# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:11:41 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 5-[[5-chloranyl-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-yl]amino]-1,3-dihydroindol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)n(n1)c2ncc(Cl)c(Nc3ccc4NC(=O)Cc4c3)n2
#
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
 TJ3  TJ3  5-[[5-chloranyl-2-(3,5-dimethylpyrazol-1-yl)pyrimidin-4-yl]amino]-1,3-dihydroindol-2-one  ligand  40  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TJ3
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
 TJ3  C4   C   CR6   0  -0.241  -1.7838   2.4986  -0.2007
 TJ3  C5   C   CR6   0   0.651  -0.8493   1.4379  -0.1160
 TJ3  C7   C   CR6   0   0.633  -2.5988  -0.0073  -0.0568
 TJ3  C10  C   CR15  0  -0.574  -4.1113  -3.2177   0.0893
 TJ3  N12  N   NR15  0  -0.741   5.1207  -1.3203   0.1078
 TJ3  C13  C   CR6   0   0.366   1.5615   0.7982  -0.0405
 TJ3  C15  C   CR16  0  -0.299   2.6158  -1.3743   0.1664
 TJ3  C17  C   CR56  0   0.021   3.9558   0.6190  -0.0714
 TJ3  C20  C   CH2   0  -0.621   5.4078   0.9684  -0.1406
 TJ3  C24  C   CR5   0   0.430  -4.2737  -1.8682  -0.0524
 TJ3  N2   N   N     0  -0.465  -3.5423   0.9072  -0.1324
 TJ3  C18  C   CR56  0   0.405   3.8473  -0.7630   0.0755
 TJ3  N8   N   NR5   0  -0.451  -3.0071  -1.3403   0.0272
 TJ3  C16  C   CR16  0  -0.441   2.8275   1.3993  -0.1293
 TJ3  N22  N   N     0  -0.290  -2.0718  -2.2944   0.2101
 TJ3  C9   C   CR5   0   0.309  -2.7214  -3.4296   0.2510
 TJ3  C19  C   CR5   0   0.513   6.1000  -0.3812  -0.0084
 TJ3  C14  C   CR16  0  -0.337   1.4667  -0.5867   0.1087
 TJ3  N6   N   N     0  -0.491  -1.2965   0.1937  -0.0495
 TJ3  CL1  CL  CL    0  -0.100  -1.2760   4.1425  -0.2916
 TJ3  O21  O   O     0  -0.460   7.2941  -0.5968  -0.0066
 TJ3  N11  N   NH1   0  -0.775   0.4732   1.6809  -0.1053
 TJ3  C3   C   CR16  0   0.025  -3.1127   2.1669  -0.2084
 TJ3  C23  C   CH3   0  -0.733  -2.0131  -4.7230   0.4490
 TJ3  H1   H   HCR5  0   0.267  -4.8931  -3.9599   0.0767
 TJ3  H3   H   HCR6  0   0.267   2.5236  -2.4464   0.2800
 TJ3  H4   H   HCH2  0   0.305   5.6941   1.4400  -1.0836
 TJ3  H5   H   HCH2  0   0.304   5.7326   1.6359   0.6610
 TJ3  H6   H   HCR6  0   0.272   2.9147   2.4742  -0.2415
 TJ3  H10  H   HCR6  0   0.322   0.5031  -1.0660   0.1794
 TJ3  H11  H   HNH1  0   0.415   0.7358   2.6528  -0.1770
 TJ3  H12  H   HCR6  0   0.297  -3.8677   2.9415  -0.2742
 TJ3  H13  H   HCH3  0   0.250  -2.1992  -5.4030  -0.3831
 TJ3  H14  H   HCH3  0   0.248  -0.9386  -4.5694   0.5307
 TJ3  H15  H   HCH3  0   0.250  -2.3573  -5.2232   1.3551
 TJ3  C25  C   CH3   0  -0.708  -5.5440  -1.1257  -0.2639
 TJ3  H2   H   HNR5  0   0.412   5.3102  -2.3068   0.2021
 TJ3  H7   H   HCH3  0   0.256  -5.7473  -0.4201   0.5393
 TJ3  H8   H   HCH3  0   0.255  -5.5383  -0.5603  -1.1946
 TJ3  H9   H   HCH3  0   0.251  -6.3586  -1.8463  -0.3050

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
 TJ3  O21  C19  double    1.213  0.020  1.213
 TJ3  N12  C19  single    1.362  0.020  1.362
 TJ3  N12  C18  single    1.390  0.020  1.390
 TJ3  C19  C20  single    1.522  0.020  1.522
 TJ3  C18  C15  aromatic  1.378  0.020  1.378
 TJ3  C18  C17  aromatic  1.394  0.020  1.394
 TJ3  C15  C14  aromatic  1.394  0.020  1.394
 TJ3  C20  C17  single    1.495  0.020  1.495
 TJ3  C17  C16  aromatic  1.373  0.020  1.373
 TJ3  C25  C24  single    1.487  0.020  1.487
 TJ3  C14  C13  aromatic  1.396  0.020  1.396
 TJ3  C10  C24  aromatic  1.367  0.020  1.367
 TJ3  C10  C9   aromatic  1.415  0.020  1.415
 TJ3  C16  C13  aromatic  1.404  0.020  1.404
 TJ3  C24  N8   aromatic  1.375  0.020  1.375
 TJ3  C13  N11  single    1.403  0.020  1.403
 TJ3  C9   C23  single    1.488  0.020  1.488
 TJ3  C9   N22  aromatic  1.309  0.020  1.309
 TJ3  N11  C5   single    1.345  0.020  1.345
 TJ3  N6   C5   aromatic  1.324  0.020  1.324
 TJ3  N6   C7   aromatic  1.318  0.020  1.318
 TJ3  N8   C7   single    1.397  0.020  1.397
 TJ3  N8   N22  aromatic  1.349  0.020  1.349
 TJ3  C5   C4   aromatic  1.416  0.020  1.416
 TJ3  C7   N2   aromatic  1.316  0.020  1.316
 TJ3  N2   C3   aromatic  1.333  0.020  1.333
 TJ3  C4   C3   aromatic  1.370  0.020  1.370
 TJ3  C4   CL1  single    1.723  0.020  1.723
 TJ3  C10  H1   single    0.930  0.020  1.080
 TJ3  N12  H2   single    0.860  0.020  1.020
 TJ3  C15  H3   single    0.930  0.020  1.080
 TJ3  C20  H4   single    0.970  0.020  1.090
 TJ3  C20  H5   single    0.970  0.020  1.090
 TJ3  C16  H6   single    0.930  0.020  1.080
 TJ3  C25  H7   single    0.970  0.020  1.090
 TJ3  C25  H8   single    0.970  0.020  1.090
 TJ3  C25  H9   single    0.970  0.020  1.090
 TJ3  C14  H10  single    0.930  0.020  1.080
 TJ3  N11  H11  single    0.860  0.020  1.020
 TJ3  C3   H12  single    0.930  0.020  1.080
 TJ3  C23  H13  single    0.970  0.020  1.090
 TJ3  C23  H14  single    0.970  0.020  1.090
 TJ3  C23  H15  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
 TJ3  C3   C4   CL1  121.12  3.000
 TJ3  CL1  C4   C5   121.55  3.000
 TJ3  C3   C4   C5   117.33  3.000
 TJ3  N11  C5   N6   120.11  3.000
 TJ3  N6   C5   C4   118.94  3.000
 TJ3  N11  C5   C4   120.94  3.000
 TJ3  N6   C7   N8   115.74  3.000
 TJ3  N8   C7   N2   117.20  3.000
 TJ3  N6   C7   N2   127.06  3.000
 TJ3  H1   C10  C9   127.62  3.000
 TJ3  H1   C10  C24  126.33  3.000
 TJ3  C9   C10  C24  106.05  3.000
 TJ3  H2   N12  C19  123.17  3.000
 TJ3  H2   N12  C18  124.48  3.000
 TJ3  C19  N12  C18  112.35  3.000
 TJ3  N11  C13  C14  125.20  3.000
 TJ3  N11  C13  C16  115.29  3.000
 TJ3  C14  C13  C16  119.51  3.000
 TJ3  H3   C15  C14  119.59  3.000
 TJ3  H3   C15  C18  121.51  3.000
 TJ3  C14  C15  C18  118.90  3.000
 TJ3  C16  C17  C18  120.26  3.000
 TJ3  C16  C17  C20  131.56  3.000
 TJ3  C18  C17  C20  108.19  3.000
 TJ3  H5   C20  H4   106.95  3.000
 TJ3  H5   C20  C19  110.05  3.000
 TJ3  H4   C20  C19  109.78  3.000
 TJ3  H5   C20  C17  113.43  3.000
 TJ3  H4   C20  C17  113.29  3.000
 TJ3  C19  C20  C17  103.32  3.000
 TJ3  C25  C24  N8   127.15  3.000
 TJ3  N8   C24  C10  105.29  3.000
 TJ3  C25  C24  C10  127.56  3.000
 TJ3  C3   N2   C7   115.40  3.000
 TJ3  C17  C18  C15  121.09  3.000
 TJ3  C17  C18  N12  109.18  3.000
 TJ3  C15  C18  N12  129.73  3.000
 TJ3  N22  N8   C24  112.04  3.000
 TJ3  N22  N8   C7   118.73  3.000
 TJ3  C24  N8   C7   129.23  3.000
 TJ3  H6   C16  C17  120.11  3.000
 TJ3  H6   C16  C13  120.23  3.000
 TJ3  C17  C16  C13  119.66  3.000
 TJ3  C9   N22  N8   105.89  3.000
 TJ3  C23  C9   N22  121.46  3.000
 TJ3  N22  C9   C10  110.74  3.000
 TJ3  C23  C9   C10  127.80  3.000
 TJ3  O21  C19  C20  127.23  3.000
 TJ3  C20  C19  N12  106.96  3.000
 TJ3  O21  C19  N12  125.81  3.000
 TJ3  H10  C14  C15  118.85  3.000
 TJ3  H10  C14  C13  120.57  3.000
 TJ3  C15  C14  C13  120.58  3.000
 TJ3  C7   N6   C5   118.49  3.000
 TJ3  H11  N11  C13  114.04  3.000
 TJ3  H11  N11  C5   115.42  3.000
 TJ3  C13  N11  C5   130.52  3.000
 TJ3  H12  C3   N2   117.03  3.000
 TJ3  H12  C3   C4   120.21  3.000
 TJ3  N2   C3   C4   122.76  3.000
 TJ3  H15  C23  H14  108.30  3.000
 TJ3  H15  C23  H13  107.10  3.000
 TJ3  H14  C23  H13  108.29  3.000
 TJ3  H15  C23  C9   111.03  3.000
 TJ3  H14  C23  C9   110.93  3.000
 TJ3  H13  C23  C9   111.05  3.000
 TJ3  H9   C25  H8   108.39  3.000
 TJ3  H9   C25  H7   108.51  3.000
 TJ3  H8   C25  H7   107.17  3.000
 TJ3  H9   C25  C24  108.31  3.000
 TJ3  H8   C25  C24  112.11  3.000
 TJ3  H7   C25  C24  112.24  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
 TJ3  CONST_01  C7   N6   C5   C4      0.00   0.0  0
 TJ3  CONST_02  C7   N2   C3   C4      0.00   0.0  0
 TJ3  CONST_03  N8   C7   N6   C5    180.00   0.0  0
 TJ3  CONST_04  N2   C7   N6   C5      0.00   0.0  0
 TJ3  CONST_05  N2   C3   C4   C5      0.00   0.0  0
 TJ3  CONST_06  C10  C24  N8   C7    180.00   0.0  0
 TJ3  CONST_07  C9   N22  N8   C7    180.00   0.0  0
 TJ3  CONST_08  N22  N8   C24  C10     0.00   0.0  0
 TJ3  CONST_09  N8   N22  C9   C10     0.00   0.0  0
 TJ3  CONST_10  C18  C15  C14  C13     0.00   0.0  0
 TJ3  CONST_11  C18  C17  C16  C13     0.00   0.0  0
 TJ3  CONST_12  C16  C17  C18  C15     0.00   0.0  0
 TJ3  CONST_13  C16  C13  C14  C15     0.00   0.0  0
 TJ3  CONST_14  C14  C15  C18  C17     0.00   0.0  0
 TJ3  CONST_15  C14  C13  C16  C17     0.00   0.0  0
 TJ3  CONST_16  N22  C9   C10  C24     0.00   0.0  0
 TJ3  CONST_17  N6   C7   N8   C24   180.00   0.0  0
 TJ3  CONST_18  N2   C7   N8   C24     0.00   0.0  0
 TJ3  CONST_19  C9   N22  N8   C24     0.00   0.0  0
 TJ3  CONST_20  N22  N8   C7   N2    180.00   0.0  0
 TJ3  CONST_21  C9   C10  C24  N8      0.00   0.0  0
 TJ3  CONST_22  C3   N2   C7   N8    180.00   0.0  0
 TJ3  CONST_23  N6   C7   N8   N22     0.00   0.0  0
 TJ3  CONST_24  C3   C4   C5   N6      0.00   0.0  0
 TJ3  CONST_25  C3   N2   C7   N6      0.00   0.0  0
 TJ3  CONST_26  C18  N12  C19  C20     0.00   0.0  0
 TJ3  CONST_27  N11  C5   N6   C7    180.00   0.0  0
 TJ3  CONST_28  C25  C24  N8   C7      0.00   0.0  0
 TJ3  CONST_29  N11  C13  C14  C15   180.00   0.0  0
 TJ3  CONST_30  N11  C13  C16  C17   180.00   0.0  0
 TJ3  CONST_31  C23  C9   C10  C24   180.00   0.0  0
 TJ3  CONST_32  CL1  C4   C3   N2    180.00   0.0  0
 TJ3  CONST_33  C23  C9   N22  N8    180.00   0.0  0
 TJ3  CONST_34  C25  C24  N8   N22   180.00   0.0  0
 TJ3  CONST_35  C9   C10  C24  C25   180.00   0.0  0
 TJ3  CONST_36  CL1  C4   C5   N6    180.00   0.0  0
 TJ3  CONST_37  C3   C4   C5   N11   180.00   0.0  0
 TJ3  CONST_38  O21  C19  N12  C18   180.00   0.0  0
 TJ3  CONST_39  H12  C3   C4   C5    180.00   0.0  0
 TJ3  CONST_40  H3   C15  C18  N12     0.00   0.0  0
 TJ3  CONST_41  H6   C16  C17  C20     0.00   0.0  0
 TJ3  CONST_42  H10  C14  C15  C18   180.00   0.0  0
 TJ3  CONST_43  H1   C10  C24  N8    180.00   0.0  0
 TJ3  CONST_44  H2   N12  C19  C20   180.00   0.0  0
 TJ3  Var_01    C13  N11  C5   C4   -179.37  30.0  2
 TJ3  Var_02    C14  C13  N11  C5     -3.97  30.0  2
 TJ3  Var_03    H4   C20  C19  N12  -120.81  30.0  1
 TJ3  Var_04    H7   C25  C24  C10   118.95  30.0  2
 TJ3  Var_05    H13  C23  C9   C10    58.84  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
 TJ3  plan-1  C7   0.020
 TJ3  plan-1  C10  0.020
 TJ3  plan-1  C24  0.020
 TJ3  plan-1  N8   0.020
 TJ3  plan-1  N22  0.020
 TJ3  plan-1  C9   0.020
 TJ3  plan-1  C23  0.020
 TJ3  plan-1  H1   0.020
 TJ3  plan-1  C25  0.020
 TJ3  plan-2  C4   0.020
 TJ3  plan-2  C5   0.020
 TJ3  plan-2  C7   0.020
 TJ3  plan-2  N2   0.020
 TJ3  plan-2  N8   0.020
 TJ3  plan-2  N6   0.020
 TJ3  plan-2  CL1  0.020
 TJ3  plan-2  N11  0.020
 TJ3  plan-2  C3   0.020
 TJ3  plan-2  H12  0.020
 TJ3  plan-3  N12  0.020
 TJ3  plan-3  C13  0.020
 TJ3  plan-3  C15  0.020
 TJ3  plan-3  C17  0.020
 TJ3  plan-3  C20  0.020
 TJ3  plan-3  C18  0.020
 TJ3  plan-3  C16  0.020
 TJ3  plan-3  C19  0.020
 TJ3  plan-3  C14  0.020
 TJ3  plan-3  O21  0.020
 TJ3  plan-3  N11  0.020
 TJ3  plan-3  H3   0.020
 TJ3  plan-3  H6   0.020
 TJ3  plan-3  H10  0.020
 TJ3  plan-3  H2   0.020

