# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 03:05:29 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2R)-4-[2-(6-chloro-3,3-dimethyl-2,3-dihydro-1H-indol-1-yl)-2-oxoethyl]-2-methylpiperazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN(CC[NH2+]1)CC(=O)N2CC(C)(C)c3ccc(Cl)cc23
#
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
 4YC  4YC  (2R)-4-[2-(6-chloro-3,3-dimethyl-2,3-dihydro-1H-indol-1-yl)-2-oxoethyl]-2-methylpiperazin-1-ium  ligand  47  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4YC
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
 4YC  C1   C   CH3   0  -0.674  -5.9390   1.4131   0.4342
 4YC  C2   C   CH1   0  -0.145  -4.9458   0.2728   0.3780
 4YC  C3   C   CH2   0  -0.268  -3.5017   0.7418   0.3527
 4YC  N4   N   NT    0  -0.422  -2.5929  -0.3828   0.2551
 4YC  C5   C   CH2   0  -0.423  -1.2191   0.0133   0.4258
 4YC  C6   C   C     0   0.534  -0.3446  -1.1708   0.8047
 4YC  C10  C   CR5   0  -0.163   3.1569  -1.8524   0.0986
 4YC  C11  C   CH3   0  -0.646   4.4038  -2.3927   0.7848
 4YC  C12  C   CH3   0  -0.633   3.0584  -2.3878  -1.3343
 4YC  C13  C   CR56  0   0.075   3.0874  -0.3466   0.0695
 4YC  C14  C   CR16  0  -0.346   4.0713   0.5641  -0.2484
 4YC  C15  C   CR16  0  -0.223   3.7826   1.9263  -0.2466
 4YC  C16  C   CR6   0  -0.050   2.5030   2.3325   0.0870
 4YC  C19  C   CR56  0   0.398   1.7966   0.0835   0.3816
 4YC  C21  C   CH2   0  -0.324  -4.2217  -1.6618  -1.0107
 4YC  O7   O   O     0  -0.461  -0.8231  -2.2225   1.1857
 4YC  N8   N   NR5   0  -0.602   1.0038  -1.0319   0.6841
 4YC  C9   C   CH2   0  -0.265   1.8821  -2.1896   0.8899
 4YC  C18  C   CR16  0  -0.256   1.4909   1.4366   0.4165
 4YC  C20  C   CH2   0  -0.311  -2.8159  -1.1102  -0.9790
 4YC  N22  N   NT2   1  -0.649  -5.1987  -0.5505  -0.8480
 4YC  H23  H   HCH3  0   0.264  -6.9644   1.0443   0.4413
 4YC  H25  H   HCH3  0   0.267  -5.7862   1.9840   1.3484
 4YC  H24  H   HCH3  0   0.248  -5.8175   2.0899  -0.4121
 4YC  H26  H   HCH1  0   0.305  -5.0906  -0.4080   1.2178
 4YC  H27  H   HCH2  0   0.224  -3.3677   1.4684  -0.4669
 4YC  H28  H   HCH2  0   0.278  -3.3187   1.2761   1.2860
 4YC  H30  H   HCH2  0   0.254  -0.8106   0.5188  -0.4631
 4YC  H29  H   HCH2  0   0.296  -1.1684   0.7355   1.2467
 4YC  H35  H   HCH3  0   0.239   4.3723  -3.4825   0.8327
 4YC  H33  H   HCH3  0   0.237   5.3053  -2.1153   0.2367
 4YC  H34  H   HCH3  0   0.236   4.4961  -2.0126   1.8029
 4YC  H37  H   HCH3  0   0.235   2.1439  -2.0495  -1.8247
 4YC  H36  H   HCH3  0   0.237   3.9045  -2.0470  -1.9323
 4YC  H38  H   HCH3  0   0.236   3.0592  -3.4794  -1.3378
 4YC  H39  H   HCR6  0   0.265   5.0705   0.2313  -0.5004
 4YC  H40  H   HCR6  0   0.279   4.5452   2.6520  -0.4923
 4YC  H44  H   HCH2  0   0.308  -4.4375  -2.1529  -1.9560
 4YC  H45  H   HCH2  0   0.297  -4.3924  -2.3598  -0.1939
 4YC  H32  H   HCH2  0   0.265   1.4034  -3.1024   0.5417
 4YC  H31  H   HCH2  0   0.262   2.0962  -2.3015   1.9569
 4YC  H41  H   HCR6  0   0.293   0.5266   1.8189   0.7100
 4YC  H43  H   HCH2  0   0.234  -2.6419  -0.4798  -1.8670
 4YC  H42  H   HCH2  0   0.282  -2.1347  -1.9573  -1.0475
 4YC  H47  H   HNT2  0   0.477  -6.1459  -0.9300  -0.8197
 4YC  H46  H   HNT2  0   0.460  -5.1722   0.0480  -1.6770
 4YC  CL1  CL  CL    0  -0.125   2.1363   4.0278   0.1217

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
 4YC  C14  C15  aromatic  1.392  0.020  1.392
 4YC  C14  C13  aromatic  1.378  0.020  1.378
 4YC  C11  C10  single    1.522  0.020  1.522
 4YC  C15  C16  aromatic  1.383  0.020  1.383
 4YC  C12  C10  single    1.533  0.020  1.533
 4YC  C13  C10  single    1.508  0.020  1.508
 4YC  C13  C19  aromatic  1.396  0.020  1.396
 4YC  C10  C9   single    1.538  0.020  1.538
 4YC  C16  CL1  single    1.735  0.020  1.735
 4YC  C16  C18  aromatic  1.391  0.020  1.391
 4YC  C19  C18  aromatic  1.388  0.020  1.388
 4YC  C19  N8   single    1.401  0.020  1.401
 4YC  C9   N8   single    1.468  0.020  1.468
 4YC  N8   C6   single    1.361  0.020  1.361
 4YC  C6   O7   double    1.217  0.020  1.217
 4YC  C6   C5   single    1.520  0.020  1.520
 4YC  C5   N4   single    1.440  0.020  1.440
 4YC  N4   C3   single    1.449  0.020  1.449
 4YC  N4   C20  single    1.450  0.020  1.450
 4YC  C3   C2   single    1.519  0.020  1.519
 4YC  C20  C21  single    1.510  0.020  1.510
 4YC  C2   C1   single    1.513  0.020  1.513
 4YC  C2   N22  single    1.498  0.020  1.498
 4YC  C21  N22  single    1.489  0.020  1.489
 4YC  C1   H23  single    0.970  0.020  1.090
 4YC  C1   H25  single    0.970  0.020  1.090
 4YC  C1   H24  single    0.970  0.020  1.090
 4YC  C2   H26  single    0.970  0.020  1.090
 4YC  C3   H27  single    0.970  0.020  1.090
 4YC  C3   H28  single    0.970  0.020  1.090
 4YC  C5   H30  single    0.970  0.020  1.090
 4YC  C5   H29  single    0.970  0.020  1.090
 4YC  C11  H35  single    0.970  0.020  1.090
 4YC  C11  H33  single    0.970  0.020  1.090
 4YC  C11  H34  single    0.970  0.020  1.090
 4YC  C12  H37  single    0.970  0.020  1.090
 4YC  C12  H36  single    0.970  0.020  1.090
 4YC  C12  H38  single    0.970  0.020  1.090
 4YC  C14  H39  single    0.930  0.020  1.080
 4YC  C15  H40  single    0.930  0.020  1.080
 4YC  C21  H44  single    0.970  0.020  1.090
 4YC  C21  H45  single    0.970  0.020  1.090
 4YC  C9   H32  single    0.970  0.020  1.090
 4YC  C9   H31  single    0.970  0.020  1.090
 4YC  C18  H41  single    0.930  0.020  1.080
 4YC  C20  H43  single    0.970  0.020  1.090
 4YC  C20  H42  single    0.970  0.020  1.090
 4YC  N22  H47  single    0.890  0.020  1.040
 4YC  N22  H46  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
 4YC  H24  C1   H25  108.10  3.000
 4YC  H24  C1   H23  108.66  3.000
 4YC  H25  C1   H23  107.70  3.000
 4YC  H24  C1   C2   111.46  3.000
 4YC  H25  C1   C2   109.52  3.000
 4YC  H23  C1   C2   111.28  3.000
 4YC  H26  C2   N22  105.34  3.000
 4YC  H26  C2   C3   109.38  3.000
 4YC  N22  C2   C3   108.45  3.000
 4YC  H26  C2   C1   110.77  3.000
 4YC  N22  C2   C1   109.49  3.000
 4YC  C3   C2   C1   113.09  3.000
 4YC  H28  C3   H27  107.01  3.000
 4YC  H28  C3   N4   109.42  3.000
 4YC  H27  C3   N4   112.63  3.000
 4YC  H28  C3   C2   107.25  3.000
 4YC  H27  C3   C2   109.34  3.000
 4YC  N4   C3   C2   110.97  3.000
 4YC  C20  N4   C5   112.68  3.000
 4YC  C20  N4   C3   110.50  3.000
 4YC  C5   N4   C3   112.14  3.000
 4YC  H29  C5   H30  106.58  3.000
 4YC  H29  C5   C6   107.48  3.000
 4YC  H30  C5   C6   110.21  3.000
 4YC  H29  C5   N4   108.33  3.000
 4YC  H30  C5   N4   112.61  3.000
 4YC  C6   C5   N4   111.36  3.000
 4YC  N8   C6   O7   120.38  3.000
 4YC  O7   C6   C5   121.68  3.000
 4YC  N8   C6   C5   117.93  3.000
 4YC  C9   C10  C13  100.99  3.000
 4YC  C9   C10  C12  110.56  3.000
 4YC  C13  C10  C12  109.14  3.000
 4YC  C9   C10  C11  111.67  3.000
 4YC  C13  C10  C11  113.63  3.000
 4YC  C12  C10  C11  110.49  3.000
 4YC  H34  C11  H33  108.09  3.000
 4YC  H34  C11  H35  108.03  3.000
 4YC  H33  C11  H35  107.45  3.000
 4YC  H34  C11  C10  111.49  3.000
 4YC  H33  C11  C10  111.11  3.000
 4YC  H35  C11  C10  110.52  3.000
 4YC  H38  C12  H36  108.06  3.000
 4YC  H38  C12  H37  108.01  3.000
 4YC  H36  C12  H37  107.87  3.000
 4YC  H38  C12  C10  110.62  3.000
 4YC  H36  C12  C10  110.71  3.000
 4YC  H37  C12  C10  111.44  3.000
 4YC  C19  C13  C14  120.55  3.000
 4YC  C19  C13  C10  110.24  3.000
 4YC  C14  C13  C10  129.18  3.000
 4YC  H39  C14  C15  119.49  3.000
 4YC  H39  C14  C13  120.62  3.000
 4YC  C15  C14  C13  119.89  3.000
 4YC  H40  C15  C16  120.68  3.000
 4YC  H40  C15  C14  120.67  3.000
 4YC  C16  C15  C14  118.64  3.000
 4YC  C18  C16  CL1  118.09  3.000
 4YC  C18  C16  C15  122.75  3.000
 4YC  CL1  C16  C15  119.16  3.000
 4YC  C18  C19  N8   130.24  3.000
 4YC  N8   C19  C13  109.04  3.000
 4YC  C18  C19  C13  120.65  3.000
 4YC  H45  C21  H44  109.38  3.000
 4YC  H45  C21  N22  107.10  3.000
 4YC  H44  C21  N22  107.58  3.000
 4YC  H45  C21  C20  111.39  3.000
 4YC  H44  C21  C20  111.59  3.000
 4YC  N22  C21  C20  109.63  3.000
 4YC  C9   N8   C19  108.64  3.000
 4YC  C9   N8   C6   120.00  3.000
 4YC  C19  N8   C6   131.36  3.000
 4YC  H31  C9   H32  108.21  3.000
 4YC  H31  C9   N8   109.55  3.000
 4YC  H32  C9   N8   110.72  3.000
 4YC  H31  C9   C10  111.23  3.000
 4YC  H32  C9   C10  112.58  3.000
 4YC  N8   C9   C10  104.53  3.000
 4YC  H41  C18  C19  123.34  3.000
 4YC  H41  C18  C16  119.13  3.000
 4YC  C19  C18  C16  117.50  3.000
 4YC  H42  C20  H43  107.18  3.000
 4YC  H42  C20  C21  107.26  3.000
 4YC  H43  C20  C21  109.80  3.000
 4YC  H42  C20  N4   110.34  3.000
 4YC  H43  C20  N4   111.99  3.000
 4YC  C21  C20  N4   110.13  3.000
 4YC  H46  N22  H47  105.31  3.000
 4YC  H46  N22  C21  109.35  3.000
 4YC  H47  N22  C21  109.54  3.000
 4YC  H46  N22  C2   109.72  3.000
 4YC  H47  N22  C2   109.77  3.000
 4YC  C21  N22  C2   112.88  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
 4YC  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 4YC  CONST_02  C16  C18  C19  C13    0.00   0.0  0
 4YC  CONST_03  C18  C16  C15  C14    0.00   0.0  0
 4YC  CONST_04  C18  C19  C13  C14    0.00   0.0  0
 4YC  CONST_05  C19  C13  C14  C15    0.00   0.0  0
 4YC  CONST_06  C19  C18  C16  C15    0.00   0.0  0
 4YC  CONST_07  CL1  C16  C15  C14  180.00   0.0  0
 4YC  CONST_08  CL1  C16  C18  C19  180.00   0.0  0
 4YC  CONST_09  H39  C14  C13  C10    0.00   0.0  0
 4YC  CONST_10  H40  C15  C14  C13  180.00   0.0  0
 4YC  CONST_11  H41  C18  C19  C13  180.00   0.0  0
 4YC  CONST_12  C19  N8   C6   C5     0.00   0.0  0
 4YC  CONST_13  C9   N8   C6   C5   180.00   0.0  0
 4YC  CONST_14  O7   C6   N8   C19  180.00   0.0  0
 4YC  CONST_15  C9   N8   C6   O7     0.00   0.0  0
 4YC  Var_01    C20  N4   C3   C2    61.87  30.0  1
 4YC  Var_02    C20  C21  N22  C2   -54.37  30.0  1
 4YC  Var_03    C21  C20  N4   C3   -61.52  30.0  1
 4YC  Var_04    N22  C21  C20  N4    56.95  30.0  1
 4YC  Var_05    C19  N8   C9   C10  -24.49  30.0  1
 4YC  Var_06    N8   C9   C10  C13   24.31  30.0  1
 4YC  Var_07    C9   N8   C19  C13   13.97  30.0  1
 4YC  Var_08    C9   C10  C13  C14  165.01  30.0  1
 4YC  Var_09    C6   C5   N4   C3   160.12  30.0  2
 4YC  Var_10    N8   C6   C5   N4   164.35  30.0  1
 4YC  Var_11    H35  C11  C10  C13  176.46  30.0  3
 4YC  Var_12    H37  C12  C10  C13  -57.18  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
 4YC  chir_01  C2  C3  C1  N22  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
 4YC  plan-1  C5   0.020
 4YC  plan-1  C6   0.020
 4YC  plan-1  C19  0.020
 4YC  plan-1  O7   0.020
 4YC  plan-1  N8   0.020
 4YC  plan-1  C9   0.020
 4YC  plan-2  C10  0.020
 4YC  plan-2  C13  0.020
 4YC  plan-2  C14  0.020
 4YC  plan-2  C15  0.020
 4YC  plan-2  C16  0.020
 4YC  plan-2  C19  0.020
 4YC  plan-2  N8   0.020
 4YC  plan-2  C18  0.020
 4YC  plan-2  H39  0.020
 4YC  plan-2  H40  0.020
 4YC  plan-2  H41  0.020
 4YC  plan-2  CL1  0.020

