# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 06:57:26 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[(1R,2R)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)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
 0LJ  0LJ  N-[(1R,2R)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluorophenyl)ethanediamide  ligand  44  27  .  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_0LJ
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
 0LJ  C10  C   C     0   0.448  -1.0382   0.1516  -0.1179
 0LJ  C15  C   CR15  0  -0.182   2.7180   0.1270  -0.5745
 0LJ  C17  C   CH2   0  -0.487   4.0526   0.4702   1.4312
 0LJ  C21  C   CR16  0  -0.328   4.6189  -2.0643   1.7114
 0LJ  C22  C   CR16  0  -0.251   4.4475  -3.3396   1.1822
 0LJ  C24  C   CR16  0  -0.314   3.1007  -2.4564  -0.6164
 0LJ  C01  C   CR16  0  -0.197  -5.6765  -0.7107  -1.3253
 0LJ  C02  C   CR6   0  -0.256  -6.2006  -0.1387  -0.1765
 0LJ  C03  C   CR6   0   0.654  -5.3279   0.3838   0.7606
 0LJ  C04  C   CR16  0  -0.487  -3.9584   0.3564   0.5932
 0LJ  C05  C   CR6   0   0.413  -3.4385  -0.2191  -0.5649
 0LJ  C06  C   CR16  0  -0.361  -4.3092  -0.7510  -1.5183
 0LJ  F08  F   F     0  -0.295  -5.8251   0.9368   1.8678
 0LJ  N09  N   NH1   0  -0.738  -2.0757  -0.2998  -0.8405
 0LJ  O11  O   O     0  -0.442  -1.0888   0.7267   0.9520
 0LJ  C12  C   C     0   0.474   0.3041  -0.1443  -0.8083
 0LJ  N13  N   NH1   0  -0.619   1.3486   0.3219  -0.1337
 0LJ  O14  O   O     0  -0.469   0.3477  -0.7423  -1.8718
 0LJ  C16  C   CR15  0  -0.163   3.6455   1.1533   0.1081
 0LJ  C18  C   CR56  0   0.105   4.0274  -0.9880   1.0690
 0LJ  C19  C   CR56  0   0.129   3.2754  -1.1896  -0.0841
 0LJ  N20  N   NH1   0  -0.642   4.7698   1.3962  -0.7651
 0LJ  C23  C   CR16  0  -0.260   3.6963  -3.5357   0.0275
 0LJ  C25  C   C     0   0.552   5.6999   2.3663  -0.4782
 0LJ  N26  N   N     0  -0.718   5.5627   3.3426   0.3418
 0LJ  N27  N   NH2   0  -0.828   6.8409   2.2755  -1.2423
 0LJ  H1   H   HCR5  0   0.292   2.7455   0.2307  -1.6605
 0LJ  H2   H   HCH2  0   0.269   5.0186   0.8200   1.7968
 0LJ  H3   H   HCH2  0   0.264   3.3220   0.6800   2.2191
 0LJ  H4   H   HCR6  0   0.252   5.2125  -1.9199   2.6058
 0LJ  H5   H   HCR6  0   0.258   4.9099  -4.1884   1.6696
 0LJ  H6   H   HCR6  0   0.254   2.5174  -2.6048  -1.5158
 0LJ  H7   H   HCR6  0   0.296  -6.3391  -1.1236  -2.0730
 0LJ  H8   H   HCR6  0   0.312  -3.3312   0.7806   1.3612
 0LJ  H9   H   HCR6  0   0.291  -3.9165  -1.1982  -2.4223
 0LJ  H10  H   HNH1  0   0.429  -1.8218  -0.7565  -1.7077
 0LJ  H11  H   HNH1  0   0.419   1.1721   0.7586   0.7605
 0LJ  H12  H   HCR5  0   0.277   3.1147   2.0934   0.2713
 0LJ  H13  H   HNH1  0   0.390   5.1097   0.5933  -1.2742
 0LJ  H14  H   HCR6  0   0.256   3.5798  -4.5336  -0.3748
 0LJ  H15  H   H     0   0.328   4.6531   3.3464   0.7850
 0LJ  H16  H   HNH2  0   0.382   7.1572   1.3487  -1.4815
 0LJ  H17  H   HNH2  0   0.380   7.5922   2.8571  -0.9076
 0LJ  CL7  CL  CL    0  -0.091  -7.8987  -0.0677   0.0965

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
 0LJ  C21  C22  aromatic  1.391  0.020  1.391
 0LJ  C21  C18  aromatic  1.386  0.020  1.386
 0LJ  C17  C18  single    1.503  0.020  1.503
 0LJ  C17  C16  single    1.544  0.020  1.544
 0LJ  N26  C25  double    1.282  0.020  1.282
 0LJ  C22  C23  aromatic  1.391  0.020  1.391
 0LJ  C18  C19  aromatic  1.391  0.020  1.391
 0LJ  C25  N27  single    1.376  0.020  1.376
 0LJ  C25  N20  single    1.374  0.020  1.374
 0LJ  C16  N20  single    1.444  0.020  1.444
 0LJ  C16  C15  single    1.543  0.020  1.543
 0LJ  C23  C24  aromatic  1.391  0.020  1.391
 0LJ  C19  C15  single    1.511  0.020  1.511
 0LJ  C19  C24  aromatic  1.385  0.020  1.385
 0LJ  C15  N13  single    1.452  0.020  1.452
 0LJ  N13  C12  single    1.328  0.020  1.328
 0LJ  C12  O14  double    1.221  0.020  1.221
 0LJ  C12  C10  single    1.538  0.020  1.538
 0LJ  O11  C10  double    1.216  0.020  1.216
 0LJ  C10  N09  single    1.343  0.020  1.343
 0LJ  N09  C05  single    1.393  0.020  1.393
 0LJ  C04  C05  aromatic  1.394  0.020  1.394
 0LJ  C04  C03  aromatic  1.380  0.020  1.380
 0LJ  C05  C06  aromatic  1.396  0.020  1.396
 0LJ  F08  C03  single    1.334  0.020  1.334
 0LJ  C03  C02  aromatic  1.383  0.020  1.383
 0LJ  C06  C01  aromatic  1.381  0.020  1.381
 0LJ  C02  C01  aromatic  1.386  0.020  1.386
 0LJ  C02  CL7  single    1.721  0.020  1.721
 0LJ  C15  H1   single    0.970  0.020  1.090
 0LJ  C17  H2   single    0.970  0.020  1.090
 0LJ  C17  H3   single    0.970  0.020  1.090
 0LJ  C21  H4   single    0.930  0.020  1.080
 0LJ  C22  H5   single    0.930  0.020  1.080
 0LJ  C24  H6   single    0.930  0.020  1.080
 0LJ  C01  H7   single    0.930  0.020  1.080
 0LJ  C04  H8   single    0.930  0.020  1.080
 0LJ  C06  H9   single    0.930  0.020  1.080
 0LJ  N09  H10  single    0.860  0.020  1.020
 0LJ  N13  H11  single    0.860  0.020  1.020
 0LJ  C16  H12  single    0.970  0.020  1.090
 0LJ  N20  H13  single    0.890  0.020  1.040
 0LJ  C23  H14  single    0.930  0.020  1.080
 0LJ  N26  H15  single    0.890  0.020  1.040
 0LJ  N27  H16  single    0.890  0.020  1.040
 0LJ  N27  H17  single    0.890  0.020  1.040

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
 0LJ  C12  C10  O11  121.49  3.000
 0LJ  O11  C10  N09  126.91  3.000
 0LJ  C12  C10  N09  111.60  3.000
 0LJ  H1   C15  C19  113.35  3.000
 0LJ  H1   C15  C16  111.21  3.000
 0LJ  C19  C15  C16  102.37  3.000
 0LJ  H1   C15  N13  108.25  3.000
 0LJ  C19  C15  N13  111.49  3.000
 0LJ  C16  C15  N13  110.09  3.000
 0LJ  H3   C17  H2   106.76  3.000
 0LJ  H3   C17  C18  110.38  3.000
 0LJ  H2   C17  C18  114.01  3.000
 0LJ  H3   C17  C16  110.86  3.000
 0LJ  H2   C17  C16  112.27  3.000
 0LJ  C18  C17  C16  102.61  3.000
 0LJ  H4   C21  C18  120.87  3.000
 0LJ  H4   C21  C22  120.25  3.000
 0LJ  C18  C21  C22  118.87  3.000
 0LJ  H5   C22  C23  119.59  3.000
 0LJ  H5   C22  C21  119.66  3.000
 0LJ  C23  C22  C21  120.75  3.000
 0LJ  H6   C24  C23  120.61  3.000
 0LJ  H6   C24  C19  120.85  3.000
 0LJ  C23  C24  C19  118.54  3.000
 0LJ  H7   C01  C06  119.93  3.000
 0LJ  H7   C01  C02  119.94  3.000
 0LJ  C06  C01  C02  120.14  3.000
 0LJ  CL7  C02  C03  119.96  3.000
 0LJ  CL7  C02  C01  121.43  3.000
 0LJ  C03  C02  C01  118.61  3.000
 0LJ  F08  C03  C04  118.61  3.000
 0LJ  F08  C03  C02  118.94  3.000
 0LJ  C04  C03  C02  122.45  3.000
 0LJ  H8   C04  C05  122.49  3.000
 0LJ  H8   C04  C03  118.88  3.000
 0LJ  C05  C04  C03  118.63  3.000
 0LJ  N09  C05  C06  116.93  3.000
 0LJ  C06  C05  C04  119.47  3.000
 0LJ  N09  C05  C04  123.60  3.000
 0LJ  H9   C06  C05  120.09  3.000
 0LJ  H9   C06  C01  119.20  3.000
 0LJ  C05  C06  C01  120.70  3.000
 0LJ  H10  N09  C05  116.17  3.000
 0LJ  H10  N09  C10  114.76  3.000
 0LJ  C05  N09  C10  129.07  3.000
 0LJ  O14  C12  N13  125.90  3.000
 0LJ  O14  C12  C10  121.09  3.000
 0LJ  N13  C12  C10  113.01  3.000
 0LJ  H11  N13  C12  117.63  3.000
 0LJ  H11  N13  C15  119.43  3.000
 0LJ  C12  N13  C15  122.72  3.000
 0LJ  H12  C16  N20  108.91  3.000
 0LJ  H12  C16  C17  112.40  3.000
 0LJ  N20  C16  C17  112.79  3.000
 0LJ  H12  C16  C15  110.28  3.000
 0LJ  N20  C16  C15  108.21  3.000
 0LJ  C17  C16  C15  104.09  3.000
 0LJ  C19  C18  C21  120.15  3.000
 0LJ  C19  C18  C17  110.45  3.000
 0LJ  C21  C18  C17  129.39  3.000
 0LJ  C18  C19  C24  121.28  3.000
 0LJ  C24  C19  C15  128.71  3.000
 0LJ  C18  C19  C15  110.00  3.000
 0LJ  H13  N20  C25  116.02  3.000
 0LJ  H13  N20  C16  115.68  3.000
 0LJ  C25  N20  C16  121.29  3.000
 0LJ  H14  C23  C24  119.83  3.000
 0LJ  H14  C23  C22  119.77  3.000
 0LJ  C24  C23  C22  120.40  3.000
 0LJ  N27  C25  N26  119.60  3.000
 0LJ  N27  C25  N20  113.50  3.000
 0LJ  N26  C25  N20  126.77  3.000
 0LJ  H15  N26  C25  112.28  3.000
 0LJ  H17  N27  H16  112.07  3.000
 0LJ  H17  N27  C25  113.32  3.000
 0LJ  H16  N27  C25  116.90  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
 0LJ  CONST_01  C24  C23  C22  C21    0.00   0.0  0
 0LJ  CONST_02  C24  C19  C18  C21    0.00   0.0  0
 0LJ  CONST_03  C19  C18  C21  C22    0.00   0.0  0
 0LJ  CONST_04  C19  C24  C23  C22    0.00   0.0  0
 0LJ  CONST_05  C04  C05  C06  C01    0.00   0.0  0
 0LJ  CONST_06  C04  C03  C02  C01    0.00   0.0  0
 0LJ  CONST_07  C05  C04  C03  C02    0.00   0.0  0
 0LJ  CONST_08  C05  C06  C01  C02    0.00   0.0  0
 0LJ  CONST_09  C06  C05  C04  C03    0.00   0.0  0
 0LJ  CONST_10  C06  C01  C02  C03    0.00   0.0  0
 0LJ  CONST_11  C23  C22  C21  C18    0.00   0.0  0
 0LJ  CONST_12  C23  C24  C19  C18    0.00   0.0  0
 0LJ  CONST_13  N09  C05  C06  C01  180.00   0.0  0
 0LJ  CONST_14  F08  C03  C02  C01  180.00   0.0  0
 0LJ  CONST_15  N09  C05  C04  C03  180.00   0.0  0
 0LJ  CONST_16  CL7  C02  C03  C04  180.00   0.0  0
 0LJ  CONST_17  F08  C03  C04  C05  180.00   0.0  0
 0LJ  CONST_18  CL7  C02  C01  C06  180.00   0.0  0
 0LJ  CONST_19  H6   C24  C19  C15    0.00   0.0  0
 0LJ  CONST_20  H4   C21  C18  C17    0.00   0.0  0
 0LJ  CONST_21  H14  C23  C22  C21  180.00   0.0  0
 0LJ  CONST_22  H5   C22  C23  C24  180.00   0.0  0
 0LJ  CONST_23  H8   C04  C03  C02  180.00   0.0  0
 0LJ  CONST_24  H9   C06  C01  C02  180.00   0.0  0
 0LJ  CONST_25  H7   C01  C02  C03  180.00   0.0  0
 0LJ  CONST_26  C04  C05  N09  C10    0.00   0.0  0
 0LJ  CONST_27  C06  C05  N09  C10  180.00   0.0  0
 0LJ  CONST_28  H10  N09  C05  C04  180.00   0.0  0
 0LJ  CONST_29  C15  N13  C12  C10  180.00   0.0  0
 0LJ  CONST_30  O14  C12  N13  C15    0.00   0.0  0
 0LJ  CONST_31  C12  C10  N09  C05  180.00   0.0  0
 0LJ  CONST_32  O11  C10  N09  C05    0.00   0.0  0
 0LJ  CONST_34  N27  C25  N20  C16  180.00   0.0  0
 0LJ  CONST_35  N13  C12  C10  N09  180.00   0.0  0
 0LJ  CONST_36  N13  C12  C10  O11    0.00   0.0  0
 0LJ  CONST_37  H11  N13  C12  C10    0.00   0.0  0
 0LJ  CONST_38  H15  N26  C25  N20    0.00   0.0  0
 0LJ  CONST_40  H17  N27  C25  N20  180.00   0.0  0
 0LJ  CONST_41  H13  N20  C25  N26  180.00   0.0  0
 0LJ  Var_01    C16  C17  C18  C21  161.42  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
 0LJ  chir_01  C15  C16  C19  N13  negativ
 0LJ  chir_02  C16  N20  C15  C17  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
 0LJ  plan-1  C01  0.020
 0LJ  plan-1  C02  0.020
 0LJ  plan-1  C03  0.020
 0LJ  plan-1  C04  0.020
 0LJ  plan-1  C05  0.020
 0LJ  plan-1  C06  0.020
 0LJ  plan-1  F08  0.020
 0LJ  plan-1  N09  0.020
 0LJ  plan-1  H7   0.020
 0LJ  plan-1  H8   0.020
 0LJ  plan-1  H9   0.020
 0LJ  plan-1  CL7  0.020
 0LJ  plan-2  C15  0.020
 0LJ  plan-2  C17  0.020
 0LJ  plan-2  C21  0.020
 0LJ  plan-2  C22  0.020
 0LJ  plan-2  C24  0.020
 0LJ  plan-2  C18  0.020
 0LJ  plan-2  C19  0.020
 0LJ  plan-2  C23  0.020
 0LJ  plan-2  H4   0.020
 0LJ  plan-2  H5   0.020
 0LJ  plan-2  H6   0.020
 0LJ  plan-2  H14  0.020
 0LJ  plan-3  C10  0.020
 0LJ  plan-3  C15  0.020
 0LJ  plan-3  C05  0.020
 0LJ  plan-3  N09  0.020
 0LJ  plan-3  O11  0.020
 0LJ  plan-3  C12  0.020
 0LJ  plan-3  N13  0.020
 0LJ  plan-3  O14  0.020
 0LJ  plan-3  H10  0.020
 0LJ  plan-3  H11  0.020
 0LJ  plan-4  C16  0.020
 0LJ  plan-4  N20  0.020
 0LJ  plan-4  C25  0.020
 0LJ  plan-4  N26  0.020
 0LJ  plan-4  N27  0.020
 0LJ  plan-4  H13  0.020
 0LJ  plan-4  H15  0.020
 0LJ  plan-4  H16  0.020
 0LJ  plan-4  H17  0.020

