# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 12:58:05 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-[[4-(pyridin-3-ylmethylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino]-1,3-dihydroindol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cnc(Nc2ccc3NC(=O)Cc3c2)nc1NCc4cccnc4
#
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
 PVT  PVT  5-[[4-(pyridin-3-ylmethylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino]-1,3-dihydroindol-2-one  ligand  44  29  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PVT
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
 PVT  C1   C  CR6   0   0.003  27.9037  -10.5377  14.6701
 PVT  C2   C  CR16  0  -0.180  27.9460   -9.5484  13.6980
 PVT  C3   C  CR16  0  -0.315  28.5739   -9.8154  12.4909
 PVT  C7   C  CH2   0  -0.340  27.2516  -10.3416  16.0160
 PVT  C9   C  CR6   0   0.595  23.5704  -10.5740  14.3539
 PVT  C11  C  CR16  0  -0.034  22.9613   -8.4739  14.8768
 PVT  C12  C  CR6   0  -0.443  24.1907   -8.2186  15.4572
 PVT  C13  C  CR6   0   0.600  25.0992   -9.3108  15.4767
 PVT  C19  C  CR16  0  -0.308  26.0425  -14.0530  13.0400
 PVT  C20  C  CR16  0  -0.295  25.3399  -12.8754  13.2775
 PVT  C21  C  CR6   0   0.348  23.9738  -12.8965  13.5516
 PVT  C22  C  CR16  0  -0.400  23.2892  -14.1186  13.5684
 PVT  C24  C  CR56  0   0.015  23.9787  -15.2815  13.3155
 PVT  N29  N  NH1   0  -0.757  23.2192  -11.7331  13.7529
 PVT  C4   C  CR16  0  -0.076  29.1430  -11.0643  12.2983
 PVT  N5   N  N     0  -0.398  29.1158  -12.0197  13.2210
 PVT  C6   C  CR16  0  -0.094  28.5096  -11.7537  14.3700
 PVT  N8   N  NH1   0  -0.682  26.3087   -9.2525  16.0557
 PVT  N10  N  N     0  -0.486  22.6216   -9.6277  14.3345
 PVT  N14  N  N     0  -0.507  24.7701  -10.4641  14.9052
 PVT  C23  C  CR56  0   0.406  25.3479  -15.2454  13.0604
 PVT  C25  C  CH2   0  -0.622  23.5319  -16.7072  13.2627
 PVT  C26  C  CR5   0   0.510  24.8137  -17.4670  12.9475
 PVT  N27  N  NR15  0  -0.741  25.8085  -16.5402  12.8499
 PVT  H1   H  HCR6  0   0.263  27.4897   -8.5814  13.8714
 PVT  H2   H  HCR6  0   0.269  28.6194   -9.0691  11.7094
 PVT  H3   H  HCH2  0   0.266  26.7712  -11.2709  16.3264
 PVT  H4   H  HCH2  0   0.286  28.0154  -10.1203  16.7624
 PVT  H5   H  HCR6  0   0.279  22.2023   -7.7006  14.8424
 PVT  H6   H  HCR6  0   0.264  27.1041  -14.0169  12.8330
 PVT  H7   H  HCR6  0   0.275  25.8721  -11.9369  13.2458
 PVT  H8   H  HCR6  0   0.266  22.2259  -14.1422  13.7786
 PVT  H9   H  HNH1  0   0.407  22.2538  -11.7663  13.4609
 PVT  H10  H  HCR6  0   0.262  29.6370  -11.3042  11.3634
 PVT  H11  H  HCR6  0   0.258  28.4895  -12.5581  15.1001
 PVT  H12  H  HNH1  0   0.410  26.6047   -8.4199  16.5328
 PVT  H13  H  HCH2  0   0.302  22.7855  -16.8986  12.4877
 PVT  H14  H  HCH2  0   0.301  23.1085  -17.0641  14.2049
 PVT  H15  H  HNR5  0   0.409  26.7673  -16.7774  12.6432
 PVT  C15  C  CT    0   1.072  24.5336   -6.8729  15.9722
 PVT  O28  O  O     0  -0.449  24.9425  -18.6641  12.8067
 PVT  F16  F  F     0  -0.300  23.5176   -6.0135  15.8649
 PVT  F17  F  F     0  -0.323  24.8933   -6.8878  17.2700
 PVT  F18  F  F     0  -0.319  25.5746   -6.3233  15.3167

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
 PVT  C4   C3   aromatic  1.386  0.020  1.386
 PVT  C4   N5   aromatic  1.328  0.020  1.328
 PVT  C3   C2   aromatic  1.387  0.020  1.387
 PVT  N5   C6   aromatic  1.326  0.020  1.326
 PVT  O28  C26  double    1.212  0.020  1.212
 PVT  N27  C26  single    1.363  0.020  1.363
 PVT  N27  C23  single    1.390  0.020  1.390
 PVT  C26  C25  single    1.523  0.020  1.523
 PVT  C23  C19  aromatic  1.380  0.020  1.380
 PVT  C23  C24  aromatic  1.393  0.020  1.393
 PVT  C25  C24  single    1.495  0.020  1.495
 PVT  C19  C20  aromatic  1.392  0.020  1.392
 PVT  C24  C22  aromatic  1.375  0.020  1.375
 PVT  C20  C21  aromatic  1.394  0.020  1.394
 PVT  C22  C21  aromatic  1.401  0.020  1.401
 PVT  C21  N29  single    1.401  0.020  1.401
 PVT  C2   C1   aromatic  1.388  0.020  1.388
 PVT  N29  C9   single    1.352  0.020  1.352
 PVT  C6   C1   aromatic  1.391  0.020  1.391
 PVT  C9   N10  aromatic  1.340  0.020  1.340
 PVT  C9   N14  aromatic  1.325  0.020  1.325
 PVT  N10  C11  aromatic  1.319  0.020  1.319
 PVT  C1   C7   single    1.508  0.020  1.508
 PVT  N14  C13  aromatic  1.329  0.020  1.329
 PVT  C11  C12  aromatic  1.383  0.020  1.383
 PVT  C13  C12  aromatic  1.421  0.020  1.421
 PVT  C13  N8   single    1.342  0.020  1.342
 PVT  C12  C15  single    1.481  0.020  1.481
 PVT  F18  C15  single    1.347  0.020  1.347
 PVT  C7   N8   single    1.441  0.020  1.441
 PVT  F16  C15  single    1.335  0.020  1.335
 PVT  C15  F17  single    1.347  0.020  1.347
 PVT  C2   H1   single    0.930  0.020  1.080
 PVT  C3   H2   single    0.930  0.020  1.080
 PVT  C7   H3   single    0.970  0.020  1.090
 PVT  C7   H4   single    0.970  0.020  1.090
 PVT  C11  H5   single    0.930  0.020  1.080
 PVT  C19  H6   single    0.930  0.020  1.080
 PVT  C20  H7   single    0.930  0.020  1.080
 PVT  C22  H8   single    0.930  0.020  1.080
 PVT  N29  H9   single    0.860  0.020  1.020
 PVT  C4   H10  single    0.930  0.020  1.080
 PVT  C6   H11  single    0.930  0.020  1.080
 PVT  N8   H12  single    0.860  0.020  1.020
 PVT  C25  H13  single    0.970  0.020  1.090
 PVT  C25  H14  single    0.970  0.020  1.090
 PVT  N27  H15  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
 PVT  C6   C1   C7   119.62  3.000
 PVT  C7   C1   C2   123.06  3.000
 PVT  C6   C1   C2   117.31  3.000
 PVT  H1   C2   C3   120.13  3.000
 PVT  H1   C2   C1   120.76  3.000
 PVT  C3   C2   C1   119.10  3.000
 PVT  H2   C3   C4   120.28  3.000
 PVT  H2   C3   C2   121.01  3.000
 PVT  C4   C3   C2   118.71  3.000
 PVT  H4   C7   H3   106.64  3.000
 PVT  H4   C7   N8   106.62  3.000
 PVT  H3   C7   N8   110.34  3.000
 PVT  H4   C7   C1   109.53  3.000
 PVT  H3   C7   C1   109.48  3.000
 PVT  N8   C7   C1   113.93  3.000
 PVT  N14  C9   N10  126.05  3.000
 PVT  N14  C9   N29  119.42  3.000
 PVT  N10  C9   N29  114.52  3.000
 PVT  H5   C11  N10  115.49  3.000
 PVT  H5   C11  C12  120.27  3.000
 PVT  N10  C11  C12  124.24  3.000
 PVT  C15  C12  C13  123.06  3.000
 PVT  C15  C12  C11  121.29  3.000
 PVT  C13  C12  C11  115.61  3.000
 PVT  N14  C13  N8   116.52  3.000
 PVT  N8   C13  C12  123.29  3.000
 PVT  N14  C13  C12  120.19  3.000
 PVT  H6   C19  C23  121.70  3.000
 PVT  H6   C19  C20  119.97  3.000
 PVT  C23  C19  C20  118.33  3.000
 PVT  H7   C20  C21  120.16  3.000
 PVT  H7   C20  C19  118.80  3.000
 PVT  C21  C20  C19  121.04  3.000
 PVT  N29  C21  C22  117.35  3.000
 PVT  N29  C21  C20  122.93  3.000
 PVT  C22  C21  C20  119.65  3.000
 PVT  H8   C22  C24  120.59  3.000
 PVT  H8   C22  C21  120.04  3.000
 PVT  C24  C22  C21  119.37  3.000
 PVT  C25  C24  C23  108.18  3.000
 PVT  C25  C24  C22  131.53  3.000
 PVT  C23  C24  C22  120.29  3.000
 PVT  H9   N29  C21  116.50  3.000
 PVT  H9   N29  C9   113.91  3.000
 PVT  C21  N29  C9   129.48  3.000
 PVT  H10  C4   N5   116.68  3.000
 PVT  H10  C4   C3   120.42  3.000
 PVT  N5   C4   C3   122.90  3.000
 PVT  C6   N5   C4   117.84  3.000
 PVT  H11  C6   N5   116.24  3.000
 PVT  H11  C6   C1   119.61  3.000
 PVT  N5   C6   C1   124.14  3.000
 PVT  H12  N8   C13  120.43  3.000
 PVT  H12  N8   C7   116.54  3.000
 PVT  C13  N8   C7   123.02  3.000
 PVT  C11  N10  C9   115.42  3.000
 PVT  C13  N14  C9   118.38  3.000
 PVT  N27  C23  C24  109.22  3.000
 PVT  C24  C23  C19  121.31  3.000
 PVT  N27  C23  C19  129.47  3.000
 PVT  H14  C25  H13  106.83  3.000
 PVT  H14  C25  C26  109.97  3.000
 PVT  H13  C25  C26  109.91  3.000
 PVT  H14  C25  C24  113.38  3.000
 PVT  H13  C25  C24  113.34  3.000
 PVT  C26  C25  C24  103.39  3.000
 PVT  N27  C26  C25  106.85  3.000
 PVT  C25  C26  O28  127.31  3.000
 PVT  N27  C26  O28  125.84  3.000
 PVT  H15  N27  C26  123.25  3.000
 PVT  H15  N27  C23  124.38  3.000
 PVT  C26  N27  C23  112.37  3.000
 PVT  F18  C15  F17  105.48  3.000
 PVT  F17  C15  F16  106.73  3.000
 PVT  F18  C15  F16  106.63  3.000
 PVT  F17  C15  C12  112.76  3.000
 PVT  F16  C15  C12  112.38  3.000
 PVT  F18  C15  C12  112.35  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
 PVT  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 PVT  CONST_02  C4   N5   C6   C1      0.00   0.0  0
 PVT  CONST_03  N5   C4   C3   C2      0.00   0.0  0
 PVT  CONST_04  N5   C6   C1   C2      0.00   0.0  0
 PVT  CONST_05  C6   N5   C4   C3      0.00   0.0  0
 PVT  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 PVT  CONST_07  C12  C11  N10  C9      0.00   0.0  0
 PVT  CONST_08  C12  C13  N14  C9      0.00   0.0  0
 PVT  CONST_09  N14  C9   N10  C11     0.00   0.0  0
 PVT  CONST_10  N14  C13  C12  C11     0.00   0.0  0
 PVT  CONST_11  N10  C9   N14  C13     0.00   0.0  0
 PVT  CONST_12  N10  C11  C12  C13     0.00   0.0  0
 PVT  CONST_13  C22  C24  C23  C19     0.00   0.0  0
 PVT  CONST_14  C22  C21  C20  C19     0.00   0.0  0
 PVT  CONST_15  C24  C23  C19  C20     0.00   0.0  0
 PVT  CONST_16  C24  C22  C21  C20     0.00   0.0  0
 PVT  CONST_17  C23  C19  C20  C21     0.00   0.0  0
 PVT  CONST_18  C23  C24  C22  C21     0.00   0.0  0
 PVT  CONST_19  C25  C26  N27  C23     0.00   0.0  0
 PVT  CONST_20  C7   C1   C2   C3    180.00   0.0  0
 PVT  CONST_21  N5   C6   C1   C7    180.00   0.0  0
 PVT  CONST_22  N8   C13  N14  C9    180.00   0.0  0
 PVT  CONST_23  N29  C9   N10  C11   180.00   0.0  0
 PVT  CONST_24  N8   C13  C12  C11   180.00   0.0  0
 PVT  CONST_25  N29  C9   N14  C13   180.00   0.0  0
 PVT  CONST_26  N10  C11  C12  C15   180.00   0.0  0
 PVT  CONST_27  N14  C13  C12  C15   180.00   0.0  0
 PVT  CONST_28  N29  C21  C20  C19   180.00   0.0  0
 PVT  CONST_29  N29  C21  C22  C24   180.00   0.0  0
 PVT  CONST_30  C23  N27  C26  O28   180.00   0.0  0
 PVT  CONST_31  H2   C3   C2   C1    180.00   0.0  0
 PVT  CONST_32  H10  C4   C3   C2    180.00   0.0  0
 PVT  CONST_33  H11  C6   C1   C2    180.00   0.0  0
 PVT  CONST_34  H5   C11  N10  C9    180.00   0.0  0
 PVT  CONST_35  H8   C22  C21  C20   180.00   0.0  0
 PVT  CONST_36  H6   C19  C20  C21   180.00   0.0  0
 PVT  CONST_37  H7   C20  C21  C22   180.00   0.0  0
 PVT  CONST_38  H1   C2   C3   C4    180.00   0.0  0
 PVT  CONST_39  H15  N27  C26  C25   180.00   0.0  0
 PVT  CONST_40  N14  C13  N8   C7      0.00   0.0  0
 PVT  CONST_41  C12  C13  N8   C7    180.00   0.0  0
 PVT  CONST_42  H12  N8   C13  C12     0.00   0.0  0
 PVT  Var_01    C20  C21  N29  C9    -35.74  30.0  1
 PVT  Var_02    N10  C9   N29  C21   177.46  30.0  2
 PVT  Var_03    H13  C25  C24  C22    61.64  30.0  1
 PVT  Var_04    C13  N8   C7   C1     73.16  30.0  3
 PVT  Var_05    N8   C7   C1   C2     19.76  30.0  2
 PVT  Var_06    F18  C15  C12  C11  -117.12  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
 PVT  plan-1  C9   0.020
 PVT  plan-1  C11  0.020
 PVT  plan-1  C12  0.020
 PVT  plan-1  C13  0.020
 PVT  plan-1  N29  0.020
 PVT  plan-1  N8   0.020
 PVT  plan-1  N10  0.020
 PVT  plan-1  N14  0.020
 PVT  plan-1  H5   0.020
 PVT  plan-1  C15  0.020
 PVT  plan-2  C1   0.020
 PVT  plan-2  C2   0.020
 PVT  plan-2  C3   0.020
 PVT  plan-2  C7   0.020
 PVT  plan-2  C4   0.020
 PVT  plan-2  N5   0.020
 PVT  plan-2  C6   0.020
 PVT  plan-2  H1   0.020
 PVT  plan-2  H2   0.020
 PVT  plan-2  H10  0.020
 PVT  plan-2  H11  0.020
 PVT  plan-3  C7   0.020
 PVT  plan-3  C13  0.020
 PVT  plan-3  N8   0.020
 PVT  plan-3  H12  0.020
 PVT  plan-4  C19  0.020
 PVT  plan-4  C20  0.020
 PVT  plan-4  C21  0.020
 PVT  plan-4  C22  0.020
 PVT  plan-4  C24  0.020
 PVT  plan-4  N29  0.020
 PVT  plan-4  C23  0.020
 PVT  plan-4  C25  0.020
 PVT  plan-4  C26  0.020
 PVT  plan-4  N27  0.020
 PVT  plan-4  H6   0.020
 PVT  plan-4  H7   0.020
 PVT  plan-4  H8   0.020
 PVT  plan-4  H15  0.020
 PVT  plan-4  O28  0.020

