# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 05:44:31 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-bromo-3-(carboxymethoxy)-5-phenylthiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1c(Br)c(sc1C(O)=O)c2ccccc2
#
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
 509  509  '4-bromo-3-(carboxymethoxy)-5-phenylthiophene-2-carboxylic acid'  ligand  27  20  .  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_509
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
 509  C1    C   CR16   0  -0.261  -5.5186  -0.1122  -0.3785
 509  C2    C   CR16   0  -0.240  -5.0336   0.9367   0.3912
 509  C3    C   CR16   0  -0.303  -3.6675   1.1561   0.4887
 509  C4    C   CR6    0   0.087  -2.7658   0.3301  -0.1855
 509  C5    C   CR16   0  -0.295  -3.2627  -0.7146  -0.9669
 509  C6    C   CR16   0  -0.240  -4.6289  -0.9351  -1.0574
 509  C7    C   CR5    0  -0.202  -1.3260   0.5856  -0.0940
 509  C8    C   CR5    0  -0.142  -0.2901  -0.2636   0.1729
 509  C9    C   CR5    0   0.436   0.9941   0.3633   0.1971
 509  C10   C   CR5    0  -0.441   0.9137   1.7025  -0.0737
 509  S1    S   S2     0   0.240  -0.7164   2.1793  -0.3367
 509  C11   C   C      0   0.425   1.9539   2.7866  -0.1609
 509  O1    O   O      0  -0.568   3.1396   2.4649   0.0138
 509  O2    O   OC    -1  -0.598   1.4892   3.9179  -0.4051
 509  O3    O   O2     0  -0.460   2.1069  -0.3303   0.4843
 509  C12   C   CH2    0  -0.292   2.8581  -0.7340  -0.6586
 509  C13   C   C      0   0.368   4.0687  -1.5826  -0.2525
 509  O4    O   O      0  -0.596   4.2722  -1.7853   0.9532
 509  O5    O   OC    -1  -0.627   4.7436  -1.9849  -1.2219
 509  BR1   BR  BR     0  -0.031  -0.4734  -2.0801   0.5885
 509  H1    H   HCR6   0   0.260  -6.5842  -0.2860  -0.4526
 509  H2    H   HCR6   0   0.261  -5.7184   1.5835   0.9237
 509  H3    H   HCR6   0   0.258  -3.2978   1.9680   1.1030
 509  H5    H   HCR6   0   0.257  -2.5825  -1.3433  -1.5257
 509  H6    H   HCR6   0   0.261  -4.9995  -1.7482  -1.6679
 509  H121  H   HCH2   0   0.228   3.2034   0.1492  -1.2038
 509  H122  H   HCH2   0   0.214   2.2230  -1.3136  -1.3398

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
 509  C1   C2    aromatic  1.389  0.020  1.389
 509  C1   C6    aromatic  1.389  0.020  1.389
 509  C1   H1    single    0.930  0.020  1.080
 509  C2   C3    aromatic  1.387  0.020  1.387
 509  C2   H2    single    0.930  0.020  1.080
 509  C3   C4    aromatic  1.396  0.020  1.396
 509  C3   H3    single    0.930  0.020  1.080
 509  C4   C5    aromatic  1.396  0.020  1.396
 509  C4   C7    single    1.465  0.020  1.465
 509  C5   C6    aromatic  1.387  0.020  1.387
 509  C5   H5    single    0.930  0.020  1.080
 509  C6   H6    single    0.930  0.020  1.080
 509  C7   C8    aromatic  1.366  0.020  1.366
 509  C7   S1    aromatic  1.723  0.020  1.723
 509  C8   C9    aromatic  1.429  0.020  1.429
 509  C8   BR1   single    1.872  0.020  1.872
 509  C9   C10   aromatic  1.369  0.020  1.369
 509  C9   O3    single    1.342  0.020  1.342
 509  C10  S1    aromatic  1.719  0.020  1.719
 509  C10  C11   single    1.505  0.020  1.505
 509  C11  O1    deloc     1.241  0.020  1.241
 509  C11  O2    deloc     1.247  0.020  1.247
 509  O3   C12   single    1.426  0.020  1.426
 509  C12  C13   single    1.533  0.020  1.533
 509  C12  H121  single    0.970  0.020  1.090
 509  C12  H122  single    0.970  0.020  1.090
 509  C13  O4    deloc     1.239  0.020  1.239
 509  C13  O5    deloc     1.248  0.020  1.248

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
 509  H1    C1   C6    120.14  3.000
 509  H1    C1   C2    120.21  3.000
 509  C6    C1   C2    119.65  3.000
 509  H2    C2   C3    119.61  3.000
 509  H2    C2   C1    120.22  3.000
 509  C3    C2   C1    120.17  3.000
 509  H3    C3   C4    119.79  3.000
 509  H3    C3   C2    119.64  3.000
 509  C4    C3   C2    120.57  3.000
 509  C7    C4   C5    121.01  3.000
 509  C7    C4   C3    120.09  3.000
 509  C5    C4   C3    118.88  3.000
 509  H5    C5   C6    119.56  3.000
 509  H5    C5   C4    120.01  3.000
 509  C6    C5   C4    120.41  3.000
 509  H6    C6   C5    119.58  3.000
 509  H6    C6   C1    120.09  3.000
 509  C5    C6   C1    120.32  3.000
 509  S1    C7   C8    109.52  3.000
 509  S1    C7   C4    120.00  3.000
 509  C8    C7   C4    130.48  3.000
 509  BR1   C8   C9    120.65  3.000
 509  BR1   C8   C7    124.91  3.000
 509  C9    C8   C7    114.34  3.000
 509  O3    C9   C10   126.63  3.000
 509  O3    C9   C8    121.46  3.000
 509  C10   C9   C8    111.90  3.000
 509  C11   C10  S1    116.54  3.000
 509  C11   C10  C9    132.51  3.000
 509  S1    C10  C9    110.94  3.000
 509  C10   S1   C7     93.29  3.000
 509  O2    C11  O1    128.23  3.000
 509  O2    C11  C10   114.03  3.000
 509  O1    C11  C10   117.75  3.000
 509  C12   O3   C9    114.30  3.000
 509  H122  C12  H121  107.45  3.000
 509  H122  C12  C13   109.22  3.000
 509  H121  C12  C13   109.24  3.000
 509  H122  C12  O3    110.02  3.000
 509  H121  C12  O3    109.71  3.000
 509  C13   C12  O3    111.12  3.000
 509  O5    C13  O4    127.89  3.000
 509  O5    C13  C12   113.57  3.000
 509  O4    C13  C12   118.54  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
 509  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 509  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 509  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 509  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 509  CONST_05  C7   C4   C3   C2    180.00   0.0  0
 509  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 509  CONST_07  C6   C5   C4   C3      0.00   0.0  0
 509  CONST_10  C9   C8   C7   C4    180.00   0.0  0
 509  CONST_11  C10  S1   C7   C4    180.00   0.0  0
 509  CONST_14  C7   C4   C5   C6    180.00   0.0  0
 509  CONST_15  C10  C9   C8   C7      0.00   0.0  0
 509  CONST_16  C9   C10  S1   C7      0.00   0.0  0
 509  CONST_17  C10  S1   C7   C8      0.00   0.0  0
 509  CONST_18  S1   C10  C9   C8      0.00   0.0  0
 509  CONST_19  S1   C7   C8   C9      0.00   0.0  0
 509  CONST_20  BR1  C8   C7   C4      0.00   0.0  0
 509  CONST_21  O3   C9   C8   C7    180.00   0.0  0
 509  CONST_22  C11  C10  S1   C7    180.00   0.0  0
 509  CONST_23  C11  C10  C9   C8    180.00   0.0  0
 509  CONST_24  BR1  C8   C9   C10   180.00   0.0  0
 509  CONST_25  BR1  C8   C7   S1    180.00   0.0  0
 509  CONST_26  O3   C9   C10  S1    180.00   0.0  0
 509  CONST_27  H3   C3   C2   C1    180.00   0.0  0
 509  CONST_28  H5   C5   C6   C1    180.00   0.0  0
 509  CONST_29  H6   C6   C1   C2    180.00   0.0  0
 509  CONST_30  H1   C1   C2   C3    180.00   0.0  0
 509  CONST_31  H2   C2   C3   C4    180.00   0.0  0
 509  Var_01    O1   C11  C10  C9      1.51  30.0  2
 509  Var_02    C13  C12  O3   C9   -176.94  30.0  3
 509  Var_03    O4   C13  C12  O3     -1.75  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
 509  plan-1  C4   0.020
 509  plan-1  C7   0.020
 509  plan-1  C8   0.020
 509  plan-1  C9   0.020
 509  plan-1  C10  0.020
 509  plan-1  S1   0.020
 509  plan-1  C11  0.020
 509  plan-1  O3   0.020
 509  plan-1  BR1  0.020
 509  plan-2  C1   0.020
 509  plan-2  C2   0.020
 509  plan-2  C3   0.020
 509  plan-2  C4   0.020
 509  plan-2  C5   0.020
 509  plan-2  C6   0.020
 509  plan-2  C7   0.020
 509  plan-2  H1   0.020
 509  plan-2  H2   0.020
 509  plan-2  H3   0.020
 509  plan-2  H5   0.020
 509  plan-2  H6   0.020
 509  plan-3  C10  0.020
 509  plan-3  C11  0.020
 509  plan-3  O1   0.020
 509  plan-3  O2   0.020
 509  plan-4  C12  0.020
 509  plan-4  C13  0.020
 509  plan-4  O4   0.020
 509  plan-4  O5   0.020

