# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:11:46 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 3-[(4-methylthiophen-2-yl)methylamino]pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1csc(CNc2cnccc2C(O)=O)c1
#
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
 AUY  AUY  '3-[(4-methylthiophen-2-yl)methylamino]pyridine-4-carboxylic acid'  ligand  29  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AUY
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
 AUY  S     S  S2    0   0.207  -2.4848  -0.1083  -1.2111
 AUY  C1    C  CR15  0  -0.241  -2.9868   0.2984   1.2541
 AUY  N1    N  N     0  -0.371   3.3594   2.2618   0.2557
 AUY  O1    O  OH1   0  -0.589   3.4802  -2.5900  -0.5719
 AUY  C01   C  CH3   0  -0.724  -5.3691  -0.6460   1.5374
 AUY  N01   N  NH1   0  -0.699   0.3835   0.1915   0.1812
 AUY  O01   O  O     0  -0.456   1.3024  -2.3363  -0.2057
 AUY  C02   C  CR5   0   0.176  -4.1552  -0.3305   0.7235
 AUY  C03   C  CR15  0  -0.531  -4.0113  -0.6065  -0.6022
 AUY  C04   C  CR5   0  -0.186  -2.0032   0.4872   0.3345
 AUY  C05   C  CH2   0  -0.328  -0.6673   1.1205   0.5330
 AUY  C06   C  CR6   0   0.334   1.6932   0.5188   0.1332
 AUY  C07   C  CR16  0  -0.169   2.1107   1.8590   0.3217
 AUY  C08   C  CR16  0  -0.106   4.3167   1.3695   0.0063
 AUY  C09   C  CR16  0  -0.321   4.0368   0.0325  -0.1772
 AUY  C10   C  CR6   0  -0.096   2.7200  -0.4240  -0.1145
 AUY  C11   C  C     0   0.568   2.4135  -1.8560  -0.2970
 AUY  H1    H  HCR5  0   0.262  -2.8869   0.5964   2.2900
 AUY  HO1   H  HOH1  0   0.491   3.2223  -3.5184  -0.6739
 AUY  H01   H  HCH3  0   0.246  -5.8223   0.2620   1.9381
 AUY  H01A  H  HCH3  0   0.246  -6.1224  -1.1628   0.9452
 AUY  H01B  H  HCH3  0   0.245  -5.1173  -1.2807   2.3882
 AUY  HN01  H  HNH1  0   0.409   0.1680  -0.7932   0.2189
 AUY  H03   H  HCR5  0   0.289  -4.7256  -1.0851  -1.2558
 AUY  H05   H  HCH2  0   0.261  -0.5922   1.4524   1.5748
 AUY  H05A  H  HCH2  0   0.265  -0.5898   2.0161  -0.0904
 AUY  H07   H  HCR6  0   0.278   1.3761   2.6244   0.5414
 AUY  H08   H  HCR6  0   0.262   5.3351   1.7346  -0.0396
 AUY  H09   H  HCR6  0   0.279   4.8506  -0.6529  -0.3647

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
 AUY  C03  S     aromatic  1.717  0.020  1.717
 AUY  C04  S     aromatic  1.725  0.020  1.725
 AUY  C02  C1    aromatic  1.429  0.020  1.429
 AUY  C1   C04   aromatic  1.360  0.020  1.360
 AUY  C1   H1    single    0.930  0.020  1.080
 AUY  C07  N1    aromatic  1.314  0.020  1.314
 AUY  N1   C08   aromatic  1.332  0.020  1.332
 AUY  C11  O1    single    1.324  0.020  1.324
 AUY  O1   HO1   single    0.850  0.020  0.980
 AUY  C01  C02   single    1.495  0.020  1.495
 AUY  C01  H01   single    0.970  0.020  1.090
 AUY  C01  H01A  single    0.970  0.020  1.090
 AUY  C01  H01B  single    0.970  0.020  1.090
 AUY  C05  N01   single    1.446  0.020  1.446
 AUY  N01  C06   single    1.351  0.020  1.351
 AUY  N01  HN01  single    0.860  0.020  1.020
 AUY  O01  C11   double    1.214  0.020  1.214
 AUY  C02  C03   aromatic  1.362  0.020  1.362
 AUY  C03  H03   single    0.930  0.020  1.080
 AUY  C04  C05   single    1.492  0.020  1.492
 AUY  C05  H05   single    0.970  0.020  1.090
 AUY  C05  H05A  single    0.970  0.020  1.090
 AUY  C06  C07   aromatic  1.416  0.020  1.416
 AUY  C06  C10   aromatic  1.416  0.020  1.416
 AUY  C07  H07   single    0.930  0.020  1.080
 AUY  C09  C08   aromatic  1.378  0.020  1.378
 AUY  C08  H08   single    0.930  0.020  1.080
 AUY  C10  C09   aromatic  1.395  0.020  1.395
 AUY  C09  H09   single    0.930  0.020  1.080
 AUY  C11  C10   single    1.476  0.020  1.476

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
 AUY  C04   S    C03    91.76  3.000
 AUY  H1    C1   C04   122.83  3.000
 AUY  H1    C1   C02   123.50  3.000
 AUY  C04   C1   C02   113.67  3.000
 AUY  C08   N1   C07   119.14  3.000
 AUY  HO1   O1   C11   109.79  3.000
 AUY  H01B  C01  H01A  107.93  3.000
 AUY  H01B  C01  H01   107.08  3.000
 AUY  H01A  C01  H01   107.89  3.000
 AUY  H01B  C01  C02   111.10  3.000
 AUY  H01A  C01  C02   111.46  3.000
 AUY  H01   C01  C02   111.19  3.000
 AUY  HN01  N01  C06   116.42  3.000
 AUY  HN01  N01  C05   117.57  3.000
 AUY  C06   N01  C05   123.89  3.000
 AUY  C03   C02  C01   124.96  3.000
 AUY  C03   C02  C1    111.36  3.000
 AUY  C01   C02  C1    123.68  3.000
 AUY  H03   C03  C02   127.52  3.000
 AUY  H03   C03  S     120.12  3.000
 AUY  C02   C03  S     112.35  3.000
 AUY  C05   C04  C1    128.08  3.000
 AUY  C05   C04  S     121.05  3.000
 AUY  C1    C04  S     110.86  3.000
 AUY  H05A  C05  H05   106.79  3.000
 AUY  H05A  C05  C04   109.59  3.000
 AUY  H05   C05  C04   108.45  3.000
 AUY  H05A  C05  N01   109.62  3.000
 AUY  H05   C05  N01   112.09  3.000
 AUY  C04   C05  N01   110.22  3.000
 AUY  C10   C06  C07   116.08  3.000
 AUY  C10   C06  N01   123.23  3.000
 AUY  C07   C06  N01   120.69  3.000
 AUY  H07   C07  C06   119.71  3.000
 AUY  H07   C07  N1    115.97  3.000
 AUY  C06   C07  N1    124.31  3.000
 AUY  H08   C08  C09   120.83  3.000
 AUY  H08   C08  N1    117.25  3.000
 AUY  C09   C08  N1    121.92  3.000
 AUY  H09   C09  C10   120.74  3.000
 AUY  H09   C09  C08   119.05  3.000
 AUY  C10   C09  C08   120.21  3.000
 AUY  C11   C10  C09   120.53  3.000
 AUY  C11   C10  C06   121.14  3.000
 AUY  C09   C10  C06   118.33  3.000
 AUY  C10   C11  O01   124.38  3.000
 AUY  C10   C11  O1    113.35  3.000
 AUY  O01   C11  O1    122.27  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
 AUY  CONST_01  C1    C02  C03  S      0.00   0.0  0
 AUY  CONST_02  C02   C1   C04  S      0.00   0.0  0
 AUY  CONST_03  C03   S    C04  C1     0.00   0.0  0
 AUY  CONST_04  C10   C06  C07  N1     0.00   0.0  0
 AUY  CONST_05  C10   C09  C08  N1     0.00   0.0  0
 AUY  CONST_06  C04   S    C03  C02    0.00   0.0  0
 AUY  CONST_07  C04   C1   C02  C03    0.00   0.0  0
 AUY  CONST_08  C08   N1   C07  C06    0.00   0.0  0
 AUY  CONST_09  C08   C09  C10  C06    0.00   0.0  0
 AUY  CONST_10  C09   C08  N1   C07    0.00   0.0  0
 AUY  CONST_11  C09   C10  C06  C07    0.00   0.0  0
 AUY  CONST_12  C01   C02  C03  S    180.00   0.0  0
 AUY  CONST_13  N01   C06  C07  N1   180.00   0.0  0
 AUY  CONST_14  C04   C1   C02  C01  180.00   0.0  0
 AUY  CONST_15  C09   C10  C06  N01  180.00   0.0  0
 AUY  CONST_16  C05   C04  C1   C02  180.00   0.0  0
 AUY  CONST_17  C05   C04  S    C03  180.00   0.0  0
 AUY  CONST_18  C11   C10  C06  C07  180.00   0.0  0
 AUY  CONST_19  C11   C10  C09  C08  180.00   0.0  0
 AUY  CONST_20  H1    C1   C04  S    180.00   0.0  0
 AUY  CONST_21  H03   C03  C02  C1   180.00   0.0  0
 AUY  CONST_22  H09   C09  C08  N1   180.00   0.0  0
 AUY  CONST_23  H08   C08  N1   C07  180.00   0.0  0
 AUY  CONST_24  H07   C07  N1   C08  180.00   0.0  0
 AUY  CONST_25  C07   C06  N01  C05    0.00   0.0  0
 AUY  CONST_26  C10   C06  N01  C05  180.00   0.0  0
 AUY  CONST_27  HN01  N01  C06  C07  180.00   0.0  0
 AUY  CONST_28  HO1   O1   C11  C10  180.00   0.0  0
 AUY  Var_01    N01   C05  C04  S    -58.90  30.0  2
 AUY  Var_02    C06   C10  C11  O1   177.48  30.0  2
 AUY  Var_03    C06   N01  C05  C04  173.34  30.0  3
 AUY  Var_04    H01   C01  C02  C1    62.08  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
 AUY  plan-1  S     0.020
 AUY  plan-1  C1    0.020
 AUY  plan-1  C01   0.020
 AUY  plan-1  C02   0.020
 AUY  plan-1  C03   0.020
 AUY  plan-1  C04   0.020
 AUY  plan-1  C05   0.020
 AUY  plan-1  H1    0.020
 AUY  plan-1  H03   0.020
 AUY  plan-2  N1    0.020
 AUY  plan-2  N01   0.020
 AUY  plan-2  C06   0.020
 AUY  plan-2  C07   0.020
 AUY  plan-2  C08   0.020
 AUY  plan-2  C09   0.020
 AUY  plan-2  C10   0.020
 AUY  plan-2  C11   0.020
 AUY  plan-2  H07   0.020
 AUY  plan-2  H08   0.020
 AUY  plan-2  H09   0.020
 AUY  plan-3  N01   0.020
 AUY  plan-3  C05   0.020
 AUY  plan-3  C06   0.020
 AUY  plan-3  HN01  0.020
 AUY  plan-4  O1    0.020
 AUY  plan-4  O01   0.020
 AUY  plan-4  C10   0.020
 AUY  plan-4  C11   0.020
 AUY  plan-4  HO1   0.020

