# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 16:00:55 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 1-({1-(2-aminopyrimidin-4-yl)-2-[(2-methoxyethyl)amino]-1H-benzimidazol-6-yl}ethynyl)cyclohexanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCNc1nc2ccc(cc2n1c3ccnc(N)n3)C#CC4(O)CCCCC4
#
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
 2OL  2OL  1-({1-(2-aminopyrimidin-4-yl)-2-[(2-methoxyethyl)amino]-1H-benzimidazol-6-yl}ethynyl)cyclohexanol  ligand  56  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2OL
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
 2OL  C1   C  CH3   0  -0.393   7.7471   0.0754   0.0557
 2OL  O2   O  O2    0  -0.487   6.5520  -0.6086   0.3361
 2OL  C3   C  CH2   0  -0.169   6.2013  -1.5350  -0.6620
 2OL  C4   C  CH2   0  -0.303   4.8438  -2.1118  -0.3305
 2OL  N5   N  NH1   0  -0.697   3.8763  -1.0406  -0.2529
 2OL  C6   C  CR5   0   0.714   2.5687  -1.2908  -0.1597
 2OL  N7   N  N     0  -0.527   2.0176  -2.4707  -0.2632
 2OL  C8   C  CR56  0   0.156   0.6683  -2.2608  -0.1513
 2OL  C9   C  CR16  0  -0.331  -0.3684  -3.1865  -0.1577
 2OL  C10  C  CR16  0  -0.312  -1.6628  -2.7313   0.0262
 2OL  C11  C  CR6   0  -0.162  -1.9356  -1.3709   0.2353
 2OL  C12  C  CR16  0  -0.351  -0.8952  -0.4316   0.2457
 2OL  C13  C  CR56  0   0.352   0.3843  -0.8960   0.0251
 2OL  N14  N  NR5   0  -0.705   1.6305  -0.2694   0.0061
 2OL  C15  C  CR6   0   0.566   1.8918   1.0999   0.0416
 2OL  C16  C  CR16  0  -0.430   0.9817   2.0324  -0.4438
 2OL  C17  C  CR16  0  -0.012   1.3737   3.3551  -0.3222
 2OL  N18  N  N     0  -0.459   2.5298   3.7411   0.1885
 2OL  C19  C  CR6   0   0.590   3.3478   2.7598   0.5856
 2OL  N20  N  N     0  -0.541   3.0579   1.4547   0.5477
 2OL  N21  N  NH2   0  -0.819   4.5543   3.1013   1.0534
 2OL  C22  C  CSP   0   0.102  -3.2764  -0.9311   0.4331
 2OL  C23  C  CSP   0   0.114  -4.4100  -0.5491   0.5901
 2OL  C24  C  CT    0   0.082  -5.7968  -0.0819   0.7530
 2OL  C25  C  CH2   0  -0.444  -5.8463   1.4429   0.6062
 2OL  C26  C  CH2   0  -0.449  -5.4615   1.8939  -0.7983
 2OL  C27  C  CH2   0  -0.429  -6.3350   1.2285  -1.8565
 2OL  C28  C  CH2   0  -0.448  -6.3048  -0.2907  -1.7281
 2OL  C29  C  CH2   0  -0.462  -6.6859  -0.7307  -0.3183
 2OL  O30  O  OH1   0  -0.665  -6.2607  -0.3851   2.0549
 2OL  H1   H  HCH3  0   0.207   7.6912   0.6287  -0.8891
 2OL  H2   H  HCH3  0   0.234   7.9247   0.7862   0.8617
 2OL  H3   H  HCH3  0   0.208   8.6053  -0.6039  -0.0028
 2OL  H4   H  HCH2  0   0.211   6.1665  -1.0507  -1.6478
 2OL  H5   H  HCH2  0   0.223   6.9327  -2.3511  -0.7247
 2OL  H6   H  HCH2  0   0.252   4.5621  -2.8113  -1.1179
 2OL  H7   H  HCH2  0   0.240   4.8868  -2.6795   0.6055
 2OL  H8   H  HNH1  0   0.415   4.1843  -0.1553   0.1290
 2OL  H9   H  HCR6  0   0.259  -0.1649  -4.2403  -0.2949
 2OL  H10  H  HCR6  0   0.255  -2.4836  -3.4358   0.0189
 2OL  H11  H  HCR6  0   0.279  -1.1173   0.6084   0.4350
 2OL  H12  H  HCR6  0   0.291   0.0528   1.7697  -0.9217
 2OL  H13  H  HCR6  0   0.281   0.7135   4.1422  -0.6692
 2OL  H14  H  HNH2  0   0.406   4.7953   4.0690   1.1716
 2OL  H15  H  HNH2  0   0.401   5.1663   2.4035   1.4365
 2OL  H16  H  HCH2  0   0.235  -6.8694   1.7649   0.8272
 2OL  H17  H  HCH2  0   0.241  -5.1947   1.9046   1.3519
 2OL  H18  H  HCH2  0   0.237  -5.5489   2.9806  -0.8637
 2OL  H19  H  HCH2  0   0.222  -4.4096   1.6573  -0.9847
 2OL  H20  H  HCH2  0   0.212  -7.3671   1.5776  -1.7432
 2OL  H21  H  HCH2  0   0.232  -6.0115   1.5294  -2.8553
 2OL  H22  H  HCH2  0   0.236  -6.9902  -0.7457  -2.4464
 2OL  H23  H  HCH2  0   0.222  -5.3059  -0.6639  -1.9743
 2OL  H24  H  HCH2  0   0.238  -6.6338  -1.8199  -0.2271
 2OL  H25  H  HCH2  0   0.235  -7.7205  -0.4391  -0.1095
 2OL  H26  H  HOH1  0   0.448  -6.3036  -1.3435   2.1477

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
 2OL  C29  C28  single    1.525  0.020  1.525
 2OL  C29  C24  single    1.536  0.020  1.536
 2OL  C28  C27  single    1.525  0.020  1.525
 2OL  C10  C9   aromatic  1.384  0.020  1.384
 2OL  C10  C11  aromatic  1.403  0.020  1.403
 2OL  O30  C24  single    1.415  0.020  1.415
 2OL  C9   C8   aromatic  1.390  0.020  1.390
 2OL  C24  C23  single    1.472  0.020  1.472
 2OL  C24  C25  single    1.533  0.020  1.533
 2OL  C23  C22  triple    1.206  0.020  1.206
 2OL  C22  C11  single    1.425  0.020  1.425
 2OL  C11  C12  aromatic  1.402  0.020  1.402
 2OL  C8   N7   aromatic  1.370  0.020  1.370
 2OL  C8   C13  aromatic  1.405  0.020  1.405
 2OL  C27  C26  single    1.525  0.020  1.525
 2OL  N7   C6   aromatic  1.306  0.020  1.306
 2OL  C12  C13  aromatic  1.379  0.020  1.379
 2OL  C13  N14  aromatic  1.395  0.020  1.395
 2OL  C25  C26  single    1.524  0.020  1.524
 2OL  C6   N14  aromatic  1.397  0.020  1.397
 2OL  C6   N5   single    1.335  0.020  1.335
 2OL  N14  C15  single    1.394  0.020  1.394
 2OL  C4   N5   single    1.446  0.020  1.446
 2OL  C4   C3   single    1.512  0.020  1.512
 2OL  O2   C3   single    1.406  0.020  1.406
 2OL  O2   C1   single    1.405  0.020  1.405
 2OL  C15  C16  aromatic  1.390  0.020  1.390
 2OL  C15  N20  aromatic  1.320  0.020  1.320
 2OL  C16  C17  aromatic  1.385  0.020  1.385
 2OL  N20  C19  aromatic  1.337  0.020  1.337
 2OL  C17  N18  aromatic  1.321  0.020  1.321
 2OL  C19  N18  aromatic  1.338  0.020  1.338
 2OL  C19  N21  single    1.338  0.020  1.338
 2OL  C1   H1   single    0.970  0.020  1.090
 2OL  C1   H2   single    0.970  0.020  1.090
 2OL  C1   H3   single    0.970  0.020  1.090
 2OL  C3   H4   single    0.970  0.020  1.090
 2OL  C3   H5   single    0.970  0.020  1.090
 2OL  C4   H6   single    0.970  0.020  1.090
 2OL  C4   H7   single    0.970  0.020  1.090
 2OL  N5   H8   single    0.890  0.020  1.040
 2OL  C9   H9   single    0.930  0.020  1.080
 2OL  C10  H10  single    0.930  0.020  1.080
 2OL  C12  H11  single    0.930  0.020  1.080
 2OL  C16  H12  single    0.930  0.020  1.080
 2OL  C17  H13  single    0.930  0.020  1.080
 2OL  N21  H14  single    0.860  0.020  1.020
 2OL  N21  H15  single    0.860  0.020  1.020
 2OL  C25  H16  single    0.970  0.020  1.090
 2OL  C25  H17  single    0.970  0.020  1.090
 2OL  C26  H18  single    0.970  0.020  1.090
 2OL  C26  H19  single    0.970  0.020  1.090
 2OL  C27  H20  single    0.970  0.020  1.090
 2OL  C27  H21  single    0.970  0.020  1.090
 2OL  C28  H22  single    0.970  0.020  1.090
 2OL  C28  H23  single    0.970  0.020  1.090
 2OL  C29  H24  single    0.970  0.020  1.090
 2OL  C29  H25  single    0.970  0.020  1.090
 2OL  O30  H26  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
 2OL  H3   C1   H2   108.44  3.000
 2OL  H3   C1   H1   107.87  3.000
 2OL  H2   C1   H1   108.46  3.000
 2OL  H3   C1   O2   112.01  3.000
 2OL  H2   C1   O2   107.98  3.000
 2OL  H1   C1   O2   111.98  3.000
 2OL  C3   O2   C1   113.02  3.000
 2OL  H5   C3   H4   107.31  3.000
 2OL  H5   C3   C4   109.10  3.000
 2OL  H4   C3   C4   109.66  3.000
 2OL  H5   C3   O2   111.35  3.000
 2OL  H4   C3   O2   110.75  3.000
 2OL  C4   C3   O2   108.64  3.000
 2OL  H7   C4   H6   107.14  3.000
 2OL  H7   C4   N5   111.37  3.000
 2OL  H6   C4   N5   109.96  3.000
 2OL  H7   C4   C3   110.48  3.000
 2OL  H6   C4   C3   108.57  3.000
 2OL  N5   C4   C3   109.27  3.000
 2OL  H8   N5   C6   115.84  3.000
 2OL  H8   N5   C4   117.70  3.000
 2OL  C6   N5   C4   121.37  3.000
 2OL  N14  C6   N7   112.74  3.000
 2OL  N14  C6   N5   121.95  3.000
 2OL  N7   C6   N5   125.25  3.000
 2OL  C8   N7   C6   105.70  3.000
 2OL  C13  C8   C9   119.79  3.000
 2OL  C13  C8   N7   110.98  3.000
 2OL  C9   C8   N7   129.21  3.000
 2OL  H9   C9   C10  120.86  3.000
 2OL  H9   C9   C8   120.60  3.000
 2OL  C10  C9   C8   118.54  3.000
 2OL  H10  C10  C11  119.01  3.000
 2OL  H10  C10  C9   119.63  3.000
 2OL  C11  C10  C9   121.36  3.000
 2OL  C22  C11  C12  119.37  3.000
 2OL  C12  C11  C10  120.43  3.000
 2OL  C22  C11  C10  120.19  3.000
 2OL  H11  C12  C13  122.89  3.000
 2OL  H11  C12  C11  119.60  3.000
 2OL  C13  C12  C11  117.51  3.000
 2OL  N14  C13  C12  132.83  3.000
 2OL  N14  C13  C8   104.72  3.000
 2OL  C12  C13  C8   122.32  3.000
 2OL  C15  N14  C13  127.45  3.000
 2OL  C15  N14  C6   126.53  3.000
 2OL  C13  N14  C6   105.85  3.000
 2OL  N20  C15  C16  122.13  3.000
 2OL  N20  C15  N14  116.06  3.000
 2OL  C16  C15  N14  121.80  3.000
 2OL  H12  C16  C17  121.06  3.000
 2OL  H12  C16  C15  123.76  3.000
 2OL  C17  C16  C15  115.13  3.000
 2OL  H13  C17  N18  116.38  3.000
 2OL  H13  C17  C16  119.52  3.000
 2OL  N18  C17  C16  124.09  3.000
 2OL  C19  N18  C17  115.81  3.000
 2OL  N21  C19  N20  117.02  3.000
 2OL  N21  C19  N18  117.90  3.000
 2OL  N20  C19  N18  125.08  3.000
 2OL  C19  N20  C15  117.69  3.000
 2OL  H15  N21  H14  118.58  3.000
 2OL  H15  N21  C19  120.37  3.000
 2OL  H14  N21  C19  120.23  3.000
 2OL  C23  C22  C11  180.00  3.000
 2OL  C24  C23  C22  180.00  3.000
 2OL  O30  C24  C29  111.19  3.000
 2OL  O30  C24  C25  106.90  3.000
 2OL  C29  C24  C25  109.56  3.000
 2OL  C25  C24  C23  109.61  3.000
 2OL  O30  C24  C23  110.03  3.000
 2OL  C29  C24  C23  109.51  3.000
 2OL  H17  C25  H16  107.17  3.000
 2OL  H17  C25  C26  110.69  3.000
 2OL  H16  C25  C26  109.56  3.000
 2OL  H17  C25  C24  109.62  3.000
 2OL  H16  C25  C24  107.66  3.000
 2OL  C26  C25  C24  111.98  3.000
 2OL  H19  C26  H18  106.37  3.000
 2OL  H19  C26  C27  109.76  3.000
 2OL  H18  C26  C27  110.29  3.000
 2OL  H19  C26  C25  109.61  3.000
 2OL  H18  C26  C25  109.23  3.000
 2OL  C27  C26  C25  111.45  3.000
 2OL  H21  C27  H20  106.61  3.000
 2OL  H21  C27  C28  110.22  3.000
 2OL  H20  C27  C28  109.11  3.000
 2OL  H21  C27  C26  110.16  3.000
 2OL  H20  C27  C26  109.20  3.000
 2OL  C28  C27  C26  111.40  3.000
 2OL  H23  C28  H22  106.43  3.000
 2OL  H23  C28  C29  109.73  3.000
 2OL  H22  C28  C29  109.33  3.000
 2OL  H23  C28  C27  109.81  3.000
 2OL  H22  C28  C27  110.32  3.000
 2OL  C29  C28  C27  111.12  3.000
 2OL  H25  C29  H24  107.11  3.000
 2OL  H25  C29  C28  109.61  3.000
 2OL  H24  C29  C28  110.63  3.000
 2OL  H25  C29  C24  107.54  3.000
 2OL  H24  C29  C24  109.56  3.000
 2OL  C28  C29  C24  112.22  3.000
 2OL  H26  O30  C24  108.43  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
 2OL  CONST_01  C9   C8   N7   C6    180.00   0.0  0
 2OL  CONST_02  C13  C8   N7   C6      0.00   0.0  0
 2OL  CONST_03  C8   C13  N14  C6      0.00   0.0  0
 2OL  CONST_04  C12  C13  N14  C6    180.00   0.0  0
 2OL  CONST_07  C10  C9   C8   N7    180.00   0.0  0
 2OL  CONST_08  C12  C13  C8   N7    180.00   0.0  0
 2OL  CONST_09  N14  C13  C8   N7      0.00   0.0  0
 2OL  CONST_10  C13  N14  C6   N7      0.00   0.0  0
 2OL  CONST_11  C15  N14  C6   N7    180.00   0.0  0
 2OL  CONST_12  C11  C10  C9   C8      0.00   0.0  0
 2OL  CONST_13  N14  C6   N7   C8      0.00   0.0  0
 2OL  CONST_14  C11  C12  C13  C8      0.00   0.0  0
 2OL  CONST_15  C15  N14  C13  C8    180.00   0.0  0
 2OL  CONST_16  C12  C11  C10  C9      0.00   0.0  0
 2OL  CONST_17  C12  C13  C8   C9      0.00   0.0  0
 2OL  CONST_18  N14  C13  C8   C9    180.00   0.0  0
 2OL  CONST_19  C13  C8   C9   C10     0.00   0.0  0
 2OL  CONST_20  C13  C12  C11  C10     0.00   0.0  0
 2OL  CONST_21  N14  C13  C12  C11   180.00   0.0  0
 2OL  CONST_22  C15  N14  C13  C12     0.00   0.0  0
 2OL  CONST_25  C17  C16  C15  N14   180.00   0.0  0
 2OL  CONST_26  C19  N20  C15  N14   180.00   0.0  0
 2OL  CONST_27  N18  C17  C16  C15     0.00   0.0  0
 2OL  CONST_28  N18  C19  N20  C15     0.00   0.0  0
 2OL  CONST_29  C19  N20  C15  C16     0.00   0.0  0
 2OL  CONST_30  C19  N18  C17  C16     0.00   0.0  0
 2OL  CONST_31  N20  C15  C16  C17     0.00   0.0  0
 2OL  CONST_32  N20  C19  N18  C17     0.00   0.0  0
 2OL  CONST_33  C8   N7   C6   N5    180.00   0.0  0
 2OL  CONST_34  C13  N14  C6   N5    180.00   0.0  0
 2OL  CONST_35  C15  N14  C6   N5      0.00   0.0  0
 2OL  CONST_36  C22  C11  C10  C9    180.00   0.0  0
 2OL  CONST_37  C22  C11  C12  C13   180.00   0.0  0
 2OL  CONST_38  N21  C19  N20  C15   180.00   0.0  0
 2OL  CONST_39  N21  C19  N18  C17   180.00   0.0  0
 2OL  CONST_40  H9   C9   C8   N7      0.00   0.0  0
 2OL  CONST_41  H10  C10  C9   C8    180.00   0.0  0
 2OL  CONST_42  H11  C12  C13  C8    180.00   0.0  0
 2OL  CONST_43  H12  C16  C15  N14     0.00   0.0  0
 2OL  CONST_44  H13  C17  C16  C15   180.00   0.0  0
 2OL  CONST_45  N7   C6   N5   C4      0.00   0.0  0
 2OL  CONST_46  N14  C6   N5   C4    180.00   0.0  0
 2OL  CONST_48  H14  N21  C19  N18     0.00   0.0  0
 2OL  CONST_49  H15  N21  C19  N18   180.00   0.0  0
 2OL  Var_01    C27  C28  C29  C24   -55.68  30.0  1
 2OL  Var_02    C27  C26  C25  C24    55.73  30.0  1
 2OL  Var_03    C28  C27  C26  C25   -54.71  30.0  1
 2OL  Var_04    C29  C28  C27  C26    54.54  30.0  1
 2OL  Var_05    C6   N5   C4   C3    170.47  30.0  3
 2OL  Var_06    C4   C3   O2   C1   -174.56  30.0  3
 2OL  Var_07    N5   C4   C3   O2     58.69  30.0  1
 2OL  Var_08    H1   C1   O2   C3     59.10  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2OL  chir_01  C24  C29  C23  C25  negativ

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
 2OL  plan-1  N14  0.020
 2OL  plan-1  C15  0.020
 2OL  plan-1  C16  0.020
 2OL  plan-1  C17  0.020
 2OL  plan-1  N18  0.020
 2OL  plan-1  C19  0.020
 2OL  plan-1  N20  0.020
 2OL  plan-1  N21  0.020
 2OL  plan-1  H12  0.020
 2OL  plan-1  H13  0.020
 2OL  plan-2  N5   0.020
 2OL  plan-2  C6   0.020
 2OL  plan-2  N7   0.020
 2OL  plan-2  C8   0.020
 2OL  plan-2  C9   0.020
 2OL  plan-2  C10  0.020
 2OL  plan-2  C11  0.020
 2OL  plan-2  C12  0.020
 2OL  plan-2  C13  0.020
 2OL  plan-2  N14  0.020
 2OL  plan-2  C15  0.020
 2OL  plan-2  C22  0.020
 2OL  plan-2  C23  0.020
 2OL  plan-2  H9   0.020
 2OL  plan-2  H10  0.020
 2OL  plan-2  H11  0.020
 2OL  plan-3  C4   0.020
 2OL  plan-3  N5   0.020
 2OL  plan-3  C6   0.020
 2OL  plan-3  H8   0.020
 2OL  plan-4  C19  0.020
 2OL  plan-4  N21  0.020
 2OL  plan-4  H14  0.020
 2OL  plan-4  H15  0.020

