# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 13:20:11 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-[[[3-(5-methoxy-2-oxidanyl-phenyl)-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl]amino]methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(O)c(c1)C2=NNC(=S)N2NCc3ccccc3C(O)=O
#
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
 PJB  PJB  '2-[[[3-(5-methoxy-2-oxidanyl-phenyl)-5-sulfanylidene-1~{H}-1,2,4-triazol-4-yl]amino]methyl]benzoic acid'  ligand  41  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PJB
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
 PJB  C10  C  CR16   0  -0.282  -29.0125  -20.7921   -6.5549
 PJB  C12  C  CR16   0  -0.259  -29.6433  -20.0639   -4.3591
 PJB  O17  O  OC    -1  -0.587  -26.6662  -22.5228   -2.8119
 PJB  C15  C  C      0   0.371  -27.0965  -22.8512   -3.9334
 PJB  O16  O  O      0  -0.583  -26.8857  -23.9264   -4.5278
 PJB  C14  C  CR6    0  -0.114  -28.0010  -21.8380   -4.6346
 PJB  C13  C  CR16   0  -0.282  -28.7535  -20.9845   -3.8276
 PJB  C11  C  CR16   0  -0.254  -29.7698  -19.9672   -5.7357
 PJB  C9   C  CR6    0   0.042  -28.1340  -21.7398   -6.0310
 PJB  C8   C  CH2    0  -0.315  -27.3389  -22.6243   -6.9700
 PJB  N7   N  NH1    0  -0.473  -27.4257  -22.1591   -8.3540
 PJB  N2   N  NR5    0  -0.329  -27.5047  -23.1488   -9.2935
 PJB  C3   C  CR5    0   0.360  -26.4912  -23.9520   -9.7326
 PJB  S6   S  S1     0  -0.400  -24.9091  -23.9768   -9.2094
 PJB  N5   N  NR15   0  -0.464  -27.0853  -24.6646  -10.6965
 PJB  N4   N  N      0  -0.232  -28.3864  -24.3569  -10.8854
 PJB  C1   C  CR5    0   0.423  -28.6293  -23.4241  -10.0267
 PJB  C18  C  C      0  -0.066  -29.9020  -22.7203   -9.8456
 PJB  C19  C  C      0   0.350  -30.6759  -22.9715   -8.7105
 PJB  O24  O  OH1    0  -0.626  -30.2283  -23.9039   -7.8479
 PJB  C20  C  C1     0  -0.351  -31.8568  -22.2675   -8.5387
 PJB  C23  C  C1     0  -0.353  -30.3203  -21.7953  -10.7894
 PJB  C22  C  C      0   0.376  -31.5079  -21.0885  -10.6147
 PJB  C21  C  C1     0  -0.364  -32.2707  -21.3302   -9.4769
 PJB  O25  O  O2     0  -0.472  -31.8288  -20.2031  -11.5817
 PJB  C26  C  CH3    0  -0.436  -33.0106  -19.4467  -11.4277
 PJB  H1   H  HCR6   0   0.248  -29.1066  -20.7003   -7.6277
 PJB  H2   H  HCR6   0   0.241  -30.2242  -19.4253   -3.7053
 PJB  H4   H  HCR6   0   0.239  -28.6396  -21.0534   -2.7539
 PJB  H5   H  HCR6   0   0.243  -30.4515  -19.2508   -6.1773
 PJB  H6   H  HCH2   0   0.261  -27.7266  -23.6392   -6.9275
 PJB  H7   H  HCH2   0   0.243  -26.2997  -22.6829   -6.6472
 PJB  H8   H  HNH1   0   0.385  -26.6588  -21.5446   -8.5978
 PJB  H9   H  HNR5   0   0.437  -26.6433  -25.3738  -11.2617
 PJB  H10  H  HOH1   0   0.478  -30.7750  -23.9242   -7.0541
 PJB  H11  H  H      0   0.278  -32.4731  -22.4436   -7.6647
 PJB  H12  H  H      0   0.270  -29.7097  -21.6083  -11.6644
 PJB  H13  H  H      0   0.286  -33.1979  -20.8034   -9.2966
 PJB  H14  H  HCH3   0   0.258  -33.0756  -18.7936  -12.2948
 PJB  H15  H  HCH3   0   0.226  -33.9027  -20.0786  -11.3986
 PJB  H16  H  HCH3   0   0.226  -32.9880  -18.8292  -10.5254

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
 PJB  C26  O25  single    1.412  0.020  1.412
 PJB  O25  C22  single    1.350  0.020  1.350
 PJB  C22  C23  aromatic  1.393  0.020  1.393
 PJB  C22  C21  aromatic  1.391  0.020  1.391
 PJB  C23  C18  aromatic  1.386  0.020  1.386
 PJB  N4   N5   single    1.350  0.020  1.350
 PJB  N4   C1   double    1.291  0.020  1.291
 PJB  C21  C20  aromatic  1.389  0.020  1.389
 PJB  N5   C3   single    1.338  0.020  1.338
 PJB  C18  C1   single    1.466  0.020  1.466
 PJB  C18  C19  aromatic  1.397  0.020  1.397
 PJB  C1   N2   single    1.370  0.020  1.370
 PJB  C20  C19  aromatic  1.386  0.020  1.386
 PJB  C19  O24  single    1.347  0.020  1.347
 PJB  C3   N2   single    1.366  0.020  1.366
 PJB  C3   S6   double    1.667  0.020  1.667
 PJB  N2   N7   single    1.367  0.020  1.367
 PJB  N7   C8   single    1.463  0.020  1.463
 PJB  C8   C9   single    1.515  0.020  1.515
 PJB  C9   C10  aromatic  1.394  0.020  1.394
 PJB  C9   C14  aromatic  1.406  0.020  1.406
 PJB  C10  C11  aromatic  1.387  0.020  1.387
 PJB  O16  C15  deloc     1.247  0.020  1.247
 PJB  C15  C14  single    1.529  0.020  1.529
 PJB  C15  O17  deloc     1.245  0.020  1.245
 PJB  C14  C13  aromatic  1.395  0.020  1.395
 PJB  C11  C12  aromatic  1.386  0.020  1.386
 PJB  C13  C12  aromatic  1.386  0.020  1.386
 PJB  C10  H1   single    0.930  0.020  1.080
 PJB  C12  H2   single    0.930  0.020  1.080
 PJB  C13  H4   single    0.930  0.020  1.080
 PJB  C11  H5   single    0.930  0.020  1.080
 PJB  C8   H6   single    0.970  0.020  1.090
 PJB  C8   H7   single    0.970  0.020  1.090
 PJB  N7   H8   single    0.890  0.020  1.040
 PJB  N5   H9   single    0.860  0.020  1.020
 PJB  O24  H10  single    0.850  0.020  0.980
 PJB  C20  H11  single    0.930  0.020  1.080
 PJB  C23  H12  single    0.930  0.020  1.080
 PJB  C21  H13  single    0.930  0.020  1.080
 PJB  C26  H14  single    0.970  0.020  1.090
 PJB  C26  H15  single    0.970  0.020  1.090
 PJB  C26  H16  single    0.970  0.020  1.090

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
 PJB  H1   C10  C9   119.04  3.000
 PJB  H1   C10  C11  119.22  3.000
 PJB  C9   C10  C11  121.74  3.000
 PJB  H2   C12  C11  120.64  3.000
 PJB  H2   C12  C13  120.29  3.000
 PJB  C11  C12  C13  119.06  3.000
 PJB  C14  C15  O16  116.95  3.000
 PJB  C14  C15  O17  116.28  3.000
 PJB  O16  C15  O17  126.76  3.000
 PJB  C9   C14  C13  118.74  3.000
 PJB  C13  C14  C15  117.35  3.000
 PJB  C9   C14  C15  123.90  3.000
 PJB  H4   C13  C14  118.58  3.000
 PJB  H4   C13  C12  119.36  3.000
 PJB  C14  C13  C12  122.05  3.000
 PJB  H5   C11  C12  120.57  3.000
 PJB  H5   C11  C10  119.74  3.000
 PJB  C12  C11  C10  119.68  3.000
 PJB  C8   C9   C14  121.67  3.000
 PJB  C14  C9   C10  118.69  3.000
 PJB  C8   C9   C10  119.63  3.000
 PJB  H7   C8   H6   106.15  3.000
 PJB  H7   C8   N7   110.74  3.000
 PJB  H6   C8   N7   108.23  3.000
 PJB  H7   C8   C9   110.38  3.000
 PJB  H6   C8   C9   109.48  3.000
 PJB  N7   C8   C9   111.69  3.000
 PJB  H8   N7   N2   108.53  3.000
 PJB  H8   N7   C8   112.08  3.000
 PJB  N2   N7   C8   115.06  3.000
 PJB  C1   N2   C3   108.59  3.000
 PJB  C3   N2   N7   127.15  3.000
 PJB  C1   N2   N7   124.10  3.000
 PJB  N5   C3   S6   129.78  3.000
 PJB  S6   C3   N2   127.76  3.000
 PJB  N5   C3   N2   102.44  3.000
 PJB  H9   N5   N4   120.26  3.000
 PJB  H9   N5   C3   125.70  3.000
 PJB  N4   N5   C3   114.03  3.000
 PJB  C1   N4   N5   104.65  3.000
 PJB  C18  C1   N4   126.34  3.000
 PJB  C18  C1   N2   123.37  3.000
 PJB  N4   C1   N2   110.28  3.000
 PJB  C23  C18  C19  120.41  3.000
 PJB  C19  C18  C1   119.69  3.000
 PJB  C23  C18  C1   119.89  3.000
 PJB  C20  C19  O24  123.75  3.000
 PJB  O24  C19  C18  117.45  3.000
 PJB  C20  C19  C18  118.80  3.000
 PJB  H10  O24  C19  110.70  3.000
 PJB  H11  C20  C21  119.00  3.000
 PJB  H11  C20  C19  120.14  3.000
 PJB  C21  C20  C19  120.86  3.000
 PJB  H12  C23  C22  119.62  3.000
 PJB  H12  C23  C18  119.68  3.000
 PJB  C22  C23  C18  120.70  3.000
 PJB  O25  C22  C21  124.73  3.000
 PJB  C21  C22  C23  118.81  3.000
 PJB  O25  C22  C23  116.46  3.000
 PJB  H13  C21  C22  121.45  3.000
 PJB  H13  C21  C20  118.13  3.000
 PJB  C22  C21  C20  120.42  3.000
 PJB  C26  O25  C22  118.19  3.000
 PJB  H16  C26  H15  108.73  3.000
 PJB  H16  C26  H14  108.66  3.000
 PJB  H15  C26  H14  108.63  3.000
 PJB  H16  C26  O25  112.04  3.000
 PJB  H15  C26  O25  112.10  3.000
 PJB  H14  C26  O25  106.55  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
 PJB  CONST_01  C13  C14  C9   C10     0.00   0.0  0
 PJB  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 PJB  CONST_03  C9   C10  C11  C12     0.00   0.0  0
 PJB  CONST_04  C9   C14  C13  C12     0.00   0.0  0
 PJB  CONST_05  C11  C10  C9   C14     0.00   0.0  0
 PJB  CONST_06  C11  C12  C13  C14     0.00   0.0  0
 PJB  CONST_07  C21  C22  C23  C18     0.00   0.0  0
 PJB  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 PJB  CONST_09  C22  C23  C18  C19     0.00   0.0  0
 PJB  CONST_10  C22  C21  C20  C19     0.00   0.0  0
 PJB  CONST_11  C23  C22  C21  C20     0.00   0.0  0
 PJB  CONST_12  C23  C18  C19  C20     0.00   0.0  0
 PJB  CONST_13  C22  C23  C18  C1    180.00   0.0  0
 PJB  CONST_14  C20  C19  C18  C1    180.00   0.0  0
 PJB  CONST_15  N5   N4   C1   N2      0.00   0.0  0
 PJB  CONST_16  N4   N5   C3   N2      0.00   0.0  0
 PJB  CONST_17  C1   N4   N5   C3      0.00   0.0  0
 PJB  CONST_18  N4   C1   N2   C3      0.00   0.0  0
 PJB  CONST_19  C18  C1   N2   C3    180.00   0.0  0
 PJB  CONST_20  C18  C1   N4   N5    180.00   0.0  0
 PJB  CONST_21  C1   N2   C3   N5      0.00   0.0  0
 PJB  CONST_22  C15  C14  C9   C10   180.00   0.0  0
 PJB  CONST_23  C15  C14  C13  C12   180.00   0.0  0
 PJB  CONST_24  C8   C9   C14  C13   180.00   0.0  0
 PJB  CONST_25  C8   C9   C10  C11   180.00   0.0  0
 PJB  CONST_26  O24  C19  C18  C1      0.00   0.0  0
 PJB  CONST_27  O25  C22  C23  C18   180.00   0.0  0
 PJB  CONST_28  C23  C18  C19  O24   180.00   0.0  0
 PJB  CONST_29  C21  C20  C19  O24   180.00   0.0  0
 PJB  CONST_30  O25  C22  C21  C20   180.00   0.0  0
 PJB  CONST_31  N4   C1   N2   N7    180.00   0.0  0
 PJB  CONST_32  C18  C1   N2   N7      0.00   0.0  0
 PJB  CONST_33  N5   C3   N2   N7    180.00   0.0  0
 PJB  CONST_34  N4   N5   C3   S6    180.00   0.0  0
 PJB  CONST_35  C1   N2   C3   S6    180.00   0.0  0
 PJB  CONST_36  H2   C12  C11  C10   180.00   0.0  0
 PJB  CONST_37  H1   C10  C11  C12   180.00   0.0  0
 PJB  CONST_38  H5   C11  C12  C13   180.00   0.0  0
 PJB  CONST_39  H4   C13  C12  C11   180.00   0.0  0
 PJB  CONST_40  H12  C23  C18  C1      0.00   0.0  0
 PJB  CONST_41  H11  C20  C19  C18   180.00   0.0  0
 PJB  CONST_42  H13  C21  C20  C19   180.00   0.0  0
 PJB  CONST_43  H9   N5   C3   N2    180.00   0.0  0
 PJB  CONST_44  S6   C3   N2   N7      0.00   0.0  0
 PJB  Var_01    C23  C18  C1   N2    106.34  30.0  2
 PJB  Var_02    N7   C8   C9   C10    11.38  30.0  2
 PJB  Var_03    C9   C14  C15  O17   152.76  30.0  2
 PJB  Var_04    N2   N7   C8   C9   -141.82  30.0  2
 PJB  Var_05    C1   N2   N7   C8    109.76  30.0  1
 PJB  Var_06    H14  C26  O25  C22   179.17  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
 PJB  plan-1  N7   0.020
 PJB  plan-1  N2   0.020
 PJB  plan-1  C3   0.020
 PJB  plan-1  S6   0.020
 PJB  plan-1  N5   0.020
 PJB  plan-1  N4   0.020
 PJB  plan-1  C1   0.020
 PJB  plan-1  C18  0.020
 PJB  plan-1  H9   0.020
 PJB  plan-2  C10  0.020
 PJB  plan-2  C12  0.020
 PJB  plan-2  C15  0.020
 PJB  plan-2  C14  0.020
 PJB  plan-2  C13  0.020
 PJB  plan-2  C11  0.020
 PJB  plan-2  C9   0.020
 PJB  plan-2  C8   0.020
 PJB  plan-2  H1   0.020
 PJB  plan-2  H2   0.020
 PJB  plan-2  H4   0.020
 PJB  plan-2  H5   0.020
 PJB  plan-3  C1   0.020
 PJB  plan-3  C18  0.020
 PJB  plan-3  C19  0.020
 PJB  plan-3  O24  0.020
 PJB  plan-3  C20  0.020
 PJB  plan-3  C23  0.020
 PJB  plan-3  C22  0.020
 PJB  plan-3  C21  0.020
 PJB  plan-3  O25  0.020
 PJB  plan-3  H11  0.020
 PJB  plan-3  H12  0.020
 PJB  plan-3  H13  0.020
 PJB  plan-4  O17  0.020
 PJB  plan-4  C15  0.020
 PJB  plan-4  O16  0.020
 PJB  plan-4  C14  0.020

