# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 04:23:32 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 1-(1'-{[3-(methylsulfanyl)-2-benzothiophen-1-yl]carbonyl}spiro[1-benzofuran-3,4'-piperidin]-5-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1sc(C(=O)N2CCC3(CC2)COc4ccc(CN)cc34)c5ccccc15
#
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
 11M  11M  1-(1'-{[3-(methylsulfanyl)-2-benzothiophen-1-yl]carbonyl}spiro[1-benzofuran-3,4'-piperidin]-5-yl)methanamine  ligand  53  29  .  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_11M
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
 11M  C4    C  CR16  0  -0.348  -5.8432  -1.3447  -0.9843
 11M  C5    C  CR16  0  -0.313  -6.1725  -0.0602  -1.4188
 11M  C6    C  CR6   0   0.099  -5.3636   1.0406  -1.1583
 11M  C8    C  CH2   0  -0.162  -3.0978  -2.3375   1.0867
 11M  C10   C  CH2   0  -0.403  -1.4312  -0.9709  -0.2822
 11M  C13   C  CH2   0  -0.335  -0.8986  -0.6027   2.5226
 11M  C15   C  CR5   0  -0.222  -2.6101  -0.9207   0.7040
 11M  C22   C  CR5   0  -0.471   4.3639  -0.3782  -0.3711
 11M  C24   C  CR16  0  -0.300   4.8984   1.8883  -1.3409
 11M  C26   C  CR16  0  -0.252   3.2758   3.6140  -0.8392
 11M  C1    C  CR16  0  -0.371  -4.1797   0.8525  -0.4350
 11M  C2    C  CR56  0   0.100  -3.8397  -0.4098   0.0003
 11M  C3    C  CR56  0   0.365  -4.6675  -1.4901  -0.2753
 11M  O13   O  O     0  -0.487  -4.1870  -2.6566   0.2087
 11M  C11   C  CH2   0  -0.340  -0.1260  -1.4119   0.3741
 11M  N22   N  NT    0  -0.458   0.1724  -0.5875   1.5382
 11M  C14   C  CH2   0  -0.423  -2.2087  -0.1008   1.9305
 11M  O61   O  O     0  -0.477   0.8581   1.4671   2.2127
 11M  C30   C  CH2   0  -0.359  -5.7535   2.4181  -1.6236
 11M  N64   N  NH2   0  -0.789  -5.9817   3.3038  -0.4895
 11M  C39   C  CR5   0  -0.471   2.2267   0.3690   0.6725
 11M  C41   C  CR56  0   0.261   2.8881   1.4021   0.0213
 11M  C42   C  CR56  0   0.245   4.1072   0.9707  -0.5986
 11M  S44   S  S2    0   0.324   3.1290  -1.0867   0.5563
 11M  C25   C  CR16  0  -0.265   4.4857   3.1795  -1.4544
 11M  C27   C  CR16  0  -0.318   2.4925   2.7633  -0.1211
 11M  C29   C  CH3   0  -0.794   5.4068  -2.9260  -0.4617
 11M  H4    H  HCR6  0   0.258  -6.4876  -2.1882  -1.1963
 11M  H5    H  HCR6  0   0.248  -7.0916   0.0806  -1.9759
 11M  H8    H  HCH2  0   0.245  -2.3382  -3.1118   0.9796
 11M  H8A   H  HCH2  0   0.238  -3.4641  -2.3554   2.1187
 11M  H10   H  HCH2  0   0.254  -1.6574  -1.6495  -1.1088
 11M  H10A  H  HCH2  0   0.246  -1.2905   0.0232  -0.7173
 11M  H13   H  HCH2  0   0.256  -1.0066  -1.6342   2.8748
 11M  H13A  H  HCH2  0   0.270  -0.6096  -0.0056   3.3837
 11M  H24   H  HCR6  0   0.257   5.8160   1.5608  -1.8135
 11M  H26   H  HCR6  0   0.262   2.9771   4.6483  -0.9499
 11M  H1    H  HCR6  0   0.242  -3.5329   1.6994  -0.2323
 11M  H11   H  HCH2  0   0.252  -0.1835  -2.4567   0.6912
 11M  H11A  H  HCH2  0   0.276   0.6718  -1.3469  -0.3595
 11M  H14   H  HCH2  0   0.251  -2.9969  -0.1452   2.6860
 11M  H14A  H  HCH2  0   0.248  -2.0906   0.9500   1.6529
 11M  H30   H  HCH2  0   0.231  -4.9394   2.8447  -2.2161
 11M  H30A  H  HCH2  0   0.211  -6.6133   2.3336  -2.3011
 11M  HN64  H  HNH2  0   0.348  -6.1828   4.2358  -0.8301
 11M  HN6A  H  HNH2  0   0.339  -6.8128   3.0047   0.0054
 11M  H25   H  HCR6  0   0.263   5.0746   3.8891  -2.0198
 11M  H27   H  HCR6  0   0.255   1.5789   3.1128   0.3370
 11M  H29   H  HCH3  0   0.285   5.3541  -3.0384   0.6199
 11M  H29A  H  HCH3  0   0.286   4.4857  -3.2737  -0.9263
 11M  H29B  H  HCH3  0   0.306   6.2358  -3.5240  -0.8337
 11M  C17   C  C     0   0.538   1.0241   0.4734   1.5159
 11M  S59   S  S2    0   0.100   5.7720  -1.2233  -0.9311

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
 11M  C4   C5    aromatic  1.395  0.020  1.395
 11M  C4   C3    aromatic  1.381  0.020  1.381
 11M  C5   C6    aromatic  1.391  0.020  1.391
 11M  C6   C1    aromatic  1.400  0.020  1.400
 11M  C6   C30   single    1.505  0.020  1.505
 11M  C8   C15   single    1.547  0.020  1.547
 11M  C8   O13   single    1.435  0.020  1.435
 11M  C10  C15   single    1.538  0.020  1.538
 11M  C10  C11   single    1.526  0.020  1.526
 11M  C13  N22   single    1.455  0.020  1.455
 11M  C13  C14   single    1.523  0.020  1.523
 11M  C15  C2    single    1.506  0.020  1.506
 11M  C15  C14   single    1.529  0.020  1.529
 11M  C17  N22   single    1.361  0.020  1.361
 11M  C17  O61   double    1.225  0.020  1.225
 11M  C17  C39   single    1.473  0.020  1.473
 11M  C22  C42   aromatic  1.392  0.020  1.392
 11M  C22  S44   aromatic  1.699  0.020  1.699
 11M  C22  S59   single    1.735  0.020  1.735
 11M  C24  C42   aromatic  1.421  0.020  1.421
 11M  C24  C25   aromatic  1.360  0.020  1.360
 11M  C26  C25   aromatic  1.425  0.020  1.425
 11M  C26  C27   aromatic  1.361  0.020  1.361
 11M  C1   C2    aromatic  1.378  0.020  1.378
 11M  C2   C3    aromatic  1.389  0.020  1.389
 11M  C3   O13   single    1.351  0.020  1.351
 11M  C11  N22   single    1.457  0.020  1.457
 11M  C30  N64   single    1.457  0.020  1.457
 11M  C39  C41   aromatic  1.389  0.020  1.389
 11M  C39  S44   aromatic  1.717  0.020  1.717
 11M  C41  C42   aromatic  1.434  0.020  1.434
 11M  C41  C27   aromatic  1.425  0.020  1.425
 11M  S59  C29   single    1.803  0.020  1.803
 11M  C4   H4    single    0.930  0.020  1.080
 11M  C5   H5    single    0.930  0.020  1.080
 11M  C8   H8    single    0.970  0.020  1.090
 11M  C8   H8A   single    0.970  0.020  1.090
 11M  C10  H10   single    0.970  0.020  1.090
 11M  C10  H10A  single    0.970  0.020  1.090
 11M  C13  H13   single    0.970  0.020  1.090
 11M  C13  H13A  single    0.970  0.020  1.090
 11M  C24  H24   single    0.930  0.020  1.080
 11M  C26  H26   single    0.930  0.020  1.080
 11M  C1   H1    single    0.930  0.020  1.080
 11M  C11  H11   single    0.970  0.020  1.090
 11M  C11  H11A  single    0.970  0.020  1.090
 11M  C14  H14   single    0.970  0.020  1.090
 11M  C14  H14A  single    0.970  0.020  1.090
 11M  C30  H30   single    0.970  0.020  1.090
 11M  C30  H30A  single    0.970  0.020  1.090
 11M  N64  HN64  single    0.890  0.020  1.040
 11M  N64  HN6A  single    0.890  0.020  1.040
 11M  C25  H25   single    0.930  0.020  1.080
 11M  C27  H27   single    0.930  0.020  1.080
 11M  C29  H29   single    0.970  0.020  1.090
 11M  C29  H29A  single    0.970  0.020  1.090
 11M  C29  H29B  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
 11M  H4    C4   C3    121.70  3.000
 11M  H4    C4   C5    121.05  3.000
 11M  C3    C4   C5    117.24  3.000
 11M  H5    C5   C6    119.13  3.000
 11M  H5    C5   C4    118.67  3.000
 11M  C6    C5   C4    122.21  3.000
 11M  C30   C6   C1    120.11  3.000
 11M  C30   C6   C5    121.05  3.000
 11M  C1    C6   C5    118.84  3.000
 11M  H8A   C8   H8    108.31  3.000
 11M  H8A   C8   O13   108.61  3.000
 11M  H8    C8   O13   108.11  3.000
 11M  H8A   C8   C15   110.71  3.000
 11M  H8    C8   C15   114.00  3.000
 11M  O13   C8   C15   106.96  3.000
 11M  H10A  C10  H10   106.86  3.000
 11M  H10A  C10  C11   108.88  3.000
 11M  H10   C10  C11   108.83  3.000
 11M  H10A  C10  C15   108.90  3.000
 11M  H10   C10  C15   110.28  3.000
 11M  C11   C10  C15   112.91  3.000
 11M  H13A  C13  H13   106.78  3.000
 11M  H13A  C13  C14   110.84  3.000
 11M  H13   C13  C14   110.52  3.000
 11M  H13A  C13  N22   109.55  3.000
 11M  H13   C13  N22   107.46  3.000
 11M  C14   C13  N22   111.52  3.000
 11M  C14   C15  C2    114.03  3.000
 11M  C14   C15  C10   109.31  3.000
 11M  C2    C15  C10   109.72  3.000
 11M  C14   C15  C8    112.05  3.000
 11M  C2    C15  C8     99.73  3.000
 11M  C10   C15  C8    111.75  3.000
 11M  S59   C22  S44   124.25  3.000
 11M  S59   C22  C42   124.67  3.000
 11M  S44   C22  C42   111.06  3.000
 11M  H24   C24  C25   120.51  3.000
 11M  H24   C24  C42   120.30  3.000
 11M  C25   C24  C42   119.19  3.000
 11M  H26   C26  C27   119.50  3.000
 11M  H26   C26  C25   118.78  3.000
 11M  C27   C26  C25   121.72  3.000
 11M  H1    C1   C2    120.60  3.000
 11M  H1    C1   C6    119.72  3.000
 11M  C2    C1   C6    119.67  3.000
 11M  C3    C2   C1    120.19  3.000
 11M  C3    C2   C15   108.39  3.000
 11M  C1    C2   C15   131.29  3.000
 11M  O13   C3   C2    112.86  3.000
 11M  O13   C3   C4    125.29  3.000
 11M  C2    C3   C4    121.85  3.000
 11M  C3    O13  C8    107.29  3.000
 11M  H11A  C11  H11   106.96  3.000
 11M  H11A  C11  N22   110.82  3.000
 11M  H11   C11  N22   108.64  3.000
 11M  H11A  C11  C10   108.70  3.000
 11M  H11   C11  C10   110.85  3.000
 11M  N22   C11  C10   110.81  3.000
 11M  C11   N22  C17   123.79  3.000
 11M  C11   N22  C13   112.57  3.000
 11M  C17   N22  C13   118.69  3.000
 11M  H14A  C14  H14   107.01  3.000
 11M  H14A  C14  C15   109.88  3.000
 11M  H14   C14  C15   110.09  3.000
 11M  H14A  C14  C13   108.82  3.000
 11M  H14   C14  C13   109.78  3.000
 11M  C15   C14  C13   111.16  3.000
 11M  H30A  C30  H30   106.18  3.000
 11M  H30A  C30  N64   113.86  3.000
 11M  H30   C30  N64   107.53  3.000
 11M  H30A  C30  C6    108.85  3.000
 11M  H30   C30  C6    109.37  3.000
 11M  N64   C30  C6    110.87  3.000
 11M  HN6A  N64  HN64  105.86  3.000
 11M  HN6A  N64  C30   109.23  3.000
 11M  HN64  N64  C30   109.20  3.000
 11M  S44   C39  C41   110.41  3.000
 11M  S44   C39  C17   121.88  3.000
 11M  C41   C39  C17   127.21  3.000
 11M  C27   C41  C42   118.70  3.000
 11M  C27   C41  C39   128.71  3.000
 11M  C42   C41  C39   112.57  3.000
 11M  C41   C42  C24   120.32  3.000
 11M  C41   C42  C22   112.19  3.000
 11M  C24   C42  C22   127.49  3.000
 11M  C39   S44  C22    93.75  3.000
 11M  H25   C25  C26   119.20  3.000
 11M  H25   C25  C24   120.07  3.000
 11M  C26   C25  C24   120.72  3.000
 11M  H27   C27  C41   120.11  3.000
 11M  H27   C27  C26   120.55  3.000
 11M  C41   C27  C26   119.34  3.000
 11M  H29B  C29  H29A  108.86  3.000
 11M  H29B  C29  H29   108.65  3.000
 11M  H29A  C29  H29   110.49  3.000
 11M  H29B  C29  S59   106.01  3.000
 11M  H29A  C29  S59   111.21  3.000
 11M  H29   C29  S59   111.46  3.000
 11M  C39   C17  O61   119.60  3.000
 11M  C39   C17  N22   117.73  3.000
 11M  O61   C17  N22   122.57  3.000
 11M  C29   S59  C22   102.21  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
 11M  CONST_01  C1    C6   C5   C4     0.00   0.0  0
 11M  CONST_02  C1    C2   C3   C4     0.00   0.0  0
 11M  CONST_03  C2    C3   C4   C5     0.00   0.0  0
 11M  CONST_04  C2    C1   C6   C5     0.00   0.0  0
 11M  CONST_05  C3    C4   C5   C6     0.00   0.0  0
 11M  CONST_06  C3    C2   C1   C6     0.00   0.0  0
 11M  CONST_07  C25   C24  C42  C22  180.00   0.0  0
 11M  CONST_08  C39   C41  C42  C22    0.00   0.0  0
 11M  CONST_09  C27   C41  C42  C22  180.00   0.0  0
 11M  CONST_10  C41   C39  S44  C22    0.00   0.0  0
 11M  CONST_11  S44   C22  C42  C24  180.00   0.0  0
 11M  CONST_12  C39   C41  C42  C24  180.00   0.0  0
 11M  CONST_13  C27   C41  C42  C24    0.00   0.0  0
 11M  CONST_14  C27   C26  C25  C24    0.00   0.0  0
 11M  CONST_15  C42   C24  C25  C26    0.00   0.0  0
 11M  CONST_16  C39   C41  C27  C26  180.00   0.0  0
 11M  CONST_17  C42   C41  C27  C26    0.00   0.0  0
 11M  CONST_18  C42   C22  S44  C39    0.00   0.0  0
 11M  CONST_19  S44   C22  C42  C41    0.00   0.0  0
 11M  CONST_20  C25   C24  C42  C41    0.00   0.0  0
 11M  CONST_21  C25   C26  C27  C41    0.00   0.0  0
 11M  CONST_22  S44   C39  C41  C42    0.00   0.0  0
 11M  CONST_23  C27   C41  C39  S44  180.00   0.0  0
 11M  CONST_24  C15   C2   C3   C4   180.00   0.0  0
 11M  CONST_25  C15   C2   C1   C6   180.00   0.0  0
 11M  CONST_26  O13   C3   C2   C15    0.00   0.0  0
 11M  CONST_27  C30   C6   C5   C4   180.00   0.0  0
 11M  CONST_28  C42   C41  C39  C17  180.00   0.0  0
 11M  CONST_29  C27   C41  C39  C17    0.00   0.0  0
 11M  CONST_30  C22   S44  C39  C17  180.00   0.0  0
 11M  CONST_31  S59   C22  C42  C24    0.00   0.0  0
 11M  CONST_32  C30   C6   C1   C2   180.00   0.0  0
 11M  CONST_33  S59   C22  S44  C39  180.00   0.0  0
 11M  CONST_34  S59   C22  C42  C41  180.00   0.0  0
 11M  CONST_35  C39   C17  N22  C13  180.00   0.0  0
 11M  CONST_37  H1    C1   C6   C5   180.00   0.0  0
 11M  CONST_38  H4    C4   C5   C6   180.00   0.0  0
 11M  CONST_39  H24   C24  C42  C22    0.00   0.0  0
 11M  CONST_40  H26   C26  C25  C24  180.00   0.0  0
 11M  CONST_41  H5    C5   C6   C1   180.00   0.0  0
 11M  CONST_42  H27   C27  C41  C39    0.00   0.0  0
 11M  CONST_43  H25   C25  C24  C42  180.00   0.0  0
 11M  CONST_44  O61   C17  N22  C13    0.00   0.0  0
 11M  Var_01    C11   C10  C15  C8   -73.31  30.0  3
 11M  Var_02    C1    C2   C15  C8   169.51  30.0  1
 11M  Var_03    C13   C14  C15  C8    72.33  30.0  3
 11M  Var_04    C2    C3   O13  C8    11.43  30.0  1
 11M  Var_05    O13   C8   C15  C10  -94.79  30.0  1
 11M  Var_06    C13   N22  C11  C10   56.85  30.0  1
 11M  Var_07    N22   C11  C10  C15  -53.51  30.0  1
 11M  Var_08    N22   C13  C14  C15   56.69  30.0  1
 11M  Var_09    C14   C13  N22  C11  -59.10  30.0  1
 11M  Var_10    C41   C39  C17  N22  149.02  30.0  2
 11M  Var_11    N64   C30  C6   C5   116.10  30.0  2
 11M  Var_12    HN64  N64  C30  C6   176.36  30.0  3
 11M  Var_13    H29   C29  S59  C22  -64.82  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
 11M  plan-1  C4   0.020
 11M  plan-1  C5   0.020
 11M  plan-1  C6   0.020
 11M  plan-1  C15  0.020
 11M  plan-1  C1   0.020
 11M  plan-1  C2   0.020
 11M  plan-1  C3   0.020
 11M  plan-1  O13  0.020
 11M  plan-1  C30  0.020
 11M  plan-1  H4   0.020
 11M  plan-1  H5   0.020
 11M  plan-1  H1   0.020
 11M  plan-2  C22  0.020
 11M  plan-2  C24  0.020
 11M  plan-2  C26  0.020
 11M  plan-2  C39  0.020
 11M  plan-2  C41  0.020
 11M  plan-2  C42  0.020
 11M  plan-2  S44  0.020
 11M  plan-2  C25  0.020
 11M  plan-2  C27  0.020
 11M  plan-2  H24  0.020
 11M  plan-2  H26  0.020
 11M  plan-2  H25  0.020
 11M  plan-2  H27  0.020
 11M  plan-2  C17  0.020
 11M  plan-2  S59  0.020
 11M  plan-3  C13  0.020
 11M  plan-3  C11  0.020
 11M  plan-3  N22  0.020
 11M  plan-3  O61  0.020
 11M  plan-3  C39  0.020
 11M  plan-3  C17  0.020

