# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 18:56:38 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[C@H]1CN(C[C@@H]1c2cn(C)c3ccccc23)Cc4c(F)cccc4Br
#
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
 82D  82D  (3R,4S)-1-[(2-bromo-6-fluorophenyl)methyl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine  ligand  52  27  .  2022-07-23  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_82D
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
 82D  C4   C   CR56  0   0.011   3.9145  -0.2309  -0.3312
 82D  C5   C   CR16  0  -0.381   4.9477   0.4097  -1.0252
 82D  C6   C   CR16  0  -0.270   6.2256  -0.1103  -0.9585
 82D  C7   C   CR16  0  -0.285   6.4986  -1.2664  -0.2081
 82D  C8   C   CR16  0  -0.316   5.5006  -1.9220   0.4886
 82D  C10  C   CR5   0   0.062   2.5127   0.0163  -0.1861
 82D  C13  C   CH2   0  -0.269   0.5507   0.5959  -1.6573
 82D  C17  C   CR6   0  -0.145  -3.0685  -0.8864   0.5081
 82D  C20  C   CR16  0  -0.249  -4.9762   0.0674   1.5933
 82D  C21  C   CR16  0  -0.403  -4.8778   1.1859   0.7834
 82D  C22  C   CR6   0   0.527  -3.8635   1.2310  -0.1526
 82D  C24  C   CH2   0  -0.304  -0.4698   1.9195  -0.1123
 82D  C19  C   CR16  0  -0.243  -4.0727  -0.9766   1.4612
 82D  C9   C   CR15  0  -0.082   2.0409  -0.9770   0.6258
 82D  C16  C   CR6   0  -0.027  -2.9320   0.2167  -0.3371
 82D  C3   C   CR56  0   0.367   4.2124  -1.3912   0.4219
 82D  C11  C   CH1   0  -0.409   1.7181   1.1189  -0.8084
 82D  C25  C   CH1   0  -0.017   1.0166   2.0411   0.2381
 82D  N2   N   NR5   0  -0.524   3.0537  -1.8206   1.0002
 82D  N14  N   NT    0  -0.396  -0.5641   0.6152  -0.7344
 82D  N27  N   NT    0  -0.419   1.4932   3.4136   0.1978
 82D  BR   BR  BR    0  -0.027  -1.8723  -2.3415   0.3629
 82D  H1   H   HCR6  0   0.237   4.7511   1.3005  -1.6104
 82D  H2   H   HCR6  0   0.244   7.0310   0.3755  -1.4940
 82D  H3   H   HCR6  0   0.247   7.5091  -1.6526  -0.1767
 82D  H4   H   HCR6  0   0.261   5.7191  -2.8160   1.0593
 82D  H5   H   HCH2  0   0.204   0.3755   1.2703  -2.5133
 82D  H6   H   HCH2  0   0.239   0.7261  -0.4059  -2.0524
 82D  H9   H   HCR6  0   0.280  -5.7606   0.0056   2.3346
 82D  H10  H   HCR6  0   0.286  -5.5697   2.0121   0.8763
 82D  H11  H   HCH2  0   0.246  -1.1228   1.9925   0.7592
 82D  H12  H   HCH2  0   0.196  -0.7476   2.7246  -0.8160
 82D  H16  H   HCR6  0   0.283  -4.1560  -1.8469   2.0974
 82D  H17  H   HCR5  0   0.278   1.0313  -1.1454   0.9691
 82D  H18  H   HCH1  0   0.251   2.3772   1.7149  -1.4431
 82D  H19  H   HCH1  0   0.209   1.1776   1.6172   1.2442
 82D  C1   C   CH3   0  -0.528   2.9055  -3.0108   1.7990
 82D  C15  C   CH2   0  -0.359  -1.8359   0.3395  -1.3619
 82D  C29  C   CH3   0  -0.528   0.6906   4.2816   1.0389
 82D  C28  C   CH3   0  -0.526   2.8810   3.4987   0.6071
 82D  F23  F   F     0  -0.308  -3.7736   2.3287  -0.9198
 82D  H7   H   HCH2  0   0.260  -1.7552  -0.5989  -1.9158
 82D  H8   H   HCH2  0   0.235  -2.0973   1.1061  -2.1056
 82D  H13  H   HCH3  0   0.236   3.5240   2.9089  -0.0453
 82D  H14  H   HCH3  0   0.235   3.2204   4.5337   0.5461
 82D  H15  H   HCH3  0   0.193   3.0463   3.1505   1.6389
 82D  H20  H   HCH3  0   0.249   2.9987  -3.9131   1.1930
 82D  H21  H   HCH3  0   0.252   3.6555  -3.0424   2.5884
 82D  H22  H   HCH3  0   0.260   1.9235  -3.0076   2.2653
 82D  H23  H   HCH3  0   0.236   1.0776   5.3001   0.9891
 82D  H24  H   HCH3  0   0.240  -0.3444   4.3131   0.6991
 82D  H25  H   HCH3  0   0.193   0.6903   3.9768   2.0975

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
 82D  F23  C22  single    1.342  0.020  1.342
 82D  C21  C22  aromatic  1.381  0.020  1.381
 82D  C21  C20  aromatic  1.384  0.020  1.384
 82D  C22  C16  aromatic  1.389  0.020  1.389
 82D  C20  C19  aromatic  1.387  0.020  1.387
 82D  C28  N27  single    1.449  0.020  1.449
 82D  C16  C15  single    1.506  0.020  1.506
 82D  C16  C17  aromatic  1.396  0.020  1.396
 82D  C15  N14  single    1.445  0.020  1.445
 82D  C24  N14  single    1.448  0.020  1.448
 82D  C24  C25  single    1.532  0.020  1.532
 82D  N27  C25  single    1.453  0.020  1.453
 82D  N27  C29  single    1.451  0.020  1.451
 82D  C19  C17  aromatic  1.387  0.020  1.387
 82D  C17  BR   single    1.889  0.020  1.889
 82D  N14  C13  single    1.447  0.020  1.447
 82D  C25  C11  single    1.561  0.020  1.561
 82D  C13  C11  single    1.535  0.020  1.535
 82D  C11  C10  single    1.495  0.020  1.495
 82D  C10  C9   aromatic  1.367  0.020  1.367
 82D  C10  C4   aromatic  1.431  0.020  1.431
 82D  C9   N2   aromatic  1.370  0.020  1.370
 82D  C5   C4   aromatic  1.400  0.020  1.400
 82D  C5   C6   aromatic  1.381  0.020  1.381
 82D  C4   C3   aromatic  1.415  0.020  1.415
 82D  N2   C3   aromatic  1.364  0.020  1.364
 82D  N2   C1   single    1.441  0.020  1.441
 82D  C6   C7   aromatic  1.405  0.020  1.405
 82D  C3   C8   aromatic  1.395  0.020  1.395
 82D  C7   C8   aromatic  1.382  0.020  1.382
 82D  C5   H1   single    0.930  0.020  1.080
 82D  C6   H2   single    0.930  0.020  1.080
 82D  C7   H3   single    0.930  0.020  1.080
 82D  C8   H4   single    0.930  0.020  1.080
 82D  C13  H5   single    0.970  0.020  1.090
 82D  C13  H6   single    0.970  0.020  1.090
 82D  C15  H7   single    0.970  0.020  1.090
 82D  C15  H8   single    0.970  0.020  1.090
 82D  C20  H9   single    0.930  0.020  1.080
 82D  C21  H10  single    0.930  0.020  1.080
 82D  C24  H11  single    0.970  0.020  1.090
 82D  C24  H12  single    0.970  0.020  1.090
 82D  C28  H13  single    0.970  0.020  1.090
 82D  C28  H14  single    0.970  0.020  1.090
 82D  C28  H15  single    0.970  0.020  1.090
 82D  C19  H16  single    0.930  0.020  1.080
 82D  C9   H17  single    0.930  0.020  1.080
 82D  C11  H18  single    0.970  0.020  1.090
 82D  C25  H19  single    0.970  0.020  1.090
 82D  C1   H20  single    0.970  0.020  1.090
 82D  C1   H21  single    0.970  0.020  1.090
 82D  C1   H22  single    0.970  0.020  1.090
 82D  C29  H23  single    0.970  0.020  1.090
 82D  C29  H24  single    0.970  0.020  1.090
 82D  C29  H25  single    0.970  0.020  1.090

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
 82D  C3   C4   C10  107.10  3.000
 82D  C3   C4   C5   118.93  3.000
 82D  C10  C4   C5   133.97  3.000
 82D  H1   C5   C6   120.22  3.000
 82D  H1   C5   C4   120.67  3.000
 82D  C6   C5   C4   119.11  3.000
 82D  H2   C6   C7   119.27  3.000
 82D  H2   C6   C5   119.70  3.000
 82D  C7   C6   C5   121.02  3.000
 82D  H3   C7   C8   119.35  3.000
 82D  H3   C7   C6   119.37  3.000
 82D  C8   C7   C6   121.27  3.000
 82D  H4   C8   C3   121.71  3.000
 82D  H4   C8   C7   120.76  3.000
 82D  C3   C8   C7   117.53  3.000
 82D  C11  C10  C9   126.85  3.000
 82D  C9   C10  C4   105.83  3.000
 82D  C11  C10  C4   127.31  3.000
 82D  H6   C13  H5   107.80  3.000
 82D  H6   C13  N14  111.52  3.000
 82D  H5   C13  N14  111.35  3.000
 82D  H6   C13  C11  113.00  3.000
 82D  H5   C13  C11  109.97  3.000
 82D  N14  C13  C11  103.21  3.000
 82D  BR   C17  C16  120.00  3.000
 82D  BR   C17  C19  117.45  3.000
 82D  C16  C17  C19  122.54  3.000
 82D  H9   C20  C19  119.66  3.000
 82D  H9   C20  C21  119.93  3.000
 82D  C19  C20  C21  120.41  3.000
 82D  H10  C21  C22  120.21  3.000
 82D  H10  C21  C20  121.42  3.000
 82D  C22  C21  C20  118.36  3.000
 82D  F23  C22  C16  118.43  3.000
 82D  C16  C22  C21  123.96  3.000
 82D  F23  C22  C21  117.60  3.000
 82D  H12  C24  H11  108.02  3.000
 82D  H12  C24  N14  111.49  3.000
 82D  H11  C24  N14  111.36  3.000
 82D  H12  C24  C25  109.38  3.000
 82D  H11  C24  C25  113.12  3.000
 82D  N14  C24  C25  103.47  3.000
 82D  H16  C19  C20  119.98  3.000
 82D  H16  C19  C17  120.81  3.000
 82D  C20  C19  C17  119.20  3.000
 82D  H17  C9   N2   120.55  3.000
 82D  H17  C9   C10  128.69  3.000
 82D  N2   C9   C10  110.76  3.000
 82D  C22  C16  C17  115.51  3.000
 82D  C17  C16  C15  123.21  3.000
 82D  C22  C16  C15  121.26  3.000
 82D  N2   C3   C8   130.11  3.000
 82D  C8   C3   C4   122.13  3.000
 82D  N2   C3   C4   107.75  3.000
 82D  H18  C11  C25  109.78  3.000
 82D  H18  C11  C13  108.87  3.000
 82D  C25  C11  C13  103.31  3.000
 82D  H18  C11  C10  108.89  3.000
 82D  C13  C11  C10  112.53  3.000
 82D  C25  C11  C10  113.30  3.000
 82D  H19  C25  N27  109.89  3.000
 82D  H19  C25  C11  108.58  3.000
 82D  N27  C25  C11  113.07  3.000
 82D  H19  C25  C24  108.64  3.000
 82D  C11  C25  C24  103.63  3.000
 82D  N27  C25  C24  112.75  3.000
 82D  C1   N2   C3   125.61  3.000
 82D  C1   N2   C9   125.72  3.000
 82D  C3   N2   C9   108.55  3.000
 82D  C24  N14  C15  114.57  3.000
 82D  C24  N14  C13  103.64  3.000
 82D  C15  N14  C13  113.49  3.000
 82D  C29  N27  C25  111.56  3.000
 82D  C29  N27  C28  109.32  3.000
 82D  C25  N27  C28  111.19  3.000
 82D  H22  C1   H21  108.13  3.000
 82D  H22  C1   H20  108.54  3.000
 82D  H21  C1   H20  108.65  3.000
 82D  H22  C1   N2   109.16  3.000
 82D  H21  C1   N2   110.78  3.000
 82D  H20  C1   N2   111.50  3.000
 82D  H8   C15  H7   105.87  3.000
 82D  H8   C15  N14  111.72  3.000
 82D  H7   C15  N14  108.61  3.000
 82D  H8   C15  C16  110.13  3.000
 82D  H7   C15  C16  109.19  3.000
 82D  N14  C15  C16  111.15  3.000
 82D  H25  C29  H24  107.90  3.000
 82D  H25  C29  H23  107.59  3.000
 82D  H24  C29  H23  107.21  3.000
 82D  H25  C29  N27  113.06  3.000
 82D  H24  C29  N27  111.22  3.000
 82D  H23  C29  N27  109.63  3.000
 82D  H15  C28  H14  107.79  3.000
 82D  H15  C28  H13  107.54  3.000
 82D  H14  C28  H13  107.25  3.000
 82D  H15  C28  N27  112.93  3.000
 82D  H14  C28  N27  109.74  3.000
 82D  H13  C28  N27  111.36  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
 82D  CONST_01  N2   C9   C10  C4     0.00   0.0  0
 82D  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 82D  CONST_03  C9   N2   C3   C4     0.00   0.0  0
 82D  CONST_04  C7   C8   C3   C4     0.00   0.0  0
 82D  CONST_05  C9   C10  C4   C5   180.00   0.0  0
 82D  CONST_06  N2   C3   C4   C5   180.00   0.0  0
 82D  CONST_07  C8   C3   C4   C5     0.00   0.0  0
 82D  CONST_08  C8   C7   C6   C5     0.00   0.0  0
 82D  CONST_09  C10  C4   C5   C6   180.00   0.0  0
 82D  CONST_10  C3   C4   C5   C6     0.00   0.0  0
 82D  CONST_11  C3   C8   C7   C6     0.00   0.0  0
 82D  CONST_12  N2   C3   C8   C7   180.00   0.0  0
 82D  CONST_13  C10  C4   C3   C8   180.00   0.0  0
 82D  CONST_14  C9   N2   C3   C8   180.00   0.0  0
 82D  CONST_15  C3   N2   C9   C10    0.00   0.0  0
 82D  CONST_16  N2   C3   C4   C10    0.00   0.0  0
 82D  CONST_17  C21  C22  C16  C17    0.00   0.0  0
 82D  CONST_18  C21  C20  C19  C17    0.00   0.0  0
 82D  CONST_19  C16  C22  C21  C20    0.00   0.0  0
 82D  CONST_20  C16  C17  C19  C20    0.00   0.0  0
 82D  CONST_21  C19  C20  C21  C22    0.00   0.0  0
 82D  CONST_22  C19  C17  C16  C22    0.00   0.0  0
 82D  CONST_23  C3   C4   C10  C9     0.00   0.0  0
 82D  CONST_24  C11  C10  C4   C5     0.00   0.0  0
 82D  CONST_25  C11  C10  C4   C3   180.00   0.0  0
 82D  CONST_26  N2   C9   C10  C11  180.00   0.0  0
 82D  CONST_27  C1   N2   C3   C4   180.00   0.0  0
 82D  CONST_28  C1   N2   C3   C8     0.00   0.0  0
 82D  CONST_29  C1   N2   C9   C10  180.00   0.0  0
 82D  CONST_30  C21  C22  C16  C15  180.00   0.0  0
 82D  CONST_31  C19  C17  C16  C15  180.00   0.0  0
 82D  CONST_32  F23  C22  C16  C17  180.00   0.0  0
 82D  CONST_33  F23  C22  C21  C20  180.00   0.0  0
 82D  CONST_34  BR   C17  C19  C20  180.00   0.0  0
 82D  CONST_35  BR   C17  C16  C22  180.00   0.0  0
 82D  CONST_36  H17  C9   C10  C4   180.00   0.0  0
 82D  CONST_37  H2   C6   C5   C4   180.00   0.0  0
 82D  CONST_38  H4   C8   C3   C4   180.00   0.0  0
 82D  CONST_39  H3   C7   C6   C5   180.00   0.0  0
 82D  CONST_40  H1   C5   C6   C7   180.00   0.0  0
 82D  CONST_41  H9   C20  C19  C17  180.00   0.0  0
 82D  CONST_42  H16  C19  C20  C21  180.00   0.0  0
 82D  CONST_43  H10  C21  C20  C19  180.00   0.0  0
 82D  Var_01    C25  C24  N14  C13  -46.10  30.0  1
 82D  Var_02    C11  C13  N14  C24   46.79  30.0  1
 82D  Var_03    C16  C15  N14  C13  173.51  30.0  1
 82D  Var_04    N14  C15  C16  C17  -73.34  30.0  2
 82D  Var_05    H20  C1   N2   C9   105.88  30.0  2
 82D  Var_06    H13  C28  N27  C25   60.10  30.0  3
 82D  Var_07    H23  C29  N27  C25  179.72  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
 82D  chir_01  C11  C25  C13  C10  positiv
 82D  chir_02  C25  N27  C24  C11  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
 82D  plan-1  C17  0.020
 82D  plan-1  C20  0.020
 82D  plan-1  C21  0.020
 82D  plan-1  C22  0.020
 82D  plan-1  C19  0.020
 82D  plan-1  C16  0.020
 82D  plan-1  BR   0.020
 82D  plan-1  H9   0.020
 82D  plan-1  H10  0.020
 82D  plan-1  H16  0.020
 82D  plan-1  C15  0.020
 82D  plan-1  F23  0.020
 82D  plan-2  C4   0.020
 82D  plan-2  C5   0.020
 82D  plan-2  C6   0.020
 82D  plan-2  C7   0.020
 82D  plan-2  C8   0.020
 82D  plan-2  C10  0.020
 82D  plan-2  C9   0.020
 82D  plan-2  C3   0.020
 82D  plan-2  C11  0.020
 82D  plan-2  N2   0.020
 82D  plan-2  H1   0.020
 82D  plan-2  H2   0.020
 82D  plan-2  H3   0.020
 82D  plan-2  H4   0.020
 82D  plan-2  H17  0.020
 82D  plan-2  C1   0.020

