# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:19:48 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 3-methoxybenzyl 3-(piperidin-4-yloxy)-1-benzothiophene-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(COC(=O)c2sc3ccccc3c2OC4CCNCC4)c1
#
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
 YBN  YBN  '3-methoxybenzyl 3-(piperidin-4-yloxy)-1-benzothiophene-2-carboxylate'  ligand  51  28  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YBN
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
 YBN  C     C  CH3   0  -0.437   7.7359  -1.8462   0.5780
 YBN  N     N  NH1   0  -0.594  -4.4640   4.0846  -0.6815
 YBN  O     O  O2    0  -0.471   6.5325  -1.2939   1.0726
 YBN  S     S  S2    0   0.250   0.0020  -1.6695  -0.2390
 YBN  C1    C  CR6   0   0.398   5.8283  -0.4686   0.2759
 YBN  O1    O  O2    0  -0.467   1.5705   0.5614   0.4187
 YBN  C2    C  CR16  0  -0.389   6.1898  -0.1362  -1.0279
 YBN  O2    O  O     0  -0.434   0.0576   1.8938   1.3969
 YBN  C3    C  CR16  0  -0.229   5.3883   0.7345  -1.7578
 YBN  O3    O  O2    0  -0.477  -2.6530   0.8125   1.1580
 YBN  C4    C  CR16  0  -0.317   4.2377   1.2758  -1.2108
 YBN  C5    C  CR6   0   0.095   3.8754   0.9434   0.0931
 YBN  C6    C  CH2   0  -0.250   2.6223   1.5007   0.6953
 YBN  C7    C  C     0   0.626   0.3424   0.8751   0.8184
 YBN  C8    C  CR5   0  -0.472  -0.5946  -0.1909   0.4604
 YBN  C9    C  CR56  0  -0.216  -1.5997  -2.3170  -0.3187
 YBN  C10   C  CR16  0  -0.280  -1.9614  -3.5771  -0.7925
 YBN  C11   C  CR16  0  -0.256  -3.2946  -3.9303  -0.7486
 YBN  C12   C  CR16  0  -0.254  -4.2600  -3.0532  -0.2322
 YBN  C13   C  CR16  0  -0.300  -3.9018  -1.8081   0.2355
 YBN  C14   C  CR56  0   0.148  -2.5559  -1.4219   0.1830
 YBN  C15   C  CR5   0   0.426  -1.9508  -0.1939   0.6239
 YBN  C16   C  CH1   0   0.033  -3.4816   1.5686   0.2509
 YBN  C17   C  CH2   0  -0.460  -4.4263   2.4064   1.0886
 YBN  C18   C  CH2   0  -0.304  -5.2977   3.2574   0.1719
 YBN  C19   C  CH2   0  -0.300  -3.6041   3.2842  -1.5346
 YBN  C20   C  CH2   0  -0.448  -2.6609   2.4450  -0.6799
 YBN  C21   C  CR16  0  -0.379   4.6670   0.0754   0.8279
 YBN  H     H  HCH3  0   0.260   8.1453  -2.4601   1.3765
 YBN  HA    H  HCH3  0   0.229   7.5683  -2.4774  -0.2987
 YBN  HB    H  HCH3  0   0.229   8.4644  -1.0726   0.3209
 YBN  H2    H  HCR6  0   0.282   7.0841  -0.5354  -1.4866
 YBN  H3    H  HCR6  0   0.262   5.6765   0.9904  -2.7689
 YBN  H4    H  HCR6  0   0.253   3.6268   1.9571  -1.7895
 YBN  H6    H  HCH2  0   0.257   2.3749   2.4690   0.2571
 YBN  H6A   H  HCH2  0   0.256   2.7253   1.6293   1.7745
 YBN  H10   H  HCR6  0   0.274  -1.2175  -4.2613  -1.1794
 YBN  H11   H  HCR6  0   0.269  -3.5987  -4.9022  -1.1133
 YBN  H12   H  HCR6  0   0.266  -5.2963  -3.3615  -0.1992
 YBN  H13   H  HCR6  0   0.265  -4.6518  -1.1429   0.6440
 YBN  H16   H  HCH1  0   0.222  -4.0720   0.8707  -0.3570
 YBN  H17   H  HCH2  0   0.245  -5.0590   1.7650   1.7062
 YBN  H17A  H  HCH2  0   0.232  -3.8514   3.0560   1.7551
 YBN  H18   H  HCH2  0   0.241  -5.9408   3.9008   0.7742
 YBN  H18A  H  HCH2  0   0.194  -5.9625   2.5912  -0.4022
 YBN  H19   H  HCH2  0   0.194  -4.1719   2.6137  -2.2007
 YBN  H19A  H  HCH2  0   0.240  -3.0226   3.9474  -2.1770
 YBN  H20   H  HCH2  0   0.235  -2.0112   3.0995  -0.0950
 YBN  H20A  H  HCH2  0   0.238  -2.0273   1.8373  -1.3302
 YBN  H21   H  HCR6  0   0.262   4.3958  -0.1834   1.8452
 YBN  HN    H  HNH1  0   0.355  -5.0522   4.6748  -1.2550

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
 YBN  C    O     single    1.413  0.020  1.413
 YBN  N    C18   single    1.452  0.020  1.452
 YBN  N    C19   single    1.452  0.020  1.452
 YBN  O    C1    single    1.346  0.020  1.346
 YBN  S    C8    aromatic  1.741  0.020  1.741
 YBN  S    C9    aromatic  1.729  0.020  1.729
 YBN  C1   C2    aromatic  1.393  0.020  1.393
 YBN  C1   C21   aromatic  1.396  0.020  1.396
 YBN  O1   C6    single    1.437  0.020  1.437
 YBN  O1   C7    single    1.329  0.020  1.329
 YBN  C2   C3    aromatic  1.390  0.020  1.390
 YBN  O2   C7    double    1.206  0.020  1.206
 YBN  C3   C4    aromatic  1.384  0.020  1.384
 YBN  O3   C15   single    1.338  0.020  1.338
 YBN  O3   C16   single    1.443  0.020  1.443
 YBN  C4   C5    aromatic  1.394  0.020  1.394
 YBN  C5   C6    single    1.498  0.020  1.498
 YBN  C5   C21   aromatic  1.386  0.020  1.386
 YBN  C7   C8    single    1.464  0.020  1.464
 YBN  C8   C15   aromatic  1.366  0.020  1.366
 YBN  C9   C10   aromatic  1.394  0.020  1.394
 YBN  C9   C14   aromatic  1.403  0.020  1.403
 YBN  C10  C11   aromatic  1.380  0.020  1.380
 YBN  C11  C12   aromatic  1.403  0.020  1.403
 YBN  C12  C13   aromatic  1.377  0.020  1.377
 YBN  C13  C14   aromatic  1.401  0.020  1.401
 YBN  C14  C15   aromatic  1.438  0.020  1.438
 YBN  C16  C17   single    1.515  0.020  1.515
 YBN  C16  C20   single    1.519  0.020  1.519
 YBN  C17  C18   single    1.524  0.020  1.524
 YBN  C19  C20   single    1.525  0.020  1.525
 YBN  C    H     single    0.970  0.020  1.090
 YBN  C    HA    single    0.970  0.020  1.090
 YBN  C    HB    single    0.970  0.020  1.090
 YBN  N    HN    single    0.890  0.020  1.040
 YBN  C2   H2    single    0.930  0.020  1.080
 YBN  C3   H3    single    0.930  0.020  1.080
 YBN  C4   H4    single    0.930  0.020  1.080
 YBN  C6   H6    single    0.970  0.020  1.090
 YBN  C6   H6A   single    0.970  0.020  1.090
 YBN  C10  H10   single    0.930  0.020  1.080
 YBN  C11  H11   single    0.930  0.020  1.080
 YBN  C12  H12   single    0.930  0.020  1.080
 YBN  C13  H13   single    0.930  0.020  1.080
 YBN  C16  H16   single    0.970  0.020  1.090
 YBN  C17  H17   single    0.970  0.020  1.090
 YBN  C17  H17A  single    0.970  0.020  1.090
 YBN  C18  H18   single    0.970  0.020  1.090
 YBN  C18  H18A  single    0.970  0.020  1.090
 YBN  C19  H19   single    0.970  0.020  1.090
 YBN  C19  H19A  single    0.970  0.020  1.090
 YBN  C20  H20   single    0.970  0.020  1.090
 YBN  C20  H20A  single    0.970  0.020  1.090
 YBN  C21  H21   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
 YBN  HB    C    HA   108.80  3.000
 YBN  HB    C    H    108.75  3.000
 YBN  HA    C    H    108.70  3.000
 YBN  HB    C    O    111.90  3.000
 YBN  HA    C    O    112.07  3.000
 YBN  H     C    O    106.51  3.000
 YBN  HN    N    C19  109.44  3.000
 YBN  HN    N    C18  109.38  3.000
 YBN  C19   N    C18  111.80  3.000
 YBN  C1    O    C    118.55  3.000
 YBN  C9    S    C8    91.09  3.000
 YBN  C21   C1   C2   119.53  3.000
 YBN  C21   C1   O    116.11  3.000
 YBN  C2    C1   O    124.37  3.000
 YBN  C7    O1   C6   117.66  3.000
 YBN  H2    C2   C3   119.02  3.000
 YBN  H2    C2   C1   121.56  3.000
 YBN  C3    C2   C1   119.42  3.000
 YBN  H3    C3   C4   119.88  3.000
 YBN  H3    C3   C2   119.02  3.000
 YBN  C4    C3   C2   121.10  3.000
 YBN  C16   O3   C15  116.39  3.000
 YBN  H4    C4   C5   120.23  3.000
 YBN  H4    C4   C3   120.26  3.000
 YBN  C5    C4   C3   119.51  3.000
 YBN  C21   C5   C6   119.86  3.000
 YBN  C21   C5   C4   119.80  3.000
 YBN  C6    C5   C4   120.33  3.000
 YBN  H6A   C6   H6   108.29  3.000
 YBN  H6A   C6   C5   111.24  3.000
 YBN  H6    C6   C5   111.00  3.000
 YBN  H6A   C6   O1   109.65  3.000
 YBN  H6    C6   O1   109.68  3.000
 YBN  C5    C6   O1   106.97  3.000
 YBN  C8    C7   O2   125.56  3.000
 YBN  C8    C7   O1   110.25  3.000
 YBN  O2    C7   O1   124.19  3.000
 YBN  C15   C8   C7   127.44  3.000
 YBN  C15   C8   S    112.73  3.000
 YBN  C7    C8   S    119.82  3.000
 YBN  C14   C9   C10  121.43  3.000
 YBN  C14   C9   S    112.09  3.000
 YBN  C10   C9   S    126.47  3.000
 YBN  H10   C10  C11  120.91  3.000
 YBN  H10   C10  C9   120.97  3.000
 YBN  C11   C10  C9   118.12  3.000
 YBN  H11   C11  C12  119.50  3.000
 YBN  H11   C11  C10  119.40  3.000
 YBN  C12   C11  C10  121.10  3.000
 YBN  H12   C12  C13  119.76  3.000
 YBN  H12   C12  C11  119.49  3.000
 YBN  C13   C12  C11  120.75  3.000
 YBN  H13   C13  C14  120.68  3.000
 YBN  H13   C13  C12  120.23  3.000
 YBN  C14   C13  C12  119.09  3.000
 YBN  C15   C14  C13  128.90  3.000
 YBN  C15   C14  C9   111.57  3.000
 YBN  C13   C14  C9   119.50  3.000
 YBN  C14   C15  C8   112.51  3.000
 YBN  C14   C15  O3   122.93  3.000
 YBN  C8    C15  O3   124.54  3.000
 YBN  H16   C16  C20  108.55  3.000
 YBN  H16   C16  C17  108.81  3.000
 YBN  C20   C16  C17  110.89  3.000
 YBN  H16   C16  O3   108.89  3.000
 YBN  C20   C16  O3   112.16  3.000
 YBN  C17   C16  O3   107.47  3.000
 YBN  H17A  C17  H17  107.97  3.000
 YBN  H17A  C17  C18  109.59  3.000
 YBN  H17   C17  C18  109.68  3.000
 YBN  H17A  C17  C16  109.73  3.000
 YBN  H17   C17  C16  110.43  3.000
 YBN  C18   C17  C16  109.42  3.000
 YBN  H18A  C18  H18  106.76  3.000
 YBN  H18A  C18  C17  108.69  3.000
 YBN  H18   C18  C17  109.52  3.000
 YBN  H18A  C18  N    112.62  3.000
 YBN  H18   C18  N    109.09  3.000
 YBN  C17   C18  N    110.08  3.000
 YBN  H19A  C19  H19  106.76  3.000
 YBN  H19A  C19  C20  109.57  3.000
 YBN  H19   C19  C20  108.81  3.000
 YBN  H19A  C19  N    109.06  3.000
 YBN  H19   C19  N    112.66  3.000
 YBN  C20   C19  N    109.90  3.000
 YBN  H20A  C20  H20  107.89  3.000
 YBN  H20A  C20  C19  109.34  3.000
 YBN  H20   C20  C19  109.78  3.000
 YBN  H20A  C20  C16  110.93  3.000
 YBN  H20   C20  C16  109.82  3.000
 YBN  C19   C20  C16  109.07  3.000
 YBN  H21   C21  C5   120.27  3.000
 YBN  H21   C21  C1   119.08  3.000
 YBN  C5    C21  C1   120.64  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
 YBN  CONST_01  C14  C15  C8   S       0.00   0.0  0
 YBN  CONST_02  C11  C10  C9   S     180.00   0.0  0
 YBN  CONST_03  C13  C14  C9   S     180.00   0.0  0
 YBN  CONST_04  C15  C14  C9   S       0.00   0.0  0
 YBN  CONST_05  C4   C3   C2   C1      0.00   0.0  0
 YBN  CONST_06  C4   C5   C21  C1      0.00   0.0  0
 YBN  CONST_07  C5   C21  C1   C2      0.00   0.0  0
 YBN  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 YBN  CONST_09  C21  C1   C2   C3      0.00   0.0  0
 YBN  CONST_10  C21  C5   C4   C3      0.00   0.0  0
 YBN  CONST_11  C10  C9   S    C8    180.00   0.0  0
 YBN  CONST_12  C14  C9   S    C8      0.00   0.0  0
 YBN  CONST_13  C9   C14  C15  C8      0.00   0.0  0
 YBN  CONST_14  C13  C14  C15  C8    180.00   0.0  0
 YBN  CONST_15  C15  C8   S    C9      0.00   0.0  0
 YBN  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 YBN  CONST_17  C12  C13  C14  C9      0.00   0.0  0
 YBN  CONST_18  C13  C14  C9   C10     0.00   0.0  0
 YBN  CONST_19  C15  C14  C9   C10   180.00   0.0  0
 YBN  CONST_20  C13  C12  C11  C10     0.00   0.0  0
 YBN  CONST_21  C14  C9   C10  C11     0.00   0.0  0
 YBN  CONST_22  C14  C13  C12  C11     0.00   0.0  0
 YBN  CONST_23  C15  C14  C13  C12   180.00   0.0  0
 YBN  CONST_24  C3   C2   C1   O     180.00   0.0  0
 YBN  CONST_25  C5   C21  C1   O     180.00   0.0  0
 YBN  CONST_26  O3   C15  C8   S     180.00   0.0  0
 YBN  CONST_27  C6   C5   C21  C1    180.00   0.0  0
 YBN  CONST_28  C6   C5   C4   C3    180.00   0.0  0
 YBN  CONST_29  C9   C14  C15  O3    180.00   0.0  0
 YBN  CONST_30  C13  C14  C15  O3      0.00   0.0  0
 YBN  CONST_31  C9   S    C8   C7    180.00   0.0  0
 YBN  CONST_32  C14  C15  C8   C7    180.00   0.0  0
 YBN  CONST_33  H10  C10  C9   S       0.00   0.0  0
 YBN  CONST_34  H3   C3   C2   C1    180.00   0.0  0
 YBN  CONST_35  H21  C21  C1   C2    180.00   0.0  0
 YBN  CONST_36  H4   C4   C3   C2    180.00   0.0  0
 YBN  CONST_37  H2   C2   C3   C4    180.00   0.0  0
 YBN  CONST_38  H11  C11  C10  C9    180.00   0.0  0
 YBN  CONST_39  H13  C13  C14  C9    180.00   0.0  0
 YBN  CONST_40  H12  C12  C11  C10   180.00   0.0  0
 YBN  Var_01    C16  C17  C18  N     -57.02  30.0  1
 YBN  Var_02    C16  C20  C19  N      57.82  30.0  1
 YBN  Var_03    C19  N    C18  C17    61.17  30.0  1
 YBN  Var_04    C20  C19  N    C18   -61.66  30.0  1
 YBN  Var_05    C2   C1   O    C       1.40  30.0  2
 YBN  Var_06    O1   C7   C8   S       5.62  30.0  1
 YBN  Var_07    C4   C5   C6   O1     91.30  30.0  2
 YBN  Var_08    C8   C7   O1   C6   -179.79  30.0  3
 YBN  Var_09    H    C    O    C1    179.10  30.0  3

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
 YBN  chir_01  C16  O3  C17  C20  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
 YBN  plan-1  O    0.020
 YBN  plan-1  C1   0.020
 YBN  plan-1  C2   0.020
 YBN  plan-1  C3   0.020
 YBN  plan-1  C4   0.020
 YBN  plan-1  C5   0.020
 YBN  plan-1  C6   0.020
 YBN  plan-1  C21  0.020
 YBN  plan-1  H2   0.020
 YBN  plan-1  H3   0.020
 YBN  plan-1  H4   0.020
 YBN  plan-1  H21  0.020
 YBN  plan-2  O1   0.020
 YBN  plan-2  O2   0.020
 YBN  plan-2  C7   0.020
 YBN  plan-2  C8   0.020
 YBN  plan-3  S    0.020
 YBN  plan-3  O3   0.020
 YBN  plan-3  C7   0.020
 YBN  plan-3  C8   0.020
 YBN  plan-3  C9   0.020
 YBN  plan-3  C10  0.020
 YBN  plan-3  C11  0.020
 YBN  plan-3  C12  0.020
 YBN  plan-3  C13  0.020
 YBN  plan-3  C14  0.020
 YBN  plan-3  C15  0.020
 YBN  plan-3  H10  0.020
 YBN  plan-3  H11  0.020
 YBN  plan-3  H12  0.020
 YBN  plan-3  H13  0.020

