# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:20:07 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 2-(4-hydroxyphenyl)-~{N}-methyl-5-oxidanyl-4-(piperidin-1-ylmethyl)-1-benzofuran-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1c(oc2ccc(O)c(CN3CCCCC3)c12)c4ccc(O)cc4
#
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
 5V8  5V8  2-(4-hydroxyphenyl)-~{N}-methyl-5-oxidanyl-4-(piperidin-1-ylmethyl)-1-benzofuran-3-carboxamide  ligand  52  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5V8
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
 5V8  C2   C  CR6   0   0.308   2.7370  -2.7141   0.6953
 5V8  C3   C  CR16  0  -0.361   2.0184  -3.8382   0.2516
 5V8  C4   C  CR16  0  -0.348   0.6842  -3.7524  -0.0869
 5V8  C5   C  CR56  0   0.319   0.0944  -2.5099   0.0486
 5V8  C10  C  CR16  0  -0.327  -4.7761  -0.3473  -1.4416
 5V8  C11  C  CR6   0   0.357  -5.2944   0.6329  -0.5960
 5V8  C15  C  CR5   0  -0.220  -0.2094  -0.3254   0.4698
 5V8  C16  C  C     0   0.436  -0.0773   1.0851   0.9199
 5V8  C18  C  CH3   0  -0.527  -0.5018   3.4084   0.3274
 5V8  C20  C  CR56  0   0.161   0.7710  -1.3823   0.5060
 5V8  C24  C  CH2   0  -0.276   3.4100   2.0328   0.6955
 5V8  C25  C  CH2   0  -0.448   3.3085   3.1369  -0.3452
 5V8  C26  C  CH2   0  -0.439   3.9540   2.7124  -1.6570
 5V8  O1   O  OH1   0  -0.636   4.0458  -2.9433   0.9559
 5V8  C7   C  CR5   0   0.413  -1.3685  -0.8939   0.0302
 5V8  C8   C  CR6   0  -0.040  -2.7123  -0.3722  -0.1775
 5V8  C9   C  CR16  0  -0.276  -3.5031  -0.8414  -1.2305
 5V8  C13  C  CR16  0  -0.370  -4.5221   1.0985   0.4668
 5V8  C14  C  CR16  0  -0.281  -3.2500   0.5960   0.6711
 5V8  C21  C  CR6   0  -0.134   2.1343  -1.4648   0.8345
 5V8  C22  C  CH2   0  -0.361   2.8807  -0.2271   1.2477
 5V8  O6   O  O     0  -0.463  -1.1942  -2.2099  -0.2354
 5V8  N17  N  NH1   0  -0.600  -0.3984   2.0070   0.0064
 5V8  O19  O  O     0  -0.493   0.2250   1.3671   2.0735
 5V8  N23  N  NT    0  -0.395   2.8458   0.7848   0.2137
 5V8  C27  C  CH2   0  -0.433   3.3611   1.3860  -2.1105
 5V8  C28  C  CH2   0  -0.270   3.4790   0.3389  -1.0149
 5V8  H1   H  HCR6  0   0.268   2.5369  -4.7844   0.1633
 5V8  H2   H  HCR6  0   0.272   0.1365  -4.6151  -0.4414
 5V8  H3   H  HCR6  0   0.270  -5.3726  -0.7177  -2.2656
 5V8  H4   H  HCH3  0   0.239   0.4405   3.8090   0.7007
 5V8  H5   H  HCH3  0   0.251  -0.7692   3.9490  -0.5759
 5V8  H6   H  HCH3  0   0.241  -1.2718   3.5919   1.0789
 5V8  H7   H  HCH2  0   0.186   4.4701   1.9065   0.9843
 5V8  H8   H  HCH2  0   0.232   2.8713   2.3251   1.5998
 5V8  H9   H  HCH2  0   0.226   2.2545   3.3686  -0.5186
 5V8  H10  H  HCH2  0   0.227   3.7756   4.0433   0.0463
 5V8  H11  H  HCH2  0   0.230   3.8196   3.4810  -2.4213
 5V8  H12  H  HCH2  0   0.208   5.0339   2.5973  -1.5129
 5V8  H13  H  HOH1  0   0.467   4.4930  -2.1327   1.2211
 5V8  H14  H  HCR6  0   0.262  -3.1189  -1.5928  -1.9080
 5V8  H15  H  HCR6  0   0.279  -4.9184   1.8450   1.1455
 5V8  H16  H  HCR6  0   0.263  -2.6869   0.9500   1.5247
 5V8  H17  H  HCH2  0   0.267   2.4162   0.1855   2.1460
 5V8  H18  H  HCH2  0   0.195   3.9202  -0.4552   1.5463
 5V8  H19  H  HOH1  0   0.478  -6.7804   1.7666  -0.2104
 5V8  H20  H  HNH1  0   0.403  -0.6007   1.7118  -0.9333
 5V8  H22  H  HCH2  0   0.215   2.3040   1.5199  -2.3592
 5V8  H23  H  HCH2  0   0.228   3.8598   1.0215  -3.0113
 5V8  H24  H  HCH2  0   0.178   4.5471   0.1004  -0.8521
 5V8  H25  H  HCH2  0   0.240   2.9991  -0.5844  -1.3441
 5V8  O12  O  OH1   0  -0.623  -6.5346   1.0836  -0.8449

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
 5V8  C18  N17  single    1.441  0.020  1.441
 5V8  N17  C16  single    1.337  0.020  1.337
 5V8  C16  O19  double    1.225  0.020  1.225
 5V8  C16  C15  single    1.486  0.020  1.486
 5V8  C22  C21  single    1.503  0.020  1.503
 5V8  C22  N23  single    1.447  0.020  1.447
 5V8  C24  C25  single    1.521  0.020  1.521
 5V8  C24  N23  single    1.452  0.020  1.452
 5V8  O12  C11  single    1.343  0.020  1.343
 5V8  C13  C11  aromatic  1.394  0.020  1.394
 5V8  C13  C14  aromatic  1.383  0.020  1.383
 5V8  C11  C10  aromatic  1.395  0.020  1.395
 5V8  C15  C7   aromatic  1.364  0.020  1.364
 5V8  C15  C20  aromatic  1.442  0.020  1.442
 5V8  C14  C8   aromatic  1.395  0.020  1.395
 5V8  C10  C9   aromatic  1.382  0.020  1.382
 5V8  C8   C9   aromatic  1.398  0.020  1.398
 5V8  C8   C7   single    1.456  0.020  1.456
 5V8  C21  C20  aromatic  1.405  0.020  1.405
 5V8  C21  C2   aromatic  1.394  0.020  1.394
 5V8  C7   O6   aromatic  1.354  0.020  1.354
 5V8  C25  C26  single    1.522  0.020  1.522
 5V8  C20  C5   aromatic  1.392  0.020  1.392
 5V8  N23  C28  single    1.452  0.020  1.452
 5V8  O1   C2   single    1.354  0.020  1.354
 5V8  C2   C3   aromatic  1.406  0.020  1.406
 5V8  O6   C5   aromatic  1.353  0.020  1.353
 5V8  C5   C4   aromatic  1.382  0.020  1.382
 5V8  C26  C27  single    1.522  0.020  1.522
 5V8  C28  C27  single    1.520  0.020  1.520
 5V8  C3   C4   aromatic  1.379  0.020  1.379
 5V8  C3   H1   single    0.930  0.020  1.080
 5V8  C4   H2   single    0.930  0.020  1.080
 5V8  C10  H3   single    0.930  0.020  1.080
 5V8  C18  H4   single    0.970  0.020  1.090
 5V8  C18  H5   single    0.970  0.020  1.090
 5V8  C18  H6   single    0.970  0.020  1.090
 5V8  C24  H7   single    0.970  0.020  1.090
 5V8  C24  H8   single    0.970  0.020  1.090
 5V8  C25  H9   single    0.970  0.020  1.090
 5V8  C25  H10  single    0.970  0.020  1.090
 5V8  C26  H11  single    0.970  0.020  1.090
 5V8  C26  H12  single    0.970  0.020  1.090
 5V8  O1   H13  single    0.850  0.020  0.980
 5V8  C9   H14  single    0.930  0.020  1.080
 5V8  C13  H15  single    0.930  0.020  1.080
 5V8  C14  H16  single    0.930  0.020  1.080
 5V8  C22  H17  single    0.970  0.020  1.090
 5V8  C22  H18  single    0.970  0.020  1.090
 5V8  O12  H19  single    0.850  0.020  0.980
 5V8  N17  H20  single    0.860  0.020  1.020
 5V8  C27  H22  single    0.970  0.020  1.090
 5V8  C27  H23  single    0.970  0.020  1.090
 5V8  C28  H24  single    0.970  0.020  1.090
 5V8  C28  H25  single    0.970  0.020  1.090

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
 5V8  C21  C2   O1   123.39  3.000
 5V8  O1   C2   C3   114.80  3.000
 5V8  C21  C2   C3   121.80  3.000
 5V8  H1   C3   C4   119.85  3.000
 5V8  H1   C3   C2   118.67  3.000
 5V8  C4   C3   C2   121.48  3.000
 5V8  H2   C4   C5   122.22  3.000
 5V8  H2   C4   C3   121.38  3.000
 5V8  C5   C4   C3   116.41  3.000
 5V8  O6   C5   C20  110.62  3.000
 5V8  O6   C5   C4   125.81  3.000
 5V8  C20  C5   C4   123.57  3.000
 5V8  H3   C10  C9   120.11  3.000
 5V8  H3   C10  C11  119.82  3.000
 5V8  C9   C10  C11  120.07  3.000
 5V8  O12  C11  C13  122.75  3.000
 5V8  C13  C11  C10  119.42  3.000
 5V8  O12  C11  C10  117.83  3.000
 5V8  C7   C15  C20  106.28  3.000
 5V8  C20  C15  C16  128.86  3.000
 5V8  C7   C15  C16  124.66  3.000
 5V8  O19  C16  N17  122.94  3.000
 5V8  O19  C16  C15  121.69  3.000
 5V8  N17  C16  C15  115.22  3.000
 5V8  H6   C18  H5   108.38  3.000
 5V8  H6   C18  H4   108.20  3.000
 5V8  H5   C18  H4   108.35  3.000
 5V8  H6   C18  N17  111.56  3.000
 5V8  H5   C18  N17  108.44  3.000
 5V8  H4   C18  N17  111.82  3.000
 5V8  C21  C20  C15  135.13  3.000
 5V8  C21  C20  C5   120.06  3.000
 5V8  C15  C20  C5   104.77  3.000
 5V8  H8   C24  H7   106.68  3.000
 5V8  H8   C24  N23  108.24  3.000
 5V8  H7   C24  N23  111.16  3.000
 5V8  H8   C24  C25  109.84  3.000
 5V8  H7   C24  C25  109.00  3.000
 5V8  N23  C24  C25  111.78  3.000
 5V8  H10  C25  H9   107.06  3.000
 5V8  H10  C25  C26  111.03  3.000
 5V8  H9   C25  C26  109.35  3.000
 5V8  H10  C25  C24  109.19  3.000
 5V8  H9   C25  C24  109.07  3.000
 5V8  C26  C25  C24  111.04  3.000
 5V8  H12  C26  H11  106.70  3.000
 5V8  H12  C26  C27  109.36  3.000
 5V8  H11  C26  C27  110.91  3.000
 5V8  H12  C26  C25  109.51  3.000
 5V8  H11  C26  C25  110.77  3.000
 5V8  C27  C26  C25  109.55  3.000
 5V8  H13  O1   C2   111.07  3.000
 5V8  O6   C7   C8   116.04  3.000
 5V8  O6   C7   C15  111.04  3.000
 5V8  C8   C7   C15  132.91  3.000
 5V8  C14  C8   C9   118.23  3.000
 5V8  C9   C8   C7   120.61  3.000
 5V8  C14  C8   C7   121.16  3.000
 5V8  H14  C9   C8   120.25  3.000
 5V8  H14  C9   C10  118.66  3.000
 5V8  C8   C9   C10  121.08  3.000
 5V8  H15  C13  C14  119.60  3.000
 5V8  H15  C13  C11  120.33  3.000
 5V8  C14  C13  C11  120.06  3.000
 5V8  H16  C14  C13  118.45  3.000
 5V8  H16  C14  C8   120.42  3.000
 5V8  C13  C14  C8   121.11  3.000
 5V8  C22  C21  C20  119.85  3.000
 5V8  C20  C21  C2   116.67  3.000
 5V8  C22  C21  C2   123.41  3.000
 5V8  H18  C22  H17  104.82  3.000
 5V8  H18  C22  N23  111.10  3.000
 5V8  H17  C22  N23  108.26  3.000
 5V8  H18  C22  C21  111.79  3.000
 5V8  H17  C22  C21  109.02  3.000
 5V8  N23  C22  C21  111.55  3.000
 5V8  C7   O6   C5   107.28  3.000
 5V8  H20  N17  C18  118.63  3.000
 5V8  H20  N17  C16  118.97  3.000
 5V8  C18  N17  C16  122.38  3.000
 5V8  C28  N23  C22  112.29  3.000
 5V8  C28  N23  C24  112.04  3.000
 5V8  C22  N23  C24  110.77  3.000
 5V8  H23  C27  H22  107.13  3.000
 5V8  H23  C27  C28  109.22  3.000
 5V8  H22  C27  C28  108.85  3.000
 5V8  H23  C27  C26  111.02  3.000
 5V8  H22  C27  C26  109.72  3.000
 5V8  C28  C27  C26  110.81  3.000
 5V8  H25  C28  H24  106.65  3.000
 5V8  H25  C28  C27  109.34  3.000
 5V8  H24  C28  C27  109.24  3.000
 5V8  H25  C28  N23  108.85  3.000
 5V8  H24  C28  N23  111.26  3.000
 5V8  C27  C28  N23  111.37  3.000
 5V8  H19  O12  C11  110.57  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
 5V8  CONST_01  C15  C20  C21  C2   180.00   0.0  0
 5V8  CONST_02  C5   C20  C21  C2     0.00   0.0  0
 5V8  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 5V8  CONST_04  C20  C21  C2   C3     0.00   0.0  0
 5V8  CONST_05  C20  C5   C4   C3     0.00   0.0  0
 5V8  CONST_06  O6   C5   C4   C3   180.00   0.0  0
 5V8  CONST_07  C15  C20  C5   C4   180.00   0.0  0
 5V8  CONST_08  C21  C20  C5   C4     0.00   0.0  0
 5V8  CONST_09  C7   O6   C5   C4   180.00   0.0  0
 5V8  CONST_10  C21  C2   C3   C4     0.00   0.0  0
 5V8  CONST_11  C7   C15  C20  C5     0.00   0.0  0
 5V8  CONST_12  C15  C7   O6   C5     0.00   0.0  0
 5V8  CONST_13  C8   C7   O6   C5   180.00   0.0  0
 5V8  CONST_14  C14  C13  C11  C10    0.00   0.0  0
 5V8  CONST_15  C14  C8   C9   C10    0.00   0.0  0
 5V8  CONST_16  C7   C8   C9   C10  180.00   0.0  0
 5V8  CONST_17  C8   C14  C13  C11    0.00   0.0  0
 5V8  CONST_18  C8   C9   C10  C11    0.00   0.0  0
 5V8  CONST_21  O6   C5   C20  C15    0.00   0.0  0
 5V8  CONST_22  C8   C7   C15  C20  180.00   0.0  0
 5V8  CONST_23  O6   C7   C15  C20    0.00   0.0  0
 5V8  CONST_24  C7   O6   C5   C20    0.00   0.0  0
 5V8  CONST_25  C21  C20  C15  C7   180.00   0.0  0
 5V8  CONST_26  C13  C14  C8   C7   180.00   0.0  0
 5V8  CONST_27  C13  C11  C10  C9     0.00   0.0  0
 5V8  CONST_28  C13  C14  C8   C9     0.00   0.0  0
 5V8  CONST_31  O6   C5   C20  C21  180.00   0.0  0
 5V8  CONST_32  C22  C21  C2   C3   180.00   0.0  0
 5V8  CONST_33  O1   C2   C3   C4   180.00   0.0  0
 5V8  CONST_34  C16  C15  C20  C5   180.00   0.0  0
 5V8  CONST_35  C22  C21  C20  C5   180.00   0.0  0
 5V8  CONST_36  C22  C21  C20  C15    0.00   0.0  0
 5V8  CONST_37  C8   C7   C15  C16    0.00   0.0  0
 5V8  CONST_38  O6   C7   C15  C16  180.00   0.0  0
 5V8  CONST_39  C21  C20  C15  C16    0.00   0.0  0
 5V8  CONST_40  O1   C2   C21  C20  180.00   0.0  0
 5V8  CONST_41  O12  C11  C10  C9   180.00   0.0  0
 5V8  CONST_42  O12  C11  C13  C14  180.00   0.0  0
 5V8  CONST_43  H2   C4   C3   C2   180.00   0.0  0
 5V8  CONST_44  H1   C3   C4   C5   180.00   0.0  0
 5V8  CONST_45  H15  C13  C11  C10  180.00   0.0  0
 5V8  CONST_46  H16  C14  C13  C11  180.00   0.0  0
 5V8  CONST_47  H14  C9   C10  C11  180.00   0.0  0
 5V8  CONST_48  H3   C10  C9   C8   180.00   0.0  0
 5V8  CONST_49  C18  N17  C16  C15  180.00   0.0  0
 5V8  CONST_50  H20  N17  C16  C15    0.00   0.0  0
 5V8  CONST_51  O19  C16  N17  C18    0.00   0.0  0
 5V8  Var_01    C27  C26  C25  C24   53.52  30.0  1
 5V8  Var_02    C27  C28  N23  C24  -57.84  30.0  1
 5V8  Var_03    C28  N23  C24  C25   57.21  30.0  1
 5V8  Var_04    C28  C27  C26  C25  -54.22  30.0  1
 5V8  Var_05    N23  C24  C25  C26  -55.24  30.0  1
 5V8  Var_06    N23  C28  C27  C26   56.60  30.0  1
 5V8  Var_07    N23  C22  C21  C2   117.91  30.0  2
 5V8  Var_08    C21  C22  N23  C24  172.22  30.0  1
 5V8  Var_09    N17  C16  C15  C20  126.45  30.0  2
 5V8  Var_10    H4   C18  N17  C16   60.40  30.0  3

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
 5V8  plan-1  C10  0.020
 5V8  plan-1  C11  0.020
 5V8  plan-1  C7   0.020
 5V8  plan-1  C8   0.020
 5V8  plan-1  C9   0.020
 5V8  plan-1  C13  0.020
 5V8  plan-1  C14  0.020
 5V8  plan-1  H3   0.020
 5V8  plan-1  H14  0.020
 5V8  plan-1  H15  0.020
 5V8  plan-1  H16  0.020
 5V8  plan-1  O12  0.020
 5V8  plan-2  C2   0.020
 5V8  plan-2  C3   0.020
 5V8  plan-2  C4   0.020
 5V8  plan-2  C5   0.020
 5V8  plan-2  C15  0.020
 5V8  plan-2  C16  0.020
 5V8  plan-2  C20  0.020
 5V8  plan-2  O1   0.020
 5V8  plan-2  C7   0.020
 5V8  plan-2  C8   0.020
 5V8  plan-2  C21  0.020
 5V8  plan-2  C22  0.020
 5V8  plan-2  O6   0.020
 5V8  plan-2  H1   0.020
 5V8  plan-2  H2   0.020
 5V8  plan-3  C15  0.020
 5V8  plan-3  C16  0.020
 5V8  plan-3  C18  0.020
 5V8  plan-3  N17  0.020
 5V8  plan-3  O19  0.020
 5V8  plan-3  H20  0.020

