# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 16:06:05 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-[(3,4-dichlorobenzyl)sulfanyl]thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sccc1SCc2ccc(Cl)c(Cl)c2
#
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
 NXY  NXY  '3-[(3,4-dichlorobenzyl)sulfanyl]thiophene-2-carboxylic acid'  ligand  26  18  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXY
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
 NXY  C1    C   CR5   0   0.001  -2.6675  -0.5046  -0.0384
 NXY  C2    C   CR5   0  -0.364  -3.8006   0.2816   0.0014
 NXY  S3    S   S2    0   0.110  -1.0627   0.1606  -0.2113
 NXY  C4    C   CR15  0  -0.175  -2.9843  -1.8856   0.0795
 NXY  S5    S   S2    0   0.285  -5.2300  -0.6644   0.1825
 NXY  C6    C   C     0   0.524  -3.8365   1.7284  -0.0908
 NXY  C7    C   CH2   0  -0.662  -0.0247  -1.3398  -0.2055
 NXY  C8    C   CR15  0  -0.441  -4.3239  -2.1031   0.2033
 NXY  O9    O   O     0  -0.443  -2.8438   2.4102  -0.2173
 NXY  O10   O   OH1   0  -0.603  -5.0708   2.2116  -0.0197
 NXY  C11   C   CR6   0   0.111   1.3903  -0.8723  -0.3629
 NXY  C12   C   CR16  0  -0.246   2.1536  -0.5723   0.7583
 NXY  C13   C   CR16  0  -0.282   1.9421  -0.6887  -1.6264
 NXY  C14   C   CR6   0   0.023   3.4535  -0.1116   0.6207
 NXY  C15   C   CR16  0  -0.199   3.2391  -0.2264  -1.7687
 NXY  C16   C   CR6   0  -0.014   3.9994   0.0648  -0.6459
 NXY  CL17  CL  CL    0  -0.094   4.3785   0.2352   2.0311
 NXY  CL18  CL  CL    0  -0.093   5.6117   0.6368  -0.8351
 NXY  H4    H   HCR5  0   0.291  -2.2628  -2.6871   0.0752
 NXY  H7    H   HCH2  0   0.305  -0.1546  -1.8796   0.7323
 NXY  H7A   H   HCH2  0   0.306  -0.3093  -1.9930  -1.0303
 NXY  H8    H   HCR5  0   0.315  -4.8170  -3.0576   0.3088
 NXY  HO10  H   HOH1  0   0.492  -5.0594   3.1785  -0.0794
 NXY  H12   H   HCR6  0   0.288   1.7394  -0.7061   1.7493
 NXY  H13   H   HCR6  0   0.274   1.3612  -0.9129  -2.5117
 NXY  H15   H   HCR6  0   0.292   3.6642  -0.0901  -2.7534

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
 NXY  C4    C1    aromatic  1.422  0.020  1.422
 NXY  C1    C2    aromatic  1.380  0.020  1.380
 NXY  C1    S3    single    1.746  0.020  1.746
 NXY  S5    C2    aromatic  1.724  0.020  1.724
 NXY  C2    C6    single    1.450  0.020  1.450
 NXY  C7    S3    single    1.824  0.020  1.824
 NXY  C8    C4    aromatic  1.363  0.020  1.363
 NXY  C4    H4    single    0.930  0.020  1.080
 NXY  C8    S5    aromatic  1.700  0.020  1.700
 NXY  C6    O9    double    1.211  0.020  1.211
 NXY  C6    O10   single    1.327  0.020  1.327
 NXY  C7    C11   single    1.498  0.020  1.498
 NXY  C7    H7    single    0.970  0.020  1.090
 NXY  C7    H7A   single    0.970  0.020  1.090
 NXY  C8    H8    single    0.930  0.020  1.080
 NXY  O10   HO10  single    0.850  0.020  0.980
 NXY  C11   C12   aromatic  1.389  0.020  1.389
 NXY  C11   C13   aromatic  1.391  0.020  1.391
 NXY  C12   C14   aromatic  1.386  0.020  1.386
 NXY  C12   H12   single    0.930  0.020  1.080
 NXY  C13   C15   aromatic  1.384  0.020  1.384
 NXY  C13   H13   single    0.930  0.020  1.080
 NXY  CL17  C14   single    1.722  0.020  1.722
 NXY  C14   C16   aromatic  1.390  0.020  1.390
 NXY  C15   C16   aromatic  1.387  0.020  1.387
 NXY  C15   H15   single    0.930  0.020  1.080
 NXY  C16   CL18  single    1.721  0.020  1.721

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
 NXY  C4    C1   S3   125.67  3.000
 NXY  S3    C1   C2   122.73  3.000
 NXY  C4    C1   C2   111.59  3.000
 NXY  C6    C2   S5   122.26  3.000
 NXY  C6    C2   C1   125.94  3.000
 NXY  S5    C2   C1   111.80  3.000
 NXY  C7    S3   C1   102.09  3.000
 NXY  H4    C4   C8   122.64  3.000
 NXY  H4    C4   C1   124.92  3.000
 NXY  C8    C4   C1   112.44  3.000
 NXY  C8    S5   C2    91.36  3.000
 NXY  O10   C6   O9   124.26  3.000
 NXY  O10   C6   C2   112.50  3.000
 NXY  O9    C6   C2   123.24  3.000
 NXY  H7A   C7   H7   108.85  3.000
 NXY  H7A   C7   C11  110.73  3.000
 NXY  H7    C7   C11  110.95  3.000
 NXY  H7A   C7   S3   109.99  3.000
 NXY  H7    C7   S3   110.01  3.000
 NXY  C11   C7   S3   106.28  3.000
 NXY  H8    C8   S5   120.39  3.000
 NXY  H8    C8   C4   126.80  3.000
 NXY  S5    C8   C4   112.81  3.000
 NXY  HO10  O10  C6   110.43  3.000
 NXY  C13   C11  C12  119.12  3.000
 NXY  C13   C11  C7   120.75  3.000
 NXY  C12   C11  C7   120.10  3.000
 NXY  H12   C12  C14  119.40  3.000
 NXY  H12   C12  C11  120.13  3.000
 NXY  C14   C12  C11  120.47  3.000
 NXY  H13   C13  C15  119.21  3.000
 NXY  H13   C13  C11  120.18  3.000
 NXY  C15   C13  C11  120.61  3.000
 NXY  CL17  C14  C16  120.64  3.000
 NXY  C16   C14  C12  120.05  3.000
 NXY  CL17  C14  C12  119.31  3.000
 NXY  H15   C15  C16  119.69  3.000
 NXY  H15   C15  C13  120.28  3.000
 NXY  C16   C15  C13  120.03  3.000
 NXY  CL18  C16  C15  119.62  3.000
 NXY  CL18  C16  C14  120.67  3.000
 NXY  C15   C16  C14  119.71  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
 NXY  CONST_01  S5    C8   C4   C1     0.00   0.0  0
 NXY  CONST_02  C8    S5   C2   C1     0.00   0.0  0
 NXY  CONST_03  C8    C4   C1   C2     0.00   0.0  0
 NXY  CONST_04  C4    C8   S5   C2     0.00   0.0  0
 NXY  CONST_05  S5    C2   C1   C4     0.00   0.0  0
 NXY  CONST_06  C16   C14  C12  C11    0.00   0.0  0
 NXY  CONST_07  C16   C15  C13  C11    0.00   0.0  0
 NXY  CONST_08  C15   C13  C11  C12    0.00   0.0  0
 NXY  CONST_09  C15   C16  C14  C12    0.00   0.0  0
 NXY  CONST_10  C14   C12  C11  C13    0.00   0.0  0
 NXY  CONST_11  C14   C16  C15  C13    0.00   0.0  0
 NXY  CONST_12  C8    C4   C1   S3   180.00   0.0  0
 NXY  CONST_13  S5    C2   C1   S3   180.00   0.0  0
 NXY  CONST_14  C6    C2   C1   C4   180.00   0.0  0
 NXY  CONST_15  C8    S5   C2   C6   180.00   0.0  0
 NXY  CONST_16  C14   C12  C11  C7   180.00   0.0  0
 NXY  CONST_17  C15   C13  C11  C7   180.00   0.0  0
 NXY  CONST_18  CL17  C14  C12  C11  180.00   0.0  0
 NXY  CONST_19  CL18  C16  C14  C12  180.00   0.0  0
 NXY  CONST_20  CL18  C16  C15  C13  180.00   0.0  0
 NXY  CONST_21  CL17  C14  C16  C15  180.00   0.0  0
 NXY  CONST_22  H8    C8   C4   C1   180.00   0.0  0
 NXY  CONST_23  H4    C4   C1   C2   180.00   0.0  0
 NXY  CONST_24  H15   C15  C13  C11  180.00   0.0  0
 NXY  CONST_25  H13   C13  C11  C12  180.00   0.0  0
 NXY  CONST_26  H12   C12  C11  C13  180.00   0.0  0
 NXY  CONST_27  HO10  O10  C6   C2   180.00   0.0  0
 NXY  Var_01    O9    C6   C2   C1     0.09  30.0  2
 NXY  Var_02    C11   C7   S3   C1   179.52  30.0  1
 NXY  Var_03    C12   C11  C7   S3    89.79  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
 NXY  plan-1  C1    0.020
 NXY  plan-1  C2    0.020
 NXY  plan-1  S3    0.020
 NXY  plan-1  C4    0.020
 NXY  plan-1  S5    0.020
 NXY  plan-1  C6    0.020
 NXY  plan-1  C8    0.020
 NXY  plan-1  H4    0.020
 NXY  plan-1  H8    0.020
 NXY  plan-2  C7    0.020
 NXY  plan-2  C11   0.020
 NXY  plan-2  C12   0.020
 NXY  plan-2  C13   0.020
 NXY  plan-2  C14   0.020
 NXY  plan-2  C15   0.020
 NXY  plan-2  C16   0.020
 NXY  plan-2  CL17  0.020
 NXY  plan-2  CL18  0.020
 NXY  plan-2  H12   0.020
 NXY  plan-2  H13   0.020
 NXY  plan-2  H15   0.020
 NXY  plan-3  C2    0.020
 NXY  plan-3  C6    0.020
 NXY  plan-3  O9    0.020
 NXY  plan-3  O10   0.020
 NXY  plan-3  HO10  0.020

