# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 01:32:45 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])NC[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
 1C1  1C1  amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methaniminium  ligand  48  28  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1C1
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
 1C1  N01  N   NH2   0  -0.814  -4.7930   4.0011  -1.0130
 1C1  C02  C   C     0   0.831  -5.0213   3.5187   0.1992
 1C1  N03  N   NH1   0  -0.639  -4.4793   2.3698   0.5864
 1C1  C04  C   CH2   0  -0.275  -3.6176   1.5374  -0.2319
 1C1  C05  C   CR15  0  -0.316  -3.5630   0.1355   0.3425
 1C1  C06  C   CH2   0  -0.477  -4.8952  -0.6293   0.3113
 1C1  C07  C   CR56  0   0.096  -4.4536  -2.0645   0.2566
 1C1  C08  C   CR16  0  -0.331  -5.1759  -3.2143   0.5343
 1C1  C09  C   CR16  0  -0.254  -4.5492  -4.4496   0.4052
 1C1  C10  C   CR16  0  -0.260  -3.2198  -4.5316   0.0028
 1C1  C11  C   CR16  0  -0.317  -2.4963  -3.3773  -0.2782
 1C1  C12  C   CR56  0   0.127  -3.1264  -2.1523  -0.1451
 1C1  C13  C   CR15  0  -0.138  -2.5740  -0.7746  -0.4121
 1C1  N14  N   NH1   0  -0.624  -1.2111  -0.5869   0.0150
 1C1  C15  C   C     0   0.470  -0.1883  -0.3551  -0.8044
 1C1  O16  O   O     0  -0.465  -0.2392  -0.2726  -2.0205
 1C1  C17  C   C     0   0.439   1.1454  -0.1810  -0.0560
 1C1  O18  O   O     0  -0.441   1.2045  -0.2389   1.1567
 1C1  N19  N   NH1   0  -0.738   2.1633   0.0366  -0.9038
 1C1  C20  C   CR6   0   0.413   3.5080   0.2641  -0.6203
 1C1  C21  C   CR16  0  -0.487   4.0298   0.2892   0.6718
 1C1  C22  C   CR6   0   0.654   5.3779   0.5324   0.8367
 1C1  F23  F   F     0  -0.295   5.8746   0.5563   2.0742
 1C1  C24  C   CR6   0  -0.256   6.2283   0.7505  -0.2319
 1C1  CL1  CL  CL    0  -0.090   7.9006   1.0492   0.0465
 1C1  C26  C   CR16  0  -0.198   5.7030   0.7211  -1.5146
 1C1  C27  C   CR16  0  -0.359   4.3566   0.4800  -1.7082
 1C1  N28  N   NC2   1  -0.820  -5.8122   4.1797   1.0341
 1C1  H1   H   HNH2  0   0.446  -4.1066   3.5998  -1.6284
 1C1  H2   H   HNH2  0   0.435  -5.2506   4.8392  -1.3295
 1C1  H3   H   HNH1  0   0.427  -4.5559   2.1347   1.5643
 1C1  H4   H   HCH2  0   0.263  -4.0185   1.4879  -1.2471
 1C1  H5   H   HCH2  0   0.273  -2.6118   1.9646  -0.2886
 1C1  H6   H   HCR5  0   0.282  -3.2213   0.1895   1.3834
 1C1  H7   H   HCH2  0   0.267  -5.5324  -0.4096   1.1683
 1C1  H8   H   HCH2  0   0.258  -5.4654  -0.3696  -0.5870
 1C1  H9   H   HCR6  0   0.252  -6.2095  -3.1561   0.8533
 1C1  H10  H   HCR6  0   0.257  -5.0984  -5.3559   0.6253
 1C1  H11  H   HCR6  0   0.257  -2.7453  -5.4999  -0.0904
 1C1  H12  H   HCR6  0   0.249  -1.4589  -3.4433  -0.5837
 1C1  H13  H   HCR5  0   0.286  -2.6124  -0.5671  -1.4859
 1C1  H14  H   HNH1  0   0.416  -1.0141  -0.6453   1.0050
 1C1  H15  H   HNH1  0   0.429   1.9077   0.0412  -1.8835
 1C1  H16  H   HCR6  0   0.313   3.4187   0.1265   1.5454
 1C1  H17  H   HCR6  0   0.297   6.3487   0.8876  -2.3657
 1C1  H18  H   HCR6  0   0.290   3.9631   0.4602  -2.7168
 1C1  H19  H   HNC2  0   0.432  -6.1939   5.0783   0.7933
 1C1  H20  H   HNC2  0   0.433  -6.0828   3.7855   1.9190

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
 1C1  N28  C02  double    1.326  0.020  1.326
 1C1  C02  N03  single    1.328  0.020  1.328
 1C1  C02  N01  single    1.325  0.020  1.325
 1C1  N03  C04  single    1.451  0.020  1.451
 1C1  C04  C05  single    1.516  0.020  1.516
 1C1  C27  C26  aromatic  1.381  0.020  1.381
 1C1  C27  C20  aromatic  1.397  0.020  1.397
 1C1  C26  C24  aromatic  1.386  0.020  1.386
 1C1  C05  C06  single    1.536  0.020  1.536
 1C1  C05  C13  single    1.541  0.020  1.541
 1C1  O16  C15  double    1.220  0.020  1.220
 1C1  C20  N19  single    1.393  0.020  1.393
 1C1  C20  C21  aromatic  1.394  0.020  1.394
 1C1  N19  C17  single    1.342  0.020  1.342
 1C1  C24  CL1  single    1.721  0.020  1.721
 1C1  C24  C22  aromatic  1.383  0.020  1.383
 1C1  C15  C17  single    1.539  0.020  1.539
 1C1  C15  N14  single    1.331  0.020  1.331
 1C1  C06  C07  single    1.503  0.020  1.503
 1C1  C13  N14  single    1.440  0.020  1.440
 1C1  C13  C12  single    1.508  0.020  1.508
 1C1  C17  O18  double    1.216  0.020  1.216
 1C1  C21  C22  aromatic  1.380  0.020  1.380
 1C1  C22  F23  single    1.334  0.020  1.334
 1C1  C07  C12  aromatic  1.389  0.020  1.389
 1C1  C07  C08  aromatic  1.386  0.020  1.386
 1C1  C12  C11  aromatic  1.384  0.020  1.384
 1C1  C08  C09  aromatic  1.391  0.020  1.391
 1C1  C11  C10  aromatic  1.391  0.020  1.391
 1C1  C09  C10  aromatic  1.391  0.020  1.391
 1C1  N01  H1   single    0.860  0.020  1.020
 1C1  N01  H2   single    0.860  0.020  1.020
 1C1  N03  H3   single    0.860  0.020  1.020
 1C1  C04  H4   single    0.970  0.020  1.090
 1C1  C04  H5   single    0.970  0.020  1.090
 1C1  C05  H6   single    0.970  0.020  1.090
 1C1  C06  H7   single    0.970  0.020  1.090
 1C1  C06  H8   single    0.970  0.020  1.090
 1C1  C08  H9   single    0.930  0.020  1.080
 1C1  C09  H10  single    0.930  0.020  1.080
 1C1  C10  H11  single    0.930  0.020  1.080
 1C1  C11  H12  single    0.930  0.020  1.080
 1C1  C13  H13  single    0.970  0.020  1.090
 1C1  N14  H14  single    0.860  0.020  1.020
 1C1  N19  H15  single    0.860  0.020  1.020
 1C1  C21  H16  single    0.930  0.020  1.080
 1C1  C26  H17  single    0.930  0.020  1.080
 1C1  C27  H18  single    0.930  0.020  1.080
 1C1  N28  H19  single    0.860  0.020  1.020
 1C1  N28  H20  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
 1C1  H2   N01  H1   116.78  3.000
 1C1  H2   N01  C02  120.86  3.000
 1C1  H1   N01  C02  122.17  3.000
 1C1  N28  C02  N03  119.40  3.000
 1C1  N03  C02  N01  120.77  3.000
 1C1  N28  C02  N01  119.82  3.000
 1C1  H3   N03  C04  117.27  3.000
 1C1  H3   N03  C02  116.95  3.000
 1C1  C04  N03  C02  125.05  3.000
 1C1  H5   C04  H4   107.87  3.000
 1C1  H5   C04  C05  110.34  3.000
 1C1  H4   C04  C05  108.87  3.000
 1C1  H5   C04  N03  110.56  3.000
 1C1  H4   C04  N03  109.40  3.000
 1C1  C05  C04  N03  109.77  3.000
 1C1  H6   C05  C13  107.09  3.000
 1C1  H6   C05  C06  108.29  3.000
 1C1  C13  C05  C06  104.63  3.000
 1C1  H6   C05  C04  108.98  3.000
 1C1  C13  C05  C04  112.56  3.000
 1C1  C06  C05  C04  114.92  3.000
 1C1  H8   C06  H7   107.01  3.000
 1C1  H8   C06  C07  110.46  3.000
 1C1  H7   C06  C07  113.13  3.000
 1C1  H8   C06  C05  110.49  3.000
 1C1  H7   C06  C05  112.99  3.000
 1C1  C07  C06  C05  102.79  3.000
 1C1  C12  C07  C08  120.22  3.000
 1C1  C08  C07  C06  129.20  3.000
 1C1  C12  C07  C06  110.58  3.000
 1C1  H9   C08  C09  120.32  3.000
 1C1  H9   C08  C07  120.78  3.000
 1C1  C09  C08  C07  118.90  3.000
 1C1  H10  C09  C10  119.62  3.000
 1C1  H10  C09  C08  119.74  3.000
 1C1  C10  C09  C08  120.64  3.000
 1C1  H11  C10  C11  119.80  3.000
 1C1  H11  C10  C09  119.77  3.000
 1C1  C11  C10  C09  120.43  3.000
 1C1  H12  C11  C12  121.13  3.000
 1C1  H12  C11  C10  120.30  3.000
 1C1  C12  C11  C10  118.57  3.000
 1C1  C13  C12  C11  128.67  3.000
 1C1  C11  C12  C07  121.24  3.000
 1C1  C13  C12  C07  110.08  3.000
 1C1  H13  C13  N14  107.42  3.000
 1C1  H13  C13  C12  109.52  3.000
 1C1  N14  C13  C12  114.40  3.000
 1C1  H13  C13  C05  110.24  3.000
 1C1  C12  C13  C05  102.57  3.000
 1C1  N14  C13  C05  112.64  3.000
 1C1  H14  N14  C15  117.59  3.000
 1C1  H14  N14  C13  117.84  3.000
 1C1  C15  N14  C13  124.56  3.000
 1C1  C17  C15  O16  120.88  3.000
 1C1  C17  C15  N14  112.72  3.000
 1C1  O16  C15  N14  126.40  3.000
 1C1  N19  C17  O18  126.94  3.000
 1C1  O18  C17  C15  121.45  3.000
 1C1  N19  C17  C15  111.61  3.000
 1C1  H15  N19  C20  116.09  3.000
 1C1  H15  N19  C17  114.86  3.000
 1C1  C20  N19  C17  129.04  3.000
 1C1  C27  C20  C21  119.47  3.000
 1C1  C21  C20  N19  123.58  3.000
 1C1  C27  C20  N19  116.96  3.000
 1C1  H16  C21  C22  118.91  3.000
 1C1  H16  C21  C20  122.42  3.000
 1C1  C22  C21  C20  118.67  3.000
 1C1  C24  C22  F23  119.02  3.000
 1C1  F23  C22  C21  118.55  3.000
 1C1  C24  C22  C21  122.43  3.000
 1C1  C26  C24  CL1  121.43  3.000
 1C1  CL1  C24  C22  119.98  3.000
 1C1  C26  C24  C22  118.59  3.000
 1C1  H17  C26  C27  119.90  3.000
 1C1  H17  C26  C24  119.92  3.000
 1C1  C27  C26  C24  120.18  3.000
 1C1  H18  C27  C26  119.20  3.000
 1C1  H18  C27  C20  120.13  3.000
 1C1  C26  C27  C20  120.67  3.000
 1C1  H20  N28  H19  117.31  3.000
 1C1  H20  N28  C02  121.25  3.000
 1C1  H19  N28  C02  121.39  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
 1C1  CONST_01  C10  C11  C12  C07     0.00   0.0  0
 1C1  CONST_02  C10  C09  C08  C07     0.00   0.0  0
 1C1  CONST_03  C11  C12  C07  C08     0.00   0.0  0
 1C1  CONST_04  C11  C10  C09  C08     0.00   0.0  0
 1C1  CONST_05  C12  C07  C08  C09     0.00   0.0  0
 1C1  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 1C1  CONST_07  C24  C26  C27  C20     0.00   0.0  0
 1C1  CONST_08  C24  C22  C21  C20     0.00   0.0  0
 1C1  CONST_09  C26  C27  C20  C21     0.00   0.0  0
 1C1  CONST_10  C26  C24  C22  C21     0.00   0.0  0
 1C1  CONST_11  C27  C26  C24  C22     0.00   0.0  0
 1C1  CONST_12  C27  C20  C21  C22     0.00   0.0  0
 1C1  CONST_13  C26  C27  C20  N19   180.00   0.0  0
 1C1  CONST_14  C22  C21  C20  N19   180.00   0.0  0
 1C1  CONST_15  F23  C22  C21  C20   180.00   0.0  0
 1C1  CONST_16  CL1  C24  C22  C21   180.00   0.0  0
 1C1  CONST_17  C26  C24  C22  F23   180.00   0.0  0
 1C1  CONST_18  C27  C26  C24  CL1   180.00   0.0  0
 1C1  CONST_19  H9   C08  C07  C06     0.00   0.0  0
 1C1  CONST_20  H12  C11  C12  C07   180.00   0.0  0
 1C1  CONST_21  H10  C09  C08  C07   180.00   0.0  0
 1C1  CONST_22  H11  C10  C09  C08   180.00   0.0  0
 1C1  CONST_23  H17  C26  C27  C20   180.00   0.0  0
 1C1  CONST_24  H18  C27  C20  C21   180.00   0.0  0
 1C1  CONST_25  H16  C21  C22  C24   180.00   0.0  0
 1C1  CONST_26  C27  C20  N19  C17   180.00   0.0  0
 1C1  CONST_27  C21  C20  N19  C17     0.00   0.0  0
 1C1  CONST_28  H15  N19  C20  C21   180.00   0.0  0
 1C1  CONST_29  O16  C15  N14  C13     0.00   0.0  0
 1C1  CONST_30  C17  C15  N14  C13   180.00   0.0  0
 1C1  CONST_31  C20  N19  C17  C15   180.00   0.0  0
 1C1  CONST_32  C20  N19  C17  O18     0.00   0.0  0
 1C1  CONST_33  N19  C17  C15  N14   180.00   0.0  0
 1C1  CONST_34  N19  C17  C15  O16     0.00   0.0  0
 1C1  CONST_35  C04  N03  C02  N01     0.00   0.0  0
 1C1  CONST_36  N28  C02  N03  C04   180.00   0.0  0
 1C1  CONST_37  H14  N14  C15  O16   180.00   0.0  0
 1C1  CONST_38  H19  N28  C02  N01     0.00   0.0  0
 1C1  CONST_39  H20  N28  C02  N01   180.00   0.0  0
 1C1  CONST_40  H3   N03  C02  N01   180.00   0.0  0
 1C1  CONST_41  H1   N01  C02  N03     0.00   0.0  0
 1C1  CONST_42  H2   N01  C02  N03   180.00   0.0  0
 1C1  Var_01    C12  C07  C06  C05   -17.90  30.0  1
 1C1  Var_02    C05  C04  N03  C02  -161.59  30.0  3

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
 1C1  chir_01  C05  C04  C06  C13  negativ
 1C1  chir_02  C13  N14  C05  C12  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
 1C1  plan-1  N19  0.020
 1C1  plan-1  C20  0.020
 1C1  plan-1  C21  0.020
 1C1  plan-1  C22  0.020
 1C1  plan-1  F23  0.020
 1C1  plan-1  C24  0.020
 1C1  plan-1  CL1  0.020
 1C1  plan-1  C26  0.020
 1C1  plan-1  C27  0.020
 1C1  plan-1  H16  0.020
 1C1  plan-1  H17  0.020
 1C1  plan-1  H18  0.020
 1C1  plan-2  C06  0.020
 1C1  plan-2  C07  0.020
 1C1  plan-2  C08  0.020
 1C1  plan-2  C09  0.020
 1C1  plan-2  C10  0.020
 1C1  plan-2  C11  0.020
 1C1  plan-2  C12  0.020
 1C1  plan-2  C13  0.020
 1C1  plan-2  H9   0.020
 1C1  plan-2  H10  0.020
 1C1  plan-2  H11  0.020
 1C1  plan-2  H12  0.020
 1C1  plan-3  C13  0.020
 1C1  plan-3  N14  0.020
 1C1  plan-3  C15  0.020
 1C1  plan-3  O16  0.020
 1C1  plan-3  C17  0.020
 1C1  plan-3  O18  0.020
 1C1  plan-3  N19  0.020
 1C1  plan-3  C20  0.020
 1C1  plan-3  H14  0.020
 1C1  plan-3  H15  0.020
 1C1  plan-4  N01  0.020
 1C1  plan-4  C02  0.020
 1C1  plan-4  N03  0.020
 1C1  plan-4  C04  0.020
 1C1  plan-4  N28  0.020
 1C1  plan-4  H1   0.020
 1C1  plan-4  H2   0.020
 1C1  plan-4  H3   0.020
 1C1  plan-4  H19  0.020
 1C1  plan-4  H20  0.020

