# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:40:47 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: (3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@H]2CC[C@@H](C1)N2Cc3ccccc3
#
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
 R9V  R9V  (3-endo)-8-benzyl-8-azabicyclo[3.2.1]octan-3-ol  ligand  35  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R9V
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
 R9V  C4   C  CR16  0  -0.318  20.5677  -1.4947  54.5522
 R9V  C5   C  CR16  0  -0.242  21.9083  -1.1282  54.5801
 R9V  C6   C  CH2   0  -0.326  18.5575  -2.6441  55.5446
 R9V  C7   C  CH1   0  -0.133  16.5780  -3.1330  56.8797
 R9V  C8   C  CH2   0  -0.451  15.6529  -2.1339  56.1500
 R9V  C9   C  CH2   0  -0.455  16.3445  -0.7744  56.3745
 R9V  C10  C  CH1   0  -0.122  17.6004  -1.1361  57.2001
 R9V  C11  C  CH2   0  -0.449  17.3626  -1.1118  58.7072
 R9V  C12  C  CH1   0   0.029  16.2230  -2.0320  59.1575
 R9V  C13  C  CH2   0  -0.426  16.2183  -3.3304  58.3519
 R9V  O    O  OH1   0  -0.669  14.9480  -1.4253  59.0199
 R9V  N    N  NT    0  -0.402  17.9050  -2.5201  56.8326
 R9V  C3   C  CR6   0   0.097  20.0006  -2.2105  55.6017
 R9V  C2   C  CR16  0  -0.287  20.8023  -2.5433  56.6923
 R9V  C1   C  CR16  0  -0.242  22.1404  -2.1783  56.7249
 R9V  C    C  CR16  0  -0.272  22.6998  -1.4693  55.6676
 R9V  H1   H  HCR6  0   0.245  19.9541  -1.2138  53.7035
 R9V  H2   H  HCR6  0   0.252  22.3303  -0.5696  53.7544
 R9V  H3   H  HCH2  0   0.214  18.0543  -2.0958  54.7330
 R9V  H4   H  HCH2  0   0.250  18.5185  -3.7002  55.2578
 R9V  H5   H  HCH1  0   0.233  16.6003  -4.1095  56.3897
 R9V  H6   H  HCH2  0   0.235  14.6319  -2.1610  56.5262
 R9V  H7   H  HCH2  0   0.229  15.6070  -2.3751  55.0862
 R9V  H8   H  HCH2  0   0.229  16.6320  -0.3221  55.4237
 R9V  H9   H  HCH2  0   0.233  15.7078  -0.0530  56.8847
 R9V  H10  H  HCH1  0   0.236  18.4477  -0.4864  56.9691
 R9V  H11  H  HCH2  0   0.228  18.2866  -1.4360  59.1940
 R9V  H12  H  HCH2  0   0.229  17.1761  -0.0889  59.0506
 R9V  H13  H  HCH1  0   0.208  16.3890  -2.2830  60.2143
 R9V  H14  H  HCH2  0   0.230  15.2440  -3.8168  58.4476
 R9V  H15  H  HCH2  0   0.228  16.9533  -4.0119  58.7872
 R9V  H16  H  HOH1  0   0.443  14.9760  -0.5719  59.4633
 R9V  H18  H  HCR6  0   0.243  20.3646  -3.0804  57.5242
 R9V  H19  H  HCR6  0   0.250  22.7503  -2.4460  57.5788
 R9V  H20  H  HCR6  0   0.252  23.7432  -1.1823  55.6950

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
 R9V  C4   C5   aromatic  1.390  0.020  1.390
 R9V  C4   C3   aromatic  1.391  0.020  1.391
 R9V  C5   C    aromatic  1.388  0.020  1.388
 R9V  C3   C6   single    1.508  0.020  1.508
 R9V  C3   C2   aromatic  1.394  0.020  1.394
 R9V  C6   N    single    1.449  0.020  1.449
 R9V  C    C1   aromatic  1.390  0.020  1.390
 R9V  C8   C9   single    1.542  0.020  1.542
 R9V  C8   C7   single    1.545  0.020  1.545
 R9V  C9   C10  single    1.546  0.020  1.546
 R9V  C2   C1   aromatic  1.387  0.020  1.387
 R9V  N    C7   single    1.462  0.020  1.462
 R9V  N    C10  single    1.464  0.020  1.464
 R9V  C7   C13  single    1.528  0.020  1.528
 R9V  C10  C11  single    1.526  0.020  1.526
 R9V  C13  C12  single    1.528  0.020  1.528
 R9V  C11  C12  single    1.532  0.020  1.532
 R9V  O    C12  single    1.419  0.020  1.419
 R9V  C4   H1   single    0.930  0.020  1.080
 R9V  C5   H2   single    0.930  0.020  1.080
 R9V  C6   H3   single    0.970  0.020  1.090
 R9V  C6   H4   single    0.970  0.020  1.090
 R9V  C7   H5   single    0.970  0.020  1.090
 R9V  C8   H6   single    0.970  0.020  1.090
 R9V  C8   H7   single    0.970  0.020  1.090
 R9V  C9   H8   single    0.970  0.020  1.090
 R9V  C9   H9   single    0.970  0.020  1.090
 R9V  C10  H10  single    0.970  0.020  1.090
 R9V  C11  H11  single    0.970  0.020  1.090
 R9V  C11  H12  single    0.970  0.020  1.090
 R9V  C12  H13  single    0.970  0.020  1.090
 R9V  C13  H14  single    0.970  0.020  1.090
 R9V  C13  H15  single    0.970  0.020  1.090
 R9V  O    H16  single    0.850  0.020  0.980
 R9V  C2   H18  single    0.930  0.020  1.080
 R9V  C1   H19  single    0.930  0.020  1.080
 R9V  C    H20  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
 R9V  H1   C4   C3   119.54  3.000
 R9V  H1   C4   C5   119.55  3.000
 R9V  C3   C4   C5   120.90  3.000
 R9V  H2   C5   C    120.15  3.000
 R9V  H2   C5   C4   119.78  3.000
 R9V  C    C5   C4   120.07  3.000
 R9V  H4   C6   H3   105.72  3.000
 R9V  H4   C6   C3   108.75  3.000
 R9V  H3   C6   C3   108.79  3.000
 R9V  H4   C6   N    107.41  3.000
 R9V  H3   C6   N    114.00  3.000
 R9V  C3   C6   N    111.88  3.000
 R9V  H5   C7   N    109.97  3.000
 R9V  H5   C7   C13  108.74  3.000
 R9V  N    C7   C13  107.38  3.000
 R9V  H5   C7   C8   112.23  3.000
 R9V  C13  C7   C8   113.43  3.000
 R9V  N    C7   C8   104.90  3.000
 R9V  H7   C8   H6   106.97  3.000
 R9V  H7   C8   C9   110.83  3.000
 R9V  H6   C8   C9   113.11  3.000
 R9V  H7   C8   C7   110.04  3.000
 R9V  H6   C8   C7   112.48  3.000
 R9V  C9   C8   C7   103.47  3.000
 R9V  H9   C9   H8   106.72  3.000
 R9V  H9   C9   C10  112.32  3.000
 R9V  H8   C9   C10  110.37  3.000
 R9V  H9   C9   C8   112.96  3.000
 R9V  H8   C9   C8   110.89  3.000
 R9V  C10  C9   C8   103.64  3.000
 R9V  H10  C10  N    110.36  3.000
 R9V  H10  C10  C11  108.67  3.000
 R9V  N    C10  C11  107.18  3.000
 R9V  H10  C10  C9   112.22  3.000
 R9V  C11  C10  C9   113.40  3.000
 R9V  N    C10  C9   104.84  3.000
 R9V  H12  C11  H11  106.34  3.000
 R9V  H12  C11  C12  110.01  3.000
 R9V  H11  C11  C12  108.64  3.000
 R9V  H12  C11  C10  110.55  3.000
 R9V  H11  C11  C10  107.65  3.000
 R9V  C12  C11  C10  113.36  3.000
 R9V  H13  C12  O    109.07  3.000
 R9V  H13  C12  C13  108.26  3.000
 R9V  O    C12  C13  108.03  3.000
 R9V  H13  C12  C11  107.90  3.000
 R9V  O    C12  C11  112.53  3.000
 R9V  C13  C12  C11  110.96  3.000
 R9V  H15  C13  H14  106.68  3.000
 R9V  H15  C13  C12  108.53  3.000
 R9V  H14  C13  C12  109.55  3.000
 R9V  H15  C13  C7   107.82  3.000
 R9V  H14  C13  C7   110.59  3.000
 R9V  C12  C13  C7   113.41  3.000
 R9V  H16  O    C12  107.97  3.000
 R9V  C10  N    C7   101.50  3.000
 R9V  C10  N    C6   113.43  3.000
 R9V  C7   N    C6   113.67  3.000
 R9V  C2   C3   C6   120.76  3.000
 R9V  C2   C3   C4   118.60  3.000
 R9V  C6   C3   C4   120.63  3.000
 R9V  H18  C2   C1   120.16  3.000
 R9V  H18  C2   C3   119.15  3.000
 R9V  C1   C2   C3   120.68  3.000
 R9V  H19  C1   C    119.93  3.000
 R9V  H19  C1   C2   119.78  3.000
 R9V  C    C1   C2   120.29  3.000
 R9V  H20  C    C1   120.25  3.000
 R9V  H20  C    C5   120.30  3.000
 R9V  C1   C    C5   119.46  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
 R9V  CONST_01  C1   C   C5  C4     0.00   0.0  0
 R9V  CONST_02  C1   C2  C3  C4     0.00   0.0  0
 R9V  CONST_03  C2   C3  C4  C5     0.00   0.0  0
 R9V  CONST_04  C2   C1  C   C5     0.00   0.0  0
 R9V  CONST_05  C    C5  C4  C3     0.00   0.0  0
 R9V  CONST_06  C    C1  C2  C3     0.00   0.0  0
 R9V  CONST_07  C6   C3  C4  C5   180.00   0.0  0
 R9V  CONST_08  C1   C2  C3  C6   180.00   0.0  0
 R9V  CONST_09  H20  C   C5  C4   180.00   0.0  0
 R9V  CONST_10  H18  C2  C3  C4   180.00   0.0  0
 R9V  CONST_11  H19  C1  C   C5   180.00   0.0  0
 R9V  CONST_12  H2   C5  C4  C3   180.00   0.0  0
 R9V  CONST_13  H1   C4  C3  C2   180.00   0.0  0
 R9V  Var_01    C10  C9  C8  C7     0.44  30.0  3
 R9V  Var_02    N    C6  C3  C4  -140.96  30.0  2
 R9V  Var_03    C3   C6  N   C7  -170.42  30.0  1

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
 R9V  chir_01  C7   C8  N    C13  negativ
 R9V  chir_02  C10  N   C9   C11  negativ
 R9V  chir_03  C12  O   C11  C13  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
 R9V  plan-1  C4   0.020
 R9V  plan-1  C5   0.020
 R9V  plan-1  C6   0.020
 R9V  plan-1  C3   0.020
 R9V  plan-1  C2   0.020
 R9V  plan-1  C1   0.020
 R9V  plan-1  C    0.020
 R9V  plan-1  H1   0.020
 R9V  plan-1  H2   0.020
 R9V  plan-1  H18  0.020
 R9V  plan-1  H19  0.020
 R9V  plan-1  H20  0.020

