# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 02:02:29 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2~{Z})-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1~{H}-pyrrolo[2,3-c]pyridin-3-ylmethylidene)-1-benzofuran-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2C(=O)\C(Oc2c1CN3CCNCC3)=C\c4c[nH]c5cnccc45
#
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
 8GX  8GX  (2~{Z})-6-methoxy-7-(piperazin-1-ylmethyl)-2-(1~{H}-pyrrolo[2,3-c]pyridin-3-ylmethylidene)-1-benzofuran-3-one  ligand  51  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_8GX
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
 8GX  C15  C  CH2   0  -0.298   1.8262   2.7890   0.9753
 8GX  C17  C  CR5   0   0.258  -0.7021  -1.7170  -0.2451
 8GX  C20  C  CR15  0  -0.037  -1.8826   1.1224   0.1548
 8GX  C22  C  CR56  0   0.258  -4.0361   1.6562   0.0321
 8GX  C24  C  CR16  0  -0.429  -5.1058  -0.4062  -0.5500
 8GX  C28  C  CR5   0   0.333  -0.0423  -2.9950  -0.5833
 8GX  C01  C  CH3   0  -0.441   6.0928  -1.7935   0.9521
 8GX  C03  C  CR6   0   0.379   3.7356  -1.6537   0.6330
 8GX  C04  C  CR16  0  -0.405   3.6939  -2.9658   0.1169
 8GX  C05  C  CR16  0  -0.289   2.5047  -3.5181  -0.3126
 8GX  C06  C  CR56  0  -0.159   1.3492  -2.7518  -0.2342
 8GX  C07  C  CR56  0   0.452   1.4236  -1.4592   0.2740
 8GX  C08  C  CR6   0  -0.146   2.5795  -0.8614   0.7339
 8GX  C09  C  CH2   0  -0.320   2.5502   0.5323   1.3016
 8GX  N10  N  NT    0  -0.404   2.0733   1.5082   0.3391
 8GX  C11  C  CH2   0  -0.280   2.9761   1.6570  -0.7879
 8GX  C12  C  CH2   0  -0.320   2.4101   2.6519  -1.7911
 8GX  N13  N  NH1   0  -0.579   2.0982   3.9481  -1.2119
 8GX  C14  C  CH2   0  -0.324   1.2688   3.7877  -0.0304
 8GX  O16  O  O     0  -0.489   0.2189  -0.8481   0.2800
 8GX  C19  C  CR5   0   0.015  -2.5369  -0.0543  -0.1794
 8GX  N21  N  NR15  0  -0.678  -2.7740   2.1261   0.2768
 8GX  C23  C  CR56  0   0.152  -3.9282   0.2865  -0.2627
 8GX  C25  C  CR16  0  -0.091  -6.2850   0.3100  -0.5249
 8GX  N26  N  N     0  -0.416  -6.3735   1.6194  -0.2419
 8GX  C27  C  CR16  0  -0.092  -5.2721   2.2912   0.0343
 8GX  O29  O  O     0  -0.418  -0.5689  -3.9881  -1.0542
 8GX  H1   H  HCH2  0   0.233   1.1094   2.6480   1.7897
 8GX  H2   H  HCH2  0   0.196   2.7463   3.2051   1.4256
 8GX  H4   H  HCR6  0   0.262  -5.1140  -1.4627  -0.7838
 8GX  H5   H  HCH3  0   0.266   6.8629  -1.1195   1.3168
 8GX  H6   H  HCH3  0   0.237   6.0926  -2.6966   1.5662
 8GX  H7   H  HCH3  0   0.237   6.3182  -2.0636  -0.0816
 8GX  H8   H  HCR6  0   0.288   4.5959  -3.5565   0.0509
 8GX  H9   H  HCR6  0   0.273   2.4811  -4.5266  -0.7045
 8GX  H10  H  HCH2  0   0.252   1.8627   0.5436   2.1533
 8GX  H11  H  HCH2  0   0.227   3.5374   0.8029   1.7012
 8GX  H13  H  HCH2  0   0.184   3.9772   1.9940  -0.4609
 8GX  H14  H  HCH2  0   0.236   3.1097   0.6880  -1.2753
 8GX  H15  H  HCH2  0   0.236   3.1155   2.7853  -2.6132
 8GX  H16  H  HCH2  0   0.218   1.4913   2.2374  -2.2186
 8GX  H17  H  HNH1  0   0.340   2.9623   4.4092  -0.9482
 8GX  H19  H  HCH2  0   0.212   0.2764   3.4563  -0.3557
 8GX  H20  H  HCH2  0   0.239   1.1366   4.7575   0.4527
 8GX  H22  H  HNR5  0   0.425  -2.5387   3.0770   0.5126
 8GX  H23  H  HCR6  0   0.259  -7.2214  -0.1904  -0.7429
 8GX  H24  H  HCR6  0   0.273  -5.3662   3.3485   0.2597
 8GX  C18  C  C1    0  -0.463  -1.9759  -1.3486  -0.4364
 8GX  O02  O  O2    0  -0.455   4.8688  -1.0865   1.0557
 8GX  H3   H  HCR5  0   0.315  -0.8273   1.3068   0.2862
 8GX  H21  H  H     0   0.279  -2.6322  -2.1131  -0.8364

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
 8GX  C12  C11  single    1.522  0.020  1.522
 8GX  C12  N13  single    1.454  0.020  1.454
 8GX  C11  N10  single    1.452  0.020  1.452
 8GX  N13  C14  single    1.452  0.020  1.452
 8GX  C01  O02  single    1.417  0.020  1.417
 8GX  O02  C03  single    1.336  0.020  1.336
 8GX  N10  C09  single    1.451  0.020  1.451
 8GX  N10  C15  single    1.451  0.020  1.451
 8GX  C14  C15  single    1.523  0.020  1.523
 8GX  C09  C08  single    1.505  0.020  1.505
 8GX  C03  C08  aromatic  1.405  0.020  1.405
 8GX  C03  C04  aromatic  1.411  0.020  1.411
 8GX  C08  C07  aromatic  1.380  0.020  1.380
 8GX  C04  C05  aromatic  1.380  0.020  1.380
 8GX  C07  C06  aromatic  1.391  0.020  1.391
 8GX  C07  O16  single    1.351  0.020  1.351
 8GX  C05  C06  aromatic  1.389  0.020  1.389
 8GX  C25  C24  aromatic  1.380  0.020  1.380
 8GX  C25  N26  aromatic  1.343  0.020  1.343
 8GX  C06  C28  single    1.455  0.020  1.455
 8GX  O16  C17  single    1.371  0.020  1.371
 8GX  C24  C23  aromatic  1.396  0.020  1.396
 8GX  N26  C27  aromatic  1.319  0.020  1.319
 8GX  C17  C28  single    1.478  0.020  1.478
 8GX  C17  C18  double    1.340  0.020  1.340
 8GX  C28  O29  double    1.219  0.020  1.219
 8GX  C27  C22  aromatic  1.390  0.020  1.390
 8GX  C23  C22  aromatic  1.405  0.020  1.405
 8GX  C23  C19  aromatic  1.435  0.020  1.435
 8GX  C22  N21  aromatic  1.369  0.020  1.369
 8GX  C18  C19  single    1.434  0.020  1.434
 8GX  C19  C20  aromatic  1.387  0.020  1.387
 8GX  N21  C20  aromatic  1.348  0.020  1.348
 8GX  C15  H1   single    0.970  0.020  1.090
 8GX  C15  H2   single    0.970  0.020  1.090
 8GX  C20  H3   single    0.930  0.020  1.080
 8GX  C24  H4   single    0.930  0.020  1.080
 8GX  C01  H5   single    0.970  0.020  1.090
 8GX  C01  H6   single    0.970  0.020  1.090
 8GX  C01  H7   single    0.970  0.020  1.090
 8GX  C04  H8   single    0.930  0.020  1.080
 8GX  C05  H9   single    0.930  0.020  1.080
 8GX  C09  H10  single    0.970  0.020  1.090
 8GX  C09  H11  single    0.970  0.020  1.090
 8GX  C11  H13  single    0.970  0.020  1.090
 8GX  C11  H14  single    0.970  0.020  1.090
 8GX  C12  H15  single    0.970  0.020  1.090
 8GX  C12  H16  single    0.970  0.020  1.090
 8GX  N13  H17  single    0.890  0.020  1.040
 8GX  C14  H19  single    0.970  0.020  1.090
 8GX  C14  H20  single    0.970  0.020  1.090
 8GX  C18  H21  single    0.930  0.020  1.080
 8GX  N21  H22  single    0.860  0.020  1.020
 8GX  C25  H23  single    0.930  0.020  1.080
 8GX  C27  H24  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
 8GX  H2   C15  H1   106.90  3.000
 8GX  H2   C15  C14  109.07  3.000
 8GX  H1   C15  C14  109.65  3.000
 8GX  H2   C15  N10  111.65  3.000
 8GX  H1   C15  N10  108.91  3.000
 8GX  C14  C15  N10  110.58  3.000
 8GX  C18  C17  O16  121.28  3.000
 8GX  C18  C17  C28  129.03  3.000
 8GX  O16  C17  C28  109.63  3.000
 8GX  H3   C20  N21  120.55  3.000
 8GX  H3   C20  C19  129.45  3.000
 8GX  N21  C20  C19  109.97  3.000
 8GX  C27  C22  C23  120.93  3.000
 8GX  C23  C22  N21  107.54  3.000
 8GX  C27  C22  N21  131.53  3.000
 8GX  H4   C24  C25  120.28  3.000
 8GX  H4   C24  C23  122.36  3.000
 8GX  C25  C24  C23  117.36  3.000
 8GX  O29  C28  C06  129.95  3.000
 8GX  O29  C28  C17  126.89  3.000
 8GX  C06  C28  C17  103.15  3.000
 8GX  H7   C01  H6   109.13  3.000
 8GX  H7   C01  H5   108.96  3.000
 8GX  H6   C01  H5   108.93  3.000
 8GX  H7   C01  O02  111.77  3.000
 8GX  H6   C01  O02  111.79  3.000
 8GX  H5   C01  O02  106.15  3.000
 8GX  C08  C03  C04  121.76  3.000
 8GX  C04  C03  O02  122.40  3.000
 8GX  C08  C03  O02  115.84  3.000
 8GX  H8   C04  C05  118.80  3.000
 8GX  H8   C04  C03  120.42  3.000
 8GX  C05  C04  C03  120.78  3.000
 8GX  H9   C05  C06  121.10  3.000
 8GX  H9   C05  C04  120.30  3.000
 8GX  C06  C05  C04  118.60  3.000
 8GX  C07  C06  C05  119.27  3.000
 8GX  C05  C06  C28  133.63  3.000
 8GX  C07  C06  C28  107.10  3.000
 8GX  O16  C07  C08  123.33  3.000
 8GX  O16  C07  C06  111.99  3.000
 8GX  C08  C07  C06  124.68  3.000
 8GX  C09  C08  C07  120.69  3.000
 8GX  C07  C08  C03  114.89  3.000
 8GX  C09  C08  C03  124.41  3.000
 8GX  H11  C09  H10  106.18  3.000
 8GX  H11  C09  N10  111.77  3.000
 8GX  H10  C09  N10  107.62  3.000
 8GX  H11  C09  C08  110.34  3.000
 8GX  H10  C09  C08  108.37  3.000
 8GX  N10  C09  C08  112.27  3.000
 8GX  C11  N10  C09  112.30  3.000
 8GX  C09  N10  C15  111.02  3.000
 8GX  C11  N10  C15  110.84  3.000
 8GX  H14  C11  H13  106.95  3.000
 8GX  H14  C11  C12  109.33  3.000
 8GX  H13  C11  C12  109.41  3.000
 8GX  H14  C11  N10  109.36  3.000
 8GX  H13  C11  N10  111.39  3.000
 8GX  C12  C11  N10  110.33  3.000
 8GX  H16  C12  H15  107.13  3.000
 8GX  H16  C12  N13  108.25  3.000
 8GX  H15  C12  N13  109.26  3.000
 8GX  H16  C12  C11  108.78  3.000
 8GX  H15  C12  C11  109.63  3.000
 8GX  N13  C12  C11  113.58  3.000
 8GX  H17  N13  C14  108.98  3.000
 8GX  H17  N13  C12  109.04  3.000
 8GX  C14  N13  C12  110.38  3.000
 8GX  H20  C14  H19  106.89  3.000
 8GX  H20  C14  N13  109.34  3.000
 8GX  H19  C14  N13  108.00  3.000
 8GX  H20  C14  C15  109.55  3.000
 8GX  H19  C14  C15  109.22  3.000
 8GX  N13  C14  C15  113.62  3.000
 8GX  C07  O16  C17  108.10  3.000
 8GX  C23  C19  C18  125.69  3.000
 8GX  C18  C19  C20  128.63  3.000
 8GX  C23  C19  C20  105.66  3.000
 8GX  H22  N21  C22  125.53  3.000
 8GX  H22  N21  C20  124.71  3.000
 8GX  C22  N21  C20  109.75  3.000
 8GX  C19  C23  C24  135.40  3.000
 8GX  C19  C23  C22  107.09  3.000
 8GX  C24  C23  C22  117.52  3.000
 8GX  H23  C25  N26  115.84  3.000
 8GX  H23  C25  C24  119.67  3.000
 8GX  N26  C25  C24  124.49  3.000
 8GX  C27  N26  C25  119.06  3.000
 8GX  H24  C27  N26  117.85  3.000
 8GX  H24  C27  C22  121.52  3.000
 8GX  N26  C27  C22  120.63  3.000
 8GX  H21  C18  C19  117.76  3.000
 8GX  H21  C18  C17  115.75  3.000
 8GX  C19  C18  C17  126.49  3.000
 8GX  C03  O02  C01  119.84  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
 8GX  CONST_01  C24  C23  C19  C20   180.00   0.0  0
 8GX  CONST_02  C22  C23  C19  C20     0.00   0.0  0
 8GX  CONST_03  C27  C22  N21  C20   180.00   0.0  0
 8GX  CONST_04  C23  C22  N21  C20     0.00   0.0  0
 8GX  CONST_05  C25  N26  C27  C22     0.00   0.0  0
 8GX  CONST_06  C25  C24  C23  C22     0.00   0.0  0
 8GX  CONST_07  C19  C20  N21  C22     0.00   0.0  0
 8GX  CONST_08  C27  N26  C25  C24     0.00   0.0  0
 8GX  CONST_09  C27  C22  C23  C24     0.00   0.0  0
 8GX  CONST_10  N21  C22  C23  C24   180.00   0.0  0
 8GX  CONST_11  C06  C07  C08  C03     0.00   0.0  0
 8GX  CONST_12  C06  C05  C04  C03     0.00   0.0  0
 8GX  CONST_13  C07  C08  C03  C04     0.00   0.0  0
 8GX  CONST_14  C07  C06  C05  C04     0.00   0.0  0
 8GX  CONST_15  C08  C03  C04  C05     0.00   0.0  0
 8GX  CONST_16  C08  C07  C06  C05     0.00   0.0  0
 8GX  CONST_17  C25  C24  C23  C19   180.00   0.0  0
 8GX  CONST_18  C27  C22  C23  C19   180.00   0.0  0
 8GX  CONST_19  N21  C22  C23  C19     0.00   0.0  0
 8GX  CONST_20  N26  C27  C22  N21   180.00   0.0  0
 8GX  CONST_21  C23  C19  C20  N21     0.00   0.0  0
 8GX  CONST_22  N26  C25  C24  C23     0.00   0.0  0
 8GX  CONST_23  N26  C27  C22  C23     0.00   0.0  0
 8GX  CONST_24  C18  C19  C23  C22   180.00   0.0  0
 8GX  CONST_25  C18  C19  C23  C24     0.00   0.0  0
 8GX  CONST_26  C07  C08  C03  O02   180.00   0.0  0
 8GX  CONST_27  C05  C04  C03  O02   180.00   0.0  0
 8GX  CONST_28  C09  C08  C03  C04   180.00   0.0  0
 8GX  CONST_29  C09  C08  C07  C06   180.00   0.0  0
 8GX  CONST_30  O16  C07  C08  C09     0.00   0.0  0
 8GX  CONST_31  N21  C20  C19  C18   180.00   0.0  0
 8GX  CONST_32  H4   C24  C23  C22   180.00   0.0  0
 8GX  CONST_33  H3   C20  N21  C22   180.00   0.0  0
 8GX  CONST_34  H9   C05  C06  C28     0.00   0.0  0
 8GX  CONST_35  H8   C04  C05  C06   180.00   0.0  0
 8GX  CONST_36  H22  N21  C20  C19   180.00   0.0  0
 8GX  CONST_37  H24  C27  C22  N21     0.00   0.0  0
 8GX  CONST_38  H23  C25  C24  C23   180.00   0.0  0
 8GX  Var_01    C12  C11  N10  C15   -57.19  30.0  1
 8GX  Var_02    C12  N13  C14  C15    51.08  30.0  1
 8GX  Var_03    N13  C12  C11  N10    55.20  30.0  1
 8GX  Var_04    N13  C14  C15  N10   -54.57  30.0  1
 8GX  Var_05    C14  N13  C12  C11   -51.46  30.0  1
 8GX  Var_06    C14  C15  N10  C11    56.93  30.0  1
 8GX  Var_07    C08  C09  N10  C15   169.69  30.0  3
 8GX  Var_08    C23  C19  C18  C17  -173.36  30.0  2
 8GX  Var_09    C19  C18  C17  C28  -174.88  30.0  2
 8GX  Var_10    N10  C09  C08  C03   120.52  30.0  2
 8GX  Var_11    C08  C03  O02  C01  -177.94  30.0  2
 8GX  Var_12    H5   C01  O02  C03   177.75  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
 8GX  plan-1  C17  0.020
 8GX  plan-1  C28  0.020
 8GX  plan-1  C03  0.020
 8GX  plan-1  C04  0.020
 8GX  plan-1  C05  0.020
 8GX  plan-1  C06  0.020
 8GX  plan-1  C07  0.020
 8GX  plan-1  C08  0.020
 8GX  plan-1  C09  0.020
 8GX  plan-1  O16  0.020
 8GX  plan-1  O29  0.020
 8GX  plan-1  H8   0.020
 8GX  plan-1  H9   0.020
 8GX  plan-1  C18  0.020
 8GX  plan-1  O02  0.020
 8GX  plan-2  C20  0.020
 8GX  plan-2  C22  0.020
 8GX  plan-2  C24  0.020
 8GX  plan-2  C19  0.020
 8GX  plan-2  N21  0.020
 8GX  plan-2  C23  0.020
 8GX  plan-2  C25  0.020
 8GX  plan-2  N26  0.020
 8GX  plan-2  C27  0.020
 8GX  plan-2  H4   0.020
 8GX  plan-2  H22  0.020
 8GX  plan-2  H23  0.020
 8GX  plan-2  H24  0.020
 8GX  plan-2  C18  0.020
 8GX  plan-2  H3   0.020

