# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 15:19:39 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-oxidanylidene-N-[(1S,2R)-2-phenylcyclopropyl]spiro[3H-chromene-2,4'-piperidine]-1'-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CC2(CCN(CC2)C(=O)N[C@H]3C[C@@H]3c4ccccc4)Oc5ccccc15
#
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
 I5T  I5T  4-oxidanylidene-N-[(1S,2R)-2-phenylcyclopropyl]spiro[3H-chromene-2,4'-piperidine]-1'-carboxamide  ligand  52  28  .  2022-09-22  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_I5T
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
 I5T  C1    C  CR16  0  -0.276  -8.5853   0.2618   0.3371
 I5T  C2    C  CR16  0  -0.266   7.2153   0.7983  -0.4089
 I5T  C3    C  CR16  0  -0.240  -7.8981   0.1866   1.5406
 I5T  C4    C  CR16  0  -0.236  -7.9052   0.0229  -0.8507
 I5T  C5    C  CR16  0  -0.234   6.5253   1.9890  -0.1760
 I5T  C6    C  CR16  0  -0.275   6.5686  -0.4038  -0.2147
 I5T  C7    C  CR16  0  -0.325  -6.5444  -0.1224   1.5529
 I5T  C8    C  CR16  0  -0.357  -6.5532  -0.2886  -0.8358
 I5T  C9    C  CR16  0  -0.355   5.2050   1.9786   0.2311
 I5T  C10   C  CR6   0  -0.136   5.2364  -0.4409   0.2097
 I5T  C11   C  CR6   0   0.233  -5.8502  -0.3632   0.3676
 I5T  C12   C  CR6   0   0.398   4.5510   0.7617   0.4221
 I5T  C13   C  C     0   0.396   4.5615  -1.7200   0.4802
 I5T  C14   C  C     0   0.737  -1.1045   0.2294  -0.9808
 I5T  C15   C  CH2   0  -0.576   3.1985  -1.5932   1.1059
 I5T  C16   C  CH2   0  -0.443   2.1125  -0.4689  -0.8800
 I5T  C17   C  CH2   0  -0.430   1.1877  -0.1198   1.4192
 I5T  C18   C  CH2   0  -0.468  -3.7451  -1.6058  -0.5621
 I5T  C19   C  CH2   0  -0.312   1.2449   0.6925  -1.3484
 I5T  C20   C  CH2   0  -0.339   0.3570   1.0360   0.8683
 I5T  C21   C  CH1   0  -0.415  -4.4026  -0.6795   0.4250
 I5T  C22   C  CH1   0  -0.036  -3.4535  -0.1487  -0.6150
 I5T  C23   C  CT    0   0.142   2.4557  -0.3600   0.6092
 I5T  N24   N  NT    0  -0.494   0.0480   0.8209  -0.5367
 I5T  N25   N  NH1   0  -0.694  -2.1917   0.3235  -0.1563
 I5T  O26   O  O     0  -0.397   5.0837  -2.7946   0.2659
 I5T  O27   O  O     0  -0.531  -1.1773  -0.3388  -2.0632
 I5T  O28   O  O2    0  -0.482   3.2721   0.8055   0.8211
 I5T  H1    H  HCR6  0   0.254  -9.6406   0.5011   0.3232
 I5T  H3    H  HCR6  0   0.254  -8.4148   0.3694   2.4741
 I5T  H4    H  HCR6  0   0.255  -8.4302   0.0794  -1.7958
 I5T  H2    H  HCR6  0   0.262   8.2468   0.8198  -0.7326
 I5T  H5    H  HCR6  0   0.270   7.0239   2.9379  -0.3252
 I5T  H6    H  HCR6  0   0.267   7.0920  -1.3368  -0.3799
 I5T  H7    H  HCR6  0   0.250  -6.0178  -0.1803   2.4985
 I5T  H8    H  HCR6  0   0.248  -6.0494  -0.4747  -1.7772
 I5T  H9    H  HCR6  0   0.272   4.6702   2.9044   0.4000
 I5T  H21   H  HCH1  0   0.269  -4.0002  -0.7218   1.4317
 I5T  H151  H  HCH2  0   0.283   2.6115  -2.4934   0.9214
 I5T  H152  H  HCH2  0   0.297   3.3468  -1.5215   2.1909
 I5T  H25   H  HNH1  0   0.398  -2.2258   1.0692   0.5193
 I5T  H161  H  HCH2  0   0.253   1.5809  -1.4097  -1.0450
 I5T  H162  H  HCH2  0   0.255   3.0182  -0.5137  -1.4916
 I5T  H191  H  HCH2  0   0.249   1.8004   1.6320  -1.2872
 I5T  H192  H  HCH2  0   0.267   0.9695   0.5566  -2.3903
 I5T  H171  H  HCH2  0   0.258   1.4457   0.0700   2.4640
 I5T  H172  H  HCH2  0   0.248   0.5872  -1.0330   1.3982
 I5T  H201  H  HCH2  0   0.261  -0.5431   1.1447   1.4670
 I5T  H202  H  HCH2  0   0.256   0.9006   1.9785   0.9616
 I5T  H181  H  HCH2  0   0.266  -2.9720  -2.2616  -0.1829
 I5T  H182  H  HCH2  0   0.259  -4.3525  -2.0308  -1.3515
 I5T  H22   H  HCH1  0   0.263  -3.9077   0.4104  -1.4304

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
 I5T  C1   C3    aromatic  1.388  0.020  1.388
 I5T  C1   C4    aromatic  1.389  0.020  1.389
 I5T  C2   C5    aromatic  1.396  0.020  1.396
 I5T  C2   C6    aromatic  1.379  0.020  1.379
 I5T  C3   C7    aromatic  1.389  0.020  1.389
 I5T  C4   C8    aromatic  1.387  0.020  1.387
 I5T  C5   C9    aromatic  1.382  0.020  1.382
 I5T  C6   C10   aromatic  1.399  0.020  1.399
 I5T  C7   C11   aromatic  1.394  0.020  1.394
 I5T  C8   C11   aromatic  1.396  0.020  1.396
 I5T  C9   C12   aromatic  1.395  0.020  1.395
 I5T  C10  C12   aromatic  1.400  0.020  1.400
 I5T  C10  C13   single    1.471  0.020  1.471
 I5T  C11  C21   single    1.483  0.020  1.483
 I5T  C12  O28   single    1.340  0.020  1.340
 I5T  C13  C15   single    1.505  0.020  1.505
 I5T  C13  O26   double    1.214  0.020  1.214
 I5T  C14  N24   single    1.369  0.020  1.369
 I5T  C14  N25   single    1.368  0.020  1.368
 I5T  C14  O27   double    1.225  0.020  1.225
 I5T  C15  C23   single    1.523  0.020  1.523
 I5T  C16  C19   single    1.524  0.020  1.524
 I5T  C16  C23   single    1.532  0.020  1.532
 I5T  C17  C20   single    1.526  0.020  1.526
 I5T  C17  C23   single    1.524  0.020  1.524
 I5T  C18  C21   single    1.505  0.020  1.505
 I5T  C18  C22   single    1.487  0.020  1.487
 I5T  C19  N24   single    1.452  0.020  1.452
 I5T  C20  N24   single    1.454  0.020  1.454
 I5T  C21  C22   single    1.505  0.020  1.505
 I5T  C22  N25   single    1.423  0.020  1.423
 I5T  C23  O28   single    1.439  0.020  1.439
 I5T  C1   H1    single    0.930  0.020  1.080
 I5T  C3   H3    single    0.930  0.020  1.080
 I5T  C4   H4    single    0.930  0.020  1.080
 I5T  C2   H2    single    0.930  0.020  1.080
 I5T  C5   H5    single    0.930  0.020  1.080
 I5T  C6   H6    single    0.930  0.020  1.080
 I5T  C7   H7    single    0.930  0.020  1.080
 I5T  C8   H8    single    0.930  0.020  1.080
 I5T  C9   H9    single    0.930  0.020  1.080
 I5T  C21  H21   single    0.970  0.020  1.090
 I5T  C15  H151  single    0.970  0.020  1.090
 I5T  C15  H152  single    0.970  0.020  1.090
 I5T  N25  H25   single    0.890  0.020  1.040
 I5T  C16  H161  single    0.970  0.020  1.090
 I5T  C16  H162  single    0.970  0.020  1.090
 I5T  C19  H191  single    0.970  0.020  1.090
 I5T  C19  H192  single    0.970  0.020  1.090
 I5T  C17  H171  single    0.970  0.020  1.090
 I5T  C17  H172  single    0.970  0.020  1.090
 I5T  C20  H201  single    0.970  0.020  1.090
 I5T  C20  H202  single    0.970  0.020  1.090
 I5T  C18  H181  single    0.970  0.020  1.090
 I5T  C18  H182  single    0.970  0.020  1.090
 I5T  C22  H22   single    0.970  0.020  1.090

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
 I5T  H1    C1   C4    120.29  3.000
 I5T  H1    C1   C3    120.40  3.000
 I5T  C4    C1   C3    119.31  3.000
 I5T  H2    C2   C6    120.46  3.000
 I5T  H2    C2   C5    120.30  3.000
 I5T  C6    C2   C5    119.24  3.000
 I5T  H3    C3   C7    119.69  3.000
 I5T  H3    C3   C1    120.15  3.000
 I5T  C7    C3   C1    120.16  3.000
 I5T  H4    C4   C8    119.58  3.000
 I5T  H4    C4   C1    120.00  3.000
 I5T  C8    C4   C1    120.42  3.000
 I5T  H5    C5   C9    119.17  3.000
 I5T  H5    C5   C2    119.82  3.000
 I5T  C9    C5   C2    121.01  3.000
 I5T  H6    C6   C10   118.94  3.000
 I5T  H6    C6   C2    120.21  3.000
 I5T  C10   C6   C2    120.84  3.000
 I5T  H7    C7   C11   119.37  3.000
 I5T  H7    C7   C3    119.55  3.000
 I5T  C11   C7   C3    121.08  3.000
 I5T  H8    C8   C11   120.37  3.000
 I5T  H8    C8   C4    118.83  3.000
 I5T  C11   C8   C4    120.80  3.000
 I5T  H9    C9   C12   119.56  3.000
 I5T  H9    C9   C5    120.78  3.000
 I5T  C12   C9   C5    119.67  3.000
 I5T  C13   C10  C12   119.62  3.000
 I5T  C13   C10  C6    121.05  3.000
 I5T  C12   C10  C6    119.30  3.000
 I5T  C21   C11  C8    122.44  3.000
 I5T  C21   C11  C7    119.33  3.000
 I5T  C8    C11  C7    118.22  3.000
 I5T  O28   C12  C10   122.70  3.000
 I5T  O28   C12  C9    117.36  3.000
 I5T  C10   C12  C9    119.94  3.000
 I5T  O26   C13  C15   122.52  3.000
 I5T  O26   C13  C10   122.67  3.000
 I5T  C15   C13  C10   114.75  3.000
 I5T  O27   C14  N25   121.17  3.000
 I5T  O27   C14  N24   122.48  3.000
 I5T  N25   C14  N24   116.35  3.000
 I5T  H152  C15  H151  107.10  3.000
 I5T  H152  C15  C23   109.60  3.000
 I5T  H151  C15  C23   110.54  3.000
 I5T  H152  C15  C13   107.11  3.000
 I5T  H151  C15  C13   110.34  3.000
 I5T  C23   C15  C13   111.98  3.000
 I5T  H162  C16  H161  106.45  3.000
 I5T  H162  C16  C23   111.16  3.000
 I5T  H161  C16  C23   108.47  3.000
 I5T  H162  C16  C19   109.32  3.000
 I5T  H161  C16  C19   109.43  3.000
 I5T  C23   C16  C19   111.85  3.000
 I5T  H172  C17  H171  107.04  3.000
 I5T  H172  C17  C23   108.37  3.000
 I5T  H171  C17  C23   109.82  3.000
 I5T  H172  C17  C20   109.07  3.000
 I5T  H171  C17  C20   110.01  3.000
 I5T  C23   C17  C20   112.36  3.000
 I5T  H182  C18  H181  114.72  3.000
 I5T  H182  C18  C22   117.94  3.000
 I5T  H181  C18  C22   117.78  3.000
 I5T  H182  C18  C21   118.34  3.000
 I5T  H181  C18  C21   117.08  3.000
 I5T  C22   C18  C21    60.39  3.000
 I5T  H192  C19  H191  106.86  3.000
 I5T  H192  C19  N24   109.78  3.000
 I5T  H191  C19  N24   108.16  3.000
 I5T  H192  C19  C16   110.11  3.000
 I5T  H191  C19  C16   110.40  3.000
 I5T  N24   C19  C16   111.41  3.000
 I5T  H202  C20  H201  106.20  3.000
 I5T  H202  C20  N24   108.42  3.000
 I5T  H201  C20  N24   111.79  3.000
 I5T  H202  C20  C17   110.60  3.000
 I5T  H201  C20  C17   109.13  3.000
 I5T  N24   C20  C17   110.63  3.000
 I5T  H21   C21  C22   114.91  3.000
 I5T  H21   C21  C18   115.00  3.000
 I5T  C22   C21  C18    59.22  3.000
 I5T  H21   C21  C11   113.97  3.000
 I5T  C22   C21  C11   120.91  3.000
 I5T  C18   C21  C11   122.17  3.000
 I5T  H22   C22  N25   116.18  3.000
 I5T  H22   C22  C21   115.85  3.000
 I5T  N25   C22  C21   116.96  3.000
 I5T  H22   C22  C18   116.64  3.000
 I5T  N25   C22  C18   119.18  3.000
 I5T  C21   C22  C18    60.39  3.000
 I5T  O28   C23  C17   105.44  3.000
 I5T  O28   C23  C16   109.14  3.000
 I5T  C17   C23  C16   109.97  3.000
 I5T  O28   C23  C15   109.34  3.000
 I5T  C17   C23  C15   111.11  3.000
 I5T  C16   C23  C15   111.63  3.000
 I5T  C20   N24  C19   112.21  3.000
 I5T  C20   N24  C14   123.77  3.000
 I5T  C19   N24  C14   118.32  3.000
 I5T  H25   N25  C22   115.59  3.000
 I5T  H25   N25  C14   118.84  3.000
 I5T  C22   N25  C14   119.18  3.000
 I5T  C23   O28  C12   118.11  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
 I5T  CONST_01  C11  C7   C3   C1      0.00   0.0  0
 I5T  CONST_02  C11  C8   C4   C1      0.00   0.0  0
 I5T  CONST_03  C12  C9   C5   C2      0.00   0.0  0
 I5T  CONST_04  C12  C10  C6   C2      0.00   0.0  0
 I5T  CONST_05  C8   C4   C1   C3      0.00   0.0  0
 I5T  CONST_06  C8   C11  C7   C3      0.00   0.0  0
 I5T  CONST_07  C7   C3   C1   C4      0.00   0.0  0
 I5T  CONST_08  C7   C11  C8   C4      0.00   0.0  0
 I5T  CONST_09  C10  C6   C2   C5      0.00   0.0  0
 I5T  CONST_10  C10  C12  C9   C5      0.00   0.0  0
 I5T  CONST_11  C9   C5   C2   C6      0.00   0.0  0
 I5T  CONST_12  C9   C12  C10  C6      0.00   0.0  0
 I5T  CONST_13  C21  C11  C7   C3    180.00   0.0  0
 I5T  CONST_14  C21  C11  C8   C4    180.00   0.0  0
 I5T  CONST_15  H7   C7   C3   C1    180.00   0.0  0
 I5T  CONST_16  H8   C8   C4   C1    180.00   0.0  0
 I5T  CONST_17  H9   C9   C5   C2    180.00   0.0  0
 I5T  CONST_18  H4   C4   C1   C3    180.00   0.0  0
 I5T  CONST_19  H3   C3   C1   C4    180.00   0.0  0
 I5T  CONST_20  H6   C6   C2   C5    180.00   0.0  0
 I5T  CONST_21  H5   C5   C2   C6    180.00   0.0  0
 I5T  CONST_22  H1   C1   C3   C7    180.00   0.0  0
 I5T  CONST_23  H2   C2   C5   C9    180.00   0.0  0
 I5T  CONST_24  O27  C14  N24  C19     0.00   0.0  0
 I5T  CONST_26  N25  C14  N24  C19   180.00   0.0  0
 I5T  CONST_28  N24  C14  N25  C22   180.00   0.0  0
 I5T  CONST_29  O27  C14  N25  C22     0.00   0.0  0
 I5T  Var_01    C15  C13  C10  C6    172.04  30.0  1
 I5T  Var_02    C18  C21  C11  C7    147.22  30.0  2
 I5T  Var_03    C23  C15  C13  C10    34.16  30.0  1
 I5T  Var_04    C22  C18  C21  C11   109.37  30.0  1
 I5T  Var_05    C15  C23  O28  C12    48.56  30.0  1
 I5T  Var_06    C19  C16  C23  C15   174.06  30.0  3
 I5T  Var_07    C20  C17  C23  C15  -174.95  30.0  3
 I5T  Var_08    C20  N24  C19  C16    59.07  30.0  1
 I5T  Var_09    C19  N24  C20  C17   -58.95  30.0  1
 I5T  Var_10    N24  C19  C16  C23   -54.57  30.0  1
 I5T  Var_11    N24  C20  C17  C23    55.19  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
 I5T  chir_01  C21  C11  C18  C22  both
 I5T  chir_02  C22  N25  C21  C18  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
 I5T  plan-1  C1   0.020
 I5T  plan-1  C3   0.020
 I5T  plan-1  C4   0.020
 I5T  plan-1  C7   0.020
 I5T  plan-1  C8   0.020
 I5T  plan-1  C11  0.020
 I5T  plan-1  C21  0.020
 I5T  plan-1  H1   0.020
 I5T  plan-1  H3   0.020
 I5T  plan-1  H4   0.020
 I5T  plan-1  H7   0.020
 I5T  plan-1  H8   0.020
 I5T  plan-2  C2   0.020
 I5T  plan-2  C5   0.020
 I5T  plan-2  C6   0.020
 I5T  plan-2  C9   0.020
 I5T  plan-2  C10  0.020
 I5T  plan-2  C12  0.020
 I5T  plan-2  C13  0.020
 I5T  plan-2  O28  0.020
 I5T  plan-2  H2   0.020
 I5T  plan-2  H5   0.020
 I5T  plan-2  H6   0.020
 I5T  plan-2  H9   0.020
 I5T  plan-3  C14  0.020
 I5T  plan-3  C19  0.020
 I5T  plan-3  C20  0.020
 I5T  plan-3  C22  0.020
 I5T  plan-3  N24  0.020
 I5T  plan-3  N25  0.020
 I5T  plan-3  O27  0.020
 I5T  plan-3  H25  0.020
 I5T  plan-4  C10  0.020
 I5T  plan-4  C13  0.020
 I5T  plan-4  C15  0.020
 I5T  plan-4  O26  0.020

