# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:18:48 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: naphtho[2,1-b]thiophen-1-ylacetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1csc2ccc3ccccc3c12
#
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
 3N4  3N4  'naphtho[2,1-b]thiophen-1-ylacetic acid'  ligand  27  17  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3N4
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
 3N4  S1    S  S2    0   0.239   2.2883  -2.1567   0.0661
 3N4  C2    C  CR56  0  -0.285   0.5970  -1.8415  -0.0283
 3N4  C3    C  CR56  0   0.210   0.2895  -0.5047   0.2296
 3N4  C4    C  CR66  0   0.110  -1.0917  -0.1105   0.1969
 3N4  C5    C  CR66  0   0.093  -2.0643  -1.0979  -0.1249
 3N4  C6    C  CR16  0  -0.337  -1.6752  -2.4409  -0.3891
 3N4  C8    C  CR16  0  -0.272  -0.3708  -2.8183  -0.3375
 3N4  C10   C  CR16  0  -0.305  -3.4297  -0.7460  -0.1756
 3N4  C12   C  CR16  0  -0.264  -3.8430   0.5329   0.0880
 3N4  C14   C  CR16  0  -0.242  -2.8913   1.5083   0.4212
 3N4  C16   C  CR16  0  -0.368  -1.5562   1.1940   0.4739
 3N4  C18   C  CR5   0   0.205   1.4870   0.2592   0.4934
 3N4  C19   C  CR15  0  -0.536   2.6019  -0.5129   0.4392
 3N4  C21   C  CH2   0  -0.753   1.6005   1.7207   0.7858
 3N4  C24   C  C     0   0.548   1.3096   2.5878  -0.4160
 3N4  O25   O  OH1   0  -0.591   1.1922   3.8651  -0.0745
 3N4  O26   O  O     0  -0.424   1.2185   2.1863  -1.5469
 3N4  H6    H  HCR6  0   0.261  -2.4422  -3.1670  -0.6284
 3N4  H8    H  HCR6  0   0.271  -0.0759  -3.8410  -0.5322
 3N4  H10   H  HCR6  0   0.258  -4.1536  -1.5130  -0.4244
 3N4  H12   H  HCR6  0   0.259  -4.8934   0.7889   0.0470
 3N4  H14   H  HCR6  0   0.262  -3.2084   2.5185   0.6440
 3N4  H16   H  HCR6  0   0.243  -0.8720   1.9780   0.7541
 3N4  H19   H  HCR5  0   0.302   3.6178  -0.1820   0.5976
 3N4  H21   H  HCH2  0   0.304   0.9856   2.0308   1.6339
 3N4  H21A  H  HCH2  0   0.328   2.6280   1.9441   1.0904
 3N4  HO25  H  HOH1  0   0.483   1.0346   4.4087  -0.8613

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
 3N4  S1   C2    aromatic  1.723  0.020  1.723
 3N4  S1   C19   aromatic  1.714  0.020  1.714
 3N4  C8   C2    aromatic  1.409  0.020  1.409
 3N4  C2   C3    aromatic  1.396  0.020  1.396
 3N4  C3   C4    aromatic  1.437  0.020  1.437
 3N4  C3   C18   aromatic  1.445  0.020  1.445
 3N4  C5   C4    aromatic  1.423  0.020  1.423
 3N4  C4   C16   aromatic  1.412  0.020  1.412
 3N4  C6   C5    aromatic  1.423  0.020  1.423
 3N4  C5   C10   aromatic  1.411  0.020  1.411
 3N4  C8   C6    aromatic  1.359  0.020  1.359
 3N4  C6   H6    single    0.930  0.020  1.080
 3N4  C8   H8    single    0.930  0.020  1.080
 3N4  C10  C12   aromatic  1.370  0.020  1.370
 3N4  C10  H10   single    0.930  0.020  1.080
 3N4  C12  C14   aromatic  1.403  0.020  1.403
 3N4  C12  H12   single    0.930  0.020  1.080
 3N4  C16  C14   aromatic  1.373  0.020  1.373
 3N4  C14  H14   single    0.930  0.020  1.080
 3N4  C16  H16   single    0.930  0.020  1.080
 3N4  C19  C18   aromatic  1.357  0.020  1.357
 3N4  C18  C21   single    1.495  0.020  1.495
 3N4  C19  H19   single    0.930  0.020  1.080
 3N4  C24  C21   single    1.510  0.020  1.510
 3N4  C21  H21   single    0.970  0.020  1.090
 3N4  C21  H21A  single    0.970  0.020  1.090
 3N4  O26  C24   double    1.204  0.020  1.204
 3N4  O25  C24   single    1.327  0.020  1.327
 3N4  O25  HO25  single    0.850  0.020  0.980

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
 3N4  C19   S1   C2    90.92  3.000
 3N4  C8    C2   C3   123.58  3.000
 3N4  C3    C2   S1   112.41  3.000
 3N4  C8    C2   S1   124.00  3.000
 3N4  C18   C3   C4   130.99  3.000
 3N4  C18   C3   C2   110.95  3.000
 3N4  C4    C3   C2   118.06  3.000
 3N4  C16   C4   C5   117.43  3.000
 3N4  C16   C4   C3   124.42  3.000
 3N4  C5    C4   C3   118.15  3.000
 3N4  C10   C5   C6   119.56  3.000
 3N4  C10   C5   C4   119.77  3.000
 3N4  C6    C5   C4   120.67  3.000
 3N4  H6    C6   C8   120.13  3.000
 3N4  H6    C6   C5   118.70  3.000
 3N4  C8    C6   C5   121.17  3.000
 3N4  H8    C8   C6   121.15  3.000
 3N4  H8    C8   C2   120.49  3.000
 3N4  C6    C8   C2   118.36  3.000
 3N4  H10   C10  C12  120.24  3.000
 3N4  H10   C10  C5   118.56  3.000
 3N4  C12   C10  C5   121.20  3.000
 3N4  H12   C12  C14  120.20  3.000
 3N4  H12   C12  C10  120.44  3.000
 3N4  C14   C12  C10  119.36  3.000
 3N4  H14   C14  C16  119.40  3.000
 3N4  H14   C14  C12  119.95  3.000
 3N4  C16   C14  C12  120.65  3.000
 3N4  H16   C16  C14  117.45  3.000
 3N4  H16   C16  C4   120.95  3.000
 3N4  C14   C16  C4   121.60  3.000
 3N4  C21   C18  C19  120.11  3.000
 3N4  C21   C18  C3   128.00  3.000
 3N4  C19   C18  C3   111.89  3.000
 3N4  H19   C19  C18  126.33  3.000
 3N4  H19   C19  S1   119.85  3.000
 3N4  C18   C19  S1   113.82  3.000
 3N4  H21A  C21  H21  104.74  3.000
 3N4  H21A  C21  C24  106.56  3.000
 3N4  H21   C21  C24  110.26  3.000
 3N4  H21A  C21  C18  108.98  3.000
 3N4  H21   C21  C18  112.75  3.000
 3N4  C24   C21  C18  113.02  3.000
 3N4  O26   C24  O25  123.79  3.000
 3N4  O25   C24  C21  111.39  3.000
 3N4  O26   C24  C21  124.81  3.000
 3N4  HO25  O25  C24  110.19  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
 3N4  CONST_01  C6    C8   C2   S1   180.00   0.0  0
 3N4  CONST_02  C4    C3   C2   S1   180.00   0.0  0
 3N4  CONST_03  C18   C3   C2   S1     0.00   0.0  0
 3N4  CONST_04  C3    C18  C19  S1     0.00   0.0  0
 3N4  CONST_05  C18   C19  S1   C2     0.00   0.0  0
 3N4  CONST_06  C5    C6   C8   C2     0.00   0.0  0
 3N4  CONST_07  C5    C4   C3   C2     0.00   0.0  0
 3N4  CONST_08  C16   C4   C3   C2   180.00   0.0  0
 3N4  CONST_09  C19   C18  C3   C2     0.00   0.0  0
 3N4  CONST_10  C19   S1   C2   C3     0.00   0.0  0
 3N4  CONST_11  C6    C8   C2   C3     0.00   0.0  0
 3N4  CONST_12  C6    C5   C4   C3     0.00   0.0  0
 3N4  CONST_13  C10   C5   C4   C3   180.00   0.0  0
 3N4  CONST_14  C14   C16  C4   C3   180.00   0.0  0
 3N4  CONST_15  C8    C2   C3   C4     0.00   0.0  0
 3N4  CONST_16  C19   C18  C3   C4   180.00   0.0  0
 3N4  CONST_17  C8    C6   C5   C4     0.00   0.0  0
 3N4  CONST_18  C12   C10  C5   C4     0.00   0.0  0
 3N4  CONST_19  C12   C14  C16  C4     0.00   0.0  0
 3N4  CONST_20  C18   C3   C4   C5   180.00   0.0  0
 3N4  CONST_21  C14   C16  C4   C5     0.00   0.0  0
 3N4  CONST_22  C14   C12  C10  C5     0.00   0.0  0
 3N4  CONST_23  C16   C4   C5   C6   180.00   0.0  0
 3N4  CONST_24  C12   C10  C5   C6   180.00   0.0  0
 3N4  CONST_25  C19   S1   C2   C8   180.00   0.0  0
 3N4  CONST_26  C18   C3   C2   C8   180.00   0.0  0
 3N4  CONST_27  C10   C5   C6   C8   180.00   0.0  0
 3N4  CONST_28  C16   C4   C5   C10    0.00   0.0  0
 3N4  CONST_29  C16   C14  C12  C10    0.00   0.0  0
 3N4  CONST_30  C18   C3   C4   C16    0.00   0.0  0
 3N4  CONST_31  C21   C18  C19  S1   180.00   0.0  0
 3N4  CONST_32  C21   C18  C3   C2   180.00   0.0  0
 3N4  CONST_33  C21   C18  C3   C4     0.00   0.0  0
 3N4  CONST_34  H8    C8   C2   S1     0.00   0.0  0
 3N4  CONST_35  H19   C19  S1   C2   180.00   0.0  0
 3N4  CONST_36  H6    C6   C8   C2   180.00   0.0  0
 3N4  CONST_37  H16   C16  C4   C3     0.00   0.0  0
 3N4  CONST_38  H10   C10  C5   C4   180.00   0.0  0
 3N4  CONST_39  H14   C14  C16  C4   180.00   0.0  0
 3N4  CONST_40  H12   C12  C10  C5   180.00   0.0  0
 3N4  CONST_41  HO25  O25  C24  C21  180.00   0.0  0
 3N4  Var_01    C24   C21  C18  C3   -70.49  30.0  2
 3N4  Var_02    O26   C24  C21  C18  -12.08  30.0  1

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
 3N4  plan-1  S1    0.020
 3N4  plan-1  C2    0.020
 3N4  plan-1  C3    0.020
 3N4  plan-1  C4    0.020
 3N4  plan-1  C5    0.020
 3N4  plan-1  C6    0.020
 3N4  plan-1  C8    0.020
 3N4  plan-1  C10   0.020
 3N4  plan-1  C12   0.020
 3N4  plan-1  C14   0.020
 3N4  plan-1  C16   0.020
 3N4  plan-1  C18   0.020
 3N4  plan-1  C19   0.020
 3N4  plan-1  C21   0.020
 3N4  plan-1  H6    0.020
 3N4  plan-1  H8    0.020
 3N4  plan-1  H10   0.020
 3N4  plan-1  H12   0.020
 3N4  plan-1  H14   0.020
 3N4  plan-1  H16   0.020
 3N4  plan-1  H19   0.020
 3N4  plan-2  C21   0.020
 3N4  plan-2  C24   0.020
 3N4  plan-2  O25   0.020
 3N4  plan-2  O26   0.020
 3N4  plan-2  HO25  0.020

