# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 15:09:41 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-[(3-bromo-4-chlorobenzyl)sulfanyl]thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sccc1SCc2ccc(Cl)c(Br)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
 NX1  NX1  '3-[(3-bromo-4-chlorobenzyl)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_NX1
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
 NX1  C1    C   CR5   0   0.001  -3.2516  -0.2303   0.4256
 NX1  C2    C   CR5   0  -0.364  -4.3786   0.2227  -0.2285
 NX1  S3    S   S2    0   0.111  -1.6628  -0.1949  -0.2963
 NX1  C4    C   CR15  0  -0.174  -3.5601  -0.7171   1.7257
 NX1  S5    S   S2    0   0.284  -5.7933   0.0505   0.7411
 NX1  C6    C   C     0   0.524  -4.4178   0.7825  -1.5658
 NX1  C7    C   CH2   0  -0.663  -0.6340  -0.9322   1.0180
 NX1  C8    C   CR15  0  -0.441  -4.8886  -0.6219   2.0142
 NX1  O9    O   OH1   0  -0.602  -5.6450   1.1241  -1.9388
 NX1  O10   O   O     0  -0.443  -3.4326   0.9192  -2.2566
 NX1  C11   C   CR6   0   0.122   0.7626  -0.9907   0.4778
 NX1  C12   C   CR16  0  -0.269   1.6284   0.0784   0.6706
 NX1  C13   C   CR16  0  -0.290   1.1961  -2.0897  -0.2563
 NX1  C14   C   CR6   0  -0.042   2.9148   0.0457   0.1509
 NX1  C15   C   CR16  0  -0.188   2.4779  -2.1282  -0.7756
 NX1  C16   C   CR6   0  -0.036   3.3426  -1.0612  -0.5749
 NX1  BR17  BR  BR    0  -0.001   4.0548   1.5079   0.4423
 NX1  CL18  CL  CL    0  -0.096   4.9321  -1.1389  -1.2320
 NX1  H4    H   HCR5  0   0.290  -2.8398  -1.1200   2.4208
 NX1  H7    H   HCH2  0   0.305  -0.6793  -0.3148   1.9151
 NX1  H7A   H   HCH2  0   0.307  -0.9987  -1.9310   1.2559
 NX1  H8    H   HCR5  0   0.315  -5.3748  -0.9230   2.9296
 NX1  HO9   H   HOH1  0   0.492  -5.6344   1.4975  -2.8328
 NX1  H12   H   HCR6  0   0.288   1.2962   0.9404   1.2354
 NX1  H13   H   HCR6  0   0.276   0.5310  -2.9273  -0.4232
 NX1  H15   H   HCR6  0   0.292   2.8116  -2.9886  -1.3391

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
 NX1  S3    C1   single    1.745  0.020  1.745
 NX1  C1    C2   aromatic  1.380  0.020  1.380
 NX1  C1    C4   aromatic  1.422  0.020  1.422
 NX1  C6    C2   single    1.450  0.020  1.450
 NX1  C2    S5   aromatic  1.724  0.020  1.724
 NX1  S3    C7   single    1.825  0.020  1.825
 NX1  C4    C8   aromatic  1.363  0.020  1.363
 NX1  C4    H4   single    0.930  0.020  1.080
 NX1  S5    C8   aromatic  1.700  0.020  1.700
 NX1  O10   C6   double    1.211  0.020  1.211
 NX1  C6    O9   single    1.327  0.020  1.327
 NX1  C11   C7   single    1.498  0.020  1.498
 NX1  C7    H7   single    0.970  0.020  1.090
 NX1  C7    H7A  single    0.970  0.020  1.090
 NX1  C8    H8   single    0.930  0.020  1.080
 NX1  O9    HO9  single    0.850  0.020  0.980
 NX1  C13   C11  aromatic  1.391  0.020  1.391
 NX1  C12   C11  aromatic  1.389  0.020  1.389
 NX1  C14   C12  aromatic  1.388  0.020  1.388
 NX1  C12   H12  single    0.930  0.020  1.080
 NX1  C15   C13  aromatic  1.384  0.020  1.384
 NX1  C13   H13  single    0.930  0.020  1.080
 NX1  C16   C14  aromatic  1.391  0.020  1.391
 NX1  BR17  C14  single    1.877  0.020  1.877
 NX1  C16   C15  aromatic  1.388  0.020  1.388
 NX1  C15   H15  single    0.930  0.020  1.080
 NX1  CL18  C16  single    1.722  0.020  1.722

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
 NX1  C4    C1   S3   125.63  3.000
 NX1  C4    C1   C2   111.63  3.000
 NX1  S3    C1   C2   122.74  3.000
 NX1  C6    C2   S5   122.35  3.000
 NX1  S5    C2   C1   111.78  3.000
 NX1  C6    C2   C1   125.88  3.000
 NX1  C7    S3   C1   101.96  3.000
 NX1  H4    C4   C8   122.72  3.000
 NX1  H4    C4   C1   124.88  3.000
 NX1  C8    C4   C1   112.40  3.000
 NX1  C8    S5   C2    91.37  3.000
 NX1  O10   C6   O9   124.25  3.000
 NX1  O9    C6   C2   112.55  3.000
 NX1  O10   C6   C2   123.20  3.000
 NX1  H7A   C7   H7   109.00  3.000
 NX1  H7A   C7   C11  110.79  3.000
 NX1  H7    C7   C11  110.95  3.000
 NX1  H7A   C7   S3   109.81  3.000
 NX1  H7    C7   S3   109.91  3.000
 NX1  C11   C7   S3   106.36  3.000
 NX1  H8    C8   S5   120.37  3.000
 NX1  H8    C8   C4   126.81  3.000
 NX1  S5    C8   C4   112.82  3.000
 NX1  HO9   O9   C6   110.39  3.000
 NX1  C13   C11  C12  119.15  3.000
 NX1  C12   C11  C7   120.06  3.000
 NX1  C13   C11  C7   120.77  3.000
 NX1  H12   C12  C14  119.90  3.000
 NX1  H12   C12  C11  119.59  3.000
 NX1  C14   C12  C11  120.51  3.000
 NX1  H13   C13  C15  119.33  3.000
 NX1  H13   C13  C11  120.08  3.000
 NX1  C15   C13  C11  120.59  3.000
 NX1  BR17  C14  C16  120.94  3.000
 NX1  BR17  C14  C12  119.11  3.000
 NX1  C16   C14  C12  119.95  3.000
 NX1  H15   C15  C16  119.66  3.000
 NX1  H15   C15  C13  120.24  3.000
 NX1  C16   C15  C13  120.10  3.000
 NX1  CL18  C16  C15  119.03  3.000
 NX1  CL18  C16  C14  121.26  3.000
 NX1  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
 NX1  CONST_01  C8    S5   C2   C1     0.00   0.0  0
 NX1  CONST_02  S5    C8   C4   C1     0.00   0.0  0
 NX1  CONST_03  C8    C4   C1   C2     0.00   0.0  0
 NX1  CONST_04  C4    C8   S5   C2     0.00   0.0  0
 NX1  CONST_05  S5    C2   C1   C4     0.00   0.0  0
 NX1  CONST_06  C16   C15  C13  C11    0.00   0.0  0
 NX1  CONST_07  C16   C14  C12  C11    0.00   0.0  0
 NX1  CONST_08  C15   C13  C11  C12    0.00   0.0  0
 NX1  CONST_09  C15   C16  C14  C12    0.00   0.0  0
 NX1  CONST_10  C14   C12  C11  C13    0.00   0.0  0
 NX1  CONST_11  C14   C16  C15  C13    0.00   0.0  0
 NX1  CONST_12  S5    C2   C1   S3   180.00   0.0  0
 NX1  CONST_13  C8    C4   C1   S3   180.00   0.0  0
 NX1  CONST_14  C6    C2   C1   C4   180.00   0.0  0
 NX1  CONST_15  C8    S5   C2   C6   180.00   0.0  0
 NX1  CONST_16  C15   C13  C11  C7   180.00   0.0  0
 NX1  CONST_17  C14   C12  C11  C7   180.00   0.0  0
 NX1  CONST_18  BR17  C14  C12  C11  180.00   0.0  0
 NX1  CONST_19  CL18  C16  C14  C12  180.00   0.0  0
 NX1  CONST_20  CL18  C16  C15  C13  180.00   0.0  0
 NX1  CONST_21  BR17  C14  C16  C15  180.00   0.0  0
 NX1  CONST_22  H8    C8   C4   C1   180.00   0.0  0
 NX1  CONST_23  H4    C4   C1   C2   180.00   0.0  0
 NX1  CONST_24  H15   C15  C13  C11  180.00   0.0  0
 NX1  CONST_25  H13   C13  C11  C12  180.00   0.0  0
 NX1  CONST_26  H12   C12  C11  C13  180.00   0.0  0
 NX1  CONST_27  HO9   O9   C6   C2   180.00   0.0  0
 NX1  Var_01    C11   C7   S3   C1   178.22  30.0  3
 NX1  Var_02    O10   C6   C2   C1    -0.53  30.0  2
 NX1  Var_03    C13   C11  C7   S3   -87.97  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
 NX1  plan-1  C1    0.020
 NX1  plan-1  C2    0.020
 NX1  plan-1  S3    0.020
 NX1  plan-1  C4    0.020
 NX1  plan-1  S5    0.020
 NX1  plan-1  C6    0.020
 NX1  plan-1  C8    0.020
 NX1  plan-1  H4    0.020
 NX1  plan-1  H8    0.020
 NX1  plan-2  C7    0.020
 NX1  plan-2  C11   0.020
 NX1  plan-2  C12   0.020
 NX1  plan-2  C13   0.020
 NX1  plan-2  C14   0.020
 NX1  plan-2  C15   0.020
 NX1  plan-2  C16   0.020
 NX1  plan-2  BR17  0.020
 NX1  plan-2  CL18  0.020
 NX1  plan-2  H12   0.020
 NX1  plan-2  H13   0.020
 NX1  plan-2  H15   0.020
 NX1  plan-3  C2    0.020
 NX1  plan-3  C6    0.020
 NX1  plan-3  O9    0.020
 NX1  plan-3  O10   0.020
 NX1  plan-3  HO9   0.020

