# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 20:25:42 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N-[(1S,2S)-2-amino-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1Cc2ccccc2[C@@H]1NC(=O)C(=O)Nc3ccc(Cl)c(F)c3
#
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
 0LL  0LL  N-[(1S,2S)-2-amino-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide  ligand  39  24  .  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_0LL
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
 0LL  C13  C   C     0   0.445  -0.3292  -0.5533   0.1286
 0LL  C15  C   CR6   0   0.413  -2.6792  -0.2049  -0.5462
 0LL  C20  C   CR6   0  -0.256  -5.4078   0.3194  -0.2902
 0LL  C21  C   CR6   0   0.653  -4.5969   0.1760   0.8209
 0LL  C22  C   CR16  0  -0.488  -3.2453  -0.0836   0.7218
 0LL  C01  C   CR16  0  -0.262   4.7155   2.2198  -1.4932
 0LL  C02  C   CR16  0  -0.317   4.0135   1.0181  -1.4931
 0LL  C03  C   CR56  0   0.156   4.0965   0.2011  -0.3780
 0LL  C04  C   CR56  0   0.099   4.8618   0.5639   0.7250
 0LL  C05  C   CR16  0  -0.328   5.5574   1.7626   0.7271
 0LL  C06  C   CR16  0  -0.254   5.4794   2.5883  -0.3906
 0LL  C07  C   CR15  0  -0.179   3.4095  -1.1182  -0.1187
 0LL  C08  C   CR15  0  -0.137   4.2369  -1.7147   1.0395
 0LL  C09  C   CH2   0  -0.496   4.7720  -0.4867   1.7952
 0LL  N10  N   NH2   0  -0.793   5.3569  -2.4330   0.4583
 0LL  N11  N   NH1   0  -0.619   2.0306  -0.9183   0.2962
 0LL  C12  C   C     0   0.472   1.0214  -0.8171  -0.5588
 0LL  N14  N   NH1   0  -0.738  -1.3287  -0.4649  -0.7638
 0LL  O16  O   O     0  -0.442  -0.4180  -0.4409   1.3359
 0LL  O17  O   O     0  -0.474   1.0964  -0.9187  -1.7741
 0LL  C18  C   CR16  0  -0.359  -3.4880  -0.0652  -1.6761
 0LL  C19  C   CR16  0  -0.197  -4.8386   0.1952  -1.5483
 0LL  CL   CL  CL    0  -0.091  -7.0870   0.6425  -0.0929
 0LL  F24  F   F     0  -0.295  -5.1378   0.2891   2.0349
 0LL  H1   H   HCR6  0   0.312  -2.6647  -0.1891   1.6247
 0LL  H3   H   HCR6  0   0.249   3.4179   0.7299  -2.3504
 0LL  H4   H   HCR6  0   0.249   6.1593   2.0537   1.5796
 0LL  H5   H   HCR6  0   0.254   6.0237   3.5240  -0.4052
 0LL  H6   H   HCR5  0   0.280   3.4076  -1.7788  -0.9876
 0LL  H7   H   HCR5  0   0.239   3.6020  -2.3382   1.6825
 0LL  H8   H   HCH2  0   0.260   5.7264  -0.6927   2.2837
 0LL  H9   H   HCH2  0   0.259   4.0781  -0.1759   2.5824
 0LL  H10  H   HNH2  0   0.352   5.9565  -2.7759   1.1985
 0LL  H11  H   HNH2  0   0.350   5.0221  -3.2541  -0.0311
 0LL  H13  H   HNH1  0   0.414   1.8336  -0.7657   1.2752
 0LL  H14  H   HNH1  0   0.428  -1.0470  -0.5824  -1.7291
 0LL  H15  H   HCR6  0   0.290  -3.0596  -0.1590  -2.6659
 0LL  H16  H   HCR6  0   0.296  -5.4529   0.3051  -2.4312
 0LL  H2   H   HCR6  0   0.254   4.6716   2.8707  -2.3569

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
 0LL  N10  C08  single    1.452  0.020  1.452
 0LL  C08  C09  single    1.538  0.020  1.538
 0LL  C08  C07  single    1.543  0.020  1.543
 0LL  C09  C04  single    1.502  0.020  1.502
 0LL  C04  C05  aromatic  1.386  0.020  1.386
 0LL  C04  C03  aromatic  1.391  0.020  1.391
 0LL  C05  C06  aromatic  1.392  0.020  1.392
 0LL  C07  C03  single    1.510  0.020  1.510
 0LL  C07  N11  single    1.454  0.020  1.454
 0LL  O17  C12  double    1.222  0.020  1.222
 0LL  C03  C02  aromatic  1.385  0.020  1.385
 0LL  C06  C01  aromatic  1.391  0.020  1.391
 0LL  C12  N11  single    1.326  0.020  1.326
 0LL  C12  C13  single    1.538  0.020  1.538
 0LL  C02  C01  aromatic  1.392  0.020  1.392
 0LL  C13  N14  single    1.343  0.020  1.343
 0LL  C13  O16  double    1.216  0.020  1.216
 0LL  N14  C15  single    1.392  0.020  1.392
 0LL  C18  C15  aromatic  1.397  0.020  1.397
 0LL  C18  C19  aromatic  1.381  0.020  1.381
 0LL  C15  C22  aromatic  1.394  0.020  1.394
 0LL  C19  C20  aromatic  1.386  0.020  1.386
 0LL  C22  C21  aromatic  1.380  0.020  1.380
 0LL  C20  C21  aromatic  1.383  0.020  1.383
 0LL  C20  CL   single    1.721  0.020  1.721
 0LL  C21  F24  single    1.334  0.020  1.334
 0LL  C22  H1   single    0.930  0.020  1.080
 0LL  C01  H2   single    0.930  0.020  1.080
 0LL  C02  H3   single    0.930  0.020  1.080
 0LL  C05  H4   single    0.930  0.020  1.080
 0LL  C06  H5   single    0.930  0.020  1.080
 0LL  C07  H6   single    0.970  0.020  1.090
 0LL  C08  H7   single    0.970  0.020  1.090
 0LL  C09  H8   single    0.970  0.020  1.090
 0LL  C09  H9   single    0.970  0.020  1.090
 0LL  N10  H10  single    0.890  0.020  1.040
 0LL  N10  H11  single    0.890  0.020  1.040
 0LL  N11  H13  single    0.860  0.020  1.020
 0LL  N14  H14  single    0.860  0.020  1.020
 0LL  C18  H15  single    0.930  0.020  1.080
 0LL  C19  H16  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
 0LL  O16  C13  N14  126.83  3.000
 0LL  O16  C13  C12  121.59  3.000
 0LL  N14  C13  C12  111.58  3.000
 0LL  C18  C15  N14  116.99  3.000
 0LL  C18  C15  C22  119.48  3.000
 0LL  N14  C15  C22  123.53  3.000
 0LL  CL   C20  C19  121.42  3.000
 0LL  CL   C20  C21  119.96  3.000
 0LL  C19  C20  C21  118.62  3.000
 0LL  F24  C21  C22  118.59  3.000
 0LL  F24  C21  C20  118.99  3.000
 0LL  C22  C21  C20  122.42  3.000
 0LL  H1   C22  C21  119.05  3.000
 0LL  H1   C22  C15  122.30  3.000
 0LL  C21  C22  C15  118.65  3.000
 0LL  H2   C01  C06  119.70  3.000
 0LL  H2   C01  C02  119.93  3.000
 0LL  C06  C01  C02  120.38  3.000
 0LL  H3   C02  C03  120.89  3.000
 0LL  H3   C02  C01  120.47  3.000
 0LL  C03  C02  C01  118.64  3.000
 0LL  C07  C03  C04  110.01  3.000
 0LL  C07  C03  C02  128.80  3.000
 0LL  C04  C03  C02  121.18  3.000
 0LL  C09  C04  C05  129.33  3.000
 0LL  C05  C04  C03  120.20  3.000
 0LL  C09  C04  C03  110.46  3.000
 0LL  H4   C05  C06  120.24  3.000
 0LL  H4   C05  C04  120.83  3.000
 0LL  C06  C05  C04  118.93  3.000
 0LL  H5   C06  C05  119.69  3.000
 0LL  H5   C06  C01  119.63  3.000
 0LL  C05  C06  C01  120.68  3.000
 0LL  H6   C07  N11  107.98  3.000
 0LL  H6   C07  C08  111.37  3.000
 0LL  N11  C07  C08  110.34  3.000
 0LL  H6   C07  C03  113.13  3.000
 0LL  N11  C07  C03  111.13  3.000
 0LL  C08  C07  C03  102.87  3.000
 0LL  H7   C08  N10  113.55  3.000
 0LL  H7   C08  C09  111.52  3.000
 0LL  N10  C08  C09  108.87  3.000
 0LL  H7   C08  C07  110.42  3.000
 0LL  C09  C08  C07  104.28  3.000
 0LL  N10  C08  C07  107.72  3.000
 0LL  H9   C09  H8   106.61  3.000
 0LL  H9   C09  C08  111.08  3.000
 0LL  H8   C09  C08  111.92  3.000
 0LL  H9   C09  C04  110.59  3.000
 0LL  H8   C09  C04  113.48  3.000
 0LL  C08  C09  C04  103.25  3.000
 0LL  H11  N10  H10  105.93  3.000
 0LL  H11  N10  C08  109.85  3.000
 0LL  H10  N10  C08  109.37  3.000
 0LL  H13  N11  C12  117.69  3.000
 0LL  H13  N11  C07  118.83  3.000
 0LL  C12  N11  C07  123.24  3.000
 0LL  O17  C12  N11  126.02  3.000
 0LL  N11  C12  C13  113.15  3.000
 0LL  O17  C12  C13  120.84  3.000
 0LL  H14  N14  C15  116.14  3.000
 0LL  H14  N14  C13  114.77  3.000
 0LL  C15  N14  C13  129.07  3.000
 0LL  H15  C18  C19  119.20  3.000
 0LL  H15  C18  C15  120.12  3.000
 0LL  C19  C18  C15  120.68  3.000
 0LL  H16  C19  C18  119.94  3.000
 0LL  H16  C19  C20  119.91  3.000
 0LL  C18  C19  C20  120.15  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
 0LL  CONST_01  C20  C19  C18  C15    0.00   0.0  0
 0LL  CONST_02  C20  C21  C22  C15    0.00   0.0  0
 0LL  CONST_03  C18  C15  C22  C21    0.00   0.0  0
 0LL  CONST_04  C18  C19  C20  C21    0.00   0.0  0
 0LL  CONST_05  C19  C18  C15  C22    0.00   0.0  0
 0LL  CONST_06  C19  C20  C21  C22    0.00   0.0  0
 0LL  CONST_07  C04  C05  C06  C01    0.00   0.0  0
 0LL  CONST_08  C04  C03  C02  C01    0.00   0.0  0
 0LL  CONST_09  C05  C04  C03  C02    0.00   0.0  0
 0LL  CONST_10  C05  C06  C01  C02    0.00   0.0  0
 0LL  CONST_11  C06  C05  C04  C03    0.00   0.0  0
 0LL  CONST_12  C06  C01  C02  C03    0.00   0.0  0
 0LL  CONST_13  F24  C21  C22  C15  180.00   0.0  0
 0LL  CONST_14  N14  C15  C22  C21  180.00   0.0  0
 0LL  CONST_15  CL   C20  C21  C22  180.00   0.0  0
 0LL  CONST_16  C19  C18  C15  N14  180.00   0.0  0
 0LL  CONST_17  CL   C20  C19  C18  180.00   0.0  0
 0LL  CONST_18  F24  C21  C20  C19  180.00   0.0  0
 0LL  CONST_19  H16  C19  C18  C15  180.00   0.0  0
 0LL  CONST_20  H15  C18  C19  C20  180.00   0.0  0
 0LL  CONST_21  H1   C22  C21  C20  180.00   0.0  0
 0LL  CONST_22  H4   C05  C06  C01  180.00   0.0  0
 0LL  CONST_23  H5   C06  C01  C02  180.00   0.0  0
 0LL  CONST_24  H2   C01  C02  C03  180.00   0.0  0
 0LL  CONST_25  H3   C02  C03  C04  180.00   0.0  0
 0LL  CONST_26  C18  C15  N14  C13  180.00   0.0  0
 0LL  CONST_27  C22  C15  N14  C13    0.00   0.0  0
 0LL  CONST_28  H14  N14  C15  C22  180.00   0.0  0
 0LL  CONST_29  C07  N11  C12  C13  180.00   0.0  0
 0LL  CONST_30  C12  C13  N14  C15  180.00   0.0  0
 0LL  CONST_31  O16  C13  N14  C15    0.00   0.0  0
 0LL  CONST_32  O17  C12  N11  C07    0.00   0.0  0
 0LL  CONST_33  N14  C13  C12  N11  180.00   0.0  0
 0LL  CONST_34  O16  C13  C12  N11    0.00   0.0  0
 0LL  CONST_35  H13  N11  C12  C13    0.00   0.0  0
 0LL  Var_01    C08  C09  C04  C03   17.53  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
 0LL  chir_01  C07  C08  C03  N11  positiv
 0LL  chir_02  C08  N10  C09  C07  negativ

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
 0LL  plan-1  C15  0.020
 0LL  plan-1  C20  0.020
 0LL  plan-1  C21  0.020
 0LL  plan-1  C22  0.020
 0LL  plan-1  N14  0.020
 0LL  plan-1  C18  0.020
 0LL  plan-1  C19  0.020
 0LL  plan-1  CL   0.020
 0LL  plan-1  F24  0.020
 0LL  plan-1  H1   0.020
 0LL  plan-1  H15  0.020
 0LL  plan-1  H16  0.020
 0LL  plan-2  C01  0.020
 0LL  plan-2  C02  0.020
 0LL  plan-2  C03  0.020
 0LL  plan-2  C04  0.020
 0LL  plan-2  C05  0.020
 0LL  plan-2  C06  0.020
 0LL  plan-2  C07  0.020
 0LL  plan-2  C09  0.020
 0LL  plan-2  H3   0.020
 0LL  plan-2  H4   0.020
 0LL  plan-2  H5   0.020
 0LL  plan-2  H2   0.020
 0LL  plan-3  C13  0.020
 0LL  plan-3  C15  0.020
 0LL  plan-3  C07  0.020
 0LL  plan-3  N11  0.020
 0LL  plan-3  C12  0.020
 0LL  plan-3  N14  0.020
 0LL  plan-3  O16  0.020
 0LL  plan-3  O17  0.020
 0LL  plan-3  H13  0.020
 0LL  plan-3  H14  0.020

