# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 01:20:44 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydro-2~{H}-isoquinolin-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)N2
#
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
 D4X  D4X  (3~{S})-3-[[(1~{S},3~{S})-3-methylcyclohexyl]methyl]-6,8-bis(oxidanyl)-3,4-dihydro-2~{H}-isoquinolin-1-one  ligand  44  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_D4X
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
 D4X  C1   C  CR6   0   0.385   2.9846  -1.0895   0.6924
 D4X  C10  C  CH2   0  -0.393  -0.9631   1.1273  -0.2824
 D4X  C11  C  CH1   0  -0.242  -2.2789   0.5212   0.2005
 D4X  C12  C  CH1   0  -0.234  -4.6897  -0.0750  -0.4091
 D4X  C13  C  CH2   0  -0.423  -5.1665   0.6750   0.8383
 D4X  C14  C  CH2   0  -0.440  -4.1100   0.7050   1.9378
 D4X  C15  C  CH2   0  -0.411  -2.7955   1.2805   1.4230
 D4X  C16  C  CH3   0  -0.666  -4.6182  -1.5850  -0.1877
 D4X  C17  C  CH2   0  -0.422  -3.3526   0.4990  -0.8892
 D4X  C2   C  CR16  0  -0.459   4.0428  -0.2478   1.0164
 D4X  C3   C  CR6   0   0.400   4.1166   1.0138   0.4409
 D4X  C4   C  CR16  0  -0.496   3.1413   1.4496  -0.4630
 D4X  C5   C  CR6   0   0.150   2.0880   0.6171  -0.7815
 D4X  C6   C  CH2   0  -0.502   1.0574   1.0108  -1.7984
 D4X  C7   C  CH1   0  -0.138  -0.3043   0.4162  -1.4675
 D4X  C8   C  C     0   0.577   0.8622  -1.5374  -0.5207
 D4X  C9   C  CR6   0  -0.267   1.9855  -0.6523  -0.2000
 D4X  N1   N  NH1   0  -0.630  -0.1421  -1.0130  -1.2311
 D4X  O1   O  OH1   0  -0.635   2.9451  -2.3016   1.2416
 D4X  O2   O  OH1   0  -0.622   5.1580   1.7855   0.7824
 D4X  O4   O  O     0  -0.543   0.8504  -2.7260  -0.1530
 D4X  H1   H  HCH2  0   0.226  -1.1304   2.1696  -0.5754
 D4X  H2   H  HCH2  0   0.231  -0.2581   1.1531   0.5562
 D4X  H3   H  HCH1  0   0.214  -2.0785  -0.5081   0.5233
 D4X  H4   H  HCH1  0   0.223  -5.4243   0.0967  -1.2032
 D4X  H5   H  HCH2  0   0.214  -5.4101   1.7051   0.5565
 D4X  H6   H  HCH2  0   0.222  -6.0938   0.2302   1.2106
 D4X  H7   H  HCH2  0   0.227  -4.4704   1.2960   2.7837
 D4X  H8   H  HCH2  0   0.213  -3.9388  -0.3044   2.3255
 D4X  H9   H  HCH2  0   0.224  -2.0397   1.2650   2.2137
 D4X  H10  H  HCH2  0   0.204  -2.9415   2.3340   1.1544
 D4X  H11  H  HCH3  0   0.226  -5.5913  -1.9843   0.1043
 D4X  H12  H  HCH3  0   0.224  -4.3143  -2.0990  -1.1021
 D4X  H13  H  HCH3  0   0.218  -3.9060  -1.8646   0.5904
 D4X  H14  H  HCH2  0   0.216  -3.5114   1.5259  -1.2415
 D4X  H15  H  HCH2  0   0.222  -3.0165  -0.0707  -1.7619
 D4X  H16  H  HCR6  0   0.271   4.8096  -0.5816   1.7043
 D4X  H17  H  HCR6  0   0.269   3.2134   2.4337  -0.9126
 D4X  H18  H  HCH2  0   0.266   0.9805   2.0962  -1.8706
 D4X  H19  H  HCH2  0   0.277   1.3813   0.6520  -2.7806
 D4X  H20  H  HCH1  0   0.276  -0.9414   0.5125  -2.3473
 D4X  H21  H  HNH1  0   0.396  -0.9243  -1.6215  -1.4218
 D4X  H22  H  HOH1  0   0.474   2.1654  -2.7657   0.8419
 D4X  H23  H  HOH1  0   0.480   5.1262   2.6263   0.3115

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
 D4X  C16  C12  single    1.528  0.020  1.528
 D4X  C12  C13  single    1.532  0.020  1.532
 D4X  C12  C17  single    1.532  0.020  1.532
 D4X  O2   C3   single    1.340  0.020  1.340
 D4X  C13  C14  single    1.525  0.020  1.525
 D4X  C4   C3   aromatic  1.399  0.020  1.399
 D4X  C4   C5   aromatic  1.380  0.020  1.380
 D4X  C6   C5   single    1.500  0.020  1.500
 D4X  C6   C7   single    1.522  0.020  1.522
 D4X  C3   C2   aromatic  1.389  0.020  1.389
 D4X  C15  C14  single    1.524  0.020  1.524
 D4X  C15  C11  single    1.529  0.020  1.529
 D4X  C10  C7   single    1.531  0.020  1.531
 D4X  C10  C11  single    1.527  0.020  1.527
 D4X  C17  C11  single    1.530  0.020  1.530
 D4X  C5   C9   aromatic  1.400  0.020  1.400
 D4X  C7   N1   single    1.458  0.020  1.458
 D4X  C2   C1   aromatic  1.390  0.020  1.390
 D4X  C9   C1   aromatic  1.409  0.020  1.409
 D4X  C9   C8   single    1.466  0.020  1.466
 D4X  N1   C8   single    1.337  0.020  1.337
 D4X  C1   O1   single    1.331  0.020  1.331
 D4X  C8   O4   double    1.244  0.020  1.244
 D4X  C10  H1   single    0.970  0.020  1.090
 D4X  C10  H2   single    0.970  0.020  1.090
 D4X  C11  H3   single    0.970  0.020  1.090
 D4X  C12  H4   single    0.970  0.020  1.090
 D4X  C13  H5   single    0.970  0.020  1.090
 D4X  C13  H6   single    0.970  0.020  1.090
 D4X  C14  H7   single    0.970  0.020  1.090
 D4X  C14  H8   single    0.970  0.020  1.090
 D4X  C15  H9   single    0.970  0.020  1.090
 D4X  C15  H10  single    0.970  0.020  1.090
 D4X  C16  H11  single    0.970  0.020  1.090
 D4X  C16  H12  single    0.970  0.020  1.090
 D4X  C16  H13  single    0.970  0.020  1.090
 D4X  C17  H14  single    0.970  0.020  1.090
 D4X  C17  H15  single    0.970  0.020  1.090
 D4X  C2   H16  single    0.930  0.020  1.080
 D4X  C4   H17  single    0.930  0.020  1.080
 D4X  C6   H18  single    0.970  0.020  1.090
 D4X  C6   H19  single    0.970  0.020  1.090
 D4X  C7   H20  single    0.970  0.020  1.090
 D4X  N1   H21  single    0.860  0.020  1.020
 D4X  O1   H22  single    0.850  0.020  0.980
 D4X  O2   H23  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
 D4X  O1   C1   C9   121.51  3.000
 D4X  O1   C1   C2   118.53  3.000
 D4X  C9   C1   C2   119.96  3.000
 D4X  H2   C10  H1   106.29  3.000
 D4X  H2   C10  C7   109.05  3.000
 D4X  H1   C10  C7   107.50  3.000
 D4X  H2   C10  C11  108.76  3.000
 D4X  H1   C10  C11  109.31  3.000
 D4X  C7   C10  C11  115.54  3.000
 D4X  H3   C11  C17  108.91  3.000
 D4X  H3   C11  C15  107.00  3.000
 D4X  C17  C11  C15  109.84  3.000
 D4X  H3   C11  C10  107.94  3.000
 D4X  C17  C11  C10  112.66  3.000
 D4X  C15  C11  C10  110.30  3.000
 D4X  H4   C12  C17  107.42  3.000
 D4X  H4   C12  C16  106.94  3.000
 D4X  C17  C12  C16  112.01  3.000
 D4X  H4   C12  C13  107.75  3.000
 D4X  C17  C12  C13  110.08  3.000
 D4X  C16  C12  C13  112.37  3.000
 D4X  H6   C13  H5   106.35  3.000
 D4X  H6   C13  C14  110.48  3.000
 D4X  H5   C13  C14  108.73  3.000
 D4X  H6   C13  C12  110.00  3.000
 D4X  H5   C13  C12  108.68  3.000
 D4X  C14  C13  C12  112.41  3.000
 D4X  H8   C14  H7   106.02  3.000
 D4X  H8   C14  C15  109.44  3.000
 D4X  H7   C14  C15  109.97  3.000
 D4X  H8   C14  C13  110.21  3.000
 D4X  H7   C14  C13  109.88  3.000
 D4X  C15  C14  C13  111.17  3.000
 D4X  H10  C15  H9   106.41  3.000
 D4X  H10  C15  C14  109.30  3.000
 D4X  H9   C15  C14  110.26  3.000
 D4X  H10  C15  C11  109.03  3.000
 D4X  H9   C15  C11  109.72  3.000
 D4X  C14  C15  C11  111.96  3.000
 D4X  H13  C16  H12  107.15  3.000
 D4X  H13  C16  H11  107.30  3.000
 D4X  H12  C16  H11  107.45  3.000
 D4X  H13  C16  C12  112.77  3.000
 D4X  H12  C16  C12  110.91  3.000
 D4X  H11  C16  C12  111.01  3.000
 D4X  H15  C17  H14  105.99  3.000
 D4X  H15  C17  C12  108.82  3.000
 D4X  H14  C17  C12  108.96  3.000
 D4X  H15  C17  C11  111.09  3.000
 D4X  H14  C17  C11  108.47  3.000
 D4X  C12  C17  C11  113.25  3.000
 D4X  H16  C2   C3   120.37  3.000
 D4X  H16  C2   C1   120.02  3.000
 D4X  C3   C2   C1   119.60  3.000
 D4X  O2   C3   C4   121.79  3.000
 D4X  C4   C3   C2   120.90  3.000
 D4X  O2   C3   C2   117.31  3.000
 D4X  H17  C4   C5   120.17  3.000
 D4X  H17  C4   C3   120.28  3.000
 D4X  C5   C4   C3   119.55  3.000
 D4X  C9   C5   C6   117.98  3.000
 D4X  C9   C5   C4   120.47  3.000
 D4X  C6   C5   C4   121.50  3.000
 D4X  H19  C6   H18  106.72  3.000
 D4X  H19  C6   C7   109.37  3.000
 D4X  H18  C6   C7   109.88  3.000
 D4X  H19  C6   C5   108.60  3.000
 D4X  H18  C6   C5   110.76  3.000
 D4X  C7   C6   C5   111.38  3.000
 D4X  H20  C7   N1   106.40  3.000
 D4X  H20  C7   C6   108.22  3.000
 D4X  N1   C7   C6   108.58  3.000
 D4X  H20  C7   C10  109.39  3.000
 D4X  N1   C7   C10  112.20  3.000
 D4X  C6   C7   C10  111.82  3.000
 D4X  O4   C8   N1   121.64  3.000
 D4X  O4   C8   C9   121.30  3.000
 D4X  N1   C8   C9   117.06  3.000
 D4X  C8   C9   C5   120.85  3.000
 D4X  C8   C9   C1   119.64  3.000
 D4X  C5   C9   C1   119.50  3.000
 D4X  H21  N1   C8   116.49  3.000
 D4X  H21  N1   C7   118.31  3.000
 D4X  C8   N1   C7   123.66  3.000
 D4X  H22  O1   C1   106.45  3.000
 D4X  H23  O2   C3   110.60  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
 D4X  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 D4X  CONST_02  C4   C5   C9   C1      0.00   0.0  0
 D4X  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 D4X  CONST_04  C5   C9   C1   C2      0.00   0.0  0
 D4X  CONST_05  C9   C5   C4   C3      0.00   0.0  0
 D4X  CONST_06  C9   C1   C2   C3      0.00   0.0  0
 D4X  CONST_07  C9   C8   N1   C7      0.00   0.0  0
 D4X  CONST_08  O2   C3   C2   C1    180.00   0.0  0
 D4X  CONST_09  O1   C1   C2   C3    180.00   0.0  0
 D4X  CONST_10  O2   C3   C4   C5    180.00   0.0  0
 D4X  CONST_11  O1   C1   C9   C5    180.00   0.0  0
 D4X  CONST_12  O1   C1   C9   C8      0.00   0.0  0
 D4X  CONST_13  O4   C8   N1   C7    180.00   0.0  0
 D4X  CONST_14  H17  C4   C3   C2    180.00   0.0  0
 D4X  CONST_15  H16  C2   C3   C4    180.00   0.0  0
 D4X  CONST_16  H21  N1   C8   C9    180.00   0.0  0
 D4X  Var_01    N1   C8   C9   C1    171.54  30.0  1
 D4X  Var_02    C13  C14  C15  C11   -55.72  30.0  1
 D4X  Var_03    C15  C14  C13  C12    54.85  30.0  1
 D4X  Var_04    C7   C6   C5   C4   -148.62  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
 D4X  chir_01  C11  C15  C10  C17  positiv
 D4X  chir_02  C12  C17  C13  C16  positiv
 D4X  chir_03  C7   N1   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
 D4X  plan-1  C7   0.020
 D4X  plan-1  C8   0.020
 D4X  plan-1  C9   0.020
 D4X  plan-1  N1   0.020
 D4X  plan-1  O4   0.020
 D4X  plan-1  H21  0.020
 D4X  plan-2  C1   0.020
 D4X  plan-2  C2   0.020
 D4X  plan-2  C3   0.020
 D4X  plan-2  C4   0.020
 D4X  plan-2  C5   0.020
 D4X  plan-2  C6   0.020
 D4X  plan-2  C8   0.020
 D4X  plan-2  C9   0.020
 D4X  plan-2  O1   0.020
 D4X  plan-2  O2   0.020
 D4X  plan-2  H16  0.020
 D4X  plan-2  H17  0.020

