# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:33:45 2021
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-[3-[2-(1~{H}-benzimidazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-1~{H}-1,2,4-triazol-5-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1c2[nH]nc(SCC(=O)Nc3[nH]c4ccccc4n3)n2
#
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
 9RX  9RX  '2-[3-[2-(1~{H}-benzimidazol-2-ylamino)-2-oxidanylidene-ethyl]sulfanyl-1~{H}-1,2,4-triazol-5-yl]benzoic acid'  ligand  42  28  .  2022-03-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9RX
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
 9RX  C10   C  CR5   0   0.164  -35.6394   9.8855   5.8263
 9RX  C15   C  CH2   0  -0.717  -36.2494  12.0911   7.2533
 9RX  C17   C  CR56  0   0.346  -38.2308   9.0111  11.8419
 9RX  C20   C  CR5   0   0.698  -37.8556  10.2237  10.0511
 9RX  C22   C  CR16  0  -0.341  -40.3501   8.0607  11.1697
 9RX  C24   C  CR16  0  -0.281  -39.3239   7.5154  13.3038
 9RX  C01   C  CR16  0  -0.240  -35.8558   5.2780  10.0175
 9RX  C02   C  CR16  0  -0.246  -35.9145   4.7725   8.7312
 9RX  C03   C  CR6   0  -0.072  -35.7714   5.6000   7.6156
 9RX  C04   C  CR6   0   0.077  -35.5786   6.9815   7.8033
 9RX  C05   C  CR16  0  -0.272  -35.5420   7.4716   9.1113
 9RX  C06   C  CR16  0  -0.217  -35.6716   6.6382  10.2066
 9RX  C07   C  CR5   0   0.454  -35.5081   8.0189   6.7637
 9RX  C14   C  C     0   0.568  -37.3989  11.3634   7.9347
 9RX  C18   C  CR56  0   0.158  -39.2641   8.8883  10.8994
 9RX  C23   C  CR16  0  -0.271  -40.3651   7.3805  12.3774
 9RX  C25   C  CR16  0  -0.302  -38.2340   8.3359  13.0526
 9RX  N08   N  NR15  0  -0.502  -35.1020   7.9238   5.4962
 9RX  N09   N  N     0  -0.256  -35.1755   9.1027   4.8776
 9RX  N11   N  N     0  -0.463  -35.8523   9.2762   6.9991
 9RX  N13   N  NH1   0  -0.742  -37.1299  11.0651   9.2430
 9RX  N19   N  NR15  0  -0.749  -37.3398   9.8816  11.2642
 9RX  N21   N  N     0  -0.475  -38.9997   9.6638   9.7914
 9RX  O16   O  O     0  -0.414  -38.4434  11.1260   7.3817
 9RX  O27   O  OH1   0  -0.574  -36.6439   3.9207   6.2519
 9RX  O28   O  O     0  -0.452  -35.1407   5.2679   5.3271
 9RX  S12   S  S2    0   0.079  -36.0130  11.5707   5.5446
 9RX  H151  H  HCH2  0   0.307  -35.3124  12.0050   7.8028
 9RX  H152  H  HCH2  0   0.341  -36.4963  13.1539   7.1929
 9RX  H221  H  HCR6  0   0.252  -41.1554   7.9526  10.4544
 9RX  H241  H  HCR6  0   0.252  -39.3693   6.9676  14.2361
 9RX  H011  H  HCR6  0   0.275  -35.9577   4.6112  10.8625
 9RX  H021  H  HCR6  0   0.281  -36.0597   3.7102   8.5962
 9RX  H051  H  HCR6  0   0.262  -35.4080   8.5325   9.2625
 9RX  H061  H  HCR6  0   0.268  -35.6293   7.0532  11.2046
 9RX  H231  H  HCR6  0   0.250  -41.1984   6.7306  12.6116
 9RX  H251  H  HCR6  0   0.265  -37.4282   8.4387  13.7674
 9RX  H1    H  HNR5  0   0.445  -34.7869   7.0850   5.0230
 9RX  H131  H  HNH1  0   0.423  -36.2192  11.3256   9.5895
 9RX  H2    H  HNR5  0   0.424  -36.4814  10.2201  11.6710
 9RX  H4    H  HOH1  0   0.496  -36.6045   3.4792   5.3892
 9RX  C26   C  C     0   0.500  -35.8102   4.9422   6.2819

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
 9RX  O28  C26   double    1.211  0.020  1.211
 9RX  O27  C26   single    1.319  0.020  1.319
 9RX  C26  C03   single    1.488  0.020  1.488
 9RX  N09  N08   aromatic  1.333  0.020  1.333
 9RX  N09  C10   aromatic  1.315  0.020  1.315
 9RX  N08  C07   aromatic  1.334  0.020  1.334
 9RX  C10  S12   single    1.749  0.020  1.749
 9RX  C10  N11   aromatic  1.339  0.020  1.339
 9RX  S12  C15   single    1.802  0.020  1.802
 9RX  C03  C02   aromatic  1.396  0.020  1.396
 9RX  C03  C04   aromatic  1.407  0.020  1.407
 9RX  C07  N11   aromatic  1.325  0.020  1.325
 9RX  C07  C04   single    1.470  0.020  1.470
 9RX  C02  C01   aromatic  1.383  0.020  1.383
 9RX  C04  C05   aromatic  1.397  0.020  1.397
 9RX  C15  C14   single    1.522  0.020  1.522
 9RX  C01  C06   aromatic  1.386  0.020  1.386
 9RX  O16  C14   double    1.205  0.020  1.205
 9RX  C05  C06   aromatic  1.382  0.020  1.382
 9RX  C14  N13   single    1.369  0.020  1.369
 9RX  N13  C20   single    1.374  0.020  1.374
 9RX  N21  C20   aromatic  1.300  0.020  1.300
 9RX  N21  C18   aromatic  1.378  0.020  1.378
 9RX  C20  N19   aromatic  1.362  0.020  1.362
 9RX  C18  C22   aromatic  1.392  0.020  1.392
 9RX  C18  C17   aromatic  1.404  0.020  1.404
 9RX  N19  C17   aromatic  1.373  0.020  1.373
 9RX  C22  C23   aromatic  1.386  0.020  1.386
 9RX  C17  C25   aromatic  1.386  0.020  1.386
 9RX  C23  C24   aromatic  1.400  0.020  1.400
 9RX  C25  C24   aromatic  1.387  0.020  1.387
 9RX  C15  H151  single    0.970  0.020  1.090
 9RX  C15  H152  single    0.970  0.020  1.090
 9RX  C22  H221  single    0.930  0.020  1.080
 9RX  C24  H241  single    0.930  0.020  1.080
 9RX  C01  H011  single    0.930  0.020  1.080
 9RX  C02  H021  single    0.930  0.020  1.080
 9RX  C05  H051  single    0.930  0.020  1.080
 9RX  C06  H061  single    0.930  0.020  1.080
 9RX  C23  H231  single    0.930  0.020  1.080
 9RX  C25  H251  single    0.930  0.020  1.080
 9RX  N08  H1    single    0.860  0.020  1.020
 9RX  N13  H131  single    0.860  0.020  1.020
 9RX  N19  H2    single    0.860  0.020  1.020
 9RX  O27  H4    single    0.850  0.020  0.980

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
 9RX  S12   C10  N11   123.07  3.000
 9RX  N11   C10  N09   114.67  3.000
 9RX  S12   C10  N09   122.20  3.000
 9RX  H152  C15  H151  107.40  3.000
 9RX  H152  C15  S12   104.97  3.000
 9RX  H151  C15  S12   110.03  3.000
 9RX  H152  C15  C14   108.61  3.000
 9RX  H151  C15  C14   112.70  3.000
 9RX  S12   C15  C14   112.68  3.000
 9RX  N19   C17  C25   132.67  3.000
 9RX  C25   C17  C18   122.82  3.000
 9RX  N19   C17  C18   104.51  3.000
 9RX  N21   C20  N19   113.77  3.000
 9RX  N19   C20  N13   118.53  3.000
 9RX  N21   C20  N13   127.67  3.000
 9RX  H221  C22  C23   121.24  3.000
 9RX  H221  C22  C18   120.76  3.000
 9RX  C23   C22  C18   118.00  3.000
 9RX  H241  C24  C25   119.23  3.000
 9RX  H241  C24  C23   119.34  3.000
 9RX  C25   C24  C23   121.43  3.000
 9RX  H011  C01  C06   120.75  3.000
 9RX  H011  C01  C02   119.83  3.000
 9RX  C06   C01  C02   119.42  3.000
 9RX  H021  C02  C03   119.77  3.000
 9RX  H021  C02  C01   118.76  3.000
 9RX  C03   C02  C01   121.47  3.000
 9RX  C04   C03  C02   119.28  3.000
 9RX  C04   C03  C26   123.86  3.000
 9RX  C02   C03  C26   116.85  3.000
 9RX  C07   C04  C05   114.40  3.000
 9RX  C05   C04  C03   118.21  3.000
 9RX  C07   C04  C03   127.22  3.000
 9RX  H051  C05  C06   119.54  3.000
 9RX  H051  C05  C04   118.61  3.000
 9RX  C06   C05  C04   121.86  3.000
 9RX  H061  C06  C05   119.74  3.000
 9RX  H061  C06  C01   120.51  3.000
 9RX  C05   C06  C01   119.75  3.000
 9RX  N11   C07  N08   108.40  3.000
 9RX  N11   C07  C04   122.11  3.000
 9RX  N08   C07  C04   129.48  3.000
 9RX  O16   C14  N13   124.46  3.000
 9RX  N13   C14  C15   112.57  3.000
 9RX  O16   C14  C15   122.91  3.000
 9RX  N21   C18  C22   129.83  3.000
 9RX  C22   C18  C17   119.72  3.000
 9RX  N21   C18  C17   110.45  3.000
 9RX  H231  C23  C24   119.16  3.000
 9RX  H231  C23  C22   119.44  3.000
 9RX  C24   C23  C22   121.41  3.000
 9RX  H251  C25  C24   121.44  3.000
 9RX  H251  C25  C17   121.93  3.000
 9RX  C24   C25  C17   116.62  3.000
 9RX  H1    N08  N09   122.16  3.000
 9RX  H1    N08  C07   126.68  3.000
 9RX  N09   N08  C07   111.15  3.000
 9RX  N08   N09  C10   102.19  3.000
 9RX  C07   N11  C10   103.59  3.000
 9RX  H131  N13  C14   116.72  3.000
 9RX  H131  N13  C20   115.66  3.000
 9RX  C14   N13  C20   126.29  3.000
 9RX  H2    N19  C20   126.69  3.000
 9RX  H2    N19  C17   126.54  3.000
 9RX  C20   N19  C17   106.76  3.000
 9RX  C18   N21  C20   104.51  3.000
 9RX  H4    O27  C26   110.31  3.000
 9RX  C15   S12  C10    98.84  3.000
 9RX  O28   C26  O27   122.68  3.000
 9RX  O27   C26  C03   112.29  3.000
 9RX  O28   C26  C03   125.00  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
 9RX  CONST_01  C07   N08  N09  C10     0.00   0.0  0
 9RX  CONST_02  N08   C07  N11  C10     0.00   0.0  0
 9RX  CONST_03  C04   C07  N11  C10   180.00   0.0  0
 9RX  CONST_04  C20   N21  C18  C17     0.00   0.0  0
 9RX  CONST_05  C23   C22  C18  C17     0.00   0.0  0
 9RX  CONST_06  N21   C20  N19  C17     0.00   0.0  0
 9RX  CONST_07  C23   C24  C25  C17     0.00   0.0  0
 9RX  CONST_08  C22   C18  N21  C20   180.00   0.0  0
 9RX  CONST_09  C18   C17  N19  C20     0.00   0.0  0
 9RX  CONST_10  C25   C17  N19  C20   180.00   0.0  0
 9RX  CONST_11  N19   C17  C18  C22   180.00   0.0  0
 9RX  CONST_12  C25   C17  C18  C22     0.00   0.0  0
 9RX  CONST_13  C25   C24  C23  C22     0.00   0.0  0
 9RX  CONST_14  C18   C22  C23  C24     0.00   0.0  0
 9RX  CONST_15  C18   C17  C25  C24     0.00   0.0  0
 9RX  CONST_16  N19   C17  C25  C24   180.00   0.0  0
 9RX  CONST_17  C04   C03  C02  C01     0.00   0.0  0
 9RX  CONST_18  C04   C05  C06  C01     0.00   0.0  0
 9RX  CONST_19  C07   C04  C03  C02   180.00   0.0  0
 9RX  CONST_20  C05   C04  C03  C02     0.00   0.0  0
 9RX  CONST_21  C05   C06  C01  C02     0.00   0.0  0
 9RX  CONST_22  C06   C01  C02  C03     0.00   0.0  0
 9RX  CONST_25  C06   C05  C04  C03     0.00   0.0  0
 9RX  CONST_26  N09   N08  C07  C04   180.00   0.0  0
 9RX  CONST_29  C07   C04  C05  C06   180.00   0.0  0
 9RX  CONST_30  N09   C10  N11  C07     0.00   0.0  0
 9RX  CONST_31  N19   C20  N21  C18     0.00   0.0  0
 9RX  CONST_32  N21   C18  C22  C23   180.00   0.0  0
 9RX  CONST_33  N21   C18  C17  C25   180.00   0.0  0
 9RX  CONST_34  N11   C10  N09  N08     0.00   0.0  0
 9RX  CONST_35  N11   C07  N08  N09     0.00   0.0  0
 9RX  CONST_36  N21   C18  C17  N19     0.00   0.0  0
 9RX  CONST_37  N13   C20  N19  C17   180.00   0.0  0
 9RX  CONST_38  C01   C02  C03  C26   180.00   0.0  0
 9RX  CONST_39  C07   C04  C03  C26     0.00   0.0  0
 9RX  CONST_40  C05   C04  C03  C26   180.00   0.0  0
 9RX  CONST_41  S12   C10  N11  C07   180.00   0.0  0
 9RX  CONST_42  N13   C20  N21  C18   180.00   0.0  0
 9RX  CONST_43  S12   C10  N09  N08   180.00   0.0  0
 9RX  CONST_44  H1    N08  N09  C10   180.00   0.0  0
 9RX  CONST_45  H221  C22  C18  C17   180.00   0.0  0
 9RX  CONST_46  H241  C24  C25  C17   180.00   0.0  0
 9RX  CONST_47  H051  C05  C06  C01   180.00   0.0  0
 9RX  CONST_48  H061  C06  C01  C02   180.00   0.0  0
 9RX  CONST_49  H011  C01  C02  C03   180.00   0.0  0
 9RX  CONST_50  H021  C02  C03  C04   180.00   0.0  0
 9RX  CONST_51  H231  C23  C22  C18   180.00   0.0  0
 9RX  CONST_52  H2    N19  C17  C18   180.00   0.0  0
 9RX  CONST_53  H251  C25  C17  C18   180.00   0.0  0
 9RX  CONST_54  N21   C20  N13  C14     0.00   0.0  0
 9RX  CONST_55  N19   C20  N13  C14   180.00   0.0  0
 9RX  CONST_56  H131  N13  C20  N19     0.00   0.0  0
 9RX  CONST_57  C20   N13  C14  C15   180.00   0.0  0
 9RX  CONST_58  O16   C14  N13  C20     0.00   0.0  0
 9RX  CONST_59  H4    O27  C26  C03   180.00   0.0  0
 9RX  Var_01    N09   C10  S12  C15  -169.04  30.0  2
 9RX  Var_02    O28   C26  C03  C02  -143.45  30.0  2
 9RX  Var_03    C14   C15  S12  C10   -61.80  30.0  3
 9RX  Var_04    S12   C15  C14  N13   141.83  30.0  1

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
 9RX  plan-1  C10   0.020
 9RX  plan-1  C04   0.020
 9RX  plan-1  C07   0.020
 9RX  plan-1  N08   0.020
 9RX  plan-1  N09   0.020
 9RX  plan-1  N11   0.020
 9RX  plan-1  S12   0.020
 9RX  plan-1  H1    0.020
 9RX  plan-2  C01   0.020
 9RX  plan-2  C02   0.020
 9RX  plan-2  C03   0.020
 9RX  plan-2  C04   0.020
 9RX  plan-2  C05   0.020
 9RX  plan-2  C06   0.020
 9RX  plan-2  C07   0.020
 9RX  plan-2  H011  0.020
 9RX  plan-2  H021  0.020
 9RX  plan-2  H051  0.020
 9RX  plan-2  H061  0.020
 9RX  plan-2  C26   0.020
 9RX  plan-3  C17   0.020
 9RX  plan-3  C20   0.020
 9RX  plan-3  C22   0.020
 9RX  plan-3  C24   0.020
 9RX  plan-3  C18   0.020
 9RX  plan-3  C23   0.020
 9RX  plan-3  C25   0.020
 9RX  plan-3  N13   0.020
 9RX  plan-3  N19   0.020
 9RX  plan-3  N21   0.020
 9RX  plan-3  H221  0.020
 9RX  plan-3  H241  0.020
 9RX  plan-3  H231  0.020
 9RX  plan-3  H251  0.020
 9RX  plan-3  H2    0.020
 9RX  plan-4  C15   0.020
 9RX  plan-4  C20   0.020
 9RX  plan-4  C14   0.020
 9RX  plan-4  N13   0.020
 9RX  plan-4  O16   0.020
 9RX  plan-4  H131  0.020
 9RX  plan-5  C03   0.020
 9RX  plan-5  O27   0.020
 9RX  plan-5  O28   0.020
 9RX  plan-5  H4    0.020
 9RX  plan-5  C26   0.020

