# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 04:59:45 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: methyl (1R,2S,3S,5S)-3-(4-fluorophenyl)-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(F)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
 42L  42L  'methyl (1R,2S,3S,5S)-3-(4-fluorophenyl)-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_42L
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
 42L  F    F  F     0  -0.319   5.3511  -0.6904   0.5684
 42L  C13  C  CR6   0   0.506   4.0120  -0.7598   0.4658
 42L  C12  C  CR16  0  -0.396   3.4517  -1.2448  -0.6996
 42L  C11  C  CR16  0  -0.299   2.0691  -1.3123  -0.7854
 42L  C14  C  CR16  0  -0.399   3.2353  -0.3496   1.5301
 42L  C15  C  CR16  0  -0.291   1.8526  -0.4207   1.4174
 42L  C10  C  CR6   0   0.160   1.2438  -0.8999   0.2610
 42L  C6   C  CH1   0  -0.335  -0.2540  -0.9835   0.0768
 42L  C7   C  CH1   0  -0.354  -0.8019   0.1723  -0.7868
 42L  C8   C  C     0   0.618  -0.3781   1.5389  -0.3104
 42L  O1   O  O2    0  -0.458  -0.2230   2.3724  -1.3373
 42L  C9   C  CH3   0  -0.424   0.1341   3.7212  -1.0414
 42L  O    O  O     0  -0.435  -0.2173   1.8752   0.8346
 42L  C1   C  CR15  0  -0.124  -2.3432   0.1131  -0.8349
 42L  C5   C  CH2   0  -0.400  -1.0677  -1.1768   1.3571
 42L  C4   C  CR15  0  -0.127  -2.5653  -1.1011   1.0649
 42L  C3   C  CH2   0  -0.474  -2.9897  -2.0894  -0.0464
 42L  C2   C  CH2   0  -0.469  -2.8297  -1.2669  -1.3394
 42L  N    N  NR5   0  -0.385  -2.8509   0.2268   0.5239
 42L  C    C  CH3   0  -0.529  -4.2549   0.5811   0.5761
 42L  H1   H  HCR6  0   0.276   4.0770  -1.5713  -1.5205
 42L  H2   H  HCR6  0   0.258   1.6231  -1.7014  -1.6932
 42L  H3   H  HCR6  0   0.275   3.6967   0.0250   2.4346
 42L  H4   H  HCR6  0   0.254   1.2560  -0.0952   2.2576
 42L  H5   H  HCH1  0   0.266  -0.4139  -1.8778  -0.5351
 42L  H6   H  HCH1  0   0.278  -0.4393   0.0440  -1.8106
 42L  H7   H  HCH3  0   0.250   0.2624   4.2150  -2.0005
 42L  H8   H  HCH3  0   0.236  -0.6501   4.2276  -0.4784
 42L  H9   H  HCH3  0   0.236   1.0677   3.7739  -0.4817
 42L  H10  H  HCR5  0   0.255  -2.7186   0.9300  -1.4557
 42L  H11  H  HCH2  0   0.234  -0.8205  -2.1478   1.7934
 42L  H12  H  HCH2  0   0.237  -0.8337  -0.4148   2.1006
 42L  H13  H  HCR5  0   0.239  -3.1210  -1.2573   1.9921
 42L  H14  H  HCH2  0   0.240  -2.3780  -2.9936  -0.0433
 42L  H15  H  HCH2  0   0.244  -4.0225  -2.4109   0.0929
 42L  H16  H  HCH2  0   0.249  -3.7815  -1.1596  -1.8606
 42L  H17  H  HCH2  0   0.243  -2.1337  -1.7175  -2.0490
 42L  H19  H  HCH3  0   0.199  -4.9281  -0.1010   0.0379
 42L  H20  H  HCH3  0   0.234  -4.5827   0.6136   1.6159
 42L  H21  H  HCH3  0   0.234  -4.3959   1.5780   0.1558

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
 42L  C2   C3   single    1.541  0.020  1.541
 42L  C2   C1   single    1.548  0.020  1.548
 42L  C3   C4   single    1.547  0.020  1.547
 42L  C1   N    single    1.455  0.020  1.455
 42L  C1   C7   single    1.543  0.020  1.543
 42L  C    N    single    1.449  0.020  1.449
 42L  N    C4   single    1.462  0.020  1.462
 42L  C4   C5   single    1.528  0.020  1.528
 42L  C7   C6   single    1.543  0.020  1.543
 42L  C7   C8   single    1.508  0.020  1.508
 42L  C6   C5   single    1.529  0.020  1.529
 42L  C6   C10  single    1.511  0.020  1.511
 42L  C15  C10  aromatic  1.392  0.020  1.392
 42L  C15  C14  aromatic  1.389  0.020  1.389
 42L  C8   O1   single    1.332  0.020  1.332
 42L  C8   O    double    1.204  0.020  1.204
 42L  C10  C11  aromatic  1.395  0.020  1.395
 42L  O1   C9   single    1.426  0.020  1.426
 42L  C14  C13  aromatic  1.380  0.020  1.380
 42L  C11  C12  aromatic  1.387  0.020  1.387
 42L  C13  C12  aromatic  1.381  0.020  1.381
 42L  C13  F    single    1.345  0.020  1.345
 42L  C12  H1   single    0.930  0.020  1.080
 42L  C11  H2   single    0.930  0.020  1.080
 42L  C14  H3   single    0.930  0.020  1.080
 42L  C15  H4   single    0.930  0.020  1.080
 42L  C6   H5   single    0.970  0.020  1.090
 42L  C7   H6   single    0.970  0.020  1.090
 42L  C9   H7   single    0.970  0.020  1.090
 42L  C9   H8   single    0.970  0.020  1.090
 42L  C9   H9   single    0.970  0.020  1.090
 42L  C1   H10  single    0.970  0.020  1.090
 42L  C5   H11  single    0.970  0.020  1.090
 42L  C5   H12  single    0.970  0.020  1.090
 42L  C4   H13  single    0.970  0.020  1.090
 42L  C3   H14  single    0.970  0.020  1.090
 42L  C3   H15  single    0.970  0.020  1.090
 42L  C2   H16  single    0.970  0.020  1.090
 42L  C2   H17  single    0.970  0.020  1.090
 42L  C    H19  single    0.970  0.020  1.090
 42L  C    H20  single    0.970  0.020  1.090
 42L  C    H21  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
 42L  C14  C13  C12  121.79  3.000
 42L  C12  C13  F    119.11  3.000
 42L  C14  C13  F    119.09  3.000
 42L  H1   C12  C11  120.95  3.000
 42L  H1   C12  C13  120.76  3.000
 42L  C11  C12  C13  118.28  3.000
 42L  H2   C11  C10  119.41  3.000
 42L  H2   C11  C12  118.66  3.000
 42L  C10  C11  C12  121.93  3.000
 42L  H3   C14  C15  120.65  3.000
 42L  H3   C14  C13  120.50  3.000
 42L  C15  C14  C13  118.85  3.000
 42L  H4   C15  C10  120.54  3.000
 42L  H4   C15  C14  118.10  3.000
 42L  C10  C15  C14  121.35  3.000
 42L  C6   C10  C15  123.62  3.000
 42L  C15  C10  C11  117.79  3.000
 42L  C6   C10  C11  118.59  3.000
 42L  H5   C6   C5   106.67  3.000
 42L  H5   C6   C7   104.30  3.000
 42L  C5   C6   C7   111.98  3.000
 42L  H5   C6   C10  104.94  3.000
 42L  C5   C6   C10  115.61  3.000
 42L  C7   C6   C10  112.25  3.000
 42L  H6   C7   C1   107.31  3.000
 42L  H6   C7   C8   107.99  3.000
 42L  C1   C7   C8   108.98  3.000
 42L  H6   C7   C6   108.56  3.000
 42L  C8   C7   C6   113.71  3.000
 42L  C1   C7   C6   110.08  3.000
 42L  O    C8   O1   122.88  3.000
 42L  O    C8   C7   126.23  3.000
 42L  O1   C8   C7   110.87  3.000
 42L  C9   O1   C8   117.46  3.000
 42L  H9   C9   H8   109.18  3.000
 42L  H9   C9   H7   109.28  3.000
 42L  H8   C9   H7   109.26  3.000
 42L  H9   C9   O1   111.51  3.000
 42L  H8   C9   O1   111.49  3.000
 42L  H7   C9   O1   106.04  3.000
 42L  H10  C1   N    110.63  3.000
 42L  H10  C1   C2   111.93  3.000
 42L  N    C1   C2   105.33  3.000
 42L  H10  C1   C7   109.40  3.000
 42L  N    C1   C7   108.45  3.000
 42L  C2   C1   C7   110.99  3.000
 42L  H12  C5   H11  107.48  3.000
 42L  H12  C5   C4   107.83  3.000
 42L  H11  C5   C4   110.01  3.000
 42L  H12  C5   C6   111.62  3.000
 42L  H11  C5   C6   109.03  3.000
 42L  C4   C5   C6   110.80  3.000
 42L  H13  C4   N    110.16  3.000
 42L  H13  C4   C3   112.27  3.000
 42L  N    C4   C3   105.12  3.000
 42L  H13  C4   C5   109.23  3.000
 42L  N    C4   C5   107.90  3.000
 42L  C3   C4   C5   112.01  3.000
 42L  H15  C3   H14  106.63  3.000
 42L  H15  C3   C2   111.28  3.000
 42L  H14  C3   C2   112.73  3.000
 42L  H15  C3   C4   110.88  3.000
 42L  H14  C3   C4   111.93  3.000
 42L  C2   C3   C4   103.49  3.000
 42L  H17  C2   H16  106.64  3.000
 42L  H17  C2   C3   113.05  3.000
 42L  H16  C2   C3   111.28  3.000
 42L  H17  C2   C1   112.32  3.000
 42L  H16  C2   C1   110.03  3.000
 42L  C3   C2   C1   103.60  3.000
 42L  C    N    C4   113.46  3.000
 42L  C4   N    C1   101.91  3.000
 42L  C    N    C1   113.01  3.000
 42L  H21  C    H20  107.53  3.000
 42L  H21  C    H19  107.42  3.000
 42L  H20  C    H19  107.53  3.000
 42L  H21  C    N    109.56  3.000
 42L  H20  C    N    109.44  3.000
 42L  H19  C    N    115.09  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
 42L  CONST_01  C10  C15  C14  C13    0.00   0.0  0
 42L  CONST_02  C10  C11  C12  C13    0.00   0.0  0
 42L  CONST_03  C15  C10  C11  C12    0.00   0.0  0
 42L  CONST_04  C15  C14  C13  C12    0.00   0.0  0
 42L  CONST_05  C14  C15  C10  C11    0.00   0.0  0
 42L  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 42L  CONST_07  C6   C10  C11  C12  180.00   0.0  0
 42L  CONST_08  C6   C10  C15  C14  180.00   0.0  0
 42L  CONST_09  C15  C14  C13  F    180.00   0.0  0
 42L  CONST_10  C11  C12  C13  F    180.00   0.0  0
 42L  CONST_11  H4   C15  C14  C13  180.00   0.0  0
 42L  CONST_12  H2   C11  C12  C13  180.00   0.0  0
 42L  CONST_13  H3   C14  C13  C12  180.00   0.0  0
 42L  CONST_14  H1   C12  C13  C14  180.00   0.0  0
 42L  Var_01    C4   C3   C2   C1    -0.54  30.0  3
 42L  Var_02    H19  C    N    C1    56.69  30.0  3
 42L  Var_03    O    C8   O1   C9    -0.76  30.0  2
 42L  Var_04    H7   C9   O1   C8   177.05  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
 42L  chir_01  C6  C7  C5  C10  positiv
 42L  chir_02  C7  C1  C6  C8   positiv
 42L  chir_03  C1  N   C7  C2   negativ
 42L  chir_04  C4  N   C3  C5   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
 42L  plan-1  F    0.020
 42L  plan-1  C13  0.020
 42L  plan-1  C12  0.020
 42L  plan-1  C11  0.020
 42L  plan-1  C14  0.020
 42L  plan-1  C15  0.020
 42L  plan-1  C10  0.020
 42L  plan-1  C6   0.020
 42L  plan-1  H1   0.020
 42L  plan-1  H2   0.020
 42L  plan-1  H3   0.020
 42L  plan-1  H4   0.020
 42L  plan-2  C7   0.020
 42L  plan-2  C8   0.020
 42L  plan-2  O1   0.020
 42L  plan-2  O    0.020

