# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:51:26 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 2-[(4-methylphenyl)sulfanyl]pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Sc2ncccc2C(O)=O)cc1
#
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
 JL1  JL1  '2-[(4-methylphenyl)sulfanyl]pyridine-3-carboxylic acid'  ligand  28  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JL1
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
 JL1  C10   C  CR16  0  -0.331   2.3511   2.6792   0.0251
 JL1  C13   C  C     0   0.533   3.3102  -0.9577  -0.0188
 JL1  C17   C  CR16  0  -0.293  -3.4799  -0.2099   1.1457
 JL1  C02   C  CR6   0   0.097  -4.1514   0.0307  -0.0517
 JL1  C03   C  CR16  0  -0.293  -3.4469  -0.1213  -1.2448
 JL1  C04   C  CR16  0  -0.209  -2.1117  -0.4954  -1.2447
 JL1  C05   C  CR6   0  -0.134  -1.4534  -0.7204  -0.0423
 JL1  S06   S  S2    0   0.090   0.2219  -1.2955  -0.0386
 JL1  C07   C  CR6   0   0.082   1.1023   0.2437  -0.0118
 JL1  N08   N  N     0  -0.391   0.3729   1.3452   0.0011
 JL1  C09   C  CR16  0  -0.043   0.9748   2.5249   0.0191
 JL1  C11   C  CR16  0  -0.132   3.1218   1.5328   0.0127
 JL1  C12   C  CR6   0  -0.139   2.5102   0.2813  -0.0059
 JL1  O14   O  O     0  -0.433   2.8233  -2.0641  -0.0339
 JL1  O15   O  OH1   0  -0.591   4.6152  -0.7370  -0.0118
 JL1  C16   C  CR16  0  -0.212  -2.1443  -0.5834   1.1549
 JL1  H101  H  HCR6  0   0.281   2.8001   3.6617   0.0391
 JL1  H171  H  HCR6  0   0.252  -4.0088  -0.1068   2.0858
 JL1  H011  H  HCH3  0   0.252  -5.6670   1.5495  -0.0020
 JL1  H012  H  HCH3  0   0.245  -6.1001   0.1433  -0.9626
 JL1  H013  H  HCH3  0   0.245  -6.1292   0.0567   0.8001
 JL1  H031  H  HCR6  0   0.252  -3.9490   0.0513  -2.1893
 JL1  H041  H  HCR6  0   0.265  -1.5831  -0.6136  -2.1820
 JL1  H091  H  HCR6  0   0.279   0.3234   3.3914   0.0293
 JL1  H111  H  HCR6  0   0.288   4.1997   1.6132   0.0170
 JL1  H1    H  HOH1  0   0.493   5.0952  -1.5787  -0.0197
 JL1  H161  H  HCR6  0   0.265  -1.6421  -0.7703   2.0954
 JL1  C01   C  CH3   0  -0.720  -5.5885   0.4615  -0.0548

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
 JL1  C17  C16   aromatic  1.387  0.020  1.387
 JL1  C17  C02   aromatic  1.394  0.020  1.394
 JL1  C16  C05   aromatic  1.389  0.020  1.389
 JL1  O14  C13   double    1.209  0.020  1.209
 JL1  O15  C13   single    1.324  0.020  1.324
 JL1  C13  C12   single    1.475  0.020  1.475
 JL1  C12  C11   aromatic  1.393  0.020  1.393
 JL1  C12  C07   aromatic  1.408  0.020  1.408
 JL1  C02  C01   single    1.500  0.020  1.500
 JL1  C02  C03   aromatic  1.394  0.020  1.394
 JL1  S06  C05   single    1.771  0.020  1.771
 JL1  S06  C07   single    1.773  0.020  1.773
 JL1  C05  C04   aromatic  1.389  0.020  1.389
 JL1  C11  C10   aromatic  1.381  0.020  1.381
 JL1  C07  N08   aromatic  1.321  0.020  1.321
 JL1  C10  C09   aromatic  1.385  0.020  1.385
 JL1  N08  C09   aromatic  1.325  0.020  1.325
 JL1  C04  C03   aromatic  1.387  0.020  1.387
 JL1  C10  H101  single    0.930  0.020  1.080
 JL1  C17  H171  single    0.930  0.020  1.080
 JL1  C01  H011  single    0.970  0.020  1.090
 JL1  C01  H012  single    0.970  0.020  1.090
 JL1  C01  H013  single    0.970  0.020  1.090
 JL1  C03  H031  single    0.930  0.020  1.080
 JL1  C04  H041  single    0.930  0.020  1.080
 JL1  C09  H091  single    0.930  0.020  1.080
 JL1  C11  H111  single    0.930  0.020  1.080
 JL1  O15  H1    single    0.850  0.020  0.980
 JL1  C16  H161  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
 JL1  H101  C10  C11   121.53  3.000
 JL1  H101  C10  C09   120.96  3.000
 JL1  C11   C10  C09   117.51  3.000
 JL1  O15   C13  O14   123.35  3.000
 JL1  O15   C13  C12   113.25  3.000
 JL1  O14   C13  C12   123.40  3.000
 JL1  H171  C17  C16   119.33  3.000
 JL1  H171  C17  C02   119.59  3.000
 JL1  C16   C17  C02   121.07  3.000
 JL1  C03   C02  C01   120.91  3.000
 JL1  C03   C02  C17   118.23  3.000
 JL1  C01   C02  C17   120.86  3.000
 JL1  H031  C03  C04   119.29  3.000
 JL1  H031  C03  C02   119.64  3.000
 JL1  C04   C03  C02   121.07  3.000
 JL1  H041  C04  C05   120.03  3.000
 JL1  H041  C04  C03   119.97  3.000
 JL1  C05   C04  C03   120.01  3.000
 JL1  C16   C05  S06   120.05  3.000
 JL1  S06   C05  C04   120.17  3.000
 JL1  C16   C05  C04   119.62  3.000
 JL1  C07   S06  C05   100.82  3.000
 JL1  C12   C07  N08   121.98  3.000
 JL1  N08   C07  S06   116.72  3.000
 JL1  C12   C07  S06   121.30  3.000
 JL1  C09   N08  C07   119.46  3.000
 JL1  H091  C09  N08   116.04  3.000
 JL1  H091  C09  C10   120.53  3.000
 JL1  N08   C09  C10   123.43  3.000
 JL1  H111  C11  C12   120.31  3.000
 JL1  H111  C11  C10   119.64  3.000
 JL1  C12   C11  C10   120.05  3.000
 JL1  C11   C12  C07   117.58  3.000
 JL1  C07   C12  C13   121.32  3.000
 JL1  C11   C12  C13   121.11  3.000
 JL1  H1    O15  C13   110.09  3.000
 JL1  H161  C16  C05   120.07  3.000
 JL1  H161  C16  C17   119.94  3.000
 JL1  C05   C16  C17   120.00  3.000
 JL1  H013  C01  H012  108.19  3.000
 JL1  H013  C01  H011  107.24  3.000
 JL1  H012  C01  H011  107.30  3.000
 JL1  H013  C01  C02   111.54  3.000
 JL1  H012  C01  C02   111.58  3.000
 JL1  H011  C01  C02   110.78  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
 JL1  CONST_01  C07   C12  C11  C10     0.00   0.0  0
 JL1  CONST_02  C07   N08  C09  C10     0.00   0.0  0
 JL1  CONST_03  C04   C05  C16  C17     0.00   0.0  0
 JL1  CONST_04  C04   C03  C02  C17     0.00   0.0  0
 JL1  CONST_05  C05   C16  C17  C02     0.00   0.0  0
 JL1  CONST_06  C05   C04  C03  C02     0.00   0.0  0
 JL1  CONST_07  C16   C17  C02  C03     0.00   0.0  0
 JL1  CONST_08  C16   C05  C04  C03     0.00   0.0  0
 JL1  CONST_09  C11   C12  C07  N08     0.00   0.0  0
 JL1  CONST_10  C11   C10  C09  N08     0.00   0.0  0
 JL1  CONST_11  C12   C11  C10  C09     0.00   0.0  0
 JL1  CONST_12  C12   C07  N08  C09     0.00   0.0  0
 JL1  CONST_13  C13   C12  C11  C10   180.00   0.0  0
 JL1  CONST_14  N08   C07  C12  C13   180.00   0.0  0
 JL1  CONST_15  S06   C05  C16  C17   180.00   0.0  0
 JL1  CONST_16  C16   C17  C02  C01   180.00   0.0  0
 JL1  CONST_17  C04   C03  C02  C01   180.00   0.0  0
 JL1  CONST_18  S06   C05  C04  C03   180.00   0.0  0
 JL1  CONST_19  C11   C12  C07  S06   180.00   0.0  0
 JL1  CONST_20  C09   N08  C07  S06   180.00   0.0  0
 JL1  CONST_21  H031  C03  C02  C17   180.00   0.0  0
 JL1  CONST_22  H161  C16  C17  C02   180.00   0.0  0
 JL1  CONST_23  H041  C04  C03  C02   180.00   0.0  0
 JL1  CONST_24  H171  C17  C02  C03   180.00   0.0  0
 JL1  CONST_25  H111  C11  C12  C07   180.00   0.0  0
 JL1  CONST_26  H091  C09  N08  C07   180.00   0.0  0
 JL1  CONST_27  H101  C10  C09  N08   180.00   0.0  0
 JL1  CONST_28  H1    O15  C13  C12   180.00   0.0  0
 JL1  Var_01    C12   C07  S06  C05  -179.80  30.0  2
 JL1  Var_02    C16   C05  S06  C07   -93.66  30.0  2
 JL1  Var_03    O14   C13  C12  C07    -0.05  30.0  2
 JL1  Var_04    H011  C01  C02  C17    88.79  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
 JL1  plan-1  C17   0.020
 JL1  plan-1  C02   0.020
 JL1  plan-1  C03   0.020
 JL1  plan-1  C04   0.020
 JL1  plan-1  C05   0.020
 JL1  plan-1  S06   0.020
 JL1  plan-1  C16   0.020
 JL1  plan-1  H171  0.020
 JL1  plan-1  H031  0.020
 JL1  plan-1  H041  0.020
 JL1  plan-1  H161  0.020
 JL1  plan-1  C01   0.020
 JL1  plan-2  C10   0.020
 JL1  plan-2  C13   0.020
 JL1  plan-2  S06   0.020
 JL1  plan-2  C07   0.020
 JL1  plan-2  N08   0.020
 JL1  plan-2  C09   0.020
 JL1  plan-2  C11   0.020
 JL1  plan-2  C12   0.020
 JL1  plan-2  H101  0.020
 JL1  plan-2  H091  0.020
 JL1  plan-2  H111  0.020
 JL1  plan-3  C13   0.020
 JL1  plan-3  C12   0.020
 JL1  plan-3  O14   0.020
 JL1  plan-3  O15   0.020
 JL1  plan-3  H1    0.020

