# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 21:33:04 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: 2-(4-{5-[(1H-benzimidazol-2-ylamino)methyl]thiophen-2-yl}-1,3-thiazol-2-yl)guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(N)=Nc1scc(n1)c2sc(CNc3[nH]c4ccccc4n3)cc2
#
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
 FR0  FR0  2-(4-{5-[(1H-benzimidazol-2-ylamino)methyl]thiophen-2-yl}-1,3-thiazol-2-yl)guanidine  ligand  40  25  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FR0
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
 FR0  N1    N  N     0  -0.532  -0.3037   1.3504  -4.8972
 FR0  C2    C  CR56  0   0.161   0.0975   0.9242  -6.1414
 FR0  C3    C  CR56  0   0.334   0.2336  -0.4751  -6.1581
 FR0  N4    N  NR15  0  -0.739  -0.0987  -0.8710  -4.8810
 FR0  C5    C  CR5   0   0.684  -0.4047   0.2567  -4.1815
 FR0  C6    C  CR16  0  -0.349   0.3662   1.6504  -7.2978
 FR0  C7    C  CR16  0  -0.271   0.7592   0.9540  -8.4334
 FR0  C8    C  CR16  0  -0.289   0.8855  -0.4379  -8.4289
 FR0  C9    C  CR16  0  -0.313   0.6230  -1.1803  -7.2831
 FR0  N10   N  NH1   0  -0.692  -0.7355   0.2403  -2.8675
 FR0  C11   C  CH2   0  -0.338  -1.1266  -0.9680  -2.1737
 FR0  C12   C  CR5   0  -0.186  -1.1070  -0.7498  -0.6993
 FR0  S15   S  S2    0   0.227   0.2425   0.0154   0.0548
 FR0  C16   C  CR5   0  -0.238  -0.4527  -0.1680   1.6260
 FR0  C17   C  CR15  0  -0.220  -1.6649  -0.7947   1.5514
 FR0  C18   C  CR15  0  -0.199  -2.0377  -1.1211   0.2213
 FR0  C19   C  CR5   0   0.422   0.2132   0.3251   2.8191
 FR0  N20   N  N     0  -0.528  -0.3758   0.0932   4.0336
 FR0  C21   C  CR5   0   0.234   0.3201   0.5934   5.0228
 FR0  S22   S  S2    0   0.176   1.7828   1.4000   4.4851
 FR0  C23   C  CR15  0  -0.618   1.3852   1.0154   2.8563
 FR0  N26   N  N     0  -0.557   0.0892   0.5803   6.3407
 FR0  C27   C  C     0   0.639  -0.9714  -0.0229   6.8489
 FR0  N28   N  NH2   0  -0.820  -1.0860  -0.0157   8.1883
 FR0  N29   N  NH2   0  -0.825  -1.9134  -0.6536   6.1449
 FR0  HN4   H  HNR5  0   0.422  -0.1361  -1.8221  -4.5523
 FR0  H6    H  HCR6  0   0.247   0.2714   2.7288  -7.3099
 FR0  H7    H  HCR6  0   0.247   0.9750   1.5005  -9.3426
 FR0  H8    H  HCR6  0   0.249   1.1943  -0.9477  -9.3320
 FR0  H9    H  HCR6  0   0.262   0.7205  -2.2582  -7.2759
 FR0  H10   H  HNH1  0   0.401  -1.1776   1.0912  -2.5531
 FR0  H111  H  HCH2  0   0.267  -0.4199  -1.7638  -2.4237
 FR0  H112  H  HCH2  0   0.267  -2.1230  -1.3207  -2.4612
 FR0  H17   H  HCR5  0   0.267  -2.2754  -1.0019   2.4183
 FR0  H18   H  HCR5  0   0.268  -2.9634  -1.6133  -0.0433
 FR0  H23   H  HCR5  0   0.293   2.0173   1.3144   2.0344
 FR0  H281  H  HNH2  0   0.405  -1.9426  -0.2885   8.6388
 FR0  H282  H  HNH2  0   0.404  -0.4736   0.5888   8.7074
 FR0  H291  H  HNH2  0   0.435  -1.8134  -0.7005   5.1399
 FR0  H292  H  HNH2  0   0.407  -2.6841  -1.1194   6.5915

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
 FR0  N1   C2    aromatic  1.375  0.020  1.375
 FR0  N1   C5    aromatic  1.311  0.020  1.311
 FR0  C2   C3    aromatic  1.406  0.020  1.406
 FR0  C2   C6    aromatic  1.392  0.020  1.392
 FR0  C3   N4    aromatic  1.378  0.020  1.378
 FR0  C3   C9    aromatic  1.384  0.020  1.384
 FR0  N4   C5    aromatic  1.362  0.020  1.362
 FR0  N4   HN4   single    0.860  0.020  1.020
 FR0  C5   N10   single    1.355  0.020  1.355
 FR0  C6   C7    aromatic  1.389  0.020  1.389
 FR0  C6   H6    single    0.930  0.020  1.080
 FR0  C7   C8    aromatic  1.398  0.020  1.398
 FR0  C7   H7    single    0.930  0.020  1.080
 FR0  C8   C9    aromatic  1.390  0.020  1.390
 FR0  C8   H8    single    0.930  0.020  1.080
 FR0  C9   H9    single    0.930  0.020  1.080
 FR0  N10  C11   single    1.447  0.020  1.447
 FR0  N10  H10   single    0.890  0.020  1.040
 FR0  C11  C12   single    1.491  0.020  1.491
 FR0  C11  H111  single    0.970  0.020  1.090
 FR0  C11  H112  single    0.970  0.020  1.090
 FR0  C12  S15   aromatic  1.725  0.020  1.725
 FR0  C12  C18   aromatic  1.361  0.020  1.361
 FR0  S15  C16   aromatic  1.728  0.020  1.728
 FR0  C16  C17   aromatic  1.367  0.020  1.367
 FR0  C16  C19   single    1.453  0.020  1.453
 FR0  C17  C18   aromatic  1.419  0.020  1.419
 FR0  C17  H17   single    0.930  0.020  1.080
 FR0  C18  H18   single    0.930  0.020  1.080
 FR0  C19  N20   aromatic  1.370  0.020  1.370
 FR0  C19  C23   aromatic  1.361  0.020  1.361
 FR0  N20  C21   aromatic  1.309  0.020  1.309
 FR0  C21  S22   aromatic  1.755  0.020  1.755
 FR0  C21  N26   single    1.338  0.020  1.338
 FR0  S22  C23   aromatic  1.720  0.020  1.720
 FR0  C23  H23   single    0.930  0.020  1.080
 FR0  N26  C27   double    1.322  0.020  1.322
 FR0  C27  N28   single    1.344  0.020  1.344
 FR0  C27  N29   single    1.334  0.020  1.334
 FR0  N28  H281  single    0.890  0.020  1.040
 FR0  N28  H282  single    0.890  0.020  1.040
 FR0  N29  H291  single    0.860  0.020  1.020
 FR0  N29  H292  single    0.860  0.020  1.020

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
 FR0  C5    N1   C2    104.95  3.000
 FR0  C6    C2   C3    119.39  3.000
 FR0  C6    C2   N1    130.28  3.000
 FR0  C3    C2   N1    110.33  3.000
 FR0  C9    C3   N4    132.46  3.000
 FR0  C9    C3   C2    122.96  3.000
 FR0  N4    C3   C2    104.58  3.000
 FR0  HN4   N4   C5    127.30  3.000
 FR0  HN4   N4   C3    125.66  3.000
 FR0  C5    N4   C3    107.00  3.000
 FR0  N10   C5   N4    122.88  3.000
 FR0  N10   C5   N1    123.94  3.000
 FR0  N4    C5   N1    113.15  3.000
 FR0  H6    C6   C7    121.01  3.000
 FR0  H6    C6   C2    120.80  3.000
 FR0  C7    C6   C2    118.19  3.000
 FR0  H7    C7   C8    119.17  3.000
 FR0  H7    C7   C6    119.34  3.000
 FR0  C8    C7   C6    121.49  3.000
 FR0  H8    C8   C9    119.35  3.000
 FR0  H8    C8   C7    119.49  3.000
 FR0  C9    C8   C7    121.16  3.000
 FR0  H9    C9   C8    121.36  3.000
 FR0  H9    C9   C3    121.83  3.000
 FR0  C8    C9   C3    116.81  3.000
 FR0  H10   N10  C11   115.87  3.000
 FR0  H10   N10  C5    113.50  3.000
 FR0  C11   N10  C5    122.75  3.000
 FR0  H112  C11  H111  107.07  3.000
 FR0  H112  C11  C12   108.59  3.000
 FR0  H111  C11  C12   108.92  3.000
 FR0  H112  C11  N10   112.89  3.000
 FR0  H111  C11  N10   108.87  3.000
 FR0  C12   C11  N10   110.39  3.000
 FR0  C18   C12  S15   111.12  3.000
 FR0  C18   C12  C11   128.34  3.000
 FR0  S15   C12  C11   120.51  3.000
 FR0  C16   S15  C12    92.05  3.000
 FR0  C19   C16  C17   127.38  3.000
 FR0  C19   C16  S15   121.77  3.000
 FR0  C17   C16  S15   110.85  3.000
 FR0  H17   C17  C18   124.02  3.000
 FR0  H17   C17  C16   123.05  3.000
 FR0  C18   C17  C16   112.92  3.000
 FR0  H18   C18  C17   123.97  3.000
 FR0  H18   C18  C12   122.97  3.000
 FR0  C17   C18  C12   113.06  3.000
 FR0  C23   C19  N20   115.61  3.000
 FR0  C23   C19  C16   126.12  3.000
 FR0  N20   C19  C16   118.28  3.000
 FR0  C21   N20  C19   112.13  3.000
 FR0  N26   C21  S22   116.75  3.000
 FR0  N26   C21  N20   130.46  3.000
 FR0  S22   C21  N20   112.78  3.000
 FR0  C23   S22  C21    89.70  3.000
 FR0  H23   C23  S22   121.59  3.000
 FR0  H23   C23  C19   128.63  3.000
 FR0  S22   C23  C19   109.77  3.000
 FR0  C27   N26  C21   121.44  3.000
 FR0  N29   C27  N28   117.90  3.000
 FR0  N29   C27  N26   125.40  3.000
 FR0  N28   C27  N26   116.68  3.000
 FR0  H282  N28  H281  116.80  3.000
 FR0  H282  N28  C27   117.77  3.000
 FR0  H281  N28  C27   121.17  3.000
 FR0  H292  N29  H291  119.72  3.000
 FR0  H292  N29  C27   121.73  3.000
 FR0  H291  N29  C27   118.46  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
 FR0  CONST_01  N4    C3   C2   N1     0.00   0.0  0
 FR0  CONST_02  C9    C3   C2   N1   180.00   0.0  0
 FR0  CONST_03  C7    C6   C2   N1   180.00   0.0  0
 FR0  CONST_04  C3    N4   C5   N1     0.00   0.0  0
 FR0  CONST_05  N4    C5   N1   C2     0.00   0.0  0
 FR0  CONST_06  C5    N4   C3   C2     0.00   0.0  0
 FR0  CONST_07  C8    C9   C3   C2     0.00   0.0  0
 FR0  CONST_08  C8    C7   C6   C2     0.00   0.0  0
 FR0  CONST_09  C5    N1   C2   C3     0.00   0.0  0
 FR0  CONST_10  C7    C6   C2   C3     0.00   0.0  0
 FR0  CONST_11  C7    C8   C9   C3     0.00   0.0  0
 FR0  CONST_12  C6    C2   C3   N4   180.00   0.0  0
 FR0  CONST_13  C8    C9   C3   N4   180.00   0.0  0
 FR0  CONST_14  C6    C2   N1   C5   180.00   0.0  0
 FR0  CONST_15  C9    C3   N4   C5   180.00   0.0  0
 FR0  CONST_16  C9    C3   C2   C6     0.00   0.0  0
 FR0  CONST_17  C9    C8   C7   C6     0.00   0.0  0
 FR0  CONST_18  C17   C16  S15  C12    0.00   0.0  0
 FR0  CONST_19  C19   C16  S15  C12  180.00   0.0  0
 FR0  CONST_20  C16   C17  C18  C12    0.00   0.0  0
 FR0  CONST_21  C17   C18  C12  S15    0.00   0.0  0
 FR0  CONST_22  C18   C17  C16  S15    0.00   0.0  0
 FR0  CONST_23  N20   C19  C16  S15  180.00   0.0  0
 FR0  CONST_24  C23   C19  C16  S15    0.00   0.0  0
 FR0  CONST_25  C18   C12  S15  C16    0.00   0.0  0
 FR0  CONST_26  C21   N20  C19  C16  180.00   0.0  0
 FR0  CONST_27  S22   C23  C19  C16  180.00   0.0  0
 FR0  CONST_28  N20   C19  C16  C17    0.00   0.0  0
 FR0  CONST_29  C23   C19  C16  C17  180.00   0.0  0
 FR0  CONST_30  C19   C16  C17  C18  180.00   0.0  0
 FR0  CONST_31  S22   C21  N20  C19    0.00   0.0  0
 FR0  CONST_32  C21   S22  C23  C19    0.00   0.0  0
 FR0  CONST_33  S22   C23  C19  N20    0.00   0.0  0
 FR0  CONST_34  C23   S22  C21  N20    0.00   0.0  0
 FR0  CONST_35  C23   C19  N20  C21    0.00   0.0  0
 FR0  CONST_36  N10   C5   N1   C2   180.00   0.0  0
 FR0  CONST_37  N10   C5   N4   C3   180.00   0.0  0
 FR0  CONST_38  C16   S15  C12  C11  180.00   0.0  0
 FR0  CONST_39  C17   C18  C12  C11  180.00   0.0  0
 FR0  CONST_40  N26   C21  N20  C19  180.00   0.0  0
 FR0  CONST_41  N26   C21  S22  C23  180.00   0.0  0
 FR0  CONST_42  H6    C6   C2   N1     0.00   0.0  0
 FR0  CONST_43  HN4   N4   C5   N1   180.00   0.0  0
 FR0  CONST_44  H9    C9   C3   C2   180.00   0.0  0
 FR0  CONST_45  H7    C7   C6   C2   180.00   0.0  0
 FR0  CONST_46  H8    C8   C9   C3   180.00   0.0  0
 FR0  CONST_47  H17   C17  C18  C12  180.00   0.0  0
 FR0  CONST_48  H18   C18  C12  S15  180.00   0.0  0
 FR0  CONST_49  H23   C23  C19  C16    0.00   0.0  0
 FR0  CONST_50  C11   N10  C5   N1   180.00   0.0  0
 FR0  CONST_53  N28   C27  N26  C21  180.00   0.0  0
 FR0  CONST_54  N29   C27  N26  C21    0.00   0.0  0
 FR0  CONST_55  H281  N28  C27  N26  180.00   0.0  0
 FR0  CONST_56  H282  N28  C27  N26    0.00   0.0  0
 FR0  CONST_57  H291  N29  C27  N26    0.00   0.0  0
 FR0  CONST_58  H292  N29  C27  N26  180.00   0.0  0
 FR0  Var_01    C12   C11  N10  C5   166.23  30.0  3
 FR0  Var_02    S15   C12  C11  N10  -47.16  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
 FR0  plan-1  C11   0.020
 FR0  plan-1  C12   0.020
 FR0  plan-1  S15   0.020
 FR0  plan-1  C16   0.020
 FR0  plan-1  C17   0.020
 FR0  plan-1  C18   0.020
 FR0  plan-1  C19   0.020
 FR0  plan-1  H17   0.020
 FR0  plan-1  H18   0.020
 FR0  plan-2  C16   0.020
 FR0  plan-2  C19   0.020
 FR0  plan-2  N20   0.020
 FR0  plan-2  C21   0.020
 FR0  plan-2  S22   0.020
 FR0  plan-2  C23   0.020
 FR0  plan-2  N26   0.020
 FR0  plan-2  H23   0.020
 FR0  plan-3  N1    0.020
 FR0  plan-3  C2    0.020
 FR0  plan-3  C3    0.020
 FR0  plan-3  N4    0.020
 FR0  plan-3  C5    0.020
 FR0  plan-3  C6    0.020
 FR0  plan-3  C7    0.020
 FR0  plan-3  C8    0.020
 FR0  plan-3  C9    0.020
 FR0  plan-3  N10   0.020
 FR0  plan-3  HN4   0.020
 FR0  plan-3  H6    0.020
 FR0  plan-3  H7    0.020
 FR0  plan-3  H8    0.020
 FR0  plan-3  H9    0.020
 FR0  plan-4  C5    0.020
 FR0  plan-4  N10   0.020
 FR0  plan-4  C11   0.020
 FR0  plan-4  H10   0.020
 FR0  plan-5  C21   0.020
 FR0  plan-5  N26   0.020
 FR0  plan-5  C27   0.020
 FR0  plan-5  N28   0.020
 FR0  plan-5  N29   0.020
 FR0  plan-5  H281  0.020
 FR0  plan-5  H282  0.020
 FR0  plan-5  H291  0.020
 FR0  plan-5  H292  0.020

