# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 00:57:08 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: (1~{R})-~{N}-(5-chloranylpyridin-2-yl)-3-oxidanylidene-1,2-dihydroindene-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(NC(=O)[C@@H]2CC(=O)c3ccccc23)nc1
#
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
 5P9  5P9  "N-(5-chloropyridin-2-yl)-3-oxo-2,3-dihydro-1H-indene-1-carboxamide"  ligand  31  20  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5P9
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
 5P9  O1   O   O     0  -0.387   6.9197   1.3638  16.6673
 5P9  C6   C   CR16  0  -0.399  10.7718  -2.1068  22.6967
 5P9  N1   N   NH1   0  -0.726   9.2789  -1.1425  21.0959
 5P9  C7   C   CR16  0  -0.086  11.9191  -2.0194  23.4552
 5P9  N2   N   N     0  -0.415  11.2039   0.0319  21.7336
 5P9  C8   C   CR6   0  -0.125  12.7084  -0.8840  23.3296
 5P9  C9   C   CR16  0  -0.031  12.3116   0.1123  22.4571
 5P9  C1   C   CR5   0   0.355   6.8853   0.7797  17.7247
 5P9  C4   C   C     0   0.575   8.8735  -0.3882  20.0351
 5P9  C5   C   CR6   0   0.530  10.4518  -1.0474  21.8403
 5P9  C3   C   CR15  0  -0.517   7.4745  -0.7334  19.5304
 5P9  C2   C   CH2   0  -0.570   7.4125  -0.6149  18.0026
 5P9  O2   O   O     0  -0.417   9.5089   0.5054  19.5231
 5P9  C10  C   CR56  0   0.144   6.5571   0.3695  20.0047
 5P9  C11  C   CR16  0  -0.296   6.0630   0.5901  21.2807
 5P9  C12  C   CR16  0  -0.234   5.2890   1.7227  21.4988
 5P9  C13  C   CR16  0  -0.256   5.0205   2.6258  20.4688
 5P9  C14  C   CR16  0  -0.272   5.5175   2.4037  19.1949
 5P9  C15  C   CR56  0  -0.026   6.2807   1.2627  18.9794
 5P9  H5   H   HCR6  0   0.293  10.1356  -2.9801  22.7644
 5P9  H4   H   HNH1  0   0.429   8.6735  -1.9081  21.3527
 5P9  H6   H   HCR6  0   0.298  12.1939  -2.8213  24.1274
 5P9  H7   H   HCR6  0   0.284  12.9061   1.0117  22.3423
 5P9  H3   H   HCR5  0   0.309   7.1461  -1.7117  19.8856
 5P9  H2   H   HCH2  0   0.304   6.6765  -1.3254  17.6148
 5P9  H1   H   HCH2  0   0.287   8.3528  -0.8132  17.4905
 5P9  H8   H   HCR6  0   0.264   6.2712  -0.0988  22.0899
 5P9  H9   H   HCR6  0   0.269   4.8874   1.9107  22.4862
 5P9  H10  H   HCR6  0   0.266   4.4160   3.5002  20.6706
 5P9  H11  H   HCR6  0   0.265   5.3097   3.0956  18.3882
 5P9  CL1  CL  CL    0  -0.115  14.1601  -0.7066  24.2442

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
 5P9  O1   C1   double    1.209  0.020  1.209
 5P9  C1   C2   single    1.517  0.020  1.517
 5P9  C1   C15  single    1.474  0.020  1.474
 5P9  C2   C3   single    1.534  0.020  1.534
 5P9  C14  C15  aromatic  1.389  0.020  1.389
 5P9  C14  C13  aromatic  1.385  0.020  1.385
 5P9  C15  C10  aromatic  1.388  0.020  1.388
 5P9  C3   C10  single    1.511  0.020  1.511
 5P9  C3   C4   single    1.527  0.020  1.527
 5P9  C13  C12  aromatic  1.396  0.020  1.396
 5P9  C10  C11  aromatic  1.386  0.020  1.386
 5P9  O2   C4   double    1.210  0.020  1.210
 5P9  C4   N1   single    1.363  0.020  1.363
 5P9  C12  C11  aromatic  1.389  0.020  1.389
 5P9  N1   C5   single    1.392  0.020  1.392
 5P9  N2   C5   aromatic  1.320  0.020  1.320
 5P9  N2   C9   aromatic  1.325  0.020  1.325
 5P9  C5   C6   aromatic  1.399  0.020  1.399
 5P9  C9   C8   aromatic  1.383  0.020  1.383
 5P9  C6   C7   aromatic  1.378  0.020  1.378
 5P9  C8   C7   aromatic  1.388  0.020  1.388
 5P9  C8   CL1  single    1.725  0.020  1.725
 5P9  C6   H5   single    0.930  0.020  1.080
 5P9  N1   H4   single    0.860  0.020  1.020
 5P9  C7   H6   single    0.930  0.020  1.080
 5P9  C9   H7   single    0.930  0.020  1.080
 5P9  C3   H3   single    0.970  0.020  1.090
 5P9  C2   H2   single    0.970  0.020  1.090
 5P9  C2   H1   single    0.970  0.020  1.090
 5P9  C11  H8   single    0.930  0.020  1.080
 5P9  C12  H9   single    0.930  0.020  1.080
 5P9  C13  H10  single    0.930  0.020  1.080
 5P9  C14  H11  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
 5P9  H5   C6   C5   120.97  3.000
 5P9  H5   C6   C7   120.40  3.000
 5P9  C5   C6   C7   118.63  3.000
 5P9  H4   N1   C5   114.90  3.000
 5P9  H4   N1   C4   116.06  3.000
 5P9  C5   N1   C4   128.95  3.000
 5P9  H6   C7   C8   121.19  3.000
 5P9  H6   C7   C6   120.43  3.000
 5P9  C8   C7   C6   118.38  3.000
 5P9  C5   N2   C9   118.80  3.000
 5P9  CL1  C8   C9   120.14  3.000
 5P9  CL1  C8   C7   120.97  3.000
 5P9  C9   C8   C7   118.90  3.000
 5P9  H7   C9   C8   120.48  3.000
 5P9  H7   C9   N2   116.79  3.000
 5P9  C8   C9   N2   122.73  3.000
 5P9  C15  C1   C2   106.73  3.000
 5P9  C15  C1   O1   126.73  3.000
 5P9  C2   C1   O1   126.50  3.000
 5P9  O2   C4   C3   120.55  3.000
 5P9  O2   C4   N1   125.57  3.000
 5P9  C3   C4   N1   113.86  3.000
 5P9  N2   C5   N1   119.52  3.000
 5P9  N2   C5   C6   122.56  3.000
 5P9  N1   C5   C6   117.91  3.000
 5P9  H3   C3   C10  111.68  3.000
 5P9  H3   C3   C2   112.42  3.000
 5P9  C10  C3   C2   103.40  3.000
 5P9  H3   C3   C4   111.77  3.000
 5P9  C10  C3   C4   106.71  3.000
 5P9  C2   C3   C4   110.42  3.000
 5P9  H1   C2   H2   107.22  3.000
 5P9  H1   C2   C3   114.80  3.000
 5P9  H2   C2   C3   109.28  3.000
 5P9  H1   C2   C1   112.43  3.000
 5P9  H2   C2   C1   107.35  3.000
 5P9  C3   C2   C1   105.52  3.000
 5P9  C15  C10  C11  120.45  3.000
 5P9  C11  C10  C3   128.43  3.000
 5P9  C15  C10  C3   111.03  3.000
 5P9  H8   C11  C12  120.56  3.000
 5P9  H8   C11  C10  121.21  3.000
 5P9  C12  C11  C10  118.23  3.000
 5P9  H9   C12  C13  119.30  3.000
 5P9  H9   C12  C11  119.45  3.000
 5P9  C13  C12  C11  121.25  3.000
 5P9  H10  C13  C14  120.10  3.000
 5P9  H10  C13  C12  119.52  3.000
 5P9  C14  C13  C12  120.38  3.000
 5P9  H11  C14  C15  120.97  3.000
 5P9  H11  C14  C13  120.91  3.000
 5P9  C15  C14  C13  118.12  3.000
 5P9  C14  C15  C10  121.56  3.000
 5P9  C10  C15  C1   109.65  3.000
 5P9  C14  C15  C1   128.78  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
 5P9  CONST_01  C9   N2   C5   C6      0.00   0.0  0
 5P9  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 5P9  CONST_03  N2   C5   C6   C7      0.00   0.0  0
 5P9  CONST_04  N2   C9   C8   C7      0.00   0.0  0
 5P9  CONST_05  C5   N2   C9   C8      0.00   0.0  0
 5P9  CONST_06  C5   C6   C7   C8      0.00   0.0  0
 5P9  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 5P9  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 5P9  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 5P9  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 5P9  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 5P9  CONST_12  C15  C10  C11  C12     0.00   0.0  0
 5P9  CONST_13  CL1  C8   C7   C6    180.00   0.0  0
 5P9  CONST_14  C9   N2   C5   N1    180.00   0.0  0
 5P9  CONST_15  C7   C6   C5   N1    180.00   0.0  0
 5P9  CONST_16  CL1  C8   C9   N2    180.00   0.0  0
 5P9  CONST_17  H7   C9   C8   C7    180.00   0.0  0
 5P9  CONST_18  H5   C6   C5   N2    180.00   0.0  0
 5P9  CONST_19  H5   C6   C7   C8    180.00   0.0  0
 5P9  CONST_20  H6   C7   C8   C9    180.00   0.0  0
 5P9  CONST_21  H11  C14  C15  C1      0.00   0.0  0
 5P9  CONST_22  H7   C9   N2   C5    180.00   0.0  0
 5P9  CONST_23  H6   C7   C6   C5    180.00   0.0  0
 5P9  CONST_24  H8   C11  C10  C3      0.00   0.0  0
 5P9  CONST_25  H11  C14  C15  C10   180.00   0.0  0
 5P9  CONST_26  H9   C12  C11  C10   180.00   0.0  0
 5P9  CONST_27  H10  C13  C12  C11   180.00   0.0  0
 5P9  CONST_28  H11  C14  C13  C12   180.00   0.0  0
 5P9  CONST_29  H8   C11  C12  C13   180.00   0.0  0
 5P9  CONST_30  H9   C12  C13  C14   180.00   0.0  0
 5P9  CONST_31  H10  C13  C14  C15   180.00   0.0  0
 5P9  CONST_32  H8   C11  C10  C15   180.00   0.0  0
 5P9  CONST_33  C3   C4   N1   C5    180.00   0.0  0
 5P9  CONST_34  C4   N1   C5   C6    180.00   0.0  0
 5P9  CONST_35  C4   N1   C5   N2      0.00   0.0  0
 5P9  CONST_36  H4   N1   C5   C6      0.00   0.0  0
 5P9  CONST_37  H4   N1   C5   N2    180.00   0.0  0
 5P9  CONST_38  O2   C4   N1   C5      0.00   0.0  0
 5P9  CONST_39  H4   N1   C4   C3      0.00   0.0  0
 5P9  CONST_40  H4   N1   C4   O2    180.00   0.0  0
 5P9  Var_01    C15  C1   C2   C3    -16.86  30.0  1
 5P9  Var_02    C14  C15  C1   C2   -170.96  30.0  1
 5P9  Var_03    C10  C15  C1   C2      7.87  30.0  1
 5P9  Var_04    C3   C2   C1   O1    165.15  30.0  1
 5P9  Var_05    C14  C15  C1   O1      7.03  30.0  1
 5P9  Var_06    C10  C15  C1   O1   -174.14  30.0  1
 5P9  Var_07    H2   C2   C1   C15    99.61  30.0  1
 5P9  Var_08    H1   C2   C1   C15  -142.71  30.0  1
 5P9  Var_09    H2   C2   C1   O1    -78.38  30.0  1
 5P9  Var_10    H1   C2   C1   O1     39.29  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 5P9  chir_01  C3  C2  C10  C4  positiv

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
 5P9  plan-1  C6   0.020
 5P9  plan-1  N1   0.020
 5P9  plan-1  C7   0.020
 5P9  plan-1  N2   0.020
 5P9  plan-1  C8   0.020
 5P9  plan-1  C9   0.020
 5P9  plan-1  C5   0.020
 5P9  plan-1  H5   0.020
 5P9  plan-1  H6   0.020
 5P9  plan-1  H7   0.020
 5P9  plan-1  CL1  0.020
 5P9  plan-2  C1   0.020
 5P9  plan-2  C3   0.020
 5P9  plan-2  C10  0.020
 5P9  plan-2  C11  0.020
 5P9  plan-2  C12  0.020
 5P9  plan-2  C13  0.020
 5P9  plan-2  C14  0.020
 5P9  plan-2  C15  0.020
 5P9  plan-2  H8   0.020
 5P9  plan-2  H9   0.020
 5P9  plan-2  H10  0.020
 5P9  plan-2  H11  0.020
 5P9  plan-3  N1   0.020
 5P9  plan-3  C4   0.020
 5P9  plan-3  C5   0.020
 5P9  plan-3  C3   0.020
 5P9  plan-3  O2   0.020
 5P9  plan-3  H4   0.020
 5P9  plan-4  O1   0.020
 5P9  plan-4  C1   0.020
 5P9  plan-4  C2   0.020
 5P9  plan-4  C15  0.020

