# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:07:34 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: (3~{R})-3-[[(3~{R})-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 E5R  E5R  (3~{R})-3-[[(3~{R})-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one  ligand  42  21  .  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_E5R
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
 E5R  N    N  NT    0  -0.426   -5.0984  16.8977  26.7904
 E5R  C    C  CR6   0   0.396   -9.9781  16.5642  22.7549
 E5R  O    O  OH1   0  -0.620   -9.7865  15.5171  21.9578
 E5R  C1   C  CR16  0  -0.452  -11.2261  17.1721  22.7510
 E5R  C10  C  CH2   0  -0.417   -3.3321  15.2727  28.4095
 E5R  C11  C  CH1   0  -0.242   -4.7936  14.8934  28.1945
 E5R  C12  C  CH3   0  -0.656   -5.3617  14.1261  29.3797
 E5R  C13  C  CH2   0  -0.261   -5.6145  16.1498  27.9234
 E5R  C14  C  CR66  0  -0.342   -8.9602  17.0600  23.5991
 E5R  C15  C  CR6   0   0.608   -7.6466  16.4328  23.5985
 E5R  C2   C  CR6   0   0.408  -11.4565  18.2807  23.5567
 E5R  C3   C  CR16  0  -0.491  -10.4456  18.7966  24.3779
 E5R  C4   C  CR66  0   0.177   -9.2119  18.1855  24.3958
 E5R  C5   C  C     0  -0.529   -8.0851  18.6978  25.2405
 E5R  C6   C  CR16  0   0.002   -7.2007  17.5437  25.6618
 E5R  C7   C  CH2   0  -0.279   -5.9558  17.9951  26.4019
 E5R  C8   C  CH2   0  -0.279   -3.7319  17.3274  27.0315
 E5R  C9   C  CH2   0  -0.439   -2.8227  16.1299  27.2585
 E5R  O2   O  O     0  -0.432   -6.7607  16.8058  24.5057
 E5R  O3   O  O     0  -0.481   -7.3134  15.5820  22.7861
 E5R  H2   H  HOH1  0   0.474   -8.8421  15.2568  22.0259
 E5R  H3   H  HCR6  0   0.276  -12.0127  16.7879  22.1137
 E5R  H4   H  HCH2  0   0.227   -2.7190  14.3750  28.5238
 E5R  H5   H  HCH2  0   0.205   -3.2467  15.8344  29.3473
 E5R  H6   H  HCH1  0   0.215   -4.8579  14.2621  27.3004
 E5R  H7   H  HCH3  0   0.228   -4.7861  13.2204  29.5770
 E5R  H8   H  HCH3  0   0.214   -5.3400  14.7343  30.2871
 E5R  H9   H  HCH3  0   0.225   -6.3972  13.8287  29.2046
 E5R  H10  H  HCH2  0   0.182   -5.6290  16.7727  28.8380
 E5R  H11  H  HCH2  0   0.235   -6.6496  15.8587  27.7296
 E5R  H12  H  HCR6  0   0.273  -10.6331  19.6636  25.0014
 E5R  H13  H  H     0   0.274   -7.5013  19.4339  24.6770
 E5R  H14  H  H     0   0.280   -8.4666  19.2056  26.1272
 E5R  H15  H  HCR6  0   0.261   -7.7898  16.8592  26.2819
 E5R  H16  H  HCH2  0   0.245   -5.3943  18.6630  25.7424
 E5R  H17  H  HCH2  0   0.214   -6.2811  18.6072  27.2597
 E5R  H18  H  HCH2  0   0.234   -3.3851  17.8954  26.1651
 E5R  H19  H  HCH2  0   0.184   -3.6667  18.0018  27.9043
 E5R  H20  H  HCH2  0   0.215   -2.7842  15.5339  26.3420
 E5R  H21  H  HCH2  0   0.229   -1.8072  16.4796  27.4563
 E5R  H22  H  HOH1  0   0.481  -12.7340  19.5915  24.0931
 E5R  O1   O  OH1   0  -0.614  -12.6769  18.8239  23.5113

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
 E5R  O    C    single    1.330  0.020  1.330
 E5R  O3   C15  double    1.223  0.020  1.223
 E5R  C    C1   aromatic  1.388  0.020  1.388
 E5R  C    C14  aromatic  1.412  0.020  1.412
 E5R  C1   C2   aromatic  1.390  0.020  1.390
 E5R  C15  C14  single    1.456  0.020  1.456
 E5R  C15  O2   single    1.322  0.020  1.322
 E5R  C14  C4   aromatic  1.402  0.020  1.402
 E5R  C2   O1   single    1.337  0.020  1.337
 E5R  C2   C3   aromatic  1.401  0.020  1.401
 E5R  O2   C6   single    1.440  0.020  1.440
 E5R  C4   C3   aromatic  1.377  0.020  1.377
 E5R  C4   C5   single    1.499  0.020  1.499
 E5R  C5   C6   single    1.514  0.020  1.514
 E5R  C6   C7   single    1.517  0.020  1.517
 E5R  C7   N    single    1.446  0.020  1.446
 E5R  N    C8   single    1.453  0.020  1.453
 E5R  N    C13  single    1.452  0.020  1.452
 E5R  C8   C9   single    1.521  0.020  1.521
 E5R  C9   C10  single    1.523  0.020  1.523
 E5R  C13  C11  single    1.525  0.020  1.525
 E5R  C11  C10  single    1.525  0.020  1.525
 E5R  C11  C12  single    1.522  0.020  1.522
 E5R  O    H2   single    0.850  0.020  0.980
 E5R  C1   H3   single    0.930  0.020  1.080
 E5R  C10  H4   single    0.970  0.020  1.090
 E5R  C10  H5   single    0.970  0.020  1.090
 E5R  C11  H6   single    0.970  0.020  1.090
 E5R  C12  H7   single    0.970  0.020  1.090
 E5R  C12  H8   single    0.970  0.020  1.090
 E5R  C12  H9   single    0.970  0.020  1.090
 E5R  C13  H10  single    0.970  0.020  1.090
 E5R  C13  H11  single    0.970  0.020  1.090
 E5R  C3   H12  single    0.930  0.020  1.080
 E5R  C5   H13  single    0.970  0.020  1.090
 E5R  C5   H14  single    0.970  0.020  1.090
 E5R  C6   H15  single    0.970  0.020  1.090
 E5R  C7   H16  single    0.970  0.020  1.090
 E5R  C7   H17  single    0.970  0.020  1.090
 E5R  C8   H18  single    0.970  0.020  1.090
 E5R  C8   H19  single    0.970  0.020  1.090
 E5R  C9   H20  single    0.970  0.020  1.090
 E5R  C9   H21  single    0.970  0.020  1.090
 E5R  O1   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
 E5R  C8   N    C7   112.21  3.000
 E5R  C8   N    C13  110.92  3.000
 E5R  C7   N    C13  112.94  3.000
 E5R  C14  C    C1   119.73  3.000
 E5R  C14  C    O    122.06  3.000
 E5R  C1   C    O    118.21  3.000
 E5R  H2   O    C    107.80  3.000
 E5R  H3   C1   C2   120.26  3.000
 E5R  H3   C1   C    119.96  3.000
 E5R  C2   C1   C    119.78  3.000
 E5R  H5   C10  H4   106.71  3.000
 E5R  H5   C10  C9   109.39  3.000
 E5R  H4   C10  C9   110.72  3.000
 E5R  H5   C10  C11  108.82  3.000
 E5R  H4   C10  C11  110.37  3.000
 E5R  C9   C10  C11  110.73  3.000
 E5R  H6   C11  C13  107.33  3.000
 E5R  H6   C11  C12  108.84  3.000
 E5R  C13  C11  C12  110.67  3.000
 E5R  H6   C11  C10  108.32  3.000
 E5R  C12  C11  C10  111.92  3.000
 E5R  C13  C11  C10  109.63  3.000
 E5R  H9   C12  H8   107.68  3.000
 E5R  H9   C12  H7   107.66  3.000
 E5R  H8   C12  H7   107.55  3.000
 E5R  H9   C12  C11  111.50  3.000
 E5R  H8   C12  C11  111.02  3.000
 E5R  H7   C12  C11  111.25  3.000
 E5R  H11  C13  H10  106.50  3.000
 E5R  H11  C13  C11  108.78  3.000
 E5R  H10  C13  C11  108.89  3.000
 E5R  H11  C13  N    109.61  3.000
 E5R  H10  C13  N    111.07  3.000
 E5R  C11  C13  N    111.82  3.000
 E5R  C4   C14  C15  120.54  3.000
 E5R  C4   C14  C    119.49  3.000
 E5R  C15  C14  C    119.93  3.000
 E5R  O3   C15  O2   118.02  3.000
 E5R  O2   C15  C14  118.88  3.000
 E5R  O3   C15  C14  123.09  3.000
 E5R  O1   C2   C3   121.94  3.000
 E5R  C3   C2   C1   120.94  3.000
 E5R  O1   C2   C1   117.12  3.000
 E5R  H12  C3   C4   120.15  3.000
 E5R  H12  C3   C2   120.46  3.000
 E5R  C4   C3   C2   119.39  3.000
 E5R  C5   C4   C3   121.96  3.000
 E5R  C5   C4   C14  117.38  3.000
 E5R  C3   C4   C14  120.65  3.000
 E5R  H14  C5   H13  106.96  3.000
 E5R  H14  C5   C6   109.46  3.000
 E5R  H13  C5   C6   110.13  3.000
 E5R  H14  C5   C4   110.75  3.000
 E5R  H13  C5   C4   109.91  3.000
 E5R  C6   C5   C4   109.61  3.000
 E5R  H15  C6   O2   107.37  3.000
 E5R  H15  C6   C7   110.55  3.000
 E5R  O2   C6   C7   107.06  3.000
 E5R  H15  C6   C5   108.65  3.000
 E5R  C7   C6   C5   112.85  3.000
 E5R  O2   C6   C5   110.22  3.000
 E5R  H17  C7   H16  106.35  3.000
 E5R  H17  C7   C6   107.62  3.000
 E5R  H16  C7   C6   107.99  3.000
 E5R  H17  C7   N    112.78  3.000
 E5R  H16  C7   N    108.73  3.000
 E5R  C6   C7   N    113.07  3.000
 E5R  H19  C8   H18  106.88  3.000
 E5R  H19  C8   C9   109.12  3.000
 E5R  H18  C8   C9   109.76  3.000
 E5R  H19  C8   N    111.54  3.000
 E5R  H18  C8   N    108.71  3.000
 E5R  C9   C8   N    110.75  3.000
 E5R  H21  C9   H20  107.07  3.000
 E5R  H21  C9   C8   109.32  3.000
 E5R  H20  C9   C8   108.97  3.000
 E5R  H21  C9   C10  110.75  3.000
 E5R  H20  C9   C10  109.77  3.000
 E5R  C8   C9   C10  110.86  3.000
 E5R  C6   O2   C15  119.39  3.000
 E5R  H22  O1   C2   110.91  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
 E5R  CONST_01  C3   C2   C1   C       0.00   0.0  0
 E5R  CONST_02  C3   C4   C14  C       0.00   0.0  0
 E5R  CONST_03  C4   C14  C    C1      0.00   0.0  0
 E5R  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 E5R  CONST_05  C2   C1   C    C14     0.00   0.0  0
 E5R  CONST_06  C2   C3   C4   C14     0.00   0.0  0
 E5R  CONST_07  O1   C2   C1   C     180.00   0.0  0
 E5R  CONST_08  C2   C1   C    O     180.00   0.0  0
 E5R  CONST_09  C15  C14  C    O       0.00   0.0  0
 E5R  CONST_10  C4   C14  C    O     180.00   0.0  0
 E5R  CONST_11  O1   C2   C3   C4    180.00   0.0  0
 E5R  CONST_12  H12  C3   C2   C1    180.00   0.0  0
 E5R  CONST_13  H3   C1   C    C14   180.00   0.0  0
 E5R  Var_01    C10  C9   C8   N     -56.53  30.0  1
 E5R  Var_02    O2   C15  C14  C    -171.99  30.0  1
 E5R  Var_03    C8   N    C13  C11   -60.66  30.0  1
 E5R  Var_04    C8   C9   C10  C11    53.14  30.0  1
 E5R  Var_05    C9   C8   N    C13    60.05  30.0  1
 E5R  Var_06    C6   C5   C4   C14   -31.51  30.0  1
 E5R  Var_07    C6   C7   N    C13   -75.16  30.0  2

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
 E5R  chir_01  C11  C13  C10  C12  negativ
 E5R  chir_02  C6   O2   C7   C5   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
 E5R  plan-1  C14  0.020
 E5R  plan-1  C15  0.020
 E5R  plan-1  O2   0.020
 E5R  plan-1  O3   0.020
 E5R  plan-2  C    0.020
 E5R  plan-2  O    0.020
 E5R  plan-2  C1   0.020
 E5R  plan-2  C14  0.020
 E5R  plan-2  C15  0.020
 E5R  plan-2  C2   0.020
 E5R  plan-2  C3   0.020
 E5R  plan-2  C4   0.020
 E5R  plan-2  C5   0.020
 E5R  plan-2  H3   0.020
 E5R  plan-2  H12  0.020
 E5R  plan-2  O1   0.020

