# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:04:52 2021
#   Inital geometry file: a 105 line input string
#   Ligand name: (3~{S})-2-(cyclopropylmethyl)-3-[(~{S})-oxidanyl(phenyl)methyl]-2-azabicyclo[2.2.2]octan-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@@H]1N(CC2CC2)C3CCC1(O)CC3)c4ccccc4
#
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
 SRJ  SRJ  (3~{S})-2-(cyclopropylmethyl)-3-[(~{S})-oxidanyl(phenyl)methyl]-2-azabicyclo[2.2.2]octan-4-ol  ligand  46  21  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SRJ
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
 SRJ  C4   C  CH2   0  -0.500  47.7533  120.5060  31.0910
 SRJ  C5   C  CH2   0  -0.484  46.5774  120.0994  31.9250
 SRJ  C6   C  CH1   0  -0.131  46.3623  116.9014  32.9686
 SRJ  C7   C  CH2   0  -0.444  46.2864  115.8796  34.1007
 SRJ  C8   C  CH2   0  -0.486  46.4972  114.4686  33.5192
 SRJ  C10  C  CH2   0  -0.441  45.9129  115.2091  31.2190
 SRJ  C13  C  CR16  0  -0.300  51.4623  116.1188  31.9086
 SRJ  C15  C  CR16  0  -0.268  52.4908  118.1553  32.6787
 SRJ  C17  C  CR16  0  -0.277  50.5395  117.2871  33.7872
 SRJ  N    N  NT    0  -0.418  47.7298  116.9305  32.4627
 SRJ  C    C  CH1   0   0.016  49.3740  115.2042  32.9948
 SRJ  O    O  OH1   0  -0.679  49.8012  113.9066  32.6203
 SRJ  C1   C  CH1   0  -0.123  48.2026  115.6023  32.0739
 SRJ  C11  C  CH2   0  -0.456  45.3701  116.4880  31.8787
 SRJ  C12  C  CR6   0   0.089  50.4921  116.2135  32.9033
 SRJ  C14  C  CR16  0  -0.244  52.4559  117.0827  31.7972
 SRJ  C16  C  CR16  0  -0.247  51.5293  118.2535  33.6762
 SRJ  C2   C  CH2   0  -0.272  48.0159  117.9619  31.4847
 SRJ  C3   C  CH1   0  -0.252  47.8723  119.3531  32.0405
 SRJ  C9   C  CT    0   0.228  47.0199  114.6046  32.0863
 SRJ  O1   O  OH1   0  -0.704  47.3677  113.3612  31.5217
 SRJ  H1   H  HCH2  0   0.239  47.7227  120.2933  30.0285
 SRJ  H2   H  HCH2  0   0.247  48.2635  121.4275  31.3411
 SRJ  H3   H  HCH2  0   0.246  46.2778  120.7435  32.7422
 SRJ  H4   H  HCH2  0   0.241  45.7533  119.6009  31.4281
 SRJ  H5   H  HCH1  0   0.250  46.1191  117.8917  33.3562
 SRJ  H7   H  HCH2  0   0.237  45.3180  115.9564  34.5980
 SRJ  H8   H  HCH2  0   0.237  45.5634  113.8996  33.5020
 SRJ  H9   H  HCH2  0   0.238  47.1971  113.8907  34.1286
 SRJ  H10  H  HCH2  0   0.236  45.1210  114.4675  31.0849
 SRJ  H11  H  HCH2  0   0.228  46.3183  115.4240  30.2257
 SRJ  H12  H  HCR6  0   0.245  51.4418  115.2899  31.2121
 SRJ  H13  H  HCR6  0   0.251  53.2648  118.9069  32.5913
 SRJ  H14  H  HCR6  0   0.239  49.7940  117.3703  34.5678
 SRJ  H16  H  HCH1  0   0.232  49.0032  115.1975  34.0278
 SRJ  H17  H  HOH1  0   0.462  50.4394  113.5889  33.2676
 SRJ  H18  H  HCH1  0   0.238  48.5848  115.6251  31.0432
 SRJ  H19  H  HCH2  0   0.235  45.2384  117.2816  31.1398
 SRJ  H20  H  HCH2  0   0.231  44.3860  116.3203  32.3235
 SRJ  H21  H  HCR6  0   0.251  53.2031  116.9963  31.0185
 SRJ  H22  H  HCR6  0   0.250  51.5519  119.0833  34.3713
 SRJ  H23  H  HCH2  0   0.193  47.3984  117.8734  30.5726
 SRJ  H24  H  HCH2  0   0.244  49.0514  117.8269  31.1637
 SRJ  H25  H  HCH1  0   0.249  48.4560  119.5299  32.9382
 SRJ  H26  H  HOH1  0   0.442  48.2041  113.0927  31.9266
 SRJ  H6   H  HCH2  0   0.232  47.0446  116.1154  34.8508

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
 SRJ  C4   C5   single    1.498  0.020  1.498
 SRJ  C4   C3   single    1.498  0.020  1.498
 SRJ  C10  C11  single    1.538  0.020  1.538
 SRJ  C10  C9   single    1.531  0.020  1.531
 SRJ  C2   C3   single    1.505  0.020  1.505
 SRJ  C2   N    single    1.450  0.020  1.450
 SRJ  O1   C9   single    1.409  0.020  1.409
 SRJ  C11  C6   single    1.531  0.020  1.531
 SRJ  C14  C13  aromatic  1.389  0.020  1.389
 SRJ  C14  C15  aromatic  1.389  0.020  1.389
 SRJ  C5   C3   single    1.499  0.020  1.499
 SRJ  C13  C12  aromatic  1.393  0.020  1.393
 SRJ  C1   C9   single    1.547  0.020  1.547
 SRJ  C1   N    single    1.462  0.020  1.462
 SRJ  C1   C    single    1.542  0.020  1.542
 SRJ  C9   C8   single    1.531  0.020  1.531
 SRJ  O    C    single    1.416  0.020  1.416
 SRJ  N    C6   single    1.458  0.020  1.458
 SRJ  C15  C16  aromatic  1.389  0.020  1.389
 SRJ  C12  C    single    1.509  0.020  1.509
 SRJ  C12  C17  aromatic  1.391  0.020  1.391
 SRJ  C6   C7   single    1.527  0.020  1.527
 SRJ  C8   C7   single    1.541  0.020  1.541
 SRJ  C16  C17  aromatic  1.388  0.020  1.388
 SRJ  C4   H1   single    0.970  0.020  1.090
 SRJ  C4   H2   single    0.970  0.020  1.090
 SRJ  C5   H3   single    0.970  0.020  1.090
 SRJ  C5   H4   single    0.970  0.020  1.090
 SRJ  C6   H5   single    0.970  0.020  1.090
 SRJ  C7   H6   single    0.970  0.020  1.090
 SRJ  C7   H7   single    0.970  0.020  1.090
 SRJ  C8   H8   single    0.970  0.020  1.090
 SRJ  C8   H9   single    0.970  0.020  1.090
 SRJ  C10  H10  single    0.970  0.020  1.090
 SRJ  C10  H11  single    0.970  0.020  1.090
 SRJ  C13  H12  single    0.930  0.020  1.080
 SRJ  C15  H13  single    0.930  0.020  1.080
 SRJ  C17  H14  single    0.930  0.020  1.080
 SRJ  C    H16  single    0.970  0.020  1.090
 SRJ  O    H17  single    0.850  0.020  0.980
 SRJ  C1   H18  single    0.970  0.020  1.090
 SRJ  C11  H19  single    0.970  0.020  1.090
 SRJ  C11  H20  single    0.970  0.020  1.090
 SRJ  C14  H21  single    0.930  0.020  1.080
 SRJ  C16  H22  single    0.930  0.020  1.080
 SRJ  C2   H23  single    0.970  0.020  1.090
 SRJ  C2   H24  single    0.970  0.020  1.090
 SRJ  C3   H25  single    0.970  0.020  1.090
 SRJ  O1   H26  single    0.850  0.020  0.980

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
 SRJ  H2   C4   H1   114.00  3.000
 SRJ  H2   C4   C3   118.11  3.000
 SRJ  H1   C4   C3   118.20  3.000
 SRJ  H2   C4   C5   118.19  3.000
 SRJ  H1   C4   C5   118.06  3.000
 SRJ  C3   C4   C5    60.04  3.000
 SRJ  H4   C5   H3   114.16  3.000
 SRJ  H4   C5   C3   117.59  3.000
 SRJ  H3   C5   C3   118.49  3.000
 SRJ  H4   C5   C4   117.81  3.000
 SRJ  H3   C5   C4   118.42  3.000
 SRJ  C3   C5   C4    60.00  3.000
 SRJ  H5   C6   C11  110.71  3.000
 SRJ  H5   C6   N    108.31  3.000
 SRJ  C11  C6   N    111.48  3.000
 SRJ  H5   C6   C7   109.45  3.000
 SRJ  N    C6   C7   108.49  3.000
 SRJ  C11  C6   C7   108.36  3.000
 SRJ  H7   C7   H6   106.73  3.000
 SRJ  H7   C7   C8   110.97  3.000
 SRJ  H6   C7   C8   111.21  3.000
 SRJ  H7   C7   C6   109.57  3.000
 SRJ  H6   C7   C6   109.28  3.000
 SRJ  C8   C7   C6   109.04  3.000
 SRJ  H9   C8   H8   106.28  3.000
 SRJ  H9   C8   C9   110.49  3.000
 SRJ  H8   C8   C9   108.84  3.000
 SRJ  H9   C8   C7   111.19  3.000
 SRJ  H8   C8   C7   111.44  3.000
 SRJ  C9   C8   C7   108.57  3.000
 SRJ  H11  C10  H10  106.87  3.000
 SRJ  H11  C10  C9   108.91  3.000
 SRJ  H10  C10  C9   109.00  3.000
 SRJ  H11  C10  C11  110.90  3.000
 SRJ  H10  C10  C11  111.17  3.000
 SRJ  C9   C10  C11  109.92  3.000
 SRJ  H12  C13  C14  119.55  3.000
 SRJ  H12  C13  C12  119.89  3.000
 SRJ  C14  C13  C12  120.57  3.000
 SRJ  H13  C15  C16  120.25  3.000
 SRJ  H13  C15  C14  120.20  3.000
 SRJ  C16  C15  C14  119.54  3.000
 SRJ  H14  C17  C16  119.69  3.000
 SRJ  H14  C17  C12  119.59  3.000
 SRJ  C16  C17  C12  120.72  3.000
 SRJ  C2   N    C1   113.76  3.000
 SRJ  C1   N    C6   112.16  3.000
 SRJ  C2   N    C6   115.67  3.000
 SRJ  H16  C    C12  108.15  3.000
 SRJ  H16  C    C1   107.87  3.000
 SRJ  C12  C    C1   110.72  3.000
 SRJ  H16  C    O    110.19  3.000
 SRJ  C12  C    O    111.92  3.000
 SRJ  C1   C    O    107.92  3.000
 SRJ  H17  O    C    108.93  3.000
 SRJ  H18  C1   C9   106.65  3.000
 SRJ  H18  C1   C    107.52  3.000
 SRJ  C9   C1   C    114.16  3.000
 SRJ  H18  C1   N    110.04  3.000
 SRJ  C    C1   N    108.74  3.000
 SRJ  C9   C1   N    109.66  3.000
 SRJ  H20  C11  H19  106.16  3.000
 SRJ  H20  C11  C10  111.39  3.000
 SRJ  H19  C11  C10  110.89  3.000
 SRJ  H20  C11  C6   109.59  3.000
 SRJ  H19  C11  C6   111.32  3.000
 SRJ  C10  C11  C6   107.52  3.000
 SRJ  C    C12  C17  120.19  3.000
 SRJ  C17  C12  C13  118.84  3.000
 SRJ  C    C12  C13  120.93  3.000
 SRJ  H21  C14  C15  120.05  3.000
 SRJ  H21  C14  C13  119.74  3.000
 SRJ  C15  C14  C13  120.21  3.000
 SRJ  H22  C16  C17  119.82  3.000
 SRJ  H22  C16  C15  120.06  3.000
 SRJ  C17  C16  C15  120.12  3.000
 SRJ  H24  C2   H23  106.10  3.000
 SRJ  H24  C2   C3   108.25  3.000
 SRJ  H23  C2   C3   109.00  3.000
 SRJ  H24  C2   N    107.30  3.000
 SRJ  H23  C2   N    112.93  3.000
 SRJ  C3   C2   N    112.93  3.000
 SRJ  H25  C3   C2   113.87  3.000
 SRJ  H25  C3   C5   116.57  3.000
 SRJ  C2   C3   C5   120.95  3.000
 SRJ  H25  C3   C4   116.20  3.000
 SRJ  C5   C3   C4    59.96  3.000
 SRJ  C2   C3   C4   119.00  3.000
 SRJ  O1   C9   C1   112.15  3.000
 SRJ  C1   C9   C10  107.08  3.000
 SRJ  O1   C9   C10  107.45  3.000
 SRJ  C1   C9   C8   109.00  3.000
 SRJ  O1   C9   C8   112.38  3.000
 SRJ  C10  C9   C8   108.57  3.000
 SRJ  H26  O1   C9   106.89  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
 SRJ  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 SRJ  CONST_02  C16  C17  C12  C13     0.00   0.0  0
 SRJ  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 SRJ  CONST_04  C12  C17  C16  C15     0.00   0.0  0
 SRJ  CONST_05  C14  C13  C12  C17     0.00   0.0  0
 SRJ  CONST_06  C14  C15  C16  C17     0.00   0.0  0
 SRJ  CONST_07  C14  C13  C12  C     180.00   0.0  0
 SRJ  CONST_08  C16  C17  C12  C     180.00   0.0  0
 SRJ  CONST_09  H13  C15  C14  C13   180.00   0.0  0
 SRJ  CONST_10  H14  C17  C12  C13   180.00   0.0  0
 SRJ  CONST_11  H12  C13  C14  C15   180.00   0.0  0
 SRJ  CONST_12  H21  C14  C13  C12   180.00   0.0  0
 SRJ  CONST_13  H22  C16  C17  C12   180.00   0.0  0
 SRJ  Var_01    C9   C10  C11  C6     14.47  30.0  1
 SRJ  Var_02    C9   C8   C7   C6     12.70  30.0  1
 SRJ  Var_03    C2   C3   C5   C4   -107.84  30.0  1
 SRJ  Var_04    N    C2   C3   C4   -163.00  30.0  1
 SRJ  Var_05    C3   C2   N    C6     63.69  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
 SRJ  chir_01  C6  C11  N   C7   positiv
 SRJ  chir_02  C   O    C1  C12  positiv
 SRJ  chir_03  C1  N    C   C9   negativ
 SRJ  chir_05  C9  C10  C1  C8   negativ
 SRJ  chir_06  C3  C4   C2  C5   both

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
 SRJ  plan-1  C13  0.020
 SRJ  plan-1  C15  0.020
 SRJ  plan-1  C17  0.020
 SRJ  plan-1  C    0.020
 SRJ  plan-1  C12  0.020
 SRJ  plan-1  C14  0.020
 SRJ  plan-1  C16  0.020
 SRJ  plan-1  H12  0.020
 SRJ  plan-1  H13  0.020
 SRJ  plan-1  H14  0.020
 SRJ  plan-1  H21  0.020
 SRJ  plan-1  H22  0.020

