# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:34:01 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2Z)-4,6-dihydroxy-2-[(8-methoxy-1,2,3,4-tetrahydropyrazino[1,2-a]indol-10-yl)methylidene]-1-benzofuran-3(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2n3CCNCc3c(\C=C4/Oc5cc(O)cc(O)c5C4=O)c2c1
#
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
 WYF  WYF  (2Z)-4,6-dihydroxy-2-[(8-methoxy-1,2,3,4-tetrahydropyrazino[1,2-a]indol-10-yl)methylidene]-1-benzofuran-3(2H)-one  ligand  46  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WYF
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
 WYF  C1    C  CH3   0  -0.434  -1.7380   5.3499  -0.0266
 WYF  N1    N  NR5   0  -0.580  -3.6460  -0.7042  -0.2394
 WYF  O1    O  O2    0  -0.479  -1.0748   4.1042  -0.0387
 WYF  C2    C  CR6   0   0.410  -1.8165   2.9740  -0.0986
 WYF  N2    N  NH1   0  -0.573  -4.2033  -3.4025   0.1041
 WYF  O2    O  O     0  -0.460   2.3135  -3.2259   0.0407
 WYF  C3    C  CR16  0  -0.408  -3.2173   2.9724  -0.1619
 WYF  O3    O  O     0  -0.505   1.5492   0.1957  -0.1708
 WYF  C4    C  CR16  0  -0.293  -3.9119   1.7748  -0.2128
 WYF  O4    O  OH1   0  -0.616   5.9346   2.1223  -0.2200
 WYF  C5    C  CR56  0   0.320  -3.1878   0.5957  -0.2038
 WYF  O5    O  OH1   0  -0.610   5.3306  -2.5070   0.0356
 WYF  C6    C  CR56  0   0.078  -1.7799   0.5690  -0.1453
 WYF  C7    C  CR16  0  -0.520  -1.0981   1.7832  -0.0911
 WYF  C8    C  CR5   0   0.051  -1.4052  -0.8292  -0.1374
 WYF  C9    C  CR5   0   0.347  -2.6017  -1.5480  -0.1846
 WYF  C10   C  CH2   0  -0.302  -5.0427  -1.0973  -0.2422
 WYF  C11   C  CH2   0  -0.347  -5.1588  -2.5727  -0.6016
 WYF  C12   C  CH2   0  -0.373  -2.8419  -3.0285  -0.2163
 WYF  C13   C  C1    0  -0.482  -0.1584  -1.5156  -0.0898
 WYF  C14   C  CR5   0   0.238   1.1257  -1.1164  -0.0958
 WYF  C15   C  CR5   0   0.344   2.2983  -2.0002  -0.0313
 WYF  C16   C  CR56  0  -0.332   3.4123  -1.0872  -0.0727
 WYF  C17   C  CR6   0   0.390   4.7966  -1.2873  -0.0416
 WYF  C18   C  CR16  0  -0.463   5.6238  -0.1774  -0.0938
 WYF  C19   C  CR6   0   0.397   5.0665   1.1068  -0.1754
 WYF  C20   C  CR16  0  -0.523   3.6842   1.3296  -0.2083
 WYF  C21   C  CR56  0   0.455   2.8979   0.2018  -0.1541
 WYF  H1    H  HCH3  0   0.225  -2.3159   5.5178  -0.9397
 WYF  H1A   H  HCH3  0   0.224  -2.4055   5.4524   0.8335
 WYF  H1B   H  HCH3  0   0.257  -0.9652   6.1118   0.0410
 WYF  HN2   H  HNH1  0   0.358  -4.3532  -3.3307   1.1035
 WYF  H3    H  HCR6  0   0.278  -3.7804   3.8952  -0.1698
 WYF  H4    H  HCR6  0   0.275  -4.9934   1.7793  -0.2538
 WYF  HO4   H  HOH1  0   0.484   5.4737   2.9682  -0.2669
 WYF  HO5   H  HOH1  0   0.479   4.6337  -3.1777   0.0706
 WYF  H7    H  HCR6  0   0.261  -0.0211   1.8272  -0.0411
 WYF  H10   H  HCH2  0   0.260  -5.4677  -0.9023   0.7458
 WYF  H10A  H  HCH2  0   0.266  -5.5833  -0.4836  -0.9637
 WYF  H11   H  HCH2  0   0.249  -5.0015  -2.7043  -1.6754
 WYF  H11A  H  HCH2  0   0.265  -6.1722  -2.9085  -0.3821
 WYF  H12   H  HCH2  0   0.275  -2.1632  -3.5322   0.4730
 WYF  H12A  H  HCH2  0   0.270  -2.5946  -3.3993  -1.2170
 WYF  H13   H  H     0   0.274  -0.2339  -2.5979  -0.0416
 WYF  H18   H  HCR6  0   0.280   6.7001  -0.2925  -0.0743
 WYF  H20   H  HCR6  0   0.289   3.2670   2.3266  -0.2732

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
 WYF  C1   O1    single    1.411  0.020  1.411
 WYF  N1   C5    aromatic  1.379  0.020  1.379
 WYF  N1   C9    aromatic  1.344  0.020  1.344
 WYF  N1   C10   single    1.451  0.020  1.451
 WYF  O1   C2    single    1.353  0.020  1.353
 WYF  C2   C3    aromatic  1.402  0.020  1.402
 WYF  C2   C7    aromatic  1.391  0.020  1.391
 WYF  N2   C11   single    1.449  0.020  1.449
 WYF  N2   C12   single    1.448  0.020  1.448
 WYF  O2   C15   double    1.228  0.020  1.228
 WYF  C3   C4    aromatic  1.385  0.020  1.385
 WYF  O3   C14   single    1.381  0.020  1.381
 WYF  O3   C21   single    1.349  0.020  1.349
 WYF  C4   C5    aromatic  1.384  0.020  1.384
 WYF  O4   C19   single    1.337  0.020  1.337
 WYF  C5   C6    aromatic  1.409  0.020  1.409
 WYF  O5   C17   single    1.334  0.020  1.334
 WYF  C6   C7    aromatic  1.394  0.020  1.394
 WYF  C6   C8    aromatic  1.448  0.020  1.448
 WYF  C8   C9    aromatic  1.397  0.020  1.397
 WYF  C8   C13   single    1.424  0.020  1.424
 WYF  C9   C12   single    1.500  0.020  1.500
 WYF  C10  C11   single    1.523  0.020  1.523
 WYF  C13  C14   double    1.345  0.020  1.345
 WYF  C14  C15   single    1.470  0.020  1.470
 WYF  C15  C16   single    1.441  0.020  1.441
 WYF  C16  C17   aromatic  1.399  0.020  1.399
 WYF  C16  C21   aromatic  1.390  0.020  1.390
 WYF  C17  C18   aromatic  1.385  0.020  1.385
 WYF  C18  C19   aromatic  1.402  0.020  1.402
 WYF  C19  C20   aromatic  1.401  0.020  1.401
 WYF  C20  C21   aromatic  1.376  0.020  1.376
 WYF  C1   H1    single    0.970  0.020  1.090
 WYF  C1   H1A   single    0.970  0.020  1.090
 WYF  C1   H1B   single    0.970  0.020  1.090
 WYF  N2   HN2   single    0.890  0.020  1.040
 WYF  C3   H3    single    0.930  0.020  1.080
 WYF  C4   H4    single    0.930  0.020  1.080
 WYF  O4   HO4   single    0.850  0.020  0.980
 WYF  O5   HO5   single    0.850  0.020  0.980
 WYF  C7   H7    single    0.930  0.020  1.080
 WYF  C10  H10   single    0.970  0.020  1.090
 WYF  C10  H10A  single    0.970  0.020  1.090
 WYF  C11  H11   single    0.970  0.020  1.090
 WYF  C11  H11A  single    0.970  0.020  1.090
 WYF  C12  H12   single    0.970  0.020  1.090
 WYF  C12  H12A  single    0.970  0.020  1.090
 WYF  C13  H13   single    0.930  0.020  1.080
 WYF  C18  H18   single    0.930  0.020  1.080
 WYF  C20  H20   single    0.930  0.020  1.080

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
 WYF  H1B   C1   H1A  108.62  3.000
 WYF  H1B   C1   H1   108.65  3.000
 WYF  H1A   C1   H1   108.65  3.000
 WYF  H1B   C1   O1   106.56  3.000
 WYF  H1A   C1   O1   112.11  3.000
 WYF  H1    C1   O1   112.13  3.000
 WYF  C10   N1   C9   125.32  3.000
 WYF  C10   N1   C5   125.12  3.000
 WYF  C9    N1   C5   109.43  3.000
 WYF  C2    O1   C1   118.69  3.000
 WYF  C7    C2   C3   121.02  3.000
 WYF  C7    C2   O1   115.58  3.000
 WYF  C3    C2   O1   123.40  3.000
 WYF  HN2   N2   C12  109.82  3.000
 WYF  HN2   N2   C11  110.02  3.000
 WYF  C12   N2   C11  111.37  3.000
 WYF  H3    C3   C4   118.46  3.000
 WYF  H3    C3   C2   121.31  3.000
 WYF  C4    C3   C2   120.23  3.000
 WYF  C21   O3   C14  108.08  3.000
 WYF  H4    C4   C5   121.79  3.000
 WYF  H4    C4   C3   119.92  3.000
 WYF  C5    C4   C3   118.29  3.000
 WYF  HO4   O4   C19  110.95  3.000
 WYF  C6    C5   C4   122.63  3.000
 WYF  C6    C5   N1   108.37  3.000
 WYF  C4    C5   N1   129.00  3.000
 WYF  HO5   O5   C17  110.34  3.000
 WYF  C8    C6   C7   135.62  3.000
 WYF  C8    C6   C5   106.09  3.000
 WYF  C7    C6   C5   118.29  3.000
 WYF  H7    C7   C6   121.71  3.000
 WYF  H7    C7   C2   118.75  3.000
 WYF  C6    C7   C2   119.54  3.000
 WYF  C13   C8   C9   120.21  3.000
 WYF  C13   C8   C6   133.82  3.000
 WYF  C9    C8   C6   105.97  3.000
 WYF  C12   C9   C8   130.22  3.000
 WYF  C12   C9   N1   119.63  3.000
 WYF  C8    C9   N1   110.13  3.000
 WYF  H10A  C10  H10  107.75  3.000
 WYF  H10A  C10  C11  110.56  3.000
 WYF  H10   C10  C11  110.88  3.000
 WYF  H10A  C10  N1   109.03  3.000
 WYF  H10   C10  N1   108.92  3.000
 WYF  C11   C10  N1   109.65  3.000
 WYF  H11A  C11  H11  107.12  3.000
 WYF  H11A  C11  C10  108.78  3.000
 WYF  H11   C11  C10  109.72  3.000
 WYF  H11A  C11  N2   109.79  3.000
 WYF  H11   C11  N2   108.33  3.000
 WYF  C10   C11  N2   112.93  3.000
 WYF  H12A  C12  H12  106.29  3.000
 WYF  H12A  C12  C9   108.49  3.000
 WYF  H12   C12  C9   110.05  3.000
 WYF  H12A  C12  N2   109.09  3.000
 WYF  H12   C12  N2   109.03  3.000
 WYF  C9    C12  N2   113.63  3.000
 WYF  H13   C13  C14  111.25  3.000
 WYF  H13   C13  C8   114.90  3.000
 WYF  C14   C13  C8   133.85  3.000
 WYF  C15   C14  C13  125.67  3.000
 WYF  C15   C14  O3   109.21  3.000
 WYF  C13   C14  O3   125.12  3.000
 WYF  C16   C15  C14  103.57  3.000
 WYF  C16   C15  O2   128.65  3.000
 WYF  C14   C15  O2   127.78  3.000
 WYF  C21   C16  C17  120.00  3.000
 WYF  C21   C16  C15  107.64  3.000
 WYF  C17   C16  C15  132.36  3.000
 WYF  C18   C17  C16  118.39  3.000
 WYF  C18   C17  O5   119.73  3.000
 WYF  C16   C17  O5   121.88  3.000
 WYF  H18   C18  C19  119.57  3.000
 WYF  H18   C18  C17  120.52  3.000
 WYF  C19   C18  C17  119.91  3.000
 WYF  C20   C19  C18  122.64  3.000
 WYF  C20   C19  O4   121.29  3.000
 WYF  C18   C19  O4   116.07  3.000
 WYF  H20   C20  C21  122.48  3.000
 WYF  H20   C20  C19  121.88  3.000
 WYF  C21   C20  C19  115.64  3.000
 WYF  C20   C21  C16  123.42  3.000
 WYF  C20   C21  O3   125.08  3.000
 WYF  C16   C21  O3   111.50  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
 WYF  CONST_01  C3   C4   C5   N1   180.00   0.0  0
 WYF  CONST_02  C7   C6   C5   N1   180.00   0.0  0
 WYF  CONST_03  C8   C6   C5   N1     0.00   0.0  0
 WYF  CONST_04  C6   C8   C9   N1     0.00   0.0  0
 WYF  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 WYF  CONST_06  C5   C6   C7   C2     0.00   0.0  0
 WYF  CONST_07  C8   C6   C7   C2   180.00   0.0  0
 WYF  CONST_08  C6   C7   C2   C3     0.00   0.0  0
 WYF  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 WYF  CONST_10  C7   C2   C3   C4     0.00   0.0  0
 WYF  CONST_11  C9   N1   C5   C4   180.00   0.0  0
 WYF  CONST_12  C7   C6   C5   C4     0.00   0.0  0
 WYF  CONST_13  C8   C6   C5   C4   180.00   0.0  0
 WYF  CONST_14  C8   C9   N1   C5     0.00   0.0  0
 WYF  CONST_15  C9   C8   C6   C5     0.00   0.0  0
 WYF  CONST_16  C9   N1   C5   C6     0.00   0.0  0
 WYF  CONST_17  C9   C8   C6   C7   180.00   0.0  0
 WYF  CONST_18  C19  C18  C17  C16    0.00   0.0  0
 WYF  CONST_19  C19  C20  C21  C16    0.00   0.0  0
 WYF  CONST_20  C20  C21  C16  C17    0.00   0.0  0
 WYF  CONST_21  C20  C19  C18  C17    0.00   0.0  0
 WYF  CONST_22  C21  C16  C17  C18    0.00   0.0  0
 WYF  CONST_23  C21  C20  C19  C18    0.00   0.0  0
 WYF  CONST_24  C13  C8   C9   N1   180.00   0.0  0
 WYF  CONST_25  C4   C3   C2   O1   180.00   0.0  0
 WYF  CONST_26  C6   C7   C2   O1   180.00   0.0  0
 WYF  CONST_27  C17  C18  C19  O4   180.00   0.0  0
 WYF  CONST_28  C21  C20  C19  O4   180.00   0.0  0
 WYF  CONST_29  C13  C8   C6   C5   180.00   0.0  0
 WYF  CONST_30  C15  C16  C17  O5     0.00   0.0  0
 WYF  CONST_31  C21  C16  C17  O5   180.00   0.0  0
 WYF  CONST_32  C19  C18  C17  O5   180.00   0.0  0
 WYF  CONST_33  C13  C8   C6   C7     0.00   0.0  0
 WYF  CONST_34  C13  C8   C9   C12    0.00   0.0  0
 WYF  CONST_35  H4   C4   C5   N1     0.00   0.0  0
 WYF  CONST_36  H7   C7   C2   C3   180.00   0.0  0
 WYF  CONST_37  H20  C20  C21  O3     0.00   0.0  0
 WYF  CONST_38  H3   C3   C4   C5   180.00   0.0  0
 WYF  CONST_39  H18  C18  C17  C16  180.00   0.0  0
 WYF  Var_01    N2   C12  C9   N1   -17.90  30.0  1
 WYF  Var_02    N2   C11  C10  N1    45.17  30.0  1
 WYF  Var_03    C11  C10  N1   C5   167.26  30.0  1
 WYF  Var_04    C11  N2   C12  C9    45.75  30.0  1
 WYF  Var_05    C12  N2   C11  C10  -61.32  30.0  1
 WYF  Var_06    C8   C13  C14  O3    -0.72  30.0  2
 WYF  Var_07    C14  C13  C8   C6    -3.60  30.0  2
 WYF  Var_08    C3   C2   O1   C1     0.60  30.0  2
 WYF  Var_09    H1   C1   O1   C2   -62.19  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
 WYF  plan-1  O2   0.020
 WYF  plan-1  O3   0.020
 WYF  plan-1  O4   0.020
 WYF  plan-1  O5   0.020
 WYF  plan-1  C13  0.020
 WYF  plan-1  C14  0.020
 WYF  plan-1  C15  0.020
 WYF  plan-1  C16  0.020
 WYF  plan-1  C17  0.020
 WYF  plan-1  C18  0.020
 WYF  plan-1  C19  0.020
 WYF  plan-1  C20  0.020
 WYF  plan-1  C21  0.020
 WYF  plan-1  H18  0.020
 WYF  plan-1  H20  0.020
 WYF  plan-2  N1   0.020
 WYF  plan-2  O1   0.020
 WYF  plan-2  C2   0.020
 WYF  plan-2  C3   0.020
 WYF  plan-2  C4   0.020
 WYF  plan-2  C5   0.020
 WYF  plan-2  C6   0.020
 WYF  plan-2  C7   0.020
 WYF  plan-2  C8   0.020
 WYF  plan-2  C9   0.020
 WYF  plan-2  C10  0.020
 WYF  plan-2  C12  0.020
 WYF  plan-2  C13  0.020
 WYF  plan-2  H3   0.020
 WYF  plan-2  H4   0.020
 WYF  plan-2  H7   0.020

