# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 19:31:53 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 1-{1'-[(2E)-3-phenylprop-2-enoyl]spiro[1-benzofuran-3,4'-piperidin]-5-yl}methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc2OCC3(CCN(CC3)C(=O)/C=C/c4ccccc4)c2c1
#
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
 11N  11N  1-{1'-[(2E)-3-phenylprop-2-enoyl]spiro[1-benzofuran-3,4'-piperidin]-5-yl}methanamine  ligand  50  26  .  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_11N
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
 11N  C4    C  CR16  0  -0.374  -3.6769   0.9541  -0.3161
 11N  C5    C  CR6   0   0.082  -4.9097   1.5580  -0.0446
 11N  C6    C  CR16  0  -0.315  -5.7761   0.9393   0.8516
 11N  C7    C  CR5   0  -0.227  -2.0942  -1.0666   0.2438
 11N  C8    C  CH2   0  -0.160  -2.5874  -2.3398   0.9725
 11N  C10   C  CH2   0  -0.406  -0.9511  -0.3759   1.0026
 11N  C13   C  CH2   0  -0.324  -0.3139  -2.1373  -1.1976
 11N  C15   C  CH2   0  -0.341  -5.2839   2.8656  -0.6958
 11N  C20   C  C1    0  -0.232   4.1242  -0.1671  -0.7939
 11N  C22   C  CR16  0  -0.308   6.4632   0.5720  -0.8119
 11N  C24   C  CR16  0  -0.262   7.3979   1.9580   0.9129
 11N  C26   C  CR16  0  -0.318   5.0871   1.2886   1.0211
 11N  C1    C  CR16  0  -0.346  -5.4541  -0.2573   1.4909
 11N  C2    C  CR56  0   0.361  -4.2291  -0.8233   1.1967
 11N  C3    C  CR56  0   0.106  -3.3473  -0.2328   0.3032
 11N  O15   O  O     0  -0.488  -3.7565  -1.9755   1.7200
 11N  C11   C  CH2   0  -0.325   0.3510  -1.1607   0.9126
 11N  N22   N  NT    0  -0.472   0.7144  -1.4110  -0.4713
 11N  C14   C  CH2   0  -0.418  -1.6288  -1.3689  -1.1808
 11N  N33   N  NH2   0  -0.792  -4.9280   2.8854  -2.1054
 11N  O37   O  O     0  -0.509   2.1247  -1.4516  -2.2306
 11N  C19   C  C1    0  -0.426   2.8859  -0.3176  -0.3116
 11N  C41   C  CR6   0   0.154   5.2196   0.5750  -0.1751
 11N  C23   C  CR16  0  -0.240   7.5443   1.2550  -0.2744
 11N  C25   C  CR16  0  -0.233   6.1647   1.9715   1.5575
 11N  H4    H  HCR6  0   0.241  -2.9959   1.4229  -1.0165
 11N  H6    H  HCR6  0   0.247  -6.7387   1.3937   1.0564
 11N  H8    H  HCH2  0   0.237  -2.8616  -3.1173   0.2513
 11N  H8A   H  HCH2  0   0.243  -1.8620  -2.7642   1.6674
 11N  H10   H  HCH2  0   0.248  -0.7958   0.6237   0.5861
 11N  H10A  H  HCH2  0   0.253  -1.2170  -0.2462   2.0548
 11N  H13   H  HCH2  0   0.274   0.0141  -2.3040  -2.2187
 11N  H13A  H  HCH2  0   0.246  -0.4420  -3.1249  -0.7379
 11N  H15   H  HCH2  0   0.211  -6.3476   3.0604  -0.5033
 11N  H15A  H  HCH2  0   0.234  -4.7388   3.6791  -0.2072
 11N  H20   H  H     0   0.259   4.3671  -0.6424  -1.7389
 11N  H24   H  HCR6  0   0.262   8.2368   2.4955   1.3351
 11N  H26   H  HCR6  0   0.257   4.1378   1.3187   1.5408
 11N  H1    H  HCR6  0   0.259  -6.1453  -0.7255   2.1797
 11N  H11   H  HCH2  0   0.275   1.1325  -0.6246   1.4397
 11N  H11A  H  HCH2  0   0.249   0.2499  -2.1248   1.4239
 11N  H14   H  HCH2  0   0.249  -2.3896  -1.9477  -1.7099
 11N  H14A  H  HCH2  0   0.245  -1.4987  -0.4330  -1.7316
 11N  HN33  H  HNH2  0   0.342  -5.5221   2.2404  -2.6113
 11N  HN3A  H  HNH2  0   0.351  -5.1222   3.8026  -2.4867
 11N  H19   H  H     0   0.273   2.6157   0.1408   0.6283
 11N  H23   H  HCR6  0   0.261   8.4992   1.2363  -0.7829
 11N  H25   H  HCR6  0   0.262   6.0442   2.5199   2.4826
 11N  C17   C  C     0   0.575   1.8852  -1.1021  -1.0769
 11N  H22   H  HCR6  0   0.259   6.5830   0.0252  -1.7396

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
 11N  C4   C5    aromatic  1.399  0.020  1.399
 11N  C4   C3    aromatic  1.379  0.020  1.379
 11N  C5   C6    aromatic  1.392  0.020  1.392
 11N  C5   C15   single    1.508  0.020  1.508
 11N  C6   C1    aromatic  1.394  0.020  1.394
 11N  C7   C8    single    1.548  0.020  1.548
 11N  C7   C10   single    1.536  0.020  1.536
 11N  C7   C3    single    1.506  0.020  1.506
 11N  C7   C14   single    1.529  0.020  1.529
 11N  C8   O15   single    1.435  0.020  1.435
 11N  C10  C11   single    1.523  0.020  1.523
 11N  C13  N22   single    1.453  0.020  1.453
 11N  C13  C14   single    1.523  0.020  1.523
 11N  C15  N33   single    1.454  0.020  1.454
 11N  C17  N22   single    1.354  0.020  1.354
 11N  C17  O37   double    1.229  0.020  1.229
 11N  C17  C19   single    1.484  0.020  1.484
 11N  C20  C19   double    1.337  0.020  1.337
 11N  C20  C41   single    1.461  0.020  1.461
 11N  C22  C41   aromatic  1.397  0.020  1.397
 11N  C22  C23   aromatic  1.387  0.020  1.387
 11N  C24  C23   aromatic  1.388  0.020  1.388
 11N  C24  C25   aromatic  1.392  0.020  1.392
 11N  C26  C41   aromatic  1.399  0.020  1.399
 11N  C26  C25   aromatic  1.384  0.020  1.384
 11N  C1   C2    aromatic  1.381  0.020  1.381
 11N  C2   C3    aromatic  1.387  0.020  1.387
 11N  C2   O15   single    1.351  0.020  1.351
 11N  C11  N22   single    1.453  0.020  1.453
 11N  C4   H4    single    0.930  0.020  1.080
 11N  C6   H6    single    0.930  0.020  1.080
 11N  C8   H8    single    0.970  0.020  1.090
 11N  C8   H8A   single    0.970  0.020  1.090
 11N  C10  H10   single    0.970  0.020  1.090
 11N  C10  H10A  single    0.970  0.020  1.090
 11N  C13  H13   single    0.970  0.020  1.090
 11N  C13  H13A  single    0.970  0.020  1.090
 11N  C15  H15   single    0.970  0.020  1.090
 11N  C15  H15A  single    0.970  0.020  1.090
 11N  C20  H20   single    0.930  0.020  1.080
 11N  C22  H22   single    0.930  0.020  1.080
 11N  C24  H24   single    0.930  0.020  1.080
 11N  C26  H26   single    0.930  0.020  1.080
 11N  C1   H1    single    0.930  0.020  1.080
 11N  C11  H11   single    0.970  0.020  1.090
 11N  C11  H11A  single    0.970  0.020  1.090
 11N  C14  H14   single    0.970  0.020  1.090
 11N  C14  H14A  single    0.970  0.020  1.090
 11N  N33  HN33  single    0.890  0.020  1.040
 11N  N33  HN3A  single    0.890  0.020  1.040
 11N  C19  H19   single    0.930  0.020  1.080
 11N  C23  H23   single    0.930  0.020  1.080
 11N  C25  H25   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
 11N  H4    C4   C3    120.84  3.000
 11N  H4    C4   C5    119.49  3.000
 11N  C3    C4   C5    119.67  3.000
 11N  C15   C5   C6    120.60  3.000
 11N  C15   C5   C4    120.60  3.000
 11N  C6    C5   C4    118.79  3.000
 11N  H6    C6   C1    118.57  3.000
 11N  H6    C6   C5    119.22  3.000
 11N  C1    C6   C5    122.21  3.000
 11N  C14   C7   C3    113.54  3.000
 11N  C14   C7   C10   108.82  3.000
 11N  C3    C7   C10   110.53  3.000
 11N  C14   C7   C8    111.91  3.000
 11N  C3    C7   C8     99.89  3.000
 11N  C10   C7   C8    111.99  3.000
 11N  H8A   C8   H8    108.05  3.000
 11N  H8A   C8   O15   107.99  3.000
 11N  H8    C8   O15   108.62  3.000
 11N  H8A   C8   C7    114.09  3.000
 11N  H8    C8   C7    110.71  3.000
 11N  O15   C8   C7    107.22  3.000
 11N  H10A  C10  H10   107.01  3.000
 11N  H10A  C10  C11   109.03  3.000
 11N  H10   C10  C11   109.09  3.000
 11N  H10A  C10  C7    110.36  3.000
 11N  H10   C10  C7    109.17  3.000
 11N  C11   C10  C7    112.05  3.000
 11N  H13A  C13  H13   106.94  3.000
 11N  H13A  C13  C14   110.41  3.000
 11N  H13   C13  C14   110.41  3.000
 11N  H13A  C13  N22   108.85  3.000
 11N  H13   C13  N22   109.45  3.000
 11N  C14   C13  N22   110.68  3.000
 11N  H15A  C15  H15   105.80  3.000
 11N  H15A  C15  N33   107.51  3.000
 11N  H15   C15  N33   113.86  3.000
 11N  H15A  C15  C5    109.16  3.000
 11N  H15   C15  C5    108.57  3.000
 11N  N33   C15  C5    111.70  3.000
 11N  H20   C20  C41   115.06  3.000
 11N  H20   C20  C19   118.15  3.000
 11N  C41   C20  C19   126.78  3.000
 11N  H22   C22  C23   119.61  3.000
 11N  H22   C22  C41   119.33  3.000
 11N  C23   C22  C41   121.06  3.000
 11N  H24   C24  C25   120.10  3.000
 11N  H24   C24  C23   120.25  3.000
 11N  C25   C24  C23   119.65  3.000
 11N  H26   C26  C25   118.88  3.000
 11N  H26   C26  C41   120.51  3.000
 11N  C25   C26  C41   120.61  3.000
 11N  H1    C1   C2    121.65  3.000
 11N  H1    C1   C6    121.03  3.000
 11N  C2    C1   C6    117.31  3.000
 11N  O15   C2   C3    112.97  3.000
 11N  O15   C2   C1    125.26  3.000
 11N  C3    C2   C1    121.77  3.000
 11N  C2    C3   C7    108.57  3.000
 11N  C2    C3   C4    120.25  3.000
 11N  C7    C3   C4    131.12  3.000
 11N  C2    O15  C8    107.45  3.000
 11N  H11A  C11  H11   105.94  3.000
 11N  H11A  C11  N22   108.42  3.000
 11N  H11   C11  N22   111.59  3.000
 11N  H11A  C11  C10   110.29  3.000
 11N  H11   C11  C10   109.43  3.000
 11N  N22   C11  C10   111.03  3.000
 11N  C11   N22  C17   127.10  3.000
 11N  C11   N22  C13   112.66  3.000
 11N  C17   N22  C13   120.16  3.000
 11N  H14A  C14  H14   107.00  3.000
 11N  H14A  C14  C13   108.87  3.000
 11N  H14   C14  C13   109.18  3.000
 11N  H14A  C14  C7    109.65  3.000
 11N  H14   C14  C7    110.12  3.000
 11N  C13   C14  C7    111.88  3.000
 11N  HN3A  N33  HN33  106.05  3.000
 11N  HN3A  N33  C15   109.31  3.000
 11N  HN33  N33  C15   109.40  3.000
 11N  H19   C19  C20   119.85  3.000
 11N  H19   C19  C17   120.29  3.000
 11N  C20   C19  C17   119.86  3.000
 11N  C26   C41  C22   118.36  3.000
 11N  C26   C41  C20   123.39  3.000
 11N  C22   C41  C20   118.25  3.000
 11N  H23   C23  C24   120.26  3.000
 11N  H23   C23  C22   119.81  3.000
 11N  C24   C23  C22   119.93  3.000
 11N  H25   C25  C26   119.64  3.000
 11N  H25   C25  C24   119.97  3.000
 11N  C26   C25  C24   120.38  3.000
 11N  C19   C17  O37   120.20  3.000
 11N  C19   C17  N22   118.24  3.000
 11N  O37   C17  N22   121.57  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
 11N  CONST_01  C1    C6   C5   C4      0.00   0.0  0
 11N  CONST_02  C1    C2   C3   C4      0.00   0.0  0
 11N  CONST_03  C2    C3   C4   C5      0.00   0.0  0
 11N  CONST_04  C2    C1   C6   C5      0.00   0.0  0
 11N  CONST_05  C3    C4   C5   C6      0.00   0.0  0
 11N  CONST_06  C3    C2   C1   C6      0.00   0.0  0
 11N  CONST_07  C25   C26  C41  C22     0.00   0.0  0
 11N  CONST_08  C25   C24  C23  C22     0.00   0.0  0
 11N  CONST_09  C41   C22  C23  C24     0.00   0.0  0
 11N  CONST_10  C41   C26  C25  C24     0.00   0.0  0
 11N  CONST_11  C23   C22  C41  C26     0.00   0.0  0
 11N  CONST_12  C23   C24  C25  C26     0.00   0.0  0
 11N  CONST_13  C7    C3   C4   C5    180.00   0.0  0
 11N  CONST_14  C1    C2   C3   C7    180.00   0.0  0
 11N  CONST_15  O15   C2   C3   C7      0.00   0.0  0
 11N  CONST_16  C3    C4   C5   C15   180.00   0.0  0
 11N  CONST_17  C1    C6   C5   C15   180.00   0.0  0
 11N  CONST_18  C23   C22  C41  C20   180.00   0.0  0
 11N  CONST_19  C25   C26  C41  C20   180.00   0.0  0
 11N  CONST_20  H6    C6   C5   C4    180.00   0.0  0
 11N  CONST_21  H1    C1   C6   C5    180.00   0.0  0
 11N  CONST_22  H4    C4   C5   C6    180.00   0.0  0
 11N  CONST_23  H26   C26  C41  C22   180.00   0.0  0
 11N  CONST_24  H24   C24  C23  C22   180.00   0.0  0
 11N  CONST_25  H22   C22  C23  C24   180.00   0.0  0
 11N  CONST_26  H23   C23  C22  C41   180.00   0.0  0
 11N  CONST_27  H25   C25  C26  C41   180.00   0.0  0
 11N  CONST_28  O37   C17  N22  C13     0.00   0.0  0
 11N  CONST_29  C19   C17  N22  C13   180.00   0.0  0
 11N  CONST_30  O37   C17  N22  C11   180.00   0.0  0
 11N  CONST_31  C19   C17  N22  C11     0.00   0.0  0
 11N  Var_01    C8    C7   C3   C4   -169.89  30.0  1
 11N  Var_02    N22   C11  C10  C7     54.96  30.0  1
 11N  Var_03    N22   C13  C14  C7    -56.37  30.0  1
 11N  Var_04    C11   C10  C7   C8     72.09  30.0  3
 11N  Var_05    C13   C14  C7   C8    -71.45  30.0  3
 11N  Var_06    C1    C2   O15  C8    169.03  30.0  1
 11N  Var_07    O15   C8   C7   C10    98.05  30.0  1
 11N  Var_08    C13   N22  C11  C10   -58.02  30.0  1
 11N  Var_09    C14   C13  N22  C11    58.63  30.0  1
 11N  Var_10    N33   C15  C5   C4     42.88  30.0  2
 11N  Var_11    C19   C20  C41  C22   177.48  30.0  2
 11N  Var_12    C41   C20  C19  C17   179.64   0.0  2
 11N  Var_13    N22   C17  C19  C20   169.87  30.0  2
 11N  Var_14    HN33  N33  C15  C5     69.01  30.0  3

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
 11N  plan-1  C20  0.020
 11N  plan-1  C22  0.020
 11N  plan-1  C24  0.020
 11N  plan-1  C26  0.020
 11N  plan-1  C41  0.020
 11N  plan-1  C23  0.020
 11N  plan-1  C25  0.020
 11N  plan-1  H24  0.020
 11N  plan-1  H26  0.020
 11N  plan-1  H23  0.020
 11N  plan-1  H25  0.020
 11N  plan-1  H22  0.020
 11N  plan-2  C4   0.020
 11N  plan-2  C5   0.020
 11N  plan-2  C6   0.020
 11N  plan-2  C7   0.020
 11N  plan-2  C15  0.020
 11N  plan-2  C1   0.020
 11N  plan-2  C2   0.020
 11N  plan-2  C3   0.020
 11N  plan-2  O15  0.020
 11N  plan-2  H4   0.020
 11N  plan-2  H6   0.020
 11N  plan-2  H1   0.020
 11N  plan-3  C13  0.020
 11N  plan-3  C11  0.020
 11N  plan-3  N22  0.020
 11N  plan-3  O37  0.020
 11N  plan-3  C19  0.020
 11N  plan-3  C17  0.020
 11N  plan-4  C20  0.020
 11N  plan-4  C19  0.020
 11N  plan-4  C41  0.020
 11N  plan-4  H20  0.020
 11N  plan-4  H19  0.020
 11N  plan-4  C17  0.020

