# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:28:59 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: (3~{E})-5-chloranyl-3-[[5-[3-[(4-methyl-1,4-diazepan-1-yl)carbonyl]phenyl]furan-2-yl]methylidene]-1~{H}-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCCN(CC1)C(=O)c2cccc(c2)c3oc(cc3)\C=C4\C(=O)Nc5ccc(Cl)cc45
#
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
 9G5  9G5  (3~{E})-5-chloranyl-3-[[5-[3-[(4-methyl-1,4-diazepan-1-yl)carbonyl]phenyl]furan-2-yl]methylidene]-1~{H}-indol-2-one  ligand  57  33  .  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_9G5
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
 9G5  N1   N   NT    0  -0.441   3.3644  -0.5355  -0.9046
 9G5  C4   C   CH2   0  -0.349   3.5618  -0.3855   0.5280
 9G5  C5   C   CH2   0  -0.258   4.9469   0.0983   0.9342
 9G5  C6   C   C     0   0.518   2.5753   0.2807  -1.6275
 9G5  C7   C   CR6   0  -0.058   2.0793   1.5425  -0.9846
 9G5  C8   C   CR16  0  -0.265   2.9370   2.6019  -0.7100
 9G5  C10  C   CR16  0  -0.320   1.0707   3.9190   0.0459
 9G5  C13  C   CR5   0   0.419  -1.2159   2.9996   0.0591
 9G5  C15  C   CR15  0  -0.302  -3.3107   3.5860   0.5158
 9G5  C20  C   CR56  0   0.386  -3.9667  -2.3517   0.0887
 9G5  C21  C   CR16  0  -0.306  -3.3182  -3.5611  -0.0595
 9G5  C22  C   CR16  0  -0.232  -1.9276  -3.5632  -0.0984
 9G5  C24  C   CR16  0  -0.341  -1.8856  -1.1512   0.1771
 9G5  C25  C   CR5   0   0.523  -5.5976  -0.7905   0.3449
 9G5  N2   N   NR15  0  -0.773  -5.3250  -2.1168   0.1749
 9G5  C23  C   CR6   0  -0.034  -1.2358  -2.3684   0.0261
 9G5  CL   CL  CL    0  -0.126   0.5026  -2.3801  -0.0082
 9G5  C19  C   CR56  0   0.038  -3.2717  -1.1328   0.1899
 9G5  C18  C   CR5   0   0.003  -4.2776  -0.0899   0.3326
 9G5  C16  C   CR5   0   0.384  -3.2419   2.2249   0.3521
 9G5  C14  C   CR15  0  -0.370  -2.0061   4.0840   0.3326
 9G5  O1   O   O     0  -0.457  -1.9635   1.8834   0.0721
 9G5  C11  C   CR6   0   0.029   0.2003   2.8598  -0.2246
 9G5  C9   C   CR16  0  -0.219   2.4250   3.7902  -0.2058
 9G5  C12  C   CR16  0  -0.324   0.7164   1.6801  -0.7630
 9G5  O    O   O     0  -0.489   2.2543   0.0404  -2.7841
 9G5  C3   C   CH2   0  -0.276   3.8786  -1.7267  -1.5746
 9G5  C2   C   CH2   0  -0.496   4.9980  -2.4195  -0.8173
 9G5  C1   C   CH2   0  -0.278   6.1631  -1.5231  -0.4067
 9G5  N    N   NT    0  -0.406   5.9830  -0.9114   0.8986
 9G5  C    C   CH3   0  -0.522   7.2269  -0.3604   1.3929
 9G5  H1   H   HCH2  0   0.281   2.8326   0.3288   0.9038
 9G5  H2   H   HCH2  0   0.258   3.3341  -1.3305   1.0263
 9G5  H3   H   HCH2  0   0.193   5.2121   0.9746   0.3169
 9G5  H4   H   HCH2  0   0.240   4.8720   0.4595   1.9635
 9G5  H5   H   HCR6  0   0.268   3.9993   2.5083  -0.8950
 9G5  H6   H   HCR6  0   0.266   0.6914   4.8423   0.4646
 9G5  H7   H   HCR5  0   0.286  -4.2017   4.1500   0.7408
 9G5  H8   H   H     0   0.292  -5.2538   1.7140   0.5644
 9G5  H9   H   HCR6  0   0.281  -3.8684  -4.4888  -0.1423
 9G5  H10  H   HCR6  0   0.285  -1.3943  -4.4957  -0.2208
 9G5  H11  H   HCR6  0   0.276  -1.3087  -0.2512   0.3012
 9G5  H12  H   HNR5  0   0.415  -6.0339  -2.8327   0.1378
 9G5  H13  H   HCR5  0   0.280  -1.6911   5.1133   0.3805
 9G5  H14  H   HCR6  0   0.271   3.0906   4.6167   0.0033
 9G5  H15  H   HCR6  0   0.258   0.0598   0.8589  -1.0190
 9G5  H16  H   HCH2  0   0.238   3.0651  -2.4384  -1.7489
 9G5  H17  H   HCH2  0   0.246   4.2519  -1.4296  -2.5555
 9G5  H18  H   HCH2  0   0.237   4.6233  -2.9432   0.0648
 9G5  H19  H   HCH2  0   0.260   5.3719  -3.1975  -1.4862
 9G5  H20  H   HCH2  0   0.239   7.0625  -2.1390  -0.3484
 9G5  H21  H   HCH2  0   0.195   6.3528  -0.7720  -1.1943
 9G5  H23  H   HCH3  0   0.193   7.6103   0.4700   0.7796
 9G5  H24  H   HCH3  0   0.233   7.0921   0.0163   2.4082
 9G5  H25  H   HCH3  0   0.234   7.9948  -1.1341   1.4250
 9G5  C17  C   C1    0  -0.431  -4.2776   1.2597   0.4233
 9G5  O2   O   O     0  -0.451  -6.7039  -0.3004   0.4653

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
 9G5  C    N    single    1.448  0.020  1.448
 9G5  C1   N    single    1.453  0.020  1.453
 9G5  C1   C2   single    1.526  0.020  1.526
 9G5  N    C5   single    1.447  0.020  1.447
 9G5  C2   C3   single    1.519  0.020  1.519
 9G5  C5   C4   single    1.522  0.020  1.522
 9G5  C3   N1   single    1.460  0.020  1.460
 9G5  C4   N1   single    1.454  0.020  1.454
 9G5  N1   C6   single    1.346  0.020  1.346
 9G5  O    C6   double    1.224  0.020  1.224
 9G5  C6   C7   single    1.500  0.020  1.500
 9G5  C7   C12  aromatic  1.388  0.020  1.388
 9G5  C7   C8   aromatic  1.390  0.020  1.390
 9G5  C12  C11  aromatic  1.396  0.020  1.396
 9G5  C8   C9   aromatic  1.389  0.020  1.389
 9G5  C14  C15  aromatic  1.408  0.020  1.408
 9G5  C14  C13  aromatic  1.369  0.020  1.369
 9G5  C11  C13  single    1.451  0.020  1.451
 9G5  C11  C10  aromatic  1.397  0.020  1.397
 9G5  C15  C16  aromatic  1.373  0.020  1.373
 9G5  C13  O1   aromatic  1.344  0.020  1.344
 9G5  C9   C10  aromatic  1.384  0.020  1.384
 9G5  C16  O1   aromatic  1.353  0.020  1.353
 9G5  C16  C17  single    1.418  0.020  1.418
 9G5  C17  C18  double    1.353  0.020  1.353
 9G5  C18  C19  single    1.456  0.020  1.456
 9G5  C18  C25  single    1.495  0.020  1.495
 9G5  C24  C19  aromatic  1.386  0.020  1.386
 9G5  C24  C23  aromatic  1.388  0.020  1.388
 9G5  C19  C20  aromatic  1.407  0.020  1.407
 9G5  O2   C25  double    1.216  0.020  1.216
 9G5  CL   C23  single    1.739  0.020  1.739
 9G5  C25  N2   single    1.365  0.020  1.365
 9G5  C23  C22  aromatic  1.386  0.020  1.386
 9G5  C20  N2   single    1.381  0.020  1.381
 9G5  C20  C21  aromatic  1.380  0.020  1.380
 9G5  C22  C21  aromatic  1.391  0.020  1.391
 9G5  C4   H1   single    0.970  0.020  1.090
 9G5  C4   H2   single    0.970  0.020  1.090
 9G5  C5   H3   single    0.970  0.020  1.090
 9G5  C5   H4   single    0.970  0.020  1.090
 9G5  C8   H5   single    0.930  0.020  1.080
 9G5  C10  H6   single    0.930  0.020  1.080
 9G5  C15  H7   single    0.930  0.020  1.080
 9G5  C17  H8   single    0.930  0.020  1.080
 9G5  C21  H9   single    0.930  0.020  1.080
 9G5  C22  H10  single    0.930  0.020  1.080
 9G5  C24  H11  single    0.930  0.020  1.080
 9G5  N2   H12  single    0.860  0.020  1.020
 9G5  C14  H13  single    0.930  0.020  1.080
 9G5  C9   H14  single    0.930  0.020  1.080
 9G5  C12  H15  single    0.930  0.020  1.080
 9G5  C3   H16  single    0.970  0.020  1.090
 9G5  C3   H17  single    0.970  0.020  1.090
 9G5  C2   H18  single    0.970  0.020  1.090
 9G5  C2   H19  single    0.970  0.020  1.090
 9G5  C1   H20  single    0.970  0.020  1.090
 9G5  C1   H21  single    0.970  0.020  1.090
 9G5  C    H23  single    0.970  0.020  1.090
 9G5  C    H24  single    0.970  0.020  1.090
 9G5  C    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
 9G5  C3   N1   C6   117.05  3.000
 9G5  C6   N1   C4   123.11  3.000
 9G5  C3   N1   C4   119.24  3.000
 9G5  H2   C4   H1   105.71  3.000
 9G5  H2   C4   C5   110.06  3.000
 9G5  H1   C4   C5   108.01  3.000
 9G5  H2   C4   N1   109.38  3.000
 9G5  H1   C4   N1   108.49  3.000
 9G5  C5   C4   N1   114.78  3.000
 9G5  H4   C5   H3   106.29  3.000
 9G5  H4   C5   N    107.62  3.000
 9G5  H3   C5   N    111.59  3.000
 9G5  H4   C5   C4   107.09  3.000
 9G5  H3   C5   C4   108.76  3.000
 9G5  N    C5   C4   115.03  3.000
 9G5  O    C6   C7   118.90  3.000
 9G5  C7   C6   N1   118.27  3.000
 9G5  O    C6   N1   122.83  3.000
 9G5  C12  C7   C8   119.92  3.000
 9G5  C8   C7   C6   121.43  3.000
 9G5  C12  C7   C6   118.45  3.000
 9G5  H5   C8   C9   119.86  3.000
 9G5  H5   C8   C7   120.39  3.000
 9G5  C9   C8   C7   119.75  3.000
 9G5  H6   C10  C9   119.52  3.000
 9G5  H6   C10  C11  120.21  3.000
 9G5  C9   C10  C11  120.26  3.000
 9G5  C11  C13  O1   117.70  3.000
 9G5  O1   C13  C14  109.56  3.000
 9G5  C11  C13  C14  132.73  3.000
 9G5  H7   C15  C14  127.42  3.000
 9G5  H7   C15  C16  125.80  3.000
 9G5  C14  C15  C16  106.78  3.000
 9G5  C19  C20  N2   109.51  3.000
 9G5  N2   C20  C21  128.16  3.000
 9G5  C19  C20  C21  122.33  3.000
 9G5  H9   C21  C22  120.33  3.000
 9G5  H9   C21  C20  121.38  3.000
 9G5  C22  C21  C20  118.29  3.000
 9G5  H10  C22  C23  120.49  3.000
 9G5  H10  C22  C21  119.84  3.000
 9G5  C23  C22  C21  119.68  3.000
 9G5  H11  C24  C19  121.59  3.000
 9G5  H11  C24  C23  119.67  3.000
 9G5  C19  C24  C23  118.73  3.000
 9G5  C18  C25  N2   106.15  3.000
 9G5  N2   C25  O2   125.86  3.000
 9G5  C18  C25  O2   127.99  3.000
 9G5  H12  N2   C25  123.66  3.000
 9G5  H12  N2   C20  124.64  3.000
 9G5  C25  N2   C20  111.69  3.000
 9G5  CL   C23  C24  118.43  3.000
 9G5  CL   C23  C22  119.44  3.000
 9G5  C24  C23  C22  122.13  3.000
 9G5  C18  C19  C24  134.52  3.000
 9G5  C24  C19  C20  118.80  3.000
 9G5  C18  C19  C20  106.65  3.000
 9G5  C19  C18  C25  105.97  3.000
 9G5  C25  C18  C17  117.85  3.000
 9G5  C19  C18  C17  136.16  3.000
 9G5  O1   C16  C17  121.94  3.000
 9G5  C17  C16  C15  129.24  3.000
 9G5  O1   C16  C15  108.81  3.000
 9G5  H13  C14  C15  127.07  3.000
 9G5  H13  C14  C13  126.63  3.000
 9G5  C15  C14  C13  106.29  3.000
 9G5  C16  O1   C13  108.55  3.000
 9G5  C12  C11  C13  121.18  3.000
 9G5  C13  C11  C10  119.80  3.000
 9G5  C12  C11  C10  119.01  3.000
 9G5  H14  C9   C10  119.74  3.000
 9G5  H14  C9   C8   119.81  3.000
 9G5  C10  C9   C8   120.44  3.000
 9G5  H15  C12  C11  120.55  3.000
 9G5  H15  C12  C7   118.88  3.000
 9G5  C11  C12  C7   120.57  3.000
 9G5  H17  C3   H16  106.75  3.000
 9G5  H17  C3   C2   108.69  3.000
 9G5  H16  C3   C2   109.29  3.000
 9G5  H17  C3   N1   108.11  3.000
 9G5  H16  C3   N1   109.98  3.000
 9G5  C2   C3   N1   113.76  3.000
 9G5  H19  C2   H18  105.70  3.000
 9G5  H19  C2   C1   108.77  3.000
 9G5  H18  C2   C1   109.04  3.000
 9G5  H19  C2   C3   105.78  3.000
 9G5  H18  C2   C3   111.63  3.000
 9G5  C1   C2   C3   115.39  3.000
 9G5  H21  C1   H20  106.27  3.000
 9G5  H21  C1   N    112.06  3.000
 9G5  H20  C1   N    106.97  3.000
 9G5  H21  C1   C2   109.79  3.000
 9G5  H20  C1   C2   108.18  3.000
 9G5  N    C1   C2   113.22  3.000
 9G5  C    N    C1   111.13  3.000
 9G5  C1   N    C5   113.87  3.000
 9G5  C    N    C5   109.96  3.000
 9G5  H25  C    H24  107.73  3.000
 9G5  H25  C    H23  107.83  3.000
 9G5  H24  C    H23  107.51  3.000
 9G5  H25  C    N    110.19  3.000
 9G5  H24  C    N    110.05  3.000
 9G5  H23  C    N    113.33  3.000
 9G5  H8   C17  C16  112.24  3.000
 9G5  H8   C17  C18  115.23  3.000
 9G5  C16  C17  C18  132.53  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
 9G5  CONST_01  C13  C11  C12  C7    180.00   0.0  0
 9G5  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 9G5  CONST_03  C10  C9   C8   C7      0.00   0.0  0
 9G5  CONST_04  C11  C12  C7   C8      0.00   0.0  0
 9G5  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 9G5  CONST_06  C14  C13  C11  C10     0.00   0.0  0
 9G5  CONST_07  O1   C13  C11  C10   180.00   0.0  0
 9G5  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 9G5  CONST_09  C9   C10  C11  C13   180.00   0.0  0
 9G5  CONST_10  C15  C16  O1   C13     0.00   0.0  0
 9G5  CONST_11  C11  C13  C14  C15   180.00   0.0  0
 9G5  CONST_12  O1   C13  C14  C15     0.00   0.0  0
 9G5  CONST_13  C23  C24  C19  C20     0.00   0.0  0
 9G5  CONST_14  C23  C22  C21  C20     0.00   0.0  0
 9G5  CONST_15  C24  C19  C20  C21     0.00   0.0  0
 9G5  CONST_16  C24  C23  C22  C21     0.00   0.0  0
 9G5  CONST_17  C19  C24  C23  C22     0.00   0.0  0
 9G5  CONST_18  C19  C20  C21  C22     0.00   0.0  0
 9G5  CONST_19  C14  C13  O1   C16     0.00   0.0  0
 9G5  CONST_20  C11  C13  O1   C16   180.00   0.0  0
 9G5  CONST_21  O1   C16  C15  C14     0.00   0.0  0
 9G5  CONST_22  C12  C11  C13  C14   180.00   0.0  0
 9G5  CONST_23  C12  C11  C13  O1      0.00   0.0  0
 9G5  CONST_24  C12  C7   C8   C9      0.00   0.0  0
 9G5  CONST_25  C12  C11  C10  C9      0.00   0.0  0
 9G5  CONST_26  C18  C25  N2   C20     0.00   0.0  0
 9G5  CONST_27  C11  C12  C7   C6    180.00   0.0  0
 9G5  CONST_28  C9   C8   C7   C6    180.00   0.0  0
 9G5  CONST_29  C17  C16  O1   C13   180.00   0.0  0
 9G5  CONST_30  C14  C15  C16  C17   180.00   0.0  0
 9G5  CONST_31  CL   C23  C22  C21   180.00   0.0  0
 9G5  CONST_32  C19  C24  C23  CL    180.00   0.0  0
 9G5  CONST_33  O2   C25  N2   C20   180.00   0.0  0
 9G5  CONST_34  H14  C9   C8   C7    180.00   0.0  0
 9G5  CONST_35  H15  C12  C7   C8    180.00   0.0  0
 9G5  CONST_36  H6   C10  C9   C8    180.00   0.0  0
 9G5  CONST_37  H5   C8   C9   C10   180.00   0.0  0
 9G5  CONST_38  H7   C15  C14  C13   180.00   0.0  0
 9G5  CONST_39  H11  C24  C19  C20   180.00   0.0  0
 9G5  CONST_40  H10  C22  C21  C20   180.00   0.0  0
 9G5  CONST_41  H9   C21  C20  N2      0.00   0.0  0
 9G5  CONST_42  H13  C14  C15  C16   180.00   0.0  0
 9G5  CONST_43  H12  N2   C25  C18   180.00   0.0  0
 9G5  Var_01    C12  C7   C6   N1   -114.78  30.0  2
 9G5  Var_02    C18  C17  C16  C15  -176.63  30.0  2
 9G5  Var_03    C16  C17  C18  C25  -175.10  30.0  2

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
 9G5  plan-1  C13  0.020
 9G5  plan-1  C15  0.020
 9G5  plan-1  C16  0.020
 9G5  plan-1  C14  0.020
 9G5  plan-1  O1   0.020
 9G5  plan-1  C11  0.020
 9G5  plan-1  H7   0.020
 9G5  plan-1  H13  0.020
 9G5  plan-1  C17  0.020
 9G5  plan-2  C6   0.020
 9G5  plan-2  C7   0.020
 9G5  plan-2  C8   0.020
 9G5  plan-2  C10  0.020
 9G5  plan-2  C13  0.020
 9G5  plan-2  C11  0.020
 9G5  plan-2  C9   0.020
 9G5  plan-2  C12  0.020
 9G5  plan-2  H5   0.020
 9G5  plan-2  H6   0.020
 9G5  plan-2  H14  0.020
 9G5  plan-2  H15  0.020
 9G5  plan-3  C20  0.020
 9G5  plan-3  C21  0.020
 9G5  plan-3  C22  0.020
 9G5  plan-3  C24  0.020
 9G5  plan-3  C25  0.020
 9G5  plan-3  N2   0.020
 9G5  plan-3  C23  0.020
 9G5  plan-3  CL   0.020
 9G5  plan-3  C19  0.020
 9G5  plan-3  C18  0.020
 9G5  plan-3  H9   0.020
 9G5  plan-3  H10  0.020
 9G5  plan-3  H11  0.020
 9G5  plan-3  H12  0.020
 9G5  plan-3  C17  0.020
 9G5  plan-3  O2   0.020
 9G5  plan-4  N1   0.020
 9G5  plan-4  C4   0.020
 9G5  plan-4  C6   0.020
 9G5  plan-4  C7   0.020
 9G5  plan-4  O    0.020
 9G5  plan-4  C3   0.020

