# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 15:30:03 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  28  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   0.201  -2.4178  -0.1419  -1.2243
 AUY  C1    C  CR15   0  -0.252  -2.9462   0.2512   1.2369
 AUY  N1    N  N      0  -0.387   3.4105   2.3042   0.2689
 AUY  O1    O  OC    -1  -0.573   3.4576  -2.5774  -0.7129
 AUY  C01   C  CH3    0  -0.724  -5.3373  -0.6804   1.4871
 AUY  N01   N  NH1    0  -0.705   0.4282   0.2183   0.0293
 AUY  O01   O  O      0  -0.594   1.3170  -2.2673  -0.2016
 AUY  C02   C  CR5    0   0.177  -4.1137  -0.3645   0.6878
 AUY  C03   C  CR15   0  -0.536  -3.9577  -0.6302  -0.6384
 AUY  C04   C  CR5    0  -0.171  -1.9500   0.4394   0.3308
 AUY  C05   C  CH2    0  -0.321  -0.6145   1.0719   0.5387
 AUY  C06   C  CR6    0   0.283   1.7450   0.5701   0.0494
 AUY  C07   C  CR16   0  -0.184   2.1525   1.8974   0.2864
 AUY  C08   C  CR16   0  -0.115   4.3606   1.4101   0.0224
 AUY  C09   C  CR16   0  -0.343   4.0726   0.0739  -0.2023
 AUY  C10   C  CR6    0  -0.120   2.7634  -0.3837  -0.1861
 AUY  C11   C  C      0   0.441   2.4916  -1.8691  -0.3903
 AUY  H1    H  HCR5   0   0.258  -2.8556   0.5377   2.2770
 AUY  H01   H  HCH3   0   0.245  -5.7901   0.2264   1.8912
 AUY  H01A  H  HCH3   0   0.245  -6.0879  -1.1880   0.8834
 AUY  H01B  H  HCH3   0   0.244  -5.0982  -1.3238   2.3351
 AUY  HN01  H  HNH1   0   0.396   0.3030  -0.7918   0.0691
 AUY  H03   H  HCR5   0   0.286  -4.6675  -1.1007  -1.3028
 AUY  H05   H  HCH2   0   0.243  -0.4993   1.2912   1.6087
 AUY  H05A  H  HCH2   0   0.252  -0.5870   2.0369   0.0226
 AUY  H07   H  HCR6   0   0.259   1.4128   2.6610   0.5011
 AUY  H08   H  HCR6   0   0.244   5.3843   1.7671   0.0123
 AUY  H09   H  HCR6   0   0.252   4.8767  -0.6261  -0.3833

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  1.718  0.020  1.718
 AUY  C04  S     aromatic  1.725  0.020  1.725
 AUY  C02  C1    aromatic  1.430  0.020  1.430
 AUY  C1   C04   aromatic  1.360  0.020  1.360
 AUY  C1   H1    single    0.930  0.020  1.080
 AUY  C07  N1    aromatic  1.322  0.020  1.322
 AUY  N1   C08   aromatic  1.328  0.020  1.328
 AUY  C11  O1    deloc     1.241  0.020  1.241
 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    1.441  0.020  1.441
 AUY  N01  C06   single    1.363  0.020  1.363
 AUY  N01  HN01  single    0.890  0.020  1.040
 AUY  O01  C11   deloc     1.255  0.020  1.255
 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  1.409  0.020  1.409
 AUY  C06  C10   aromatic  1.415  0.020  1.415
 AUY  C07  H07   single    0.930  0.020  1.080
 AUY  C09  C08   aromatic  1.385  0.020  1.385
 AUY  C08  H08   single    0.930  0.020  1.080
 AUY  C10  C09   aromatic  1.387  0.020  1.387
 AUY  C09  H09   single    0.930  0.020  1.080
 AUY  C11  C10   single    1.524  0.020  1.524

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    91.80  3.000
 AUY  H1    C1   C04   122.84  3.000
 AUY  H1    C1   C02   123.46  3.000
 AUY  C04   C1   C02   113.70  3.000
 AUY  C08   N1   C07   118.43  3.000
 AUY  H01B  C01  H01A  107.88  3.000
 AUY  H01B  C01  H01   107.05  3.000
 AUY  H01A  C01  H01   107.86  3.000
 AUY  H01B  C01  C02   111.14  3.000
 AUY  H01A  C01  C02   111.49  3.000
 AUY  H01   C01  C02   111.22  3.000
 AUY  HN01  N01  C06   111.97  3.000
 AUY  HN01  N01  C05   119.00  3.000
 AUY  C06   N01  C05   122.76  3.000
 AUY  C03   C02  C01   124.97  3.000
 AUY  C03   C02  C1    111.39  3.000
 AUY  C01   C02  C1    123.64  3.000
 AUY  H03   C03  C02   127.51  3.000
 AUY  H03   C03  S     120.20  3.000
 AUY  C02   C03  S     112.29  3.000
 AUY  C05   C04  C1    128.42  3.000
 AUY  C05   C04  S     120.74  3.000
 AUY  C1    C04  S     110.82  3.000
 AUY  H05A  C05  H05   106.30  3.000
 AUY  H05A  C05  C04   109.30  3.000
 AUY  H05   C05  C04   108.32  3.000
 AUY  H05A  C05  N01   109.72  3.000
 AUY  H05   C05  N01   112.76  3.000
 AUY  C04   C05  N01   110.33  3.000
 AUY  C10   C06  C07   117.06  3.000
 AUY  C10   C06  N01   121.25  3.000
 AUY  C07   C06  N01   121.68  3.000
 AUY  H07   C07  C06   119.96  3.000
 AUY  H07   C07  N1    115.78  3.000
 AUY  C06   C07  N1    124.26  3.000
 AUY  H08   C08  C09   120.82  3.000
 AUY  H08   C08  N1    117.11  3.000
 AUY  C09   C08  N1    122.06  3.000
 AUY  H09   C09  C10   119.35  3.000
 AUY  H09   C09  C08   119.80  3.000
 AUY  C10   C09  C08   120.84  3.000
 AUY  C11   C10  C09   119.24  3.000
 AUY  C11   C10  C06   123.43  3.000
 AUY  C09   C10  C06   117.32  3.000
 AUY  C10   C11  O01   117.15  3.000
 AUY  C10   C11  O1    116.91  3.000
 AUY  O01   C11  O1    125.94  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  Var_01    N01   C05  C04  S    -51.69  30.0  2
 AUY  Var_02    C06   C10  C11  O1   173.39  30.0  2
 AUY  Var_03    C06   N01  C05  C04  177.80  30.0  3
 AUY  Var_04    H01   C01  C02  C1    62.21  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

