# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 00:25:24 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (2~{Z})-2-(1~{H}-indol-3-ylmethylidene)-6-methoxy-7-(piperazin-1-ylmethyl)-1-benzofuran-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2C(=O)\C(Oc2c1CN3CCNCC3)=C\c4c[nH]c5ccccc45
#
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
 8GR  8GR  (2~{Z})-2-(1~{H}-indol-3-ylmethylidene)-6-methoxy-7-(piperazin-1-ylmethyl)-1-benzofuran-3-one  ligand  52  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8GR
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
 8GR  C15  C  CH2   0  -0.288  -2.9037   3.2067  -0.6976
 8GR  C17  C  CR5   0   0.255   0.8640  -1.7545   0.1310
 8GR  C20  C  CR15  0  -0.045   2.5605   0.7599  -0.6783
 8GR  C22  C  CR56  0   0.359   4.7876   0.8694  -0.6248
 8GR  C24  C  CR16  0  -0.371   5.4192  -1.3200   0.1833
 8GR  C26  C  CR16  0  -0.282   7.0841   0.3613  -0.3537
 8GR  C28  C  CR5   0   0.330   0.0757  -2.9312   0.5420
 8GR  C01  C  CH3   0  -0.442  -5.9645  -0.9945  -0.5440
 8GR  C03  C  CR6   0   0.380  -3.5975  -1.1273  -0.3350
 8GR  C04  C  CR16  0  -0.406  -3.6737  -2.4383   0.1717
 8GR  C05  C  CR16  0  -0.288  -2.5244  -3.1323   0.4952
 8GR  C06  C  CR56  0  -0.154  -1.2968  -2.5136   0.3087
 8GR  C07  C  CR56  0   0.426  -1.2518  -1.2162  -0.1953
 8GR  C08  C  CR6   0  -0.114  -2.3650  -0.4786  -0.5378
 8GR  C09  C  CH2   0  -0.335  -2.2915   0.9234  -1.0732
 8GR  N10  N  NT    0  -0.404  -2.6846   1.9093  -0.0847
 8GR  C11  C  CH2   0  -0.287  -1.7312   2.0120   1.0050
 8GR  C12  C  CH2   0  -0.319  -2.2137   3.0198   2.0395
 8GR  N13  N  NH1   0  -0.580  -2.5040   4.3318   1.4861
 8GR  C14  C  CH2   0  -0.323  -3.3882   4.2112   0.3388
 8GR  O16  O  O     0  -0.501   0.0205  -0.7598  -0.3037
 8GR  C19  C  CR5   0   0.031   2.9801  -0.4760  -0.2177
 8GR  N21  N  NR15  0  -0.672   3.6314   1.5460  -0.9140
 8GR  C23  C  CR56  0   0.052   4.4196  -0.4135  -0.1798
 8GR  C25  C  CR16  0  -0.260   6.7400  -0.9245   0.0929
 8GR  C27  C  CR16  0  -0.294   6.1154   1.2764  -0.7190
 8GR  O29  O  O     0  -0.424   0.5076  -3.9870   0.9738
 8GR  H1   H  HCH2  0   0.184  -1.9834   3.5940  -1.1731
 8GR  H2   H  HCH2  0   0.233  -3.6519   3.1030  -1.4881
 8GR  H4   H  HCR6  0   0.248   5.1687  -2.3158   0.5285
 8GR  H5   H  HCR6  0   0.255   8.1278   0.6404  -0.4144
 8GR  H6   H  HCH3  0   0.265  -6.6682  -0.2384  -0.8812
 8GR  H7   H  HCH3  0   0.236  -6.0730  -1.8837  -1.1688
 8GR  H8   H  HCH3  0   0.236  -6.1946  -1.2546   0.4913
 8GR  H9   H  HCR6  0   0.288  -4.6309  -2.9172   0.3189
 8GR  H10  H  HCR6  0   0.273  -2.5874  -4.1388   0.8880
 8GR  H11  H  HCH2  0   0.222  -1.2804   1.1199  -1.4641
 8GR  H12  H  HCH2  0   0.252  -2.9678   1.0118  -1.9265
 8GR  H14  H  HCH2  0   0.236  -1.6155   1.0369   1.4850
 8GR  H15  H  HCH2  0   0.182  -0.7307   2.3120   0.6400
 8GR  H16  H  HCH2  0   0.217  -3.1256   2.6354   2.5078
 8GR  H17  H  HCH2  0   0.236  -1.4664   3.1196   2.8288
 8GR  H18  H  HNH1  0   0.339  -1.6352   4.7635   1.1891
 8GR  H20  H  HCH2  0   0.236  -3.5085   5.1906  -0.1280
 8GR  H21  H  HCH2  0   0.218  -4.3753   3.9024   0.6977
 8GR  H23  H  HNR5  0   0.421   3.5776   2.4909  -1.2591
 8GR  H24  H  HCR6  0   0.253   7.5257  -1.6158   0.3690
 8GR  H25  H  HCR6  0   0.267   6.3794   2.2674  -1.0648
 8GR  C18  C  C1    0  -0.466   2.1969  -1.6112   0.1608
 8GR  O02  O  O2    0  -0.446  -4.6762  -0.4173  -0.6675
 8GR  H3   H  HCR5  0   0.296   1.5663   1.1354  -0.8535
 8GR  H22  H  H     0   0.275   2.7337  -2.4811   0.5238

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
 8GR  C14  C15  single    1.522  0.020  1.522
 8GR  C14  N13  single    1.454  0.020  1.454
 8GR  C15  N10  single    1.452  0.020  1.452
 8GR  N13  C12  single    1.453  0.020  1.453
 8GR  C01  O02  single    1.417  0.020  1.417
 8GR  O02  C03  single    1.333  0.020  1.333
 8GR  N10  C09  single    1.450  0.020  1.450
 8GR  N10  C11  single    1.451  0.020  1.451
 8GR  C12  C11  single    1.523  0.020  1.523
 8GR  C09  C08  single    1.503  0.020  1.503
 8GR  C03  C08  aromatic  1.407  0.020  1.407
 8GR  C03  C04  aromatic  1.408  0.020  1.408
 8GR  C08  C07  aromatic  1.379  0.020  1.379
 8GR  C04  C05  aromatic  1.381  0.020  1.381
 8GR  C07  C06  aromatic  1.393  0.020  1.393
 8GR  C07  O16  single    1.356  0.020  1.356
 8GR  C25  C26  aromatic  1.404  0.020  1.404
 8GR  C25  C24  aromatic  1.382  0.020  1.382
 8GR  C05  C06  aromatic  1.387  0.020  1.387
 8GR  C26  C27  aromatic  1.382  0.020  1.382
 8GR  C06  C28  single    1.453  0.020  1.453
 8GR  C24  C23  aromatic  1.397  0.020  1.397
 8GR  O16  C17  single    1.375  0.020  1.375
 8GR  C27  C22  aromatic  1.392  0.020  1.392
 8GR  C17  C28  single    1.475  0.020  1.475
 8GR  C17  C18  double    1.341  0.020  1.341
 8GR  C28  O29  double    1.220  0.020  1.220
 8GR  C23  C22  aromatic  1.407  0.020  1.407
 8GR  C23  C19  aromatic  1.441  0.020  1.441
 8GR  C22  N21  aromatic  1.370  0.020  1.370
 8GR  C18  C19  single    1.430  0.020  1.430
 8GR  C19  C20  aromatic  1.384  0.020  1.384
 8GR  N21  C20  aromatic  1.349  0.020  1.349
 8GR  C15  H1   single    0.970  0.020  1.090
 8GR  C15  H2   single    0.970  0.020  1.090
 8GR  C20  H3   single    0.930  0.020  1.080
 8GR  C24  H4   single    0.930  0.020  1.080
 8GR  C26  H5   single    0.930  0.020  1.080
 8GR  C01  H6   single    0.970  0.020  1.090
 8GR  C01  H7   single    0.970  0.020  1.090
 8GR  C01  H8   single    0.970  0.020  1.090
 8GR  C04  H9   single    0.930  0.020  1.080
 8GR  C05  H10  single    0.930  0.020  1.080
 8GR  C09  H11  single    0.970  0.020  1.090
 8GR  C09  H12  single    0.970  0.020  1.090
 8GR  C11  H14  single    0.970  0.020  1.090
 8GR  C11  H15  single    0.970  0.020  1.090
 8GR  C12  H16  single    0.970  0.020  1.090
 8GR  C12  H17  single    0.970  0.020  1.090
 8GR  N13  H18  single    0.890  0.020  1.040
 8GR  C14  H20  single    0.970  0.020  1.090
 8GR  C14  H21  single    0.970  0.020  1.090
 8GR  C18  H22  single    0.930  0.020  1.080
 8GR  N21  H23  single    0.860  0.020  1.020
 8GR  C25  H24  single    0.930  0.020  1.080
 8GR  C27  H25  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
 8GR  H2   C15  H1   106.97  3.000
 8GR  H2   C15  C14  109.69  3.000
 8GR  H1   C15  C14  109.06  3.000
 8GR  H2   C15  N10  108.89  3.000
 8GR  H1   C15  N10  111.65  3.000
 8GR  C14  C15  N10  110.51  3.000
 8GR  C18  C17  O16  122.65  3.000
 8GR  C18  C17  C28  127.62  3.000
 8GR  O16  C17  C28  109.73  3.000
 8GR  H3   C20  N21  120.07  3.000
 8GR  H3   C20  C19  130.19  3.000
 8GR  N21  C20  C19  109.74  3.000
 8GR  C27  C22  C23  122.52  3.000
 8GR  C23  C22  N21  107.23  3.000
 8GR  C27  C22  N21  130.25  3.000
 8GR  H4   C24  C25  120.33  3.000
 8GR  H4   C24  C23  120.91  3.000
 8GR  C25  C24  C23  118.76  3.000
 8GR  H5   C26  C27  119.38  3.000
 8GR  H5   C26  C25  119.37  3.000
 8GR  C27  C26  C25  121.25  3.000
 8GR  O29  C28  C06  129.78  3.000
 8GR  O29  C28  C17  126.88  3.000
 8GR  C06  C28  C17  103.34  3.000
 8GR  H8   C01  H7   109.12  3.000
 8GR  H8   C01  H6   108.87  3.000
 8GR  H7   C01  H6   108.95  3.000
 8GR  H8   C01  O02  111.79  3.000
 8GR  H7   C01  O02  111.84  3.000
 8GR  H6   C01  O02  106.16  3.000
 8GR  C08  C03  C04  121.91  3.000
 8GR  C04  C03  O02  122.81  3.000
 8GR  C08  C03  O02  115.28  3.000
 8GR  H9   C04  C05  118.86  3.000
 8GR  H9   C04  C03  120.65  3.000
 8GR  C05  C04  C03  120.49  3.000
 8GR  H10  C05  C06  121.00  3.000
 8GR  H10  C05  C04  120.26  3.000
 8GR  C06  C05  C04  118.74  3.000
 8GR  C07  C06  C05  119.52  3.000
 8GR  C05  C06  C28  133.31  3.000
 8GR  C07  C06  C28  107.17  3.000
 8GR  O16  C07  C08  123.89  3.000
 8GR  O16  C07  C06  111.89  3.000
 8GR  C08  C07  C06  124.22  3.000
 8GR  C09  C08  C07  123.25  3.000
 8GR  C07  C08  C03  115.13  3.000
 8GR  C09  C08  C03  121.62  3.000
 8GR  H12  C09  H11  106.06  3.000
 8GR  H12  C09  N10  108.03  3.000
 8GR  H11  C09  N10  111.67  3.000
 8GR  H12  C09  C08  108.88  3.000
 8GR  H11  C09  C08  109.74  3.000
 8GR  N10  C09  C08  112.22  3.000
 8GR  C11  N10  C09  112.44  3.000
 8GR  C11  N10  C15  110.67  3.000
 8GR  C09  N10  C15  111.14  3.000
 8GR  H15  C11  H14  106.92  3.000
 8GR  H15  C11  C12  109.34  3.000
 8GR  H14  C11  C12  109.01  3.000
 8GR  H15  C11  N10  111.43  3.000
 8GR  H14  C11  N10  109.64  3.000
 8GR  C12  C11  N10  110.41  3.000
 8GR  H17  C12  H16  107.04  3.000
 8GR  H17  C12  N13  109.25  3.000
 8GR  H16  C12  N13  108.27  3.000
 8GR  H17  C12  C11  109.56  3.000
 8GR  H16  C12  C11  108.79  3.000
 8GR  N13  C12  C11  113.71  3.000
 8GR  H18  N13  C14  108.97  3.000
 8GR  H18  N13  C12  108.94  3.000
 8GR  C14  N13  C12  110.32  3.000
 8GR  H21  C14  H20  107.09  3.000
 8GR  H21  C14  N13  108.25  3.000
 8GR  H20  C14  N13  109.27  3.000
 8GR  H21  C14  C15  108.91  3.000
 8GR  H20  C14  C15  109.63  3.000
 8GR  N13  C14  C15  113.48  3.000
 8GR  C07  O16  C17  107.87  3.000
 8GR  C23  C19  C18  125.06  3.000
 8GR  C18  C19  C20  129.11  3.000
 8GR  C23  C19  C20  105.83  3.000
 8GR  H23  N21  C22  125.48  3.000
 8GR  H23  N21  C20  124.33  3.000
 8GR  C22  N21  C20  110.19  3.000
 8GR  C19  C23  C24  133.88  3.000
 8GR  C19  C23  C22  107.01  3.000
 8GR  C24  C23  C22  119.11  3.000
 8GR  H24  C25  C26  119.22  3.000
 8GR  H24  C25  C24  119.63  3.000
 8GR  C26  C25  C24  121.15  3.000
 8GR  H25  C27  C26  121.32  3.000
 8GR  H25  C27  C22  121.47  3.000
 8GR  C26  C27  C22  117.21  3.000
 8GR  H22  C18  C19  117.01  3.000
 8GR  H22  C18  C17  114.43  3.000
 8GR  C19  C18  C17  128.56  3.000
 8GR  C03  O02  C01  119.79  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
 8GR  CONST_01  C24  C23  C19  C20   180.00   0.0  0
 8GR  CONST_02  C22  C23  C19  C20     0.00   0.0  0
 8GR  CONST_03  C27  C22  N21  C20   180.00   0.0  0
 8GR  CONST_04  C23  C22  N21  C20     0.00   0.0  0
 8GR  CONST_05  C25  C26  C27  C22     0.00   0.0  0
 8GR  CONST_06  C25  C24  C23  C22     0.00   0.0  0
 8GR  CONST_07  C19  C20  N21  C22     0.00   0.0  0
 8GR  CONST_08  C27  C26  C25  C24     0.00   0.0  0
 8GR  CONST_09  C27  C22  C23  C24     0.00   0.0  0
 8GR  CONST_10  N21  C22  C23  C24   180.00   0.0  0
 8GR  CONST_11  C23  C24  C25  C26     0.00   0.0  0
 8GR  CONST_12  C23  C22  C27  C26     0.00   0.0  0
 8GR  CONST_13  N21  C22  C27  C26   180.00   0.0  0
 8GR  CONST_14  C06  C07  C08  C03     0.00   0.0  0
 8GR  CONST_15  C06  C05  C04  C03     0.00   0.0  0
 8GR  CONST_16  C07  C08  C03  C04     0.00   0.0  0
 8GR  CONST_17  C07  C06  C05  C04     0.00   0.0  0
 8GR  CONST_18  C08  C03  C04  C05     0.00   0.0  0
 8GR  CONST_19  C08  C07  C06  C05     0.00   0.0  0
 8GR  CONST_20  C25  C24  C23  C19   180.00   0.0  0
 8GR  CONST_21  C27  C22  C23  C19   180.00   0.0  0
 8GR  CONST_22  N21  C22  C23  C19     0.00   0.0  0
 8GR  CONST_23  C23  C19  C20  N21     0.00   0.0  0
 8GR  CONST_24  C18  C19  C23  C22   180.00   0.0  0
 8GR  CONST_25  C18  C19  C23  C24     0.00   0.0  0
 8GR  CONST_26  C07  C08  C03  O02   180.00   0.0  0
 8GR  CONST_27  C05  C04  C03  O02   180.00   0.0  0
 8GR  CONST_28  C09  C08  C03  C04   180.00   0.0  0
 8GR  CONST_29  C09  C08  C07  C06   180.00   0.0  0
 8GR  CONST_30  O16  C07  C08  C09     0.00   0.0  0
 8GR  CONST_31  N21  C20  C19  C18   180.00   0.0  0
 8GR  CONST_32  H5   C26  C27  C22   180.00   0.0  0
 8GR  CONST_33  H4   C24  C23  C22   180.00   0.0  0
 8GR  CONST_34  H3   C20  N21  C22   180.00   0.0  0
 8GR  CONST_35  H10  C05  C06  C28     0.00   0.0  0
 8GR  CONST_36  H9   C04  C05  C06   180.00   0.0  0
 8GR  CONST_37  H23  N21  C20  C19   180.00   0.0  0
 8GR  CONST_38  H25  C27  C22  N21     0.00   0.0  0
 8GR  CONST_39  H24  C25  C24  C23   180.00   0.0  0
 8GR  Var_01    C12  N13  C14  C15   -51.26  30.0  1
 8GR  Var_02    C12  C11  N10  C15    57.15  30.0  1
 8GR  Var_03    N13  C14  C15  N10    55.18  30.0  1
 8GR  Var_04    N13  C12  C11  N10   -54.89  30.0  1
 8GR  Var_05    C14  C15  N10  C11   -57.39  30.0  1
 8GR  Var_06    C14  N13  C12  C11    51.20  30.0  1
 8GR  Var_07    C08  C09  N10  C15  -166.82  30.0  3
 8GR  Var_08    C23  C19  C18  C17  -178.68  30.0  2
 8GR  Var_09    C19  C18  C17  C28  -179.21  30.0  2
 8GR  Var_10    N10  C09  C08  C03    73.76  30.0  2
 8GR  Var_11    C08  C03  O02  C01   177.91  30.0  2
 8GR  Var_12    H6   C01  O02  C03  -179.31  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
 8GR  plan-1  C17  0.020
 8GR  plan-1  C28  0.020
 8GR  plan-1  C03  0.020
 8GR  plan-1  C04  0.020
 8GR  plan-1  C05  0.020
 8GR  plan-1  C06  0.020
 8GR  plan-1  C07  0.020
 8GR  plan-1  C08  0.020
 8GR  plan-1  C09  0.020
 8GR  plan-1  O16  0.020
 8GR  plan-1  O29  0.020
 8GR  plan-1  H9   0.020
 8GR  plan-1  H10  0.020
 8GR  plan-1  C18  0.020
 8GR  plan-1  O02  0.020
 8GR  plan-2  C20  0.020
 8GR  plan-2  C22  0.020
 8GR  plan-2  C24  0.020
 8GR  plan-2  C26  0.020
 8GR  plan-2  C19  0.020
 8GR  plan-2  N21  0.020
 8GR  plan-2  C23  0.020
 8GR  plan-2  C25  0.020
 8GR  plan-2  C27  0.020
 8GR  plan-2  H4   0.020
 8GR  plan-2  H5   0.020
 8GR  plan-2  H23  0.020
 8GR  plan-2  H24  0.020
 8GR  plan-2  H25  0.020
 8GR  plan-2  C18  0.020
 8GR  plan-2  H3   0.020

