# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 05:44:50 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-chloranyl-6-(4,6-dimethoxypyrimidin-2-yl)sulfanyl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)nc(Sc2cccc(Cl)c2C(O)=O)n1
#
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
 6QK  6QK  '2-chloranyl-6-(4,6-dimethoxypyrimidin-2-yl)sulfanyl-benzoic acid'  ligand  31  21  .  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_6QK
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
 6QK  C11   C   CR6    0   0.560  -3.5978  -0.1610  -0.1311
 6QK  C02   C   CR6    0  -0.092   3.0312  -0.1590   0.1941
 6QK  C03   C   CR6    0   0.145   1.8289   0.5075   0.0018
 6QK  C04   C   C      0   0.343   1.3525   0.8867  -1.3972
 6QK  O05   O   OC    -1  -0.585   1.5184   2.0783  -1.7018
 6QK  O06   O   O      0  -0.562   0.8681  -0.0289  -2.0762
 6QK  C07   C   CR6    0  -0.194   1.0995   0.8290   1.1477
 6QK  S08   S   S2     0   0.080  -0.4439   1.6909   1.0143
 6QK  C09   C   CR6    0   0.232  -1.5198   0.3931   0.5033
 6QK  N10   N   N      0  -0.493  -2.7630   0.7858   0.2758
 6QK  O12   O   O2     0  -0.463  -4.8643   0.1466  -0.3702
 6QK  C13   C   CH3    0  -0.419  -5.2900   1.4896  -0.1608
 6QK  C14   C   CR16   0  -0.500  -3.2020  -1.4781  -0.3405
 6QK  C15   C   CR6    0   0.567  -1.8656  -1.7426  -0.0703
 6QK  O16   O   O2     0  -0.464  -1.4043  -2.9656  -0.2744
 6QK  C17   C   CH3    0  -0.424  -0.0001  -3.1765  -0.1110
 6QK  N18   N   N      0  -0.428  -1.0326  -0.8169   0.3802
 6QK  C19   C   CR16   0  -0.216   1.5598   0.5107   2.4183
 6QK  C20   C   CR16   0  -0.280   2.7758  -0.1380   2.5712
 6QK  C21   C   CR16   0  -0.206   3.5183  -0.4789   1.4523
 6QK  H2    H   HCH3   0   0.236  -4.7544   2.1877  -0.8040
 6QK  H3    H   HCH3   0   0.251  -6.3470   1.5055  -0.4118
 6QK  H4    H   HCH3   0   0.235  -5.1606   1.7951   0.8775
 6QK  H5    H   HCR6   0   0.281  -3.8849  -2.2359  -0.6972
 6QK  H6    H   HCH3   0   0.231   0.2998  -3.0753   0.9321
 6QK  H7    H   HCH3   0   0.243   0.1837  -4.1945  -0.4437
 6QK  H8    H   HCH3   0   0.248   0.5764  -2.4721  -0.7107
 6QK  H9    H   HCR6   0   0.268   0.9674   0.7671   3.2867
 6QK  H10   H   HCR6   0   0.267   3.1449  -0.3815   3.5581
 6QK  H11   H   HCR6   0   0.277   4.4676  -0.9872   1.5578
 6QK  CL01  CL  CL     0  -0.136   3.9957  -0.5895  -1.1895

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
 6QK  C20  C19   aromatic  1.387  0.020  1.387
 6QK  C20  C21   aromatic  1.385  0.020  1.385
 6QK  C19  C07   aromatic  1.388  0.020  1.388
 6QK  C17  O16   single    1.429  0.020  1.429
 6QK  C21  C02   aromatic  1.387  0.020  1.387
 6QK  C07  S08   single    1.773  0.020  1.773
 6QK  C07  C03   aromatic  1.396  0.020  1.396
 6QK  S08  C09   single    1.762  0.020  1.762
 6QK  N18  C09   aromatic  1.310  0.020  1.310
 6QK  N18  C15   aromatic  1.324  0.020  1.324
 6QK  C02  C03   aromatic  1.388  0.020  1.388
 6QK  C02  CL01  single    1.741  0.020  1.741
 6QK  C03  C04   single    1.526  0.020  1.526
 6QK  O16  C15   single    1.323  0.020  1.323
 6QK  C09  N10   aromatic  1.323  0.020  1.323
 6QK  O06  C04   deloc     1.239  0.020  1.239
 6QK  C15  C14   aromatic  1.389  0.020  1.389
 6QK  C04  O05   deloc     1.241  0.020  1.241
 6QK  N10  C11   aromatic  1.326  0.020  1.326
 6QK  C14  C11   aromatic  1.391  0.020  1.391
 6QK  C11  O12   single    1.325  0.020  1.325
 6QK  O12  C13   single    1.424  0.020  1.424
 6QK  C13  H2    single    0.970  0.020  1.090
 6QK  C13  H3    single    0.970  0.020  1.090
 6QK  C13  H4    single    0.970  0.020  1.090
 6QK  C14  H5    single    0.930  0.020  1.080
 6QK  C17  H6    single    0.970  0.020  1.090
 6QK  C17  H7    single    0.970  0.020  1.090
 6QK  C17  H8    single    0.970  0.020  1.090
 6QK  C19  H9    single    0.930  0.020  1.080
 6QK  C20  H10   single    0.930  0.020  1.080
 6QK  C21  H11   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
 6QK  C14  C11  O12   117.68  3.000
 6QK  O12  C11  N10   119.43  3.000
 6QK  C14  C11  N10   122.89  3.000
 6QK  C21  C02  C03   122.73  3.000
 6QK  C03  C02  CL01  119.25  3.000
 6QK  C21  C02  CL01  118.01  3.000
 6QK  C07  C03  C04   122.16  3.000
 6QK  C04  C03  C02   121.12  3.000
 6QK  C07  C03  C02   116.71  3.000
 6QK  O06  C04  O05   128.86  3.000
 6QK  O05  C04  C03   114.96  3.000
 6QK  O06  C04  C03   116.17  3.000
 6QK  C19  C07  S08   117.96  3.000
 6QK  S08  C07  C03   120.34  3.000
 6QK  C19  C07  C03   121.68  3.000
 6QK  C09  S08  C07   101.27  3.000
 6QK  N18  C09  N10   127.39  3.000
 6QK  N10  C09  S08   113.89  3.000
 6QK  N18  C09  S08   118.72  3.000
 6QK  C09  N10  C11   115.61  3.000
 6QK  C13  O12  C11   118.55  3.000
 6QK  H4   C13  H3    109.35  3.000
 6QK  H4   C13  H2    108.92  3.000
 6QK  H3   C13  H2    109.41  3.000
 6QK  H4   C13  O12   111.65  3.000
 6QK  H3   C13  O12   105.70  3.000
 6QK  H2   C13  O12   111.74  3.000
 6QK  H5   C14  C15   122.59  3.000
 6QK  H5   C14  C11   122.26  3.000
 6QK  C15  C14  C11   115.14  3.000
 6QK  N18  C15  O16   118.64  3.000
 6QK  O16  C15  C14   118.79  3.000
 6QK  N18  C15  C14   122.57  3.000
 6QK  C17  O16  C15   117.47  3.000
 6QK  H8   C17  H7    110.34  3.000
 6QK  H8   C17  H6    108.72  3.000
 6QK  H7   C17  H6    109.47  3.000
 6QK  H8   C17  O16   111.18  3.000
 6QK  H7   C17  O16   105.63  3.000
 6QK  H6   C17  O16   111.47  3.000
 6QK  C15  N18  C09   116.34  3.000
 6QK  H9   C19  C20   120.16  3.000
 6QK  H9   C19  C07   119.91  3.000
 6QK  C20  C19  C07   119.93  3.000
 6QK  H10  C20  C21   119.92  3.000
 6QK  H10  C20  C19   120.35  3.000
 6QK  C21  C20  C19   119.74  3.000
 6QK  H11  C21  C20   120.47  3.000
 6QK  H11  C21  C02   120.33  3.000
 6QK  C20  C21  C02   119.20  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
 6QK  CONST_01  N18  C09  N10  C11      0.00   0.0  0
 6QK  CONST_02  N18  C15  C14  C11      0.00   0.0  0
 6QK  CONST_03  C19  C20  C21  C02      0.00   0.0  0
 6QK  CONST_04  C19  C07  C03  C02      0.00   0.0  0
 6QK  CONST_05  C20  C19  C07  C03      0.00   0.0  0
 6QK  CONST_06  C20  C21  C02  C03      0.00   0.0  0
 6QK  CONST_07  C21  C20  C19  C07      0.00   0.0  0
 6QK  CONST_08  C21  C02  C03  C07      0.00   0.0  0
 6QK  CONST_09  C14  C15  N18  C09      0.00   0.0  0
 6QK  CONST_10  C14  C11  N10  C09      0.00   0.0  0
 6QK  CONST_11  C15  N18  C09  N10      0.00   0.0  0
 6QK  CONST_12  C15  C14  C11  N10      0.00   0.0  0
 6QK  CONST_13  S08  C09  N10  C11    180.00   0.0  0
 6QK  CONST_14  O16  C15  C14  C11    180.00   0.0  0
 6QK  CONST_15  C20  C21  C02  CL01   180.00   0.0  0
 6QK  CONST_16  C07  C03  C02  CL01   180.00   0.0  0
 6QK  CONST_17  S08  C07  C03  C02    180.00   0.0  0
 6QK  CONST_18  C19  C07  C03  C04    180.00   0.0  0
 6QK  CONST_19  C21  C02  C03  C04    180.00   0.0  0
 6QK  CONST_20  C20  C19  C07  S08    180.00   0.0  0
 6QK  CONST_21  C15  N18  C09  S08    180.00   0.0  0
 6QK  CONST_22  O16  C15  N18  C09    180.00   0.0  0
 6QK  CONST_23  O12  C11  N10  C09    180.00   0.0  0
 6QK  CONST_24  C15  C14  C11  O12    180.00   0.0  0
 6QK  CONST_25  H10  C20  C21  C02    180.00   0.0  0
 6QK  CONST_26  H9   C19  C07  C03    180.00   0.0  0
 6QK  CONST_27  H11  C21  C02  C03    180.00   0.0  0
 6QK  CONST_28  H5   C14  C11  N10    180.00   0.0  0
 6QK  Var_01    N18  C09  S08  C07      1.97  30.0  2
 6QK  Var_02    C19  C07  S08  C09   -103.85  30.0  2
 6QK  Var_03    O06  C04  C03  C02     77.35  30.0  2
 6QK  Var_04    C14  C11  O12  C13    179.95  30.0  1
 6QK  Var_05    N18  C15  O16  C17     -5.66  30.0  2
 6QK  Var_06    H2   C13  O12  C11     61.33  30.0  3
 6QK  Var_07    H6   C17  O16  C15     68.22  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
 6QK  plan-1  C11   0.020
 6QK  plan-1  S08   0.020
 6QK  plan-1  C09   0.020
 6QK  plan-1  N10   0.020
 6QK  plan-1  O12   0.020
 6QK  plan-1  C14   0.020
 6QK  plan-1  C15   0.020
 6QK  plan-1  O16   0.020
 6QK  plan-1  N18   0.020
 6QK  plan-1  H5    0.020
 6QK  plan-2  C02   0.020
 6QK  plan-2  C03   0.020
 6QK  plan-2  C04   0.020
 6QK  plan-2  C07   0.020
 6QK  plan-2  S08   0.020
 6QK  plan-2  C19   0.020
 6QK  plan-2  C20   0.020
 6QK  plan-2  C21   0.020
 6QK  plan-2  H9    0.020
 6QK  plan-2  H10   0.020
 6QK  plan-2  H11   0.020
 6QK  plan-2  CL01  0.020
 6QK  plan-3  C03   0.020
 6QK  plan-3  C04   0.020
 6QK  plan-3  O05   0.020
 6QK  plan-3  O06   0.020

