# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 05:32:43 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: methyl (1R,2S,3S,5S)-3-(4-iodophenyl)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H]1[C@H]2CC[C@@H](C[C@@H]1c3ccc(I)cc3)N2C
#
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
 42F  42F  'methyl (1R,2S,3S,5S)-3-(4-iodophenyl)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylate'  ligand  40  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_42F
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
 42F  O    O  O     0  -0.434   1.8760  -1.8892   0.7832
 42F  C14  C  C     0   0.619   2.1136  -1.5626  -0.3511
 42F  O1   O  O2    0  -0.459   2.0928  -2.4190  -1.3700
 42F  C15  C  CH3   0  -0.422   1.7934  -3.7828  -1.0790
 42F  C5   C  CH1   0  -0.356   2.5025  -0.1825  -0.8198
 42F  C4   C  CR15  0  -0.125   4.0420  -0.0806  -0.8314
 42F  C3   C  CH2   0  -0.469   4.5082   1.3124  -1.3161
 42F  C2   C  CH2   0  -0.473   4.6147   2.1320  -0.0156
 42F  N    N  NR5   0  -0.386   4.5149  -0.1899   0.5403
 42F  C    C  CH3   0  -0.530   5.9244  -0.5151   0.6290
 42F  C6   C  CH1   0  -0.339   1.9050   0.9570   0.0314
 42F  C7   C  CH2   0  -0.401   2.6788   1.1698   1.3329
 42F  C1   C  CR15  0  -0.127   4.1849   1.1281   1.0797
 42F  C8   C  CR6   0   0.176   0.4056   0.8356   0.1729
 42F  C13  C  CR16  0  -0.308  -0.3976   1.2119  -0.9031
 42F  C12  C  CR16  0  -0.209  -1.7800   1.1110  -0.8567
 42F  C11  C  CR6   0  -0.241  -2.3778   0.6291   0.2983
 42F  I    I  I     0   0.042  -4.4744   0.4676   0.3955
 42F  C10  C  CR16  0  -0.208  -1.6093   0.2549   1.3891
 42F  C9   C  CR16  0  -0.301  -0.2257   0.3606   1.3180
 42F  H1   H  HCH3  0   0.236   0.8123  -3.8874  -0.6160
 42F  H2   H  HCH3  0   0.249   1.7957  -4.3001  -2.0342
 42F  H3   H  HCH3  0   0.236   2.5457  -4.2268  -0.4270
 42F  H4   H  HCH1  0   0.280   2.1590  -0.0650  -1.8520
 42F  H5   H  HCR5  0   0.256   4.4534  -0.8854  -1.4451
 42F  H6   H  HCH2  0   0.250   5.4773   1.2287  -1.8089
 42F  H7   H  HCH2  0   0.244   3.8233   1.7497  -2.0444
 42F  H8   H  HCH2  0   0.245   5.6358   2.4766   0.1519
 42F  H9   H  HCH2  0   0.240   3.9816   3.0212  -0.0247
 42F  H11  H  HCH3  0   0.200   6.5960   0.1792   0.1046
 42F  H12  H  HCH3  0   0.234   6.2272  -0.5372   1.6765
 42F  H13  H  HCH3  0   0.234   6.0951  -1.5107   0.2172
 42F  H14  H  HCH1  0   0.270   2.0567   1.8571  -0.5743
 42F  H15  H  HCH2  0   0.235   2.4017   2.1385   1.7564
 42F  H16  H  HCH2  0   0.238   2.4406   0.4084   2.0756
 42F  H17  H  HCR5  0   0.239   4.7119   1.2916   2.0223
 42F  H18  H  HCR6  0   0.258   0.0632   1.5995  -1.8046
 42F  H19  H  HCR6  0   0.276  -2.3682   1.4147  -1.7120
 42F  H20  H  HCR6  0   0.276  -2.0672  -0.1171   2.2955
 42F  H21  H  HCR6  0   0.254   0.3505   0.0681   2.1843

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
 42F  I    C11  single    2.105  0.020  2.105
 42F  C12  C11  aromatic  1.387  0.020  1.387
 42F  C12  C13  aromatic  1.387  0.020  1.387
 42F  C11  C10  aromatic  1.386  0.020  1.386
 42F  C13  C8   aromatic  1.394  0.020  1.394
 42F  C10  C9   aromatic  1.389  0.020  1.389
 42F  O1   C14  single    1.331  0.020  1.331
 42F  O1   C15  single    1.426  0.020  1.426
 42F  O    C14  double    1.204  0.020  1.204
 42F  C8   C9   aromatic  1.391  0.020  1.391
 42F  C8   C6   single    1.511  0.020  1.511
 42F  C14  C5   single    1.508  0.020  1.508
 42F  C7   C6   single    1.529  0.020  1.529
 42F  C7   C1   single    1.528  0.020  1.528
 42F  C6   C5   single    1.543  0.020  1.543
 42F  C5   C4   single    1.543  0.020  1.543
 42F  C1   N    single    1.462  0.020  1.462
 42F  C1   C2   single    1.547  0.020  1.547
 42F  N    C4   single    1.455  0.020  1.455
 42F  N    C    single    1.449  0.020  1.449
 42F  C4   C3   single    1.547  0.020  1.547
 42F  C2   C3   single    1.541  0.020  1.541
 42F  C15  H1   single    0.970  0.020  1.090
 42F  C15  H2   single    0.970  0.020  1.090
 42F  C15  H3   single    0.970  0.020  1.090
 42F  C5   H4   single    0.970  0.020  1.090
 42F  C4   H5   single    0.970  0.020  1.090
 42F  C3   H6   single    0.970  0.020  1.090
 42F  C3   H7   single    0.970  0.020  1.090
 42F  C2   H8   single    0.970  0.020  1.090
 42F  C2   H9   single    0.970  0.020  1.090
 42F  C    H11  single    0.970  0.020  1.090
 42F  C    H12  single    0.970  0.020  1.090
 42F  C    H13  single    0.970  0.020  1.090
 42F  C6   H14  single    0.970  0.020  1.090
 42F  C7   H15  single    0.970  0.020  1.090
 42F  C7   H16  single    0.970  0.020  1.090
 42F  C1   H17  single    0.970  0.020  1.090
 42F  C13  H18  single    0.930  0.020  1.080
 42F  C12  H19  single    0.930  0.020  1.080
 42F  C10  H20  single    0.930  0.020  1.080
 42F  C9   H21  single    0.930  0.020  1.080

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
 42F  C5   C14  O1   110.78  3.000
 42F  C5   C14  O    126.28  3.000
 42F  O1   C14  O    122.91  3.000
 42F  C15  O1   C14  117.54  3.000
 42F  H3   C15  H2   109.30  3.000
 42F  H3   C15  H1   109.16  3.000
 42F  H2   C15  H1   109.26  3.000
 42F  H3   C15  O1   111.50  3.000
 42F  H2   C15  O1   105.99  3.000
 42F  H1   C15  O1   111.55  3.000
 42F  H4   C5   C6   108.64  3.000
 42F  H4   C5   C4   107.40  3.000
 42F  C6   C5   C4   109.99  3.000
 42F  H4   C5   C14  108.08  3.000
 42F  C4   C5   C14  108.66  3.000
 42F  C6   C5   C14  113.86  3.000
 42F  H5   C4   N    110.60  3.000
 42F  H5   C4   C3   111.96  3.000
 42F  N    C4   C3   105.38  3.000
 42F  H5   C4   C5   109.34  3.000
 42F  C3   C4   C5   111.26  3.000
 42F  N    C4   C5   108.20  3.000
 42F  H7   C3   H6   106.67  3.000
 42F  H7   C3   C2   113.17  3.000
 42F  H6   C3   C2   111.15  3.000
 42F  H7   C3   C4   112.39  3.000
 42F  H6   C3   C4   109.90  3.000
 42F  C2   C3   C4   103.61  3.000
 42F  H9   C2   H8   106.67  3.000
 42F  H9   C2   C1   111.93  3.000
 42F  H8   C2   C1   110.88  3.000
 42F  H9   C2   C3   112.72  3.000
 42F  H8   C2   C3   111.25  3.000
 42F  C1   C2   C3   103.49  3.000
 42F  C1   N    C    113.53  3.000
 42F  C    N    C4   112.99  3.000
 42F  C1   N    C4   101.93  3.000
 42F  H13  C    H12  107.49  3.000
 42F  H13  C    H11  107.50  3.000
 42F  H12  C    H11  107.53  3.000
 42F  H13  C    N    109.51  3.000
 42F  H12  C    N    109.47  3.000
 42F  H11  C    N    115.05  3.000
 42F  H14  C6   C8   104.79  3.000
 42F  H14  C6   C7   106.63  3.000
 42F  C8   C6   C7   115.70  3.000
 42F  H14  C6   C5   104.37  3.000
 42F  C7   C6   C5   112.11  3.000
 42F  C8   C6   C5   112.13  3.000
 42F  H16  C7   H15  107.44  3.000
 42F  H16  C7   C1   108.02  3.000
 42F  H15  C7   C1   109.78  3.000
 42F  H16  C7   C6   111.85  3.000
 42F  H15  C7   C6   108.95  3.000
 42F  C1   C7   C6   110.73  3.000
 42F  H17  C1   C7   109.18  3.000
 42F  H17  C1   N    110.15  3.000
 42F  C7   C1   N    107.96  3.000
 42F  H17  C1   C2   112.33  3.000
 42F  N    C1   C2   105.14  3.000
 42F  C7   C1   C2   111.94  3.000
 42F  C9   C8   C13  117.77  3.000
 42F  C9   C8   C6   123.70  3.000
 42F  C13  C8   C6   118.53  3.000
 42F  H18  C13  C12  118.52  3.000
 42F  H18  C13  C8   119.57  3.000
 42F  C12  C13  C8   121.91  3.000
 42F  H19  C12  C11  121.45  3.000
 42F  H19  C12  C13  119.68  3.000
 42F  C11  C12  C13  118.87  3.000
 42F  C10  C11  I    119.69  3.000
 42F  C10  C11  C12  120.68  3.000
 42F  I    C11  C12  119.63  3.000
 42F  H20  C10  C9   119.39  3.000
 42F  H20  C10  C11  121.18  3.000
 42F  C9   C10  C11  119.43  3.000
 42F  H21  C9   C10  117.99  3.000
 42F  H21  C9   C8   120.68  3.000
 42F  C10  C9   C8   121.33  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
 42F  CONST_01  C11  C12  C13  C8     0.00   0.0  0
 42F  CONST_02  C11  C10  C9   C8     0.00   0.0  0
 42F  CONST_03  C10  C11  C12  C13    0.00   0.0  0
 42F  CONST_04  C10  C9   C8   C13    0.00   0.0  0
 42F  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 42F  CONST_06  C9   C8   C13  C12    0.00   0.0  0
 42F  CONST_07  C12  C13  C8   C6   180.00   0.0  0
 42F  CONST_08  C10  C9   C8   C6   180.00   0.0  0
 42F  CONST_09  I    C11  C12  C13  180.00   0.0  0
 42F  CONST_10  C9   C10  C11  I    180.00   0.0  0
 42F  CONST_11  H18  C13  C8   C6     0.00   0.0  0
 42F  CONST_12  H21  C9   C8   C6     0.00   0.0  0
 42F  CONST_13  H19  C12  C13  C8   180.00   0.0  0
 42F  CONST_14  H20  C10  C9   C8   180.00   0.0  0
 42F  Var_01    C1   C2   C3   C4    -0.54  30.0  3
 42F  Var_02    H11  C    N    C4    56.19  30.0  3
 42F  Var_03    C5   C14  O1   C15  177.56  30.0  3
 42F  Var_04    H1   C15  O1   C14   59.45  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
 42F  chir_01  C5  C14  C6  C4  negativ
 42F  chir_02  C4  N    C3  C5  positiv
 42F  chir_03  C6  C5   C7  C8  positiv
 42F  chir_04  C1  N    C2  C7  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
 42F  plan-1  C6   0.020
 42F  plan-1  C8   0.020
 42F  plan-1  C13  0.020
 42F  plan-1  C12  0.020
 42F  plan-1  C11  0.020
 42F  plan-1  I    0.020
 42F  plan-1  C10  0.020
 42F  plan-1  C9   0.020
 42F  plan-1  H18  0.020
 42F  plan-1  H19  0.020
 42F  plan-1  H20  0.020
 42F  plan-1  H21  0.020
 42F  plan-2  O    0.020
 42F  plan-2  C14  0.020
 42F  plan-2  O1   0.020
 42F  plan-2  C5   0.020

