# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:31:41 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: ~{N}-[(3~{R})-1-azabicyclo[2.2.2]octan-3-yl]-7-chloranyl-1-benzothiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc2cc(sc12)C(=O)N[C@H]3CN4CCC3CC4
#
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
 I33  I33  ~{N}-[(3~{R})-1-azabicyclo[2.2.2]octan-3-yl]-7-chloranyl-1-benzothiophene-2-carboxamide  ligand  38  21  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_I33
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
 I33  C02   C   C     0   0.554  143.1498  139.4983  90.2097
 I33  C03   C   CR5   0  -0.297  143.8242  138.2549  90.6533
 I33  C04   C   CR15  0  -0.246  143.3574  136.9980  90.8523
 I33  C05   C   CR56  0   0.222  144.3687  136.1051  91.3253
 I33  C06   C   CR56  0  -0.127  145.6030  136.7630  91.4691
 I33  C07   C   CR6   0  -0.096  146.7216  136.0719  91.9225
 I33  C09   C   CR16  0  -0.232  146.6174  134.7333  92.2318
 I33  C10   C   CR16  0  -0.267  145.3881  134.0765  92.0888
 I33  C11   C   CR16  0  -0.300  144.2689  134.7457  91.6426
 I33  C14   C   CH1   0  -0.075  141.0520  140.4694  89.3485
 I33  C15   C   CH2   0  -0.341  140.4529  140.2341  87.9339
 I33  C16   C   CH1   0  -0.259  139.8787  140.7083  90.3089
 I33  C17   C   CH2   0  -0.462  139.1451  141.9645  89.8337
 I33  C18   C   CH2   0  -0.326  138.6449  141.7138  88.3894
 I33  C21   C   CH2   0  -0.474  138.9075  139.5282  90.2605
 I33  N13   N   NH1   0  -0.665  141.8930  139.3669  89.7664
 I33  N19   N   NT    0  -0.391  139.0074  140.3798  87.9257
 I33  O01   O   O     0  -0.482  143.7637  140.5566  90.2701
 I33  S12   S   S2    0   0.275  145.5106  138.4296  91.0369
 I33  CL08  CL  CL    0  -0.114  148.2182  136.9163  92.0919
 I33  H1    H   HCR5  0   0.280  142.3342  136.6840  90.6922
 I33  H2    H   HCR6  0   0.285  147.4834  134.1909  92.5862
 I33  H3    H   HCR6  0   0.272  145.3265  133.0257  92.3371
 I33  H4    H   HCR6  0   0.266  143.3223  134.2321  91.5372
 I33  H5    H   HCH1  0   0.267  141.6807  141.3596  89.3475
 I33  H6    H   HCH2  0   0.245  140.7010  139.2291  87.5800
 I33  H7    H   HCH2  0   0.251  140.8853  140.9360  87.2175
 I33  H8    H   HCH1  0   0.245  140.2611  140.8517  91.3217
 I33  H9    H   HCH2  0   0.237  139.8132  142.8285  89.8735
 I33  H10   H   HCH2  0   0.238  138.3131  142.1787  90.5081
 I33  H11   H   HCH2  0   0.237  139.0693  142.4443  87.6972
 I33  H12   H   HCH2  0   0.237  137.5593  141.8144  88.3273
 I33  H13   H   HCH2  0   0.238  137.3245  139.4789  88.7463
 I33  H14   H   HCH2  0   0.237  138.6558  138.3897  88.4062
 I33  H15   H   HCH2  0   0.242  138.0768  139.7175  90.9437
 I33  H16   H   HCH2  0   0.235  139.3859  138.6111  90.6127
 I33  H17   H   HNH1  0   0.415  141.4907  138.4432  89.7283
 I33  C20   C   CH2   0  -0.325  138.4105  139.3779  88.8022

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
 I33  N19  C15   single    1.453  0.020  1.453
 I33  N19  C18   single    1.458  0.020  1.458
 I33  N19  C20   single    1.459  0.020  1.459
 I33  C15  C14   single    1.554  0.020  1.554
 I33  C18  C17   single    1.549  0.020  1.549
 I33  C20  C21   single    1.548  0.020  1.548
 I33  C14  N13   single    1.448  0.020  1.448
 I33  C14  C16   single    1.535  0.020  1.535
 I33  O01  C02   double    1.225  0.020  1.225
 I33  C17  C16   single    1.530  0.020  1.530
 I33  N13  C02   single    1.339  0.020  1.339
 I33  C02  C03   single    1.482  0.020  1.482
 I33  C21  C16   single    1.529  0.020  1.529
 I33  C03  S12   aromatic  1.738  0.020  1.738
 I33  C03  C04   aromatic  1.355  0.020  1.355
 I33  S12  C06   aromatic  1.724  0.020  1.724
 I33  C04  C05   aromatic  1.430  0.020  1.430
 I33  C05  C06   aromatic  1.406  0.020  1.406
 I33  C05  C11   aromatic  1.400  0.020  1.400
 I33  C06  C07   aromatic  1.391  0.020  1.391
 I33  C11  C10   aromatic  1.378  0.020  1.378
 I33  C07  CL08  single    1.727  0.020  1.727
 I33  C07  C09   aromatic  1.378  0.020  1.378
 I33  C10  C09   aromatic  1.401  0.020  1.401
 I33  C04  H1    single    0.930  0.020  1.080
 I33  C09  H2    single    0.930  0.020  1.080
 I33  C10  H3    single    0.930  0.020  1.080
 I33  C11  H4    single    0.930  0.020  1.080
 I33  C14  H5    single    0.970  0.020  1.090
 I33  C15  H6    single    0.970  0.020  1.090
 I33  C15  H7    single    0.970  0.020  1.090
 I33  C16  H8    single    0.970  0.020  1.090
 I33  C17  H9    single    0.970  0.020  1.090
 I33  C17  H10   single    0.970  0.020  1.090
 I33  C18  H11   single    0.970  0.020  1.090
 I33  C18  H12   single    0.970  0.020  1.090
 I33  C20  H13   single    0.970  0.020  1.090
 I33  C20  H14   single    0.970  0.020  1.090
 I33  C21  H15   single    0.970  0.020  1.090
 I33  C21  H16   single    0.970  0.020  1.090
 I33  N13  H17   single    0.860  0.020  1.020

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
 I33  O01   C02  N13  124.85  3.000
 I33  N13   C02  C03  116.34  3.000
 I33  O01   C02  C03  118.80  3.000
 I33  S12   C03  C04  113.26  3.000
 I33  C04   C03  C02  131.68  3.000
 I33  S12   C03  C02  115.03  3.000
 I33  H1    C04  C05  122.45  3.000
 I33  H1    C04  C03  124.96  3.000
 I33  C05   C04  C03  112.59  3.000
 I33  C11   C05  C06  119.60  3.000
 I33  C11   C05  C04  129.15  3.000
 I33  C06   C05  C04  111.26  3.000
 I33  S12   C06  C07  127.24  3.000
 I33  C07   C06  C05  120.46  3.000
 I33  S12   C06  C05  112.31  3.000
 I33  CL08  C07  C09  121.24  3.000
 I33  C09   C07  C06  119.67  3.000
 I33  CL08  C07  C06  119.08  3.000
 I33  H2    C09  C10  120.06  3.000
 I33  H2    C09  C07  120.01  3.000
 I33  C10   C09  C07  119.93  3.000
 I33  H3    C10  C11  119.99  3.000
 I33  H3    C10  C09  118.81  3.000
 I33  C11   C10  C09  121.19  3.000
 I33  H4    C11  C10  120.76  3.000
 I33  H4    C11  C05  120.08  3.000
 I33  C10   C11  C05  119.15  3.000
 I33  H5    C14  N13  106.68  3.000
 I33  H5    C14  C16  108.33  3.000
 I33  N13   C14  C16  112.45  3.000
 I33  H5    C14  C15  110.19  3.000
 I33  C16   C14  C15  107.36  3.000
 I33  N13   C14  C15  111.80  3.000
 I33  H7    C15  H6   106.77  3.000
 I33  H7    C15  N19  109.01  3.000
 I33  H6    C15  N19  108.42  3.000
 I33  H7    C15  C14  110.31  3.000
 I33  H6    C15  C14  110.25  3.000
 I33  N19   C15  C14  111.93  3.000
 I33  H8    C16  C21  110.67  3.000
 I33  H8    C16  C17  110.37  3.000
 I33  C21   C16  C17  108.62  3.000
 I33  H8    C16  C14  109.46  3.000
 I33  C21   C16  C14  110.22  3.000
 I33  C17   C16  C14  107.45  3.000
 I33  H10   C17  H9   106.75  3.000
 I33  H10   C17  C18  111.20  3.000
 I33  H9    C17  C18  111.06  3.000
 I33  H10   C17  C16  109.54  3.000
 I33  H9    C17  C16  110.15  3.000
 I33  C18   C17  C16  108.15  3.000
 I33  H12   C18  H11  106.78  3.000
 I33  H12   C18  N19  108.26  3.000
 I33  H11   C18  N19  108.29  3.000
 I33  H12   C18  C17  111.04  3.000
 I33  H11   C18  C17  110.93  3.000
 I33  N19   C18  C17  111.37  3.000
 I33  H16   C21  H15  106.07  3.000
 I33  H16   C21  C20  111.27  3.000
 I33  H15   C21  C20  111.22  3.000
 I33  H16   C21  C16  111.07  3.000
 I33  H15   C21  C16  109.24  3.000
 I33  C20   C21  C16  107.98  3.000
 I33  H17   N13  C14  117.05  3.000
 I33  H17   N13  C02  118.48  3.000
 I33  C14   N13  C02  124.46  3.000
 I33  C20   N19  C18  109.60  3.000
 I33  C20   N19  C15  109.56  3.000
 I33  C18   N19  C15  109.72  3.000
 I33  C06   S12  C03   90.58  3.000
 I33  H14   C20  H13  106.76  3.000
 I33  H14   C20  N19  108.15  3.000
 I33  H13   C20  N19  108.22  3.000
 I33  H14   C20  C21  110.93  3.000
 I33  H13   C20  C21  111.01  3.000
 I33  N19   C20  C21  111.59  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
 I33  CONST_01  C05   C06  S12  C03    0.00   0.0  0
 I33  CONST_02  C07   C06  S12  C03  180.00   0.0  0
 I33  CONST_03  C06   C05  C04  C03    0.00   0.0  0
 I33  CONST_04  C11   C05  C04  C03  180.00   0.0  0
 I33  CONST_05  C06   S12  C03  C04    0.00   0.0  0
 I33  CONST_06  S12   C06  C05  C04    0.00   0.0  0
 I33  CONST_07  C07   C06  C05  C04  180.00   0.0  0
 I33  CONST_08  C10   C11  C05  C04  180.00   0.0  0
 I33  CONST_09  S12   C03  C04  C05    0.00   0.0  0
 I33  CONST_10  C09   C07  C06  C05    0.00   0.0  0
 I33  CONST_11  C09   C10  C11  C05    0.00   0.0  0
 I33  CONST_12  C10   C11  C05  C06    0.00   0.0  0
 I33  CONST_13  C10   C09  C07  C06    0.00   0.0  0
 I33  CONST_14  C11   C05  C06  C07    0.00   0.0  0
 I33  CONST_15  C11   C10  C09  C07    0.00   0.0  0
 I33  CONST_16  S12   C06  C07  C09  180.00   0.0  0
 I33  CONST_17  S12   C06  C05  C11  180.00   0.0  0
 I33  CONST_18  C06   S12  C03  C02  180.00   0.0  0
 I33  CONST_19  C05   C04  C03  C02  180.00   0.0  0
 I33  CONST_20  CL08  C07  C06  C05  180.00   0.0  0
 I33  CONST_21  CL08  C07  C09  C10  180.00   0.0  0
 I33  CONST_22  CL08  C07  C06  S12    0.00   0.0  0
 I33  CONST_23  H4    C11  C05  C04    0.00   0.0  0
 I33  CONST_24  H3    C10  C11  C05  180.00   0.0  0
 I33  CONST_25  H1    C04  C05  C06  180.00   0.0  0
 I33  CONST_26  H2    C09  C07  C06  180.00   0.0  0
 I33  CONST_27  C14   N13  C02  C03  180.00   0.0  0
 I33  CONST_28  O01   C02  N13  C14    0.00   0.0  0
 I33  CONST_29  H17   N13  C02  C03    0.00   0.0  0
 I33  Var_01    C18   N19  C15  C14   58.36  30.0  1
 I33  Var_02    C17   C18  N19  C15  -60.39  30.0  1
 I33  Var_03    C21   C20  N19  C15   59.99  30.0  3
 I33  Var_04    N19   C18  C17  C16    0.36  30.0  1
 I33  Var_05    N19   C20  C21  C16    0.27  30.0  3
 I33  Var_06    O01   C02  C03  C04  170.82  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
 I33  chir_01  C14  C15  N13  C16  positiv
 I33  chir_02  C16  C21  C17  C14  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
 I33  plan-1  C02   0.020
 I33  plan-1  C03   0.020
 I33  plan-1  C04   0.020
 I33  plan-1  C05   0.020
 I33  plan-1  C06   0.020
 I33  plan-1  C07   0.020
 I33  plan-1  C09   0.020
 I33  plan-1  C10   0.020
 I33  plan-1  C11   0.020
 I33  plan-1  S12   0.020
 I33  plan-1  CL08  0.020
 I33  plan-1  H1    0.020
 I33  plan-1  H2    0.020
 I33  plan-1  H3    0.020
 I33  plan-1  H4    0.020
 I33  plan-2  C02   0.020
 I33  plan-2  C03   0.020
 I33  plan-2  C14   0.020
 I33  plan-2  N13   0.020
 I33  plan-2  O01   0.020
 I33  plan-2  H17   0.020

