# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 23:32:29 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2,2'-[5-(thiophen-2-yl)benzene-1,3-diyl]diacetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1cc(CC(O)=O)cc(c1)c2sccc2
#
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
 LNX  LNX  '2,2'-[5-(thiophen-2-yl)benzene-1,3-diyl]diacetic acid'  ligand  31  19  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LNX
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
 LNX  C1   C  CH2   0  -0.696   2.1289   2.3367   1.0209
 LNX  C2   C  CR6   0   0.193   1.2240   1.1553   0.8405
 LNX  C3   C  CR16  0  -0.359   1.7239  -0.1377   0.9476
 LNX  O1   O  OH1   0  -0.593   3.5514   3.8358  -0.0846
 LNX  O2   O  O     0  -0.432   1.7019  -2.6427  -1.5042
 LNX  O3   O  OH1   0  -0.593   2.3822  -4.4034  -0.3139
 LNX  C11  C  CR15  0  -0.172  -4.3963   1.4316  -0.5840
 LNX  C12  C  CR15  0  -0.469  -4.8651   0.2676  -0.0560
 LNX  C13  C  CR16  0  -0.392  -0.1244   1.3407   0.5747
 LNX  C    C  C     0   0.559   2.7754   2.7742  -0.2707
 LNX  O    O  O     0  -0.432   2.6206   2.2420  -1.3391
 LNX  C8   C  CR6   0   0.192  -0.9809   0.2509   0.4070
 LNX  C7   C  CR16  0  -0.389  -0.4537  -1.0356   0.5149
 LNX  C4   C  CR6   0   0.190   0.8921  -1.2382   0.7889
 LNX  C5   C  CH2   0  -0.696   1.4403  -2.6293   0.8944
 LNX  C6   C  C     0   0.558   1.8449  -3.1958  -0.4449
 LNX  C9   C  CR5   0  -0.219  -2.3987   0.4723   0.1266
 LNX  C10  C  CR15  0  -0.245  -2.9864   1.5494  -0.4791
 LNX  S    S  S2    0   0.213  -3.5952  -0.6910   0.5758
 LNX  H1   H  HCH2  0   0.306   1.5824   3.1874   1.4364
 LNX  H2   H  HCH2  0   0.307   2.9229   2.1141   1.7394
 LNX  H3   H  HCR6  0   0.253   2.7751  -0.2876   1.1681
 LNX  H4   H  HOH1  0   0.482   3.9600   4.1000  -0.9225
 LNX  H5   H  HOH1  0   0.482   2.6213  -4.7572  -1.1836
 LNX  H6   H  HCR5  0   0.269  -5.0315   2.1795  -1.0362
 LNX  H7   H  HCR5  0   0.298  -5.8860  -0.0773  -0.0015
 LNX  H8   H  HCR6  0   0.254  -0.5207   2.3481   0.5215
 LNX  H9   H  HCR6  0   0.252  -1.0968  -1.8982   0.3788
 LNX  H10  H  HCH2  0   0.306   2.3083  -2.6595   1.5580
 LNX  H11  H  HCH2  0   0.308   0.7044  -3.3072   1.3363
 LNX  H12  H  HCR5  0   0.265  -2.4279   2.3936  -0.8588

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
 LNX  C11  C12  aromatic  1.361  0.020  1.361
 LNX  C11  C10  aromatic  1.419  0.020  1.419
 LNX  C12  S    aromatic  1.712  0.020  1.712
 LNX  C10  C9   aromatic  1.368  0.020  1.368
 LNX  S    C9   aromatic  1.728  0.020  1.728
 LNX  C9   C8   single    1.462  0.020  1.462
 LNX  C8   C7   aromatic  1.395  0.020  1.395
 LNX  C8   C13  aromatic  1.396  0.020  1.396
 LNX  C7   C4   aromatic  1.388  0.020  1.388
 LNX  C13  C2   aromatic  1.387  0.020  1.387
 LNX  C4   C5   single    1.499  0.020  1.499
 LNX  C4   C3   aromatic  1.389  0.020  1.389
 LNX  C2   C3   aromatic  1.390  0.020  1.390
 LNX  C2   C1   single    1.499  0.020  1.499
 LNX  C5   C6   single    1.509  0.020  1.509
 LNX  C6   O2   double    1.204  0.020  1.204
 LNX  C6   O3   single    1.328  0.020  1.328
 LNX  C1   C    single    1.509  0.020  1.509
 LNX  O    C    double    1.204  0.020  1.204
 LNX  C    O1   single    1.328  0.020  1.328
 LNX  C1   H1   single    0.970  0.020  1.090
 LNX  C1   H2   single    0.970  0.020  1.090
 LNX  C3   H3   single    0.930  0.020  1.080
 LNX  O1   H4   single    0.850  0.020  0.980
 LNX  O3   H5   single    0.850  0.020  0.980
 LNX  C11  H6   single    0.930  0.020  1.080
 LNX  C12  H7   single    0.930  0.020  1.080
 LNX  C13  H8   single    0.930  0.020  1.080
 LNX  C7   H9   single    0.930  0.020  1.080
 LNX  C5   H10  single    0.970  0.020  1.090
 LNX  C5   H11  single    0.970  0.020  1.090
 LNX  C10  H12  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
 LNX  H2   C1   H1   105.76  3.000
 LNX  H2   C1   C    108.08  3.000
 LNX  H1   C1   C    108.29  3.000
 LNX  H2   C1   C2   110.91  3.000
 LNX  H1   C1   C2   110.93  3.000
 LNX  C    C1   C2   112.59  3.000
 LNX  C13  C2   C3   119.25  3.000
 LNX  C3   C2   C1   120.44  3.000
 LNX  C13  C2   C1   120.31  3.000
 LNX  H3   C3   C4   119.62  3.000
 LNX  H3   C3   C2   119.52  3.000
 LNX  C4   C3   C2   120.85  3.000
 LNX  H4   O1   C    110.07  3.000
 LNX  H5   O3   C6   110.08  3.000
 LNX  H6   C11  C10  123.90  3.000
 LNX  H6   C11  C12  123.48  3.000
 LNX  C10  C11  C12  112.62  3.000
 LNX  H7   C12  S    120.28  3.000
 LNX  H7   C12  C11  128.22  3.000
 LNX  S    C12  C11  111.49  3.000
 LNX  H8   C13  C8   119.69  3.000
 LNX  H8   C13  C2   119.29  3.000
 LNX  C8   C13  C2   121.00  3.000
 LNX  O    C    O1   123.57  3.000
 LNX  O1   C    C1   111.23  3.000
 LNX  O    C    C1   125.20  3.000
 LNX  C9   C8   C7   121.40  3.000
 LNX  C7   C8   C13  118.62  3.000
 LNX  C9   C8   C13  119.98  3.000
 LNX  H9   C7   C4   118.91  3.000
 LNX  H9   C7   C8   120.00  3.000
 LNX  C4   C7   C8   121.09  3.000
 LNX  C5   C4   C7   120.26  3.000
 LNX  C5   C4   C3   120.56  3.000
 LNX  C7   C4   C3   119.18  3.000
 LNX  H11  C5   H10  105.77  3.000
 LNX  H11  C5   C6   107.83  3.000
 LNX  H10  C5   C6   108.39  3.000
 LNX  H11  C5   C4   110.95  3.000
 LNX  H10  C5   C4   111.03  3.000
 LNX  C6   C5   C4   112.58  3.000
 LNX  C5   C6   O3   111.23  3.000
 LNX  O3   C6   O2   123.55  3.000
 LNX  C5   C6   O2   125.21  3.000
 LNX  S    C9   C10  110.34  3.000
 LNX  S    C9   C8   121.30  3.000
 LNX  C10  C9   C8   128.35  3.000
 LNX  H12  C10  C9   123.25  3.000
 LNX  H12  C10  C11  123.53  3.000
 LNX  C9   C10  C11  113.21  3.000
 LNX  C9   S    C12   92.34  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
 LNX  CONST_01  C9   C8   C13  C2   180.00   0.0  0
 LNX  CONST_02  C7   C8   C13  C2     0.00   0.0  0
 LNX  CONST_03  C7   C4   C3   C2     0.00   0.0  0
 LNX  CONST_04  C8   C7   C4   C3     0.00   0.0  0
 LNX  CONST_05  C8   C13  C2   C3     0.00   0.0  0
 LNX  CONST_06  C9   S    C12  C11    0.00   0.0  0
 LNX  CONST_07  S    C9   C10  C11    0.00   0.0  0
 LNX  CONST_08  C8   C9   C10  C11  180.00   0.0  0
 LNX  CONST_09  C9   C10  C11  C12    0.00   0.0  0
 LNX  CONST_10  C10  C9   S    C12    0.00   0.0  0
 LNX  CONST_11  C8   C9   S    C12  180.00   0.0  0
 LNX  CONST_14  C4   C7   C8   C13    0.00   0.0  0
 LNX  CONST_15  C4   C3   C2   C13    0.00   0.0  0
 LNX  CONST_18  C9   C8   C7   C4   180.00   0.0  0
 LNX  CONST_19  S    C12  C11  C10    0.00   0.0  0
 LNX  CONST_20  C8   C13  C2   C1   180.00   0.0  0
 LNX  CONST_21  C4   C3   C2   C1   180.00   0.0  0
 LNX  CONST_22  C5   C4   C3   C2   180.00   0.0  0
 LNX  CONST_23  C5   C4   C7   C8   180.00   0.0  0
 LNX  CONST_24  H9   C7   C4   C3   180.00   0.0  0
 LNX  CONST_25  H8   C13  C2   C3   180.00   0.0  0
 LNX  CONST_26  H12  C10  C11  C12  180.00   0.0  0
 LNX  CONST_27  H3   C3   C2   C13  180.00   0.0  0
 LNX  CONST_28  H6   C11  C10  C9   180.00   0.0  0
 LNX  CONST_29  H7   C12  S    C9   180.00   0.0  0
 LNX  CONST_30  H4   O1   C    C1   180.00   0.0  0
 LNX  CONST_31  H5   O3   C6   O2     0.00   0.0  0
 LNX  Var_01    C6   C5   C4   C3   -93.10  30.0  2
 LNX  Var_02    C    C1   C2   C3    89.05  30.0  2
 LNX  Var_03    O    C    C1   C2    -1.19  30.0  3
 LNX  Var_04    C4   C5   C6   O2    -3.14  30.0  2

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
 LNX  plan-1  C11  0.020
 LNX  plan-1  C12  0.020
 LNX  plan-1  C8   0.020
 LNX  plan-1  C9   0.020
 LNX  plan-1  C10  0.020
 LNX  plan-1  S    0.020
 LNX  plan-1  H6   0.020
 LNX  plan-1  H7   0.020
 LNX  plan-1  H12  0.020
 LNX  plan-2  C1   0.020
 LNX  plan-2  C2   0.020
 LNX  plan-2  C3   0.020
 LNX  plan-2  C13  0.020
 LNX  plan-2  C8   0.020
 LNX  plan-2  C7   0.020
 LNX  plan-2  C4   0.020
 LNX  plan-2  C5   0.020
 LNX  plan-2  C9   0.020
 LNX  plan-2  H3   0.020
 LNX  plan-2  H8   0.020
 LNX  plan-2  H9   0.020
 LNX  plan-3  C1   0.020
 LNX  plan-3  O1   0.020
 LNX  plan-3  C    0.020
 LNX  plan-3  O    0.020
 LNX  plan-3  H4   0.020
 LNX  plan-4  O2   0.020
 LNX  plan-4  O3   0.020
 LNX  plan-4  C5   0.020
 LNX  plan-4  C6   0.020
 LNX  plan-4  H5   0.020

