# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 21:26:29 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (3R)-1-azabicyclo[2.2.2]oct-3-yl[bis(5-chlorothiophen-2-yl)]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC([C@H]1CN2CCC1CC2)(c3sc(Cl)cc3)c4sc(Cl)cc4
#
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
 0H7  0H7  (3R)-1-azabicyclo[2.2.2]oct-3-yl[bis(5-chlorothiophen-2-yl)]methanol  ligand  39  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0H7
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
 0H7  O1   O   OH1   0  -0.647   0.1071  -1.0714  -2.1051
 0H7  C2   C   CT    0   0.136  -0.0371  -0.5354  -0.8192
 0H7  C3   C   CH1   0  -0.271   0.4222  -1.4992   0.3024
 0H7  C4   C   CH2   0  -0.319  -0.3503  -2.8488   0.3105
 0H7  N5   N   NT    0  -0.390   0.5500  -3.9896   0.3381
 0H7  C6   C   CH2   0  -0.333   1.4158  -3.9666  -0.8360
 0H7  C7   C   CH2   0  -0.452   2.3468  -2.7331  -0.8287
 0H7  C8   C   CH1   0  -0.248   1.9222  -1.8327   0.3331
 0H7  C9   C   CH2   0  -0.460   2.1676  -2.6135   1.6280
 0H7  C10  C   CH2   0  -0.327   1.3614  -3.9347   1.5491
 0H7  C11  C   CR5   0  -0.134   0.8162   0.7124  -0.8137
 0H7  C12  C   CR15  0  -0.224   1.6748   1.1486  -1.7740
 0H7  C13  C   CR15  0  -0.127   2.3594   2.3449  -1.4188
 0H7  C14  C   CR5   0  -0.251   1.9990   2.7819  -0.1874
 0H7  CL1  CL  CL    0  -0.082   2.5635   4.1740   0.6260
 0H7  S16  S   S2    0   0.266   0.8245   1.7660   0.5548
 0H7  C17  C   CR5   0  -0.175  -1.4928  -0.1452  -0.6145
 0H7  C18  C   CR15  0  -0.224  -2.4000   0.1624  -1.5823
 0H7  C19  C   CR15  0  -0.124  -3.6702   0.5427  -1.0705
 0H7  C20  C   CR5   0  -0.250  -3.6909   0.5178   0.2862
 0H7  CL2  CL  CL    0  -0.078  -5.0057   0.8930   1.3092
 0H7  S22  S   S2    0   0.268  -2.1881   0.0220   0.9578
 0H7  H1   H   HOH1  0   0.459  -0.4592  -1.8464  -2.1895
 0H7  H2   H   HCH1  0   0.244   0.2169  -0.9823   1.2486
 0H7  H3   H   HCH2  0   0.253  -1.0037  -2.9044   1.1829
 0H7  H4   H   HCH2  0   0.231  -1.0078  -2.9557  -0.5586
 0H7  H6   H   HCH2  0   0.239   1.9921  -4.8945  -0.8579
 0H7  H7   H   HCH2  0   0.230   0.7804  -3.9762  -1.7258
 0H7  H8   H   HCH2  0   0.229   3.3852  -3.0351  -0.6686
 0H7  H9   H   HCH2  0   0.244   2.3226  -2.2035  -1.7794
 0H7  H10  H   HCH1  0   0.248   2.5147  -0.9160   0.3370
 0H7  H11  H   HCH2  0   0.237   3.2354  -2.8130   1.7414
 0H7  H12  H   HCH2  0   0.234   1.8634  -2.0175   2.4925
 0H7  H13  H   HCH2  0   0.237   0.6994  -4.0397   2.4118
 0H7  H14  H   HCH2  0   0.237   2.0260  -4.8017   1.5543
 0H7  H15  H   HCR5  0   0.271   1.8318   0.6390  -2.7127
 0H7  H16  H   HCR5  0   0.286   3.0781   2.8462  -2.0502
 0H7  H17  H   HCR5  0   0.275  -2.1752   0.1302  -2.6387
 0H7  H18  H   HCR5  0   0.288  -4.5174   0.8175  -1.6814

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
 0H7  CL2  C20  single    1.708  0.020  1.708
 0H7  C19  C20  aromatic  1.357  0.020  1.357
 0H7  C19  C18  aromatic  1.421  0.020  1.421
 0H7  C20  S22  aromatic  1.719  0.020  1.719
 0H7  C18  C17  aromatic  1.362  0.020  1.362
 0H7  S22  C17  aromatic  1.727  0.020  1.727
 0H7  C17  C2   single    1.521  0.020  1.521
 0H7  S16  C14  aromatic  1.721  0.020  1.721
 0H7  S16  C11  aromatic  1.727  0.020  1.727
 0H7  CL1  C14  single    1.708  0.020  1.708
 0H7  O1   C2   single    1.401  0.020  1.401
 0H7  C14  C13  aromatic  1.355  0.020  1.355
 0H7  C2   C11  single    1.512  0.020  1.512
 0H7  C2   C3   single    1.548  0.020  1.548
 0H7  C11  C12  aromatic  1.360  0.020  1.360
 0H7  C13  C12  aromatic  1.423  0.020  1.423
 0H7  C4   C3   single    1.555  0.020  1.555
 0H7  C4   N5   single    1.454  0.020  1.454
 0H7  C3   C8   single    1.537  0.020  1.537
 0H7  C6   N5   single    1.459  0.020  1.459
 0H7  C6   C7   single    1.545  0.020  1.545
 0H7  N5   C10  single    1.459  0.020  1.459
 0H7  C7   C8   single    1.530  0.020  1.530
 0H7  C8   C9   single    1.532  0.020  1.532
 0H7  C10  C9   single    1.550  0.020  1.550
 0H7  O1   H1   single    0.850  0.020  0.980
 0H7  C3   H2   single    0.970  0.020  1.090
 0H7  C4   H3   single    0.970  0.020  1.090
 0H7  C4   H4   single    0.970  0.020  1.090
 0H7  C6   H6   single    0.970  0.020  1.090
 0H7  C6   H7   single    0.970  0.020  1.090
 0H7  C7   H8   single    0.970  0.020  1.090
 0H7  C7   H9   single    0.970  0.020  1.090
 0H7  C8   H10  single    0.970  0.020  1.090
 0H7  C9   H11  single    0.970  0.020  1.090
 0H7  C9   H12  single    0.970  0.020  1.090
 0H7  C10  H13  single    0.970  0.020  1.090
 0H7  C10  H14  single    0.970  0.020  1.090
 0H7  C12  H15  single    0.930  0.020  1.080
 0H7  C13  H16  single    0.930  0.020  1.080
 0H7  C18  H17  single    0.930  0.020  1.080
 0H7  C19  H18  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
 0H7  H1   O1   C2   109.13  3.000
 0H7  C17  C2   C11  109.15  3.000
 0H7  C11  C2   C3   110.11  3.000
 0H7  C17  C2   C3   110.25  3.000
 0H7  C3   C2   O1   113.35  3.000
 0H7  C11  C2   O1   105.13  3.000
 0H7  C17  C2   O1   108.68  3.000
 0H7  H2   C3   C8   105.52  3.000
 0H7  H2   C3   C4   108.14  3.000
 0H7  C8   C3   C4   107.24  3.000
 0H7  H2   C3   C2   106.01  3.000
 0H7  C8   C3   C2   116.04  3.000
 0H7  C4   C3   C2   113.36  3.000
 0H7  H4   C4   H3   105.66  3.000
 0H7  H4   C4   N5   108.08  3.000
 0H7  H3   C4   N5   108.40  3.000
 0H7  H4   C4   C3   112.27  3.000
 0H7  H3   C4   C3   110.23  3.000
 0H7  N5   C4   C3   111.93  3.000
 0H7  C10  N5   C6   109.71  3.000
 0H7  C10  N5   C4   109.31  3.000
 0H7  C6   N5   C4   109.87  3.000
 0H7  H7   C6   H6   106.43  3.000
 0H7  H7   C6   C7   111.16  3.000
 0H7  H6   C6   C7   111.11  3.000
 0H7  H7   C6   N5   108.05  3.000
 0H7  H6   C6   N5   108.41  3.000
 0H7  C7   C6   N5   111.49  3.000
 0H7  H9   C7   H8   106.46  3.000
 0H7  H9   C7   C8   111.76  3.000
 0H7  H8   C7   C8   108.36  3.000
 0H7  H9   C7   C6   111.76  3.000
 0H7  H8   C7   C6   110.64  3.000
 0H7  C8   C7   C6   107.83  3.000
 0H7  H10  C8   C9   109.76  3.000
 0H7  H10  C8   C7   110.26  3.000
 0H7  C9   C8   C7   107.31  3.000
 0H7  H10  C8   C3   110.34  3.000
 0H7  C9   C8   C3   106.49  3.000
 0H7  C7   C8   C3   112.55  3.000
 0H7  H12  C9   H11  106.83  3.000
 0H7  H12  C9   C10  111.12  3.000
 0H7  H11  C9   C10  110.99  3.000
 0H7  H12  C9   C8   110.25  3.000
 0H7  H11  C9   C8   109.72  3.000
 0H7  C10  C9   C8   107.95  3.000
 0H7  H14  C10  H13  106.77  3.000
 0H7  H14  C10  C9   111.09  3.000
 0H7  H13  C10  C9   110.91  3.000
 0H7  H14  C10  N5   108.21  3.000
 0H7  H13  C10  N5   108.35  3.000
 0H7  C9   C10  N5   111.33  3.000
 0H7  S16  C11  C12  111.15  3.000
 0H7  C12  C11  C2   128.21  3.000
 0H7  S16  C11  C2   120.60  3.000
 0H7  H15  C12  C13  122.94  3.000
 0H7  H15  C12  C11  123.67  3.000
 0H7  C13  C12  C11  113.39  3.000
 0H7  H16  C13  C14  123.95  3.000
 0H7  H16  C13  C12  124.35  3.000
 0H7  C14  C13  C12  111.70  3.000
 0H7  S16  C14  CL1  120.08  3.000
 0H7  CL1  C14  C13  127.41  3.000
 0H7  S16  C14  C13  112.51  3.000
 0H7  C14  S16  C11   91.24  3.000
 0H7  S22  C17  C18  110.91  3.000
 0H7  S22  C17  C2   122.18  3.000
 0H7  C18  C17  C2   126.87  3.000
 0H7  H17  C18  C19  123.09  3.000
 0H7  H17  C18  C17  123.33  3.000
 0H7  C19  C18  C17  113.57  3.000
 0H7  H18  C19  C20  123.93  3.000
 0H7  H18  C19  C18  124.43  3.000
 0H7  C20  C19  C18  111.64  3.000
 0H7  S22  C20  CL2  120.16  3.000
 0H7  S22  C20  C19  112.49  3.000
 0H7  CL2  C20  C19  127.35  3.000
 0H7  C20  S22  C17   91.38  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
 0H7  CONST_01  C13  C14  S16  C11     0.00   0.0  0
 0H7  CONST_02  C14  C13  C12  C11     0.00   0.0  0
 0H7  CONST_03  C14  S16  C11  C12     0.00   0.0  0
 0H7  CONST_04  S16  C14  C13  C12     0.00   0.0  0
 0H7  CONST_05  S16  C11  C12  C13     0.00   0.0  0
 0H7  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 0H7  CONST_07  C19  C20  S22  C17     0.00   0.0  0
 0H7  CONST_08  S22  C20  C19  C18     0.00   0.0  0
 0H7  CONST_09  C20  S22  C17  C18     0.00   0.0  0
 0H7  CONST_10  S22  C17  C18  C19     0.00   0.0  0
 0H7  CONST_11  C19  C18  C17  C2    180.00   0.0  0
 0H7  CONST_12  C20  S22  C17  C2    180.00   0.0  0
 0H7  CONST_13  C14  S16  C11  C2    180.00   0.0  0
 0H7  CONST_14  C13  C12  C11  C2    180.00   0.0  0
 0H7  CONST_15  CL1  C14  S16  C11   180.00   0.0  0
 0H7  CONST_16  CL1  C14  C13  C12   180.00   0.0  0
 0H7  CONST_17  CL2  C20  S22  C17   180.00   0.0  0
 0H7  CONST_18  CL2  C20  C19  C18   180.00   0.0  0
 0H7  CONST_19  H16  C13  C12  C11   180.00   0.0  0
 0H7  CONST_20  H15  C12  C13  C14   180.00   0.0  0
 0H7  CONST_21  H18  C19  C18  C17   180.00   0.0  0
 0H7  CONST_22  H17  C18  C19  C20   180.00   0.0  0
 0H7  Var_01    C6   N5   C4   C3    -59.74  30.0  1
 0H7  Var_02    C7   C6   N5   C4     64.43  30.0  1
 0H7  Var_03    C9   C10  N5   C4    -57.97  30.0  3
 0H7  Var_04    C8   C7   C6   N5     -7.31  30.0  1
 0H7  Var_05    C8   C9   C10  N5     -4.24  30.0  3
 0H7  Var_06    C18  C17  C2   C3   -149.29  30.0  3
 0H7  Var_07    S16  C11  C2   C3    -62.70  30.0  2

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
 0H7  chir_01  C3  C2  C4  C8  negativ
 0H7  chir_02  C8  C9  C7  C3  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
 0H7  plan-1  C2   0.020
 0H7  plan-1  C11  0.020
 0H7  plan-1  C12  0.020
 0H7  plan-1  C13  0.020
 0H7  plan-1  C14  0.020
 0H7  plan-1  CL1  0.020
 0H7  plan-1  S16  0.020
 0H7  plan-1  H15  0.020
 0H7  plan-1  H16  0.020
 0H7  plan-2  C2   0.020
 0H7  plan-2  C17  0.020
 0H7  plan-2  C18  0.020
 0H7  plan-2  C19  0.020
 0H7  plan-2  C20  0.020
 0H7  plan-2  CL2  0.020
 0H7  plan-2  S22  0.020
 0H7  plan-2  H17  0.020
 0H7  plan-2  H18  0.020

