
 E5C  H19  C7   H18  106.24  3.000
 E5C  H19  C7   C6   108.46  3.000
 E5C  H18  C7   C6   106.04  3.000
 E5C  H19  C7   N    108.78  3.000
 E5C  H18  C7   N    108.04  3.000
 E5C  C6   C7   N    118.61  3.000
 E5C  H21  C8   H20  106.55  3.000
 E5C  H21  C8   C12  108.10  3.000
 E5C  H20  C8   C12  110.20  3.000
 E5C  H21  C8   N    112.47  3.000
 E5C  H20  C8   N    108.20  3.000
 E5C  C12  C8   N    111.22  3.000
 E5C  H23  C9   H22  106.84  3.000
 E5C  H23  C9   C10  108.46  3.000
 E5C  H22  C9   C10  110.25  3.000
 E5C  H23  C9   N    112.79  3.000
 E5C  H22  C9   N    108.71  3.000
 E5C  C10  C9   N    109.75  3.000
 E5C  C6   O2   C16  120.23  3.000
 E5C  H24  O1   C2   111.01  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
 E5C  CONST_01  C3   C4   C15  C       0.00   0.0  0
 E5C  CONST_02  C3   C2   C1   C       0.00   0.0  0
 E5C  CONST_03  C4   C15  C    C1      0.00   0.0  0
 E5C  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 E5C  CONST_05  C2   C3   C4   C15     0.00   0.0  0
 E5C  CONST_06  C2   C1   C    C15     0.00   0.0  0
 E5C  CONST_07  O1   C2   C1   C     180.00   0.0  0
 E5C  CONST_08  C16  C15  C    O       0.00   0.0  0
 E5C  CONST_09  C4   C15  C    O     180.00   0.0  0
 E5C  CONST_10  C2   C1   C    O     180.00   0.0  0
 E5C  CONST_11  O1   C2   C3   C4    180.00   0.0  0
 E5C  CONST_12  H14  C3   C2   C1    180.00   0.0  0
 E5C  CONST_13  H3   C1   C    C15   180.00   0.0  0
 E5C  Var_01    C11  C10  C9   N      56.47  30.0  1
 E5C  Var_02    O2   C16  C15  C    -173.68  30.0  1
 E5C  Var_03    C8   N    C9   C10   -60.08  30.0  1
 E5C  Var_04    C9   C10  C11  C12   -54.42  30.0  1
 E5C  Var_05    C9   N    C8   C12    59.75  30.0  1
 E5C  Var_06    C6   C5   C4   C15   -31.44  30.0  1
 E5C  Var_07    H11  C14  C13  C12  -175.12  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
 E5C  chir_01  C12  C11  C8  C13  negativ
 E5C  chir_02  C6   O2   C5  C7   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
 E5C  plan-1  C15  0.020
 E5C  plan-1  C16  0.020
 E5C  plan-1  O2   0.020
 E5C  plan-1  O3   0.020
 E5C  plan-2  C    0.020
 E5C  plan-2  O    0.020
 E5C  plan-2  C1   0.020
 E5C  plan-2  C15  0.020
 E5C  plan-2  C16  0.020
 E5C  plan-2  C2   0.020
 E5C  plan-2  C3   0.020
 E5C  plan-2  C4   0.020
 E5C  plan-2  C5   0.020
 E5C  plan-2  H3   0.020
 E5C  plan-2  H14  0.020
 E5C  plan-2  O1   0.020

