# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:44:36 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CC(O)=O)cc1c2sccc2
#
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
 5V5  5V5  '2-(4-methoxy-3-thiophen-2-yl-phenyl)ethanoic acid'  ligand  29  17  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5V5
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
 5V5  C1   C  CH2   0  -0.693   3.2210   0.4556   0.9271
 5V5  C2   C  CR6   0   0.151   1.9279  -0.2570   0.6711
 5V5  C3   C  CR16  0  -0.298   1.8942  -1.6285   0.4613
 5V5  O2   O  OH1   0  -0.593   5.0392   1.5428  -0.0799
 5V5  C11  C  CR15  0  -0.479  -3.9918   1.5834   0.0363
 5V5  C12  C  CR16  0  -0.377   0.7332   0.4458   0.6173
 5V5  O    O  O     0  -0.435   3.4149   0.8537  -1.4450
 5V5  C    C  C     0   0.556   3.8743   0.9581  -0.3370
 5V5  C4   C  CR16  0  -0.367   0.6976  -2.2781   0.2007
 5V5  C5   C  CR6   0   0.344  -0.4935  -1.5616   0.1532
 5V5  C6   C  CH3   0  -0.436  -1.7680  -3.5130  -0.3373
 5V5  C7   C  CR6   0   0.061  -0.4942  -0.1718   0.3743
 5V5  C8   C  CR5   0  -0.193  -1.7203   0.6294   0.3713
 5V5  C9   C  CR15  0  -0.254  -1.8578   1.9087   0.8514
 5V5  C10  C  CR15  0  -0.173  -3.1503   2.4530   0.6610
 5V5  S    S  S2    0   0.227  -3.2237   0.0953  -0.3071
 5V5  H1   H  HCH2  0   0.304   3.0730   1.3097   1.5946
 5V5  H2   H  HCH2  0   0.304   3.9318  -0.1973   1.4415
 5V5  H3   H  HCR6  0   0.259   2.8080  -2.2091   0.4969
 5V5  H4   H  HOH1  0   0.481   5.4424   1.8566  -0.9034
 5V5  H5   H  HCR5  0   0.292  -5.0294   1.7317  -0.2214
 5V5  H6   H  HCR6  0   0.252   0.7606   1.5186   0.7623
 5V5  H7   H  HCR6  0   0.284   0.7075  -3.3476   0.0408
 5V5  H8   H  HCH3  0   0.233  -1.4251  -4.0939   0.5220
 5V5  H9   H  HCH3  0   0.263  -2.8175  -3.7321  -0.5152
 5V5  H10  H  HCH3  0   0.233  -1.1913  -3.8057  -1.2180
 5V5  H11  H  HCR5  0   0.262  -1.0599   2.4496   1.3398
 5V5  H12  H  HCR5  0   0.265  -3.4385   3.4436   0.9819
 5V5  O1   O  O2    0  -0.473  -1.6879  -2.1222  -0.0940

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
 5V5  C11  C10  aromatic  1.362  0.020  1.362
 5V5  C11  S    aromatic  1.709  0.020  1.709
 5V5  C10  C9   aromatic  1.415  0.020  1.415
 5V5  C9   C8   aromatic  1.373  0.020  1.373
 5V5  S    C8   aromatic  1.734  0.020  1.734
 5V5  C8   C7   single    1.465  0.020  1.465
 5V5  C7   C12  aromatic  1.395  0.020  1.395
 5V5  C7   C5   aromatic  1.407  0.020  1.407
 5V5  O1   C5   single    1.342  0.020  1.342
 5V5  O1   C6   single    1.414  0.020  1.414
 5V5  C12  C2   aromatic  1.387  0.020  1.387
 5V5  C5   C4   aromatic  1.391  0.020  1.391
 5V5  C2   C1   single    1.499  0.020  1.499
 5V5  C2   C3   aromatic  1.388  0.020  1.388
 5V5  C4   C3   aromatic  1.386  0.020  1.386
 5V5  O    C    double    1.204  0.020  1.204
 5V5  C1   C    single    1.509  0.020  1.509
 5V5  C    O2   single    1.329  0.020  1.329
 5V5  C1   H1   single    0.970  0.020  1.090
 5V5  C1   H2   single    0.970  0.020  1.090
 5V5  C3   H3   single    0.930  0.020  1.080
 5V5  O2   H4   single    0.850  0.020  0.980
 5V5  C11  H5   single    0.930  0.020  1.080
 5V5  C12  H6   single    0.930  0.020  1.080
 5V5  C4   H7   single    0.930  0.020  1.080
 5V5  C6   H8   single    0.970  0.020  1.090
 5V5  C6   H9   single    0.970  0.020  1.090
 5V5  C6   H10  single    0.970  0.020  1.090
 5V5  C9   H11  single    0.930  0.020  1.080
 5V5  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
 5V5  H2   C1   H1   105.48  3.000
 5V5  H2   C1   C    108.15  3.000
 5V5  H1   C1   C    108.04  3.000
 5V5  H2   C1   C2   110.93  3.000
 5V5  H1   C1   C2   111.02  3.000
 5V5  C    C1   C2   112.88  3.000
 5V5  C12  C2   C3   118.29  3.000
 5V5  C3   C2   C1   121.11  3.000
 5V5  C12  C2   C1   120.59  3.000
 5V5  H3   C3   C4   118.89  3.000
 5V5  H3   C3   C2   120.28  3.000
 5V5  C4   C3   C2   120.83  3.000
 5V5  H4   O2   C    110.05  3.000
 5V5  H5   C11  S    120.24  3.000
 5V5  H5   C11  C10  128.01  3.000
 5V5  S    C11  C10  111.74  3.000
 5V5  H6   C12  C7   118.96  3.000
 5V5  H6   C12  C2   118.35  3.000
 5V5  C7   C12  C2   122.69  3.000
 5V5  O    C    O2   123.42  3.000
 5V5  O2   C    C1   111.35  3.000
 5V5  O    C    C1   125.23  3.000
 5V5  H7   C4   C5   120.82  3.000
 5V5  H7   C4   C3   118.90  3.000
 5V5  C5   C4   C3   120.28  3.000
 5V5  C7   C5   C4   120.25  3.000
 5V5  C4   C5   O1   123.58  3.000
 5V5  C7   C5   O1   116.17  3.000
 5V5  H10  C6   H9   108.89  3.000
 5V5  H10  C6   H8   109.02  3.000
 5V5  H9   C6   H8   108.95  3.000
 5V5  H10  C6   O1   111.85  3.000
 5V5  H9   C6   O1   106.33  3.000
 5V5  H8   C6   O1   111.70  3.000
 5V5  C8   C7   C5   122.70  3.000
 5V5  C5   C7   C12  117.65  3.000
 5V5  C8   C7   C12  119.64  3.000
 5V5  S    C8   C9   109.69  3.000
 5V5  S    C8   C7   123.93  3.000
 5V5  C9   C8   C7   126.35  3.000
 5V5  H11  C9   C10  122.86  3.000
 5V5  H11  C9   C8   123.39  3.000
 5V5  C10  C9   C8   113.75  3.000
 5V5  H12  C10  C9   123.80  3.000
 5V5  H12  C10  C11  123.84  3.000
 5V5  C9   C10  C11  112.36  3.000
 5V5  C8   S    C11   92.46  3.000
 5V5  C6   O1   C5   119.53  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
 5V5  CONST_01  C8   C7   C12  C2   180.00   0.0  0
 5V5  CONST_02  C5   C7   C12  C2     0.00   0.0  0
 5V5  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 5V5  CONST_04  C7   C12  C2   C3     0.00   0.0  0
 5V5  CONST_05  C7   C5   C4   C3     0.00   0.0  0
 5V5  CONST_06  C8   C9   C10  C11    0.00   0.0  0
 5V5  CONST_07  C9   C8   S    C11    0.00   0.0  0
 5V5  CONST_08  C7   C8   S    C11  180.00   0.0  0
 5V5  CONST_09  C9   C8   C7   C12    0.00   0.0  0
 5V5  CONST_11  C4   C5   C7   C12    0.00   0.0  0
 5V5  CONST_12  C4   C3   C2   C12    0.00   0.0  0
 5V5  CONST_13  C8   C7   C5   C4   180.00   0.0  0
 5V5  CONST_14  C9   C8   C7   C5   180.00   0.0  0
 5V5  CONST_16  C10  C9   C8   C7   180.00   0.0  0
 5V5  CONST_17  C10  C11  S    C8     0.00   0.0  0
 5V5  CONST_18  S    C11  C10  C9     0.00   0.0  0
 5V5  CONST_19  S    C8   C9   C10    0.00   0.0  0
 5V5  CONST_20  C7   C12  C2   C1   180.00   0.0  0
 5V5  CONST_21  C4   C3   C2   C1   180.00   0.0  0
 5V5  CONST_22  O1   C5   C4   C3   180.00   0.0  0
 5V5  CONST_23  C8   C7   C5   O1     0.00   0.0  0
 5V5  CONST_24  C12  C7   C5   O1   180.00   0.0  0
 5V5  CONST_25  H7   C4   C3   C2   180.00   0.0  0
 5V5  CONST_26  H6   C12  C2   C3   180.00   0.0  0
 5V5  CONST_27  H11  C9   C10  C11  180.00   0.0  0
 5V5  CONST_28  H3   C3   C2   C12  180.00   0.0  0
 5V5  CONST_29  H12  C10  C9   C8   180.00   0.0  0
 5V5  CONST_30  H5   C11  S    C8   180.00   0.0  0
 5V5  CONST_31  H4   O2   C    C1   180.00   0.0  0
 5V5  Var_01    C    C1   C2   C3    90.88  30.0  2
 5V5  Var_02    C7   C5   O1   C6   179.48  30.0  2
 5V5  Var_03    O    C    C1   C2     2.26  30.0  3
 5V5  Var_04    H8   C6   O1   C5    61.61  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
 5V5  plan-1  C11  0.020
 5V5  plan-1  C7   0.020
 5V5  plan-1  C8   0.020
 5V5  plan-1  C9   0.020
 5V5  plan-1  C10  0.020
 5V5  plan-1  S    0.020
 5V5  plan-1  H5   0.020
 5V5  plan-1  H11  0.020
 5V5  plan-1  H12  0.020
 5V5  plan-2  C1   0.020
 5V5  plan-2  C2   0.020
 5V5  plan-2  C3   0.020
 5V5  plan-2  C12  0.020
 5V5  plan-2  C4   0.020
 5V5  plan-2  C5   0.020
 5V5  plan-2  C7   0.020
 5V5  plan-2  C8   0.020
 5V5  plan-2  H3   0.020
 5V5  plan-2  H6   0.020
 5V5  plan-2  H7   0.020
 5V5  plan-2  O1   0.020
 5V5  plan-3  C1   0.020
 5V5  plan-3  O2   0.020
 5V5  plan-3  O    0.020
 5V5  plan-3  C    0.020
 5V5  plan-3  H4   0.020

