# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 22:20:24 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 1-[(2-aminopyridin-4-yl)methyl]-5-chloro-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(Cn2c3ccc(Cl)cc3c(C4=CC=CNC4=O)c2C(O)=O)ccn1
#
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
 08E  08E  '1-[(2-aminopyridin-4-yl)methyl]-5-chloro-3-(2-oxo-1,2-dihydropyridin-3-yl)-1H-indole-2-carboxylic acid'  ligand  42  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_08E
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
 08E  C10  C   CR16   0  -0.306   0.3486   2.7128   0.7140
 08E  C9   C   CR16   0  -0.247  -0.5551   3.5800   0.1317
 08E  C21  C   CR16   0  -0.425   3.7855   1.6999   0.4079
 08E  C2   C   CR16   0  -0.347  -1.9928   1.7355  -0.5487
 08E  C25  C   CR16   0  -0.439   3.5512  -0.6406   0.0130
 08E  C22  C   CR16   0  -0.053   4.7506   1.7079  -0.5811
 08E  C4   C   CR56   0   0.068  -1.0781   0.8481   0.0266
 08E  C8   C   CR5    0   0.000  -1.0388  -0.5734   0.1559
 08E  C20  C   CR6    0   0.238   3.1651   0.4868   0.7105
 08E  C5   C   CR56   0   0.361   0.0753   1.3476   0.6650
 08E  C3   C   CR6    0  -0.050  -1.7097   3.0822  -0.4862
 08E  C7   C   CR5    0   0.164   0.1001  -0.8797   0.8624
 08E  C24  C   CR6    0   0.462   4.5380  -0.5275  -0.9806
 08E  C18  C   CR16   0  -0.386  -3.4942  -2.3554  -2.1019
 08E  C17  C   CR16   0  -0.190  -2.4811  -1.4877  -1.6266
 08E  C19  C   CR16   0   0.037  -4.0514  -3.2190  -1.2203
 08E  C1   C   CR6    0  -0.212  -2.0632  -1.4970  -0.3269
 08E  C15  C   CR6    0   0.510  -2.6947  -2.3950   0.6248
 08E  C11  C   C      0   0.397   0.5588  -2.2662   1.2572
 08E  N23  N   N      0  -0.461   5.1249   0.6342  -1.2668
 08E  N6   N   NR5    0  -0.572   0.7651   0.2845   1.1811
 08E  N16  N   NR16   0  -0.657  -3.6516  -3.2213   0.0731
 08E  N27  N   NH2    0  -0.835   4.9095  -1.6097  -1.7233
 08E  O28  O   O      0  -0.493  -2.4556  -2.4473   1.8268
 08E  O13  O   O      0  -0.575   0.2689  -3.1654   0.4537
 08E  O14  O   OC    -1  -0.590   1.1665  -2.3787   2.3399
 08E  CL2  CL  CL     0  -0.148  -2.8234   4.2177  -1.1938
 08E  H1   H   HCR6   0   0.266   1.2319   3.1090   1.1953
 08E  H2   H   HCR6   0   0.272  -0.3703   4.6451   0.1565
 08E  H4   H   HCR6   0   0.264  -2.8961   1.3775  -1.0255
 08E  H6   H   HCR6   0   0.257   5.2561   2.6337  -0.8354
 08E  H7   H   HCR6   0   0.271  -3.8075  -2.3436  -3.1344
 08E  H8   H   HCR6   0   0.265  -2.0102  -0.8060  -2.3250
 08E  H9   H   HCR6   0   0.305  -4.8221  -3.9299  -1.4792
 08E  H13  H   HNH2   0   0.390   4.7238  -2.5222  -1.3419
 08E  H14  H   HNH2   0   0.382   5.7920  -1.5376  -2.2029
 08E  H10  H   HNR6   0   0.418  -4.1025  -3.8640   0.7098
 08E  C12  C   CH2    0  -0.447   2.0880   0.4054   1.7636
 08E  H3   H   HCR6   0   0.256   3.5334   2.6114   0.9332
 08E  H11  H   HCH2   0   0.305   2.2441  -0.4506   2.4135
 08E  H12  H   HCH2   0   0.279   2.1065   1.2978   2.3901
 08E  H5   H   HCR6   0   0.269   3.1166  -1.6086   0.2284

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
 08E  C22  N23  aromatic  1.328  0.020  1.328
 08E  C22  C21  aromatic  1.382  0.020  1.382
 08E  N23  C24  aromatic  1.333  0.020  1.333
 08E  C21  C20  aromatic  1.396  0.020  1.396
 08E  O13  C11  deloc     1.240  0.020  1.240
 08E  C24  N27  single    1.364  0.020  1.364
 08E  C24  C25  aromatic  1.405  0.020  1.405
 08E  C20  C12  single    1.509  0.020  1.509
 08E  C20  C25  aromatic  1.381  0.020  1.381
 08E  O14  C11  deloc     1.247  0.020  1.247
 08E  C11  C7   single    1.513  0.020  1.513
 08E  C12  N6   single    1.451  0.020  1.451
 08E  O28  C15  double    1.227  0.020  1.227
 08E  C7   N6   aromatic  1.378  0.020  1.378
 08E  C7   C8   aromatic  1.375  0.020  1.375
 08E  N6   C5   aromatic  1.368  0.020  1.368
 08E  C15  N16  single    1.379  0.020  1.379
 08E  C15  C1   single    1.453  0.020  1.453
 08E  N16  C19  single    1.354  0.020  1.354
 08E  C8   C1   single    1.461  0.020  1.461
 08E  C8   C4   aromatic  1.428  0.020  1.428
 08E  C5   C10  aromatic  1.393  0.020  1.393
 08E  C5   C4   aromatic  1.410  0.020  1.410
 08E  C1   C17  double    1.365  0.020  1.365
 08E  C19  C18  double    1.354  0.020  1.354
 08E  C10  C9   aromatic  1.381  0.020  1.381
 08E  C4   C2   aromatic  1.398  0.020  1.398
 08E  C17  C18  single    1.416  0.020  1.416
 08E  C9   C3   aromatic  1.401  0.020  1.401
 08E  C2   C3   aromatic  1.378  0.020  1.378
 08E  C3   CL2  single    1.741  0.020  1.741
 08E  C10  H1   single    0.930  0.020  1.080
 08E  C9   H2   single    0.930  0.020  1.080
 08E  C21  H3   single    0.930  0.020  1.080
 08E  C2   H4   single    0.930  0.020  1.080
 08E  C25  H5   single    0.930  0.020  1.080
 08E  C22  H6   single    0.930  0.020  1.080
 08E  C18  H7   single    0.930  0.020  1.080
 08E  C17  H8   single    0.930  0.020  1.080
 08E  C19  H9   single    0.930  0.020  1.080
 08E  C12  H11  single    0.970  0.020  1.090
 08E  C12  H12  single    0.970  0.020  1.090
 08E  N27  H13  single    0.890  0.020  1.040
 08E  N27  H14  single    0.890  0.020  1.040
 08E  N16  H10  single    0.860  0.020  1.020

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
 08E  H1   C10  C5   122.35  3.000
 08E  H1   C10  C9   119.48  3.000
 08E  C5   C10  C9   118.17  3.000
 08E  H2   C9   C3   120.07  3.000
 08E  H2   C9   C10  119.79  3.000
 08E  C3   C9   C10  120.13  3.000
 08E  H3   C21  C20  121.56  3.000
 08E  H3   C21  C22  120.35  3.000
 08E  C20  C21  C22  118.08  3.000
 08E  H4   C2   C3   120.99  3.000
 08E  H4   C2   C4   121.15  3.000
 08E  C3   C2   C4   117.86  3.000
 08E  H5   C25  C24  119.64  3.000
 08E  H5   C25  C20  121.14  3.000
 08E  C24  C25  C20  119.21  3.000
 08E  H6   C22  N23  115.95  3.000
 08E  H6   C22  C21  119.87  3.000
 08E  N23  C22  C21  124.18  3.000
 08E  C5   C4   C8   106.81  3.000
 08E  C5   C4   C2   119.78  3.000
 08E  C8   C4   C2   133.39  3.000
 08E  C1   C8   C7   127.57  3.000
 08E  C1   C8   C4   125.45  3.000
 08E  C7   C8   C4   106.92  3.000
 08E  C12  C20  C25  120.55  3.000
 08E  C25  C20  C21  118.41  3.000
 08E  C12  C20  C21  121.04  3.000
 08E  N6   C5   C4   107.94  3.000
 08E  C4   C5   C10  121.58  3.000
 08E  N6   C5   C10  130.48  3.000
 08E  CL2  C3   C2   119.19  3.000
 08E  CL2  C3   C9   118.34  3.000
 08E  C2   C3   C9   122.47  3.000
 08E  N6   C7   C11  124.58  3.000
 08E  N6   C7   C8   109.29  3.000
 08E  C11  C7   C8   126.12  3.000
 08E  N27  C24  N23  117.05  3.000
 08E  N27  C24  C25  120.83  3.000
 08E  N23  C24  C25  122.10  3.000
 08E  H7   C18  C19  120.70  3.000
 08E  H7   C18  C17  121.48  3.000
 08E  C19  C18  C17  117.81  3.000
 08E  H8   C17  C1   119.00  3.000
 08E  H8   C17  C18  118.69  3.000
 08E  C1   C17  C18  122.30  3.000
 08E  H9   C19  N16  116.02  3.000
 08E  H9   C19  C18  123.87  3.000
 08E  N16  C19  C18  120.11  3.000
 08E  C15  C1   C17  119.65  3.000
 08E  C17  C1   C8   121.65  3.000
 08E  C15  C1   C8   118.62  3.000
 08E  O28  C15  N16  120.10  3.000
 08E  N16  C15  C1   114.19  3.000
 08E  O28  C15  C1   125.70  3.000
 08E  O14  C11  O13  127.68  3.000
 08E  O14  C11  C7   117.20  3.000
 08E  O13  C11  C7   115.12  3.000
 08E  C24  N23  C22  118.02  3.000
 08E  C12  N6   C7   127.11  3.000
 08E  C7   N6   C5   109.02  3.000
 08E  C12  N6   C5   123.12  3.000
 08E  H10  N16  C15  116.00  3.000
 08E  H10  N16  C19  118.11  3.000
 08E  C15  N16  C19  125.87  3.000
 08E  H14  N27  H13  114.03  3.000
 08E  H14  N27  C24  116.17  3.000
 08E  H13  N27  C24  117.57  3.000
 08E  H12  C12  H11  107.39  3.000
 08E  H12  C12  N6   108.32  3.000
 08E  H11  C12  N6   107.80  3.000
 08E  H12  C12  C20  110.17  3.000
 08E  H11  C12  C20  110.96  3.000
 08E  N6   C12  C20  112.04  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
 08E  CONST_01  C7   N6   C5   C10   180.00   0.0  0
 08E  CONST_02  C8   C4   C5   C10   180.00   0.0  0
 08E  CONST_03  C2   C4   C5   C10     0.00   0.0  0
 08E  CONST_04  C2   C3   C9   C10     0.00   0.0  0
 08E  CONST_05  N6   C5   C10  C9    180.00   0.0  0
 08E  CONST_06  C4   C5   C10  C9      0.00   0.0  0
 08E  CONST_07  C4   C2   C3   C9      0.00   0.0  0
 08E  CONST_08  C24  N23  C22  C21     0.00   0.0  0
 08E  CONST_09  C24  C25  C20  C21     0.00   0.0  0
 08E  CONST_10  C7   C8   C4   C2    180.00   0.0  0
 08E  CONST_11  N6   C5   C4   C2    180.00   0.0  0
 08E  CONST_12  C22  N23  C24  C25     0.00   0.0  0
 08E  CONST_13  C22  C21  C20  C25     0.00   0.0  0
 08E  CONST_14  N6   C7   C8   C4      0.00   0.0  0
 08E  CONST_15  C7   N6   C5   C4      0.00   0.0  0
 08E  CONST_16  C5   N6   C7   C8      0.00   0.0  0
 08E  CONST_17  N6   C5   C4   C8      0.00   0.0  0
 08E  CONST_18  C3   C2   C4   C8    180.00   0.0  0
 08E  CONST_19  N23  C22  C21  C20     0.00   0.0  0
 08E  CONST_20  N23  C24  C25  C20     0.00   0.0  0
 08E  CONST_21  C3   C9   C10  C5      0.00   0.0  0
 08E  CONST_22  C7   C8   C4   C5      0.00   0.0  0
 08E  CONST_23  C3   C2   C4   C5      0.00   0.0  0
 08E  CONST_24  C1   C8   C4   C2      0.00   0.0  0
 08E  CONST_25  C1   C8   C4   C5    180.00   0.0  0
 08E  CONST_26  N6   C7   C8   C1    180.00   0.0  0
 08E  CONST_27  C1   C15  N16  C19     0.00   0.0  0
 08E  CONST_28  C12  N6   C5   C10     0.00   0.0  0
 08E  CONST_29  CL2  C3   C9   C10   180.00   0.0  0
 08E  CONST_30  N27  C24  N23  C22   180.00   0.0  0
 08E  CONST_31  C12  C20  C21  C22   180.00   0.0  0
 08E  CONST_32  C11  C7   C8   C4    180.00   0.0  0
 08E  CONST_33  C12  N6   C5   C4    180.00   0.0  0
 08E  CONST_34  CL2  C3   C2   C4    180.00   0.0  0
 08E  CONST_35  C12  N6   C7   C8    180.00   0.0  0
 08E  CONST_36  N27  C24  C25  C20   180.00   0.0  0
 08E  CONST_37  C11  C7   N6   C5    180.00   0.0  0
 08E  CONST_38  C12  C20  C25  C24   180.00   0.0  0
 08E  CONST_39  C11  C7   C8   C1      0.00   0.0  0
 08E  CONST_40  O28  C15  N16  C19   180.00   0.0  0
 08E  CONST_41  H4   C2   C3   C9    180.00   0.0  0
 08E  CONST_42  H5   C25  C20  C21   180.00   0.0  0
 08E  CONST_43  H2   C9   C3   C2    180.00   0.0  0
 08E  CONST_44  H3   C21  C20  C25   180.00   0.0  0
 08E  CONST_45  H1   C10  C5   C4    180.00   0.0  0
 08E  CONST_46  H6   C22  C21  C20   180.00   0.0  0
 08E  CONST_47  H10  N16  C15  C1    180.00   0.0  0
 08E  Var_01    C15  C1   C8   C4   -122.56  30.0  2
 08E  Var_02    N6   C12  C20  C21   104.38  30.0  2
 08E  Var_03    C7   N6   C12  C20    90.17  30.0  2
 08E  Var_04    O13  C11  C7   C8     32.72  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
 08E  plan-1  C21  0.020
 08E  plan-1  C25  0.020
 08E  plan-1  C22  0.020
 08E  plan-1  C20  0.020
 08E  plan-1  C24  0.020
 08E  plan-1  N23  0.020
 08E  plan-1  N27  0.020
 08E  plan-1  H6   0.020
 08E  plan-1  C12  0.020
 08E  plan-1  H3   0.020
 08E  plan-1  H5   0.020
 08E  plan-2  C8   0.020
 08E  plan-2  C18  0.020
 08E  plan-2  C17  0.020
 08E  plan-2  C19  0.020
 08E  plan-2  C1   0.020
 08E  plan-2  C15  0.020
 08E  plan-2  N16  0.020
 08E  plan-2  O28  0.020
 08E  plan-2  H7   0.020
 08E  plan-2  H8   0.020
 08E  plan-2  H9   0.020
 08E  plan-2  H10  0.020
 08E  plan-3  C10  0.020
 08E  plan-3  C9   0.020
 08E  plan-3  C2   0.020
 08E  plan-3  C4   0.020
 08E  plan-3  C8   0.020
 08E  plan-3  C5   0.020
 08E  plan-3  C3   0.020
 08E  plan-3  C7   0.020
 08E  plan-3  C1   0.020
 08E  plan-3  C11  0.020
 08E  plan-3  N6   0.020
 08E  plan-3  CL2  0.020
 08E  plan-3  H1   0.020
 08E  plan-3  H2   0.020
 08E  plan-3  H4   0.020
 08E  plan-3  C12  0.020
 08E  plan-4  C24  0.020
 08E  plan-4  N27  0.020
 08E  plan-4  H13  0.020
 08E  plan-4  H14  0.020
 08E  plan-5  C7   0.020
 08E  plan-5  C11  0.020
 08E  plan-5  O13  0.020
 08E  plan-5  O14  0.020

