# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 12:02:34 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-[1-(4-amino-1,3,5-triazin-2-yl)-2-(ethylamino)-1H-benzimidazol-6-yl]-2-methylbut-3-yn-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNc1nc2ccc(cc2n1c3ncnc(N)n3)C#CC(C)(C)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
 2OO  2OO  4-[1-(4-amino-1,3,5-triazin-2-yl)-2-(ethylamino)-1H-benzimidazol-6-yl]-2-methylbut-3-yn-2-ol  ligand  44  25  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2OO
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
 2OO  C1   C  CH3   0  -0.703   6.0109  -2.0865   0.0385
 2OO  C2   C  CH2   0  -0.262   4.5520  -2.4877   0.1356
 2OO  N3   N  NH1   0  -0.692   3.7078  -1.3170   0.0099
 2OO  C4   C  CR5   0   0.730   2.3830  -1.4118   0.0106
 2OO  N5   N  N     0  -0.530   1.7264  -2.5401   0.0433
 2OO  C6   C  CR56  0   0.152   0.3997  -2.2034   0.0217
 2OO  C7   C  CR16  0  -0.336  -0.7072  -3.0435   0.0421
 2OO  C8   C  CR16  0  -0.304  -1.9687  -2.4758   0.0232
 2OO  C9   C  CR6   0  -0.153  -2.1380  -1.0842  -0.0116
 2OO  C10  C  CR16  0  -0.328  -1.0267  -0.2296  -0.0376
 2OO  C11  C  CR56  0   0.339   0.2250  -0.8105  -0.0236
 2OO  N12  N  NR5   0  -0.711   1.5314  -0.2934  -0.0329
 2OO  C13  C  CR6   0   0.694   1.8931   1.0394  -0.0709
 2OO  N14  N  N     0  -0.476   0.9085   1.9244  -0.1384
 2OO  C15  C  CR16  0   0.106   1.3175   3.1854  -0.1758
 2OO  N16  N  N     0  -0.452   2.5589   3.6093  -0.1507
 2OO  C17  C  CR6   0   0.617   3.4787   2.6324  -0.0781
 2OO  N18  N  N     0  -0.543   3.1790   1.3276  -0.0374
 2OO  N19  N  NH2   0  -0.802   4.7574   2.9796  -0.0454
 2OO  C20  C  CSP   0   0.137  -3.4502  -0.5271  -0.0101
 2OO  C21  C  CSP   0   0.127  -4.5612  -0.0593   0.0026
 2OO  C22  C  CT    0  -0.002  -5.9117   0.5159   0.0080
 2OO  C23  C  CH3   0  -0.666  -5.8227   2.0287   0.2252
 2OO  C24  C  CH3   0  -0.670  -6.6106   0.2081  -1.3189
 2OO  O25  O  OH1   0  -0.669  -6.5926  -0.1068   1.0866
 2OO  H1   H  HCH3  0   0.234   6.2810  -1.3716   0.8171
 2OO  H2   H  HCH3  0   0.248   6.6448  -2.9633   0.1589
 2OO  H3   H  HCH3  0   0.236   6.2363  -1.6397  -0.9303
 2OO  H4   H  HCH2  0   0.237   4.3070  -3.2036  -0.6517
 2OO  H5   H  HCH2  0   0.234   4.3604  -2.9887   1.0887
 2OO  H6   H  HNH1  0   0.424   4.1051  -0.3875   0.0355
 2OO  H7   H  HCR6  0   0.257  -0.5809  -4.1176   0.0733
 2OO  H8   H  HCR6  0   0.255  -2.8426  -3.1133   0.0393
 2OO  H9   H  HCR6  0   0.283  -1.1590   0.8391  -0.0650
 2OO  H10  H  HCR6  0   0.277   0.5415   3.9408  -0.2341
 2OO  H11  H  HNH2  0   0.416   5.0204   3.9499  -0.0683
 2OO  H12  H  HNH2  0   0.413   5.4806   2.2846   0.0214
 2OO  H13  H  HCH3  0   0.235  -5.2536   2.5070  -0.5712
 2OO  H14  H  HCH3  0   0.237  -6.8245   2.4639   0.2289
 2OO  H15  H  HCH3  0   0.242  -5.3434   2.2590   1.1766
 2OO  H16  H  HCH3  0   0.243  -6.6647  -0.8664  -1.4931
 2OO  H17  H  HCH3  0   0.237  -7.6272   0.6077  -1.3046
 2OO  H18  H  HCH3  0   0.235  -6.0837   0.6656  -2.1555
 2OO  H19  H  HOH1  0   0.451  -7.4985   0.2233   1.0890

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
 2OO  C1   C2   single    1.516  0.020  1.516
 2OO  C2   N3   single    1.449  0.020  1.449
 2OO  C7   C6   aromatic  1.390  0.020  1.390
 2OO  C7   C8   aromatic  1.384  0.020  1.384
 2OO  N5   C6   aromatic  1.369  0.020  1.369
 2OO  N5   C4   aromatic  1.306  0.020  1.306
 2OO  C6   C11  aromatic  1.405  0.020  1.405
 2OO  C8   C9   aromatic  1.402  0.020  1.402
 2OO  N3   C4   single    1.328  0.020  1.328
 2OO  C4   N12  aromatic  1.406  0.020  1.406
 2OO  C11  N12  aromatic  1.405  0.020  1.405
 2OO  C11  C10  aromatic  1.380  0.020  1.380
 2OO  C9   C10  aromatic  1.402  0.020  1.402
 2OO  C9   C20  single    1.426  0.020  1.426
 2OO  N12  C13  single    1.382  0.020  1.382
 2OO  C20  C21  triple    1.205  0.020  1.205
 2OO  N14  C13  aromatic  1.326  0.020  1.326
 2OO  N14  C15  aromatic  1.326  0.020  1.326
 2OO  C13  N18  aromatic  1.318  0.020  1.318
 2OO  O25  C22  single    1.419  0.020  1.419
 2OO  C21  C22  single    1.468  0.020  1.468
 2OO  C15  N16  aromatic  1.312  0.020  1.312
 2OO  C22  C23  single    1.531  0.020  1.531
 2OO  C22  C24  single    1.531  0.020  1.531
 2OO  N18  C17  aromatic  1.339  0.020  1.339
 2OO  N16  C17  aromatic  1.344  0.020  1.344
 2OO  C17  N19  single    1.325  0.020  1.325
 2OO  C1   H1   single    0.970  0.020  1.090
 2OO  C1   H2   single    0.970  0.020  1.090
 2OO  C1   H3   single    0.970  0.020  1.090
 2OO  C2   H4   single    0.970  0.020  1.090
 2OO  C2   H5   single    0.970  0.020  1.090
 2OO  N3   H6   single    0.860  0.020  1.020
 2OO  C7   H7   single    0.930  0.020  1.080
 2OO  C8   H8   single    0.930  0.020  1.080
 2OO  C10  H9   single    0.930  0.020  1.080
 2OO  C15  H10  single    0.930  0.020  1.080
 2OO  N19  H11  single    0.860  0.020  1.020
 2OO  N19  H12  single    0.860  0.020  1.020
 2OO  C23  H13  single    0.970  0.020  1.090
 2OO  C23  H14  single    0.970  0.020  1.090
 2OO  C23  H15  single    0.970  0.020  1.090
 2OO  C24  H16  single    0.970  0.020  1.090
 2OO  C24  H17  single    0.970  0.020  1.090
 2OO  C24  H18  single    0.970  0.020  1.090
 2OO  O25  H19  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
 2OO  H3   C1   H2   107.93  3.000
 2OO  H3   C1   H1   108.33  3.000
 2OO  H2   C1   H1   107.74  3.000
 2OO  H3   C1   C2   111.36  3.000
 2OO  H2   C1   C2   109.88  3.000
 2OO  H1   C1   C2   111.46  3.000
 2OO  H5   C2   H4   106.78  3.000
 2OO  H5   C2   N3   110.10  3.000
 2OO  H4   C2   N3   109.66  3.000
 2OO  H5   C2   C1   110.22  3.000
 2OO  H4   C2   C1   110.08  3.000
 2OO  N3   C2   C1   109.96  3.000
 2OO  H6   N3   C4   117.23  3.000
 2OO  H6   N3   C2   120.77  3.000
 2OO  C4   N3   C2   121.56  3.000
 2OO  N12  C4   N5   112.55  3.000
 2OO  N12  C4   N3   123.17  3.000
 2OO  N5   C4   N3   124.28  3.000
 2OO  C6   N5   C4   105.92  3.000
 2OO  C11  C6   C7   120.06  3.000
 2OO  C11  C6   N5   111.41  3.000
 2OO  C7   C6   N5   128.53  3.000
 2OO  H7   C7   C8   120.94  3.000
 2OO  H7   C7   C6   120.51  3.000
 2OO  C8   C7   C6   118.55  3.000
 2OO  H8   C8   C9   119.19  3.000
 2OO  H8   C8   C7   119.63  3.000
 2OO  C9   C8   C7   121.18  3.000
 2OO  C20  C9   C10  119.43  3.000
 2OO  C20  C9   C8   119.93  3.000
 2OO  C10  C9   C8   120.64  3.000
 2OO  H9   C10  C11  121.96  3.000
 2OO  H9   C10  C9   120.52  3.000
 2OO  C11  C10  C9   117.52  3.000
 2OO  N12  C11  C10  133.50  3.000
 2OO  C10  C11  C6   122.04  3.000
 2OO  N12  C11  C6   104.45  3.000
 2OO  C13  N12  C11  126.77  3.000
 2OO  C13  N12  C4   127.56  3.000
 2OO  C11  N12  C4   105.67  3.000
 2OO  N18  C13  N14  125.44  3.000
 2OO  N18  C13  N12  117.75  3.000
 2OO  N14  C13  N12  116.81  3.000
 2OO  C15  N14  C13  114.03  3.000
 2OO  H10  C15  N16  116.93  3.000
 2OO  H10  C15  N14  116.31  3.000
 2OO  N16  C15  N14  126.76  3.000
 2OO  C17  N16  C15  114.44  3.000
 2OO  N19  C17  N18  118.06  3.000
 2OO  N19  C17  N16  118.11  3.000
 2OO  N18  C17  N16  123.83  3.000
 2OO  C17  N18  C13  115.50  3.000
 2OO  H12  N19  H11  118.71  3.000
 2OO  H12  N19  C17  120.97  3.000
 2OO  H11  N19  C17  120.30  3.000
 2OO  C21  C20  C9   180.00  3.000
 2OO  C22  C21  C20  180.00  3.000
 2OO  O25  C22  C24  110.58  3.000
 2OO  C24  C22  C23  110.38  3.000
 2OO  O25  C22  C23  110.71  3.000
 2OO  C24  C22  C21  109.75  3.000
 2OO  C23  C22  C21  109.53  3.000
 2OO  O25  C22  C21  105.80  3.000
 2OO  H15  C23  H14  108.43  3.000
 2OO  H15  C23  H13  108.40  3.000
 2OO  H14  C23  H13  107.85  3.000
 2OO  H15  C23  C22  110.99  3.000
 2OO  H14  C23  C22  109.93  3.000
 2OO  H13  C23  C22  111.13  3.000
 2OO  H18  C24  H17  107.85  3.000
 2OO  H18  C24  H16  108.38  3.000
 2OO  H17  C24  H16  108.45  3.000
 2OO  H18  C24  C22  111.12  3.000
 2OO  H17  C24  C22  109.87  3.000
 2OO  H16  C24  C22  111.06  3.000
 2OO  H19  O25  C22  107.60  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
 2OO  CONST_01  C7   C6   N5   C4   180.00   0.0  0
 2OO  CONST_02  C11  C6   N5   C4     0.00   0.0  0
 2OO  CONST_03  C6   C11  N12  C4     0.00   0.0  0
 2OO  CONST_04  C10  C11  N12  C4   180.00   0.0  0
 2OO  CONST_05  N14  C13  N12  C4   180.00   0.0  0
 2OO  CONST_06  N18  C13  N12  C4     0.00   0.0  0
 2OO  CONST_07  C8   C7   C6   N5   180.00   0.0  0
 2OO  CONST_08  N12  C11  C6   N5     0.00   0.0  0
 2OO  CONST_09  C10  C11  C6   N5   180.00   0.0  0
 2OO  CONST_10  C11  N12  C4   N5     0.00   0.0  0
 2OO  CONST_11  C13  N12  C4   N5   180.00   0.0  0
 2OO  CONST_12  C9   C8   C7   C6     0.00   0.0  0
 2OO  CONST_13  N12  C4   N5   C6     0.00   0.0  0
 2OO  CONST_14  C13  N12  C11  C6   180.00   0.0  0
 2OO  CONST_15  C9   C10  C11  C6     0.00   0.0  0
 2OO  CONST_16  N12  C11  C6   C7   180.00   0.0  0
 2OO  CONST_17  C10  C11  C6   C7     0.00   0.0  0
 2OO  CONST_18  C10  C9   C8   C7     0.00   0.0  0
 2OO  CONST_19  C11  C6   C7   C8     0.00   0.0  0
 2OO  CONST_20  C11  C10  C9   C8     0.00   0.0  0
 2OO  CONST_21  N12  C11  C10  C9   180.00   0.0  0
 2OO  CONST_22  C13  N12  C11  C10    0.00   0.0  0
 2OO  CONST_23  N14  C13  N12  C11    0.00   0.0  0
 2OO  CONST_24  N18  C13  N12  C11  180.00   0.0  0
 2OO  CONST_25  C15  N14  C13  N12  180.00   0.0  0
 2OO  CONST_26  C17  N18  C13  N12  180.00   0.0  0
 2OO  CONST_27  N16  C15  N14  C13    0.00   0.0  0
 2OO  CONST_28  N16  C17  N18  C13    0.00   0.0  0
 2OO  CONST_29  C17  N18  C13  N14    0.00   0.0  0
 2OO  CONST_30  C17  N16  C15  N14    0.00   0.0  0
 2OO  CONST_31  N18  C13  N14  C15    0.00   0.0  0
 2OO  CONST_32  N18  C17  N16  C15    0.00   0.0  0
 2OO  CONST_33  C6   N5   C4   N3   180.00   0.0  0
 2OO  CONST_34  C11  N12  C4   N3   180.00   0.0  0
 2OO  CONST_35  C13  N12  C4   N3     0.00   0.0  0
 2OO  CONST_36  C20  C9   C8   C7   180.00   0.0  0
 2OO  CONST_37  C20  C9   C10  C11  180.00   0.0  0
 2OO  CONST_38  N19  C17  N18  C13  180.00   0.0  0
 2OO  CONST_39  N19  C17  N16  C15  180.00   0.0  0
 2OO  CONST_40  H7   C7   C6   N5     0.00   0.0  0
 2OO  CONST_41  H8   C8   C7   C6   180.00   0.0  0
 2OO  CONST_42  H9   C10  C11  C6   180.00   0.0  0
 2OO  CONST_43  H10  C15  N14  C13  180.00   0.0  0
 2OO  CONST_44  N5   C4   N3   C2     0.00   0.0  0
 2OO  CONST_45  N12  C4   N3   C2   180.00   0.0  0
 2OO  CONST_46  H6   N3   C4   N5   180.00   0.0  0
 2OO  CONST_47  H11  N19  C17  N16    0.00   0.0  0
 2OO  CONST_48  H12  N19  C17  N16  180.00   0.0  0
 2OO  Var_01    C4   N3   C2   C1   177.36  30.0  3
 2OO  Var_02    O25  C22  C21  C20  173.17  30.0  3
 2OO  Var_03    H1   C1   C2   N3    59.18  30.0  3
 2OO  Var_04    H13  C23  C22  C21   60.59  30.0  3
 2OO  Var_05    H16  C24  C22  C21   58.21  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
 2OO  plan-1  N12  0.020
 2OO  plan-1  C13  0.020
 2OO  plan-1  N14  0.020
 2OO  plan-1  C15  0.020
 2OO  plan-1  N16  0.020
 2OO  plan-1  C17  0.020
 2OO  plan-1  N18  0.020
 2OO  plan-1  N19  0.020
 2OO  plan-1  H10  0.020
 2OO  plan-2  N3   0.020
 2OO  plan-2  C4   0.020
 2OO  plan-2  N5   0.020
 2OO  plan-2  C6   0.020
 2OO  plan-2  C7   0.020
 2OO  plan-2  C8   0.020
 2OO  plan-2  C9   0.020
 2OO  plan-2  C10  0.020
 2OO  plan-2  C11  0.020
 2OO  plan-2  N12  0.020
 2OO  plan-2  C13  0.020
 2OO  plan-2  C20  0.020
 2OO  plan-2  C21  0.020
 2OO  plan-2  H7   0.020
 2OO  plan-2  H8   0.020
 2OO  plan-2  H9   0.020
 2OO  plan-3  C2   0.020
 2OO  plan-3  N3   0.020
 2OO  plan-3  C4   0.020
 2OO  plan-3  H6   0.020
 2OO  plan-4  C17  0.020
 2OO  plan-4  N19  0.020
 2OO  plan-4  H11  0.020
 2OO  plan-4  H12  0.020

