# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 20:08:13 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-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)[C@H]4CCc5cccc(F)c45
#
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
 82G  82G  (3R,4S)-1-[(1S)-7-fluoro-2,3-dihydro-1H-inden-1-yl]-N,N-dimethyl-4-(1-methyl-1H-indol-3-yl)pyrrolidin-3-amine  ligand  56  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_82G
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
 82G  C4   C  CR16  0  -0.379   3.5582  -0.3627  -1.8805
 82G  C5   C  CR16  0  -0.339  -4.8698  -1.6501  -1.1718
 82G  C6   C  CR16  0  -0.315   4.4776  -2.4303  -0.1719
 82G  C7   C  CR16  0  -0.426  -3.2796  -2.8138   0.2254
 82G  C8   C  CR15  0  -0.082   1.6471  -0.6824   1.1748
 82G  C10  C  CR56  0   0.102  -4.2590  -0.4508  -0.8364
 82G  C13  C  CR56  0   0.368   3.3852  -1.6360   0.1756
 82G  C15  C  CH2   0  -0.494  -4.6532   0.9412  -1.2427
 82G  C17  C  CH2   0  -0.266  -0.4837   0.6957  -0.8568
 82G  C20  C  CR15  0  -0.092  -2.6858   1.0035   0.2394
 82G  C21  C  CH1   0  -0.021   0.7581   2.2785   0.5240
 82G  C24  C  CH3   0  -0.531   1.1523   4.5891   1.0441
 82G  C1   C  CR16  0  -0.271   4.6404  -1.1477  -2.2291
 82G  C2   C  CR16  0  -0.284   5.0954  -2.1716  -1.3815
 82G  C3   C  CR16  0  -0.245  -4.3669  -2.8314  -0.6407
 82G  C9   C  CR56  0   0.008   2.9118  -0.5991  -0.6617
 82G  C11  C  CR5   0   0.061   1.7971   0.0039   0.0024
 82G  C12  C  CR56  0  -0.129  -3.1579  -0.4129   0.0132
 82G  C14  C  CR6   0   0.508  -2.6986  -1.6002   0.5498
 82G  C16  C  CH2   0  -0.487  -3.4248   1.7848  -0.8785
 82G  C18  C  CH2   0  -0.299  -0.7591   2.4668   0.5686
 82G  C19  C  CH1   0  -0.399   0.9546   1.1276  -0.5063
 82G  C23  C  CH3   0  -0.524   2.9122   3.2631   0.1702
 82G  N25  N  NR5   0  -0.525   2.5964  -1.6642   1.2883
 82G  N26  N  NT    0  -0.420  -1.2497   1.1372   0.2884
 82G  N27  N  NT    0  -0.417   1.4799   3.4843   0.1643
 82G  F28  F  F     0  -0.304  -1.6663  -1.5960   1.4081
 82G  H1   H  HCR6  0   0.238   3.2132   0.4205  -2.5457
 82G  H3   H  HCR6  0   0.260   4.8374  -3.2214   0.4744
 82G  H4   H  HCR6  0   0.273  -2.8898  -3.7313   0.6470
 82G  H5   H  HCR5  0   0.275   0.9104  -0.5455   1.9511
 82G  H6   H  HCH2  0   0.253  -4.9225   1.0141  -2.2974
 82G  H7   H  HCH2  0   0.253  -5.5313   1.2565  -0.6713
 82G  H8   H  HCH2  0   0.204  -0.7944   1.1863  -1.7933
 82G  H9   H  HCH2  0   0.238  -0.5701  -0.3802  -1.0103
 82G  H10  H  HCR5  0   0.262  -3.0641   1.3415   1.2133
 82G  H11  H  HCH1  0   0.206   1.0823   1.9218   1.5177
 82G  H15  H  HCH3  0   0.236   1.7098   5.4760   0.7402
 82G  H16  H  HCH3  0   0.241   0.0926   4.8382   0.9863
 82G  H17  H  HCH3  0   0.193   1.3945   4.3888   2.1003
 82G  H18  H  HCR6  0   0.244   5.1465  -0.9760  -3.1705
 82G  H19  H  HCR6  0   0.247   5.9461  -2.7698  -1.6822
 82G  H20  H  HCR6  0   0.263  -4.8232  -3.7791  -0.8948
 82G  H21  H  HCH2  0   0.242  -2.7755   1.8721  -1.7520
 82G  H22  H  HCH2  0   0.244  -3.6864   2.7950  -0.5664
 82G  H23  H  HCH2  0   0.241  -1.1211   2.8193   1.5373
 82G  H24  H  HCH2  0   0.197  -1.0603   3.2055  -0.1942
 82G  H25  H  HCH1  0   0.249   1.4236   1.5352  -1.4061
 82G  H26  H  HCH3  0   0.237   3.1943   2.4897  -0.5438
 82G  H27  H  HCH3  0   0.234   3.4267   4.1802  -0.1204
 82G  H28  H  HCH3  0   0.191   3.2981   2.9598   1.1565
 82G  C22  C  CH3   0  -0.528   2.7320  -2.5911   2.3833
 82G  H2   H  HCR6  0   0.250  -5.7242  -1.6683  -1.8367
 82G  H12  H  HCH3  0   0.249   2.5431  -3.6153   2.0602
 82G  H13  H  HCH3  0   0.250   3.7320  -2.5411   2.8142
 82G  H14  H  HCH3  0   0.261   2.0140  -2.3365   3.1583

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
 82G  F28  C14  single    1.342  0.020  1.342
 82G  C7   C14  aromatic  1.384  0.020  1.384
 82G  C7   C3   aromatic  1.390  0.020  1.390
 82G  C14  C12  aromatic  1.382  0.020  1.382
 82G  C3   C5   aromatic  1.389  0.020  1.389
 82G  C23  N27  single    1.449  0.020  1.449
 82G  C12  C20  single    1.510  0.020  1.510
 82G  C12  C10  aromatic  1.391  0.020  1.391
 82G  C20  N26  single    1.443  0.020  1.443
 82G  C20  C16  single    1.551  0.020  1.551
 82G  C18  N26  single    1.445  0.020  1.445
 82G  C18  C21  single    1.529  0.020  1.529
 82G  C5   C10  aromatic  1.387  0.020  1.387
 82G  N27  C21  single    1.451  0.020  1.451
 82G  N27  C24  single    1.450  0.020  1.450
 82G  C10  C15  single    1.503  0.020  1.503
 82G  N26  C17  single    1.447  0.020  1.447
 82G  C16  C15  single    1.534  0.020  1.534
 82G  C21  C19  single    1.557  0.020  1.557
 82G  C17  C19  single    1.542  0.020  1.542
 82G  C19  C11  single    1.494  0.020  1.494
 82G  C11  C8   aromatic  1.367  0.020  1.367
 82G  C11  C9   aromatic  1.431  0.020  1.431
 82G  C8   N25  aromatic  1.370  0.020  1.370
 82G  C4   C9   aromatic  1.400  0.020  1.400
 82G  C4   C1   aromatic  1.382  0.020  1.382
 82G  C9   C13  aromatic  1.414  0.020  1.414
 82G  N25  C13  aromatic  1.364  0.020  1.364
 82G  N25  C22  single    1.441  0.020  1.441
 82G  C1   C2   aromatic  1.405  0.020  1.405
 82G  C13  C6   aromatic  1.395  0.020  1.395
 82G  C2   C6   aromatic  1.383  0.020  1.383
 82G  C4   H1   single    0.930  0.020  1.080
 82G  C5   H2   single    0.930  0.020  1.080
 82G  C6   H3   single    0.930  0.020  1.080
 82G  C7   H4   single    0.930  0.020  1.080
 82G  C8   H5   single    0.930  0.020  1.080
 82G  C15  H6   single    0.970  0.020  1.090
 82G  C15  H7   single    0.970  0.020  1.090
 82G  C17  H8   single    0.970  0.020  1.090
 82G  C17  H9   single    0.970  0.020  1.090
 82G  C20  H10  single    0.970  0.020  1.090
 82G  C21  H11  single    0.970  0.020  1.090
 82G  C22  H12  single    0.970  0.020  1.090
 82G  C22  H13  single    0.970  0.020  1.090
 82G  C22  H14  single    0.970  0.020  1.090
 82G  C24  H15  single    0.970  0.020  1.090
 82G  C24  H16  single    0.970  0.020  1.090
 82G  C24  H17  single    0.970  0.020  1.090
 82G  C1   H18  single    0.930  0.020  1.080
 82G  C2   H19  single    0.930  0.020  1.080
 82G  C3   H20  single    0.930  0.020  1.080
 82G  C16  H21  single    0.970  0.020  1.090
 82G  C16  H22  single    0.970  0.020  1.090
 82G  C18  H23  single    0.970  0.020  1.090
 82G  C18  H24  single    0.970  0.020  1.090
 82G  C19  H25  single    0.970  0.020  1.090
 82G  C23  H26  single    0.970  0.020  1.090
 82G  C23  H27  single    0.970  0.020  1.090
 82G  C23  H28  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
 82G  H1   C4   C9   120.63  3.000
 82G  H1   C4   C1   120.33  3.000
 82G  C9   C4   C1   119.04  3.000
 82G  H2   C5   C3   120.40  3.000
 82G  H2   C5   C10  120.70  3.000
 82G  C3   C5   C10  118.90  3.000
 82G  H3   C6   C2   120.68  3.000
 82G  H3   C6   C13  121.84  3.000
 82G  C2   C6   C13  117.48  3.000
 82G  H4   C7   C14  120.05  3.000
 82G  H4   C7   C3   120.90  3.000
 82G  C14  C7   C3   119.04  3.000
 82G  H5   C8   N25  120.29  3.000
 82G  H5   C8   C11  128.93  3.000
 82G  N25  C8   C11  110.78  3.000
 82G  C12  C10  C15  110.33  3.000
 82G  C15  C10  C5   128.32  3.000
 82G  C12  C10  C5   121.32  3.000
 82G  N25  C13  C9   107.72  3.000
 82G  N25  C13  C6   130.12  3.000
 82G  C9   C13  C6   122.16  3.000
 82G  H7   C15  H6   106.71  3.000
 82G  H7   C15  C16  111.11  3.000
 82G  H6   C15  C16  112.98  3.000
 82G  H7   C15  C10  109.65  3.000
 82G  H6   C15  C10  112.84  3.000
 82G  C16  C15  C10  103.60  3.000
 82G  H9   C17  H8   107.30  3.000
 82G  H9   C17  N26  111.75  3.000
 82G  H8   C17  N26  112.80  3.000
 82G  H9   C17  C19  112.48  3.000
 82G  H8   C17  C19  109.36  3.000
 82G  N26  C17  C19  103.21  3.000
 82G  H10  C20  N26  106.51  3.000
 82G  H10  C20  C16  108.66  3.000
 82G  N26  C20  C16  116.86  3.000
 82G  H10  C20  C12  108.29  3.000
 82G  C16  C20  C12  102.45  3.000
 82G  N26  C20  C12  113.77  3.000
 82G  H11  C21  N27  110.21  3.000
 82G  H11  C21  C19  108.64  3.000
 82G  N27  C21  C19  112.80  3.000
 82G  H11  C21  C18  107.74  3.000
 82G  C19  C21  C18  103.62  3.000
 82G  N27  C21  C18  113.48  3.000
 82G  H17  C24  H16  107.82  3.000
 82G  H17  C24  H15  107.61  3.000
 82G  H16  C24  H15  107.23  3.000
 82G  H17  C24  N27  113.17  3.000
 82G  H16  C24  N27  111.20  3.000
 82G  H15  C24  N27  109.57  3.000
 82G  H18  C1   C2   119.27  3.000
 82G  H18  C1   C4   119.70  3.000
 82G  C2   C1   C4   121.03  3.000
 82G  H19  C2   C1   119.32  3.000
 82G  H19  C2   C6   119.39  3.000
 82G  C1   C2   C6   121.29  3.000
 82G  H20  C3   C7   119.16  3.000
 82G  H20  C3   C5   120.14  3.000
 82G  C7   C3   C5   120.70  3.000
 82G  C11  C9   C13  107.16  3.000
 82G  C13  C9   C4   118.99  3.000
 82G  C11  C9   C4   133.85  3.000
 82G  C19  C11  C9   126.75  3.000
 82G  C9   C11  C8   105.78  3.000
 82G  C19  C11  C8   127.44  3.000
 82G  C14  C12  C20  130.09  3.000
 82G  C20  C12  C10  111.38  3.000
 82G  C14  C12  C10  118.48  3.000
 82G  F28  C14  C12  120.08  3.000
 82G  C12  C14  C7   121.53  3.000
 82G  F28  C14  C7   118.39  3.000
 82G  H22  C16  H21  107.33  3.000
 82G  H22  C16  C20  112.03  3.000
 82G  H21  C16  C20  109.48  3.000
 82G  H22  C16  C15  112.69  3.000
 82G  H21  C16  C15  109.28  3.000
 82G  C20  C16  C15  106.00  3.000
 82G  H24  C18  H23  107.84  3.000
 82G  H24  C18  N26  112.90  3.000
 82G  H23  C18  N26  110.88  3.000
 82G  H24  C18  C21  109.45  3.000
 82G  H23  C18  C21  113.22  3.000
 82G  N26  C18  C21  102.59  3.000
 82G  H25  C19  C11  108.58  3.000
 82G  H25  C19  C21  108.85  3.000
 82G  C11  C19  C21  113.69  3.000
 82G  H25  C19  C17  108.51  3.000
 82G  C11  C19  C17  113.12  3.000
 82G  C21  C19  C17  103.87  3.000
 82G  H28  C23  H27  107.74  3.000
 82G  H28  C23  H26  107.49  3.000
 82G  H27  C23  H26  107.46  3.000
 82G  H28  C23  N27  113.07  3.000
 82G  H27  C23  N27  109.68  3.000
 82G  H26  C23  N27  111.19  3.000
 82G  C22  N25  C13  125.36  3.000
 82G  C22  N25  C8   126.08  3.000
 82G  C13  N25  C8   108.56  3.000
 82G  C18  N26  C20  115.46  3.000
 82G  C18  N26  C17  104.75  3.000
 82G  C20  N26  C17  118.15  3.000
 82G  C23  N27  C24  109.70  3.000
 82G  C24  N27  C21  111.75  3.000
 82G  C23  N27  C21  111.34  3.000
 82G  H14  C22  H13  108.27  3.000
 82G  H14  C22  H12  108.47  3.000
 82G  H13  C22  H12  108.61  3.000
 82G  H14  C22  N25  109.21  3.000
 82G  H13  C22  N25  110.93  3.000
 82G  H12  C22  N25  111.26  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
 82G  CONST_01  C8   C11  C9   C4    180.00   0.0  0
 82G  CONST_02  N25  C13  C9   C4    180.00   0.0  0
 82G  CONST_03  C6   C13  C9   C4      0.00   0.0  0
 82G  CONST_04  C6   C2   C1   C4      0.00   0.0  0
 82G  CONST_05  C14  C7   C3   C5      0.00   0.0  0
 82G  CONST_06  C14  C12  C10  C5      0.00   0.0  0
 82G  CONST_07  C11  C9   C13  C6    180.00   0.0  0
 82G  CONST_08  C8   N25  C13  C6    180.00   0.0  0
 82G  CONST_09  C10  C12  C14  C7      0.00   0.0  0
 82G  CONST_10  C10  C5   C3   C7      0.00   0.0  0
 82G  CONST_11  C13  C9   C11  C8      0.00   0.0  0
 82G  CONST_12  C9   C13  N25  C8      0.00   0.0  0
 82G  CONST_13  C1   C4   C9   C13     0.00   0.0  0
 82G  CONST_14  C11  C8   N25  C13     0.00   0.0  0
 82G  CONST_15  C1   C2   C6   C13     0.00   0.0  0
 82G  CONST_16  C11  C9   C4   C1    180.00   0.0  0
 82G  CONST_17  C9   C4   C1   C2      0.00   0.0  0
 82G  CONST_18  C9   C13  C6   C2      0.00   0.0  0
 82G  CONST_19  N25  C13  C6   C2    180.00   0.0  0
 82G  CONST_20  C12  C14  C7   C3      0.00   0.0  0
 82G  CONST_21  C12  C10  C5   C3      0.00   0.0  0
 82G  CONST_22  N25  C8   C11  C9      0.00   0.0  0
 82G  CONST_23  N25  C13  C9   C11     0.00   0.0  0
 82G  CONST_24  C19  C11  C9   C4      0.00   0.0  0
 82G  CONST_25  C19  C11  C9   C13   180.00   0.0  0
 82G  CONST_26  N25  C8   C11  C19   180.00   0.0  0
 82G  CONST_27  C22  N25  C13  C6      0.00   0.0  0
 82G  CONST_28  F28  C14  C12  C10   180.00   0.0  0
 82G  CONST_29  F28  C14  C12  C20     0.00   0.0  0
 82G  CONST_30  C11  C8   N25  C22   180.00   0.0  0
 82G  CONST_31  C9   C13  N25  C22   180.00   0.0  0
 82G  CONST_32  F28  C14  C7   C3    180.00   0.0  0
 82G  CONST_33  H19  C2   C1   C4    180.00   0.0  0
 82G  CONST_34  H4   C7   C3   C5    180.00   0.0  0
 82G  CONST_35  H18  C1   C2   C6    180.00   0.0  0
 82G  CONST_36  H2   C5   C3   C7    180.00   0.0  0
 82G  CONST_37  H20  C3   C5   C10   180.00   0.0  0
 82G  CONST_38  H1   C4   C9   C13   180.00   0.0  0
 82G  CONST_39  H5   C8   N25  C13   180.00   0.0  0
 82G  CONST_40  H3   C6   C2   C1    180.00   0.0  0
 82G  Var_01    C16  C15  C10  C5   -165.94  30.0  1
 82G  Var_02    C20  C16  C15  C10   -24.35  30.0  1
 82G  Var_03    C21  C18  N26  C17   -47.19  30.0  1
 82G  Var_04    C19  C17  N26  C20   174.20  30.0  1
 82G  Var_05    H12  C22  N25  C8    114.71  30.0  2
 82G  Var_06    H26  C23  N27  C21    60.31  30.0  3
 82G  Var_07    H15  C24  N27  C21  -179.77  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
 82G  chir_01  C20  C12  N26  C16  negativ
 82G  chir_02  C21  N27  C18  C19  negativ
 82G  chir_03  C19  C21  C17  C11  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
 82G  plan-1  C4   0.020
 82G  plan-1  C6   0.020
 82G  plan-1  C8   0.020
 82G  plan-1  C13  0.020
 82G  plan-1  C1   0.020
 82G  plan-1  C2   0.020
 82G  plan-1  C9   0.020
 82G  plan-1  C11  0.020
 82G  plan-1  C19  0.020
 82G  plan-1  N25  0.020
 82G  plan-1  H1   0.020
 82G  plan-1  H3   0.020
 82G  plan-1  H5   0.020
 82G  plan-1  H18  0.020
 82G  plan-1  H19  0.020
 82G  plan-1  C22  0.020
 82G  plan-2  C5   0.020
 82G  plan-2  C7   0.020
 82G  plan-2  C10  0.020
 82G  plan-2  C15  0.020
 82G  plan-2  C20  0.020
 82G  plan-2  C3   0.020
 82G  plan-2  C12  0.020
 82G  plan-2  C14  0.020
 82G  plan-2  F28  0.020
 82G  plan-2  H4   0.020
 82G  plan-2  H20  0.020
 82G  plan-2  H2   0.020

