# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 19:44:33 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 1-methyl-~{N}-[2-[[(2~{S})-2-methylpyrrolidin-1-yl]methyl]-3~{H}-benzimidazol-5-yl]indazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CCCN1Cc2[nH]c3cc(NC(=O)c4ccc5n(C)ncc5c4)ccc3n2
#
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
 GQ5  GQ5  1-methyl-~{N}-[2-[[(2~{S})-2-methylpyrrolidin-1-yl]methyl]-3~{H}-benzimidazol-5-yl]indazole-5-carboxamide  ligand  53  29  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GQ5
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
 GQ5  C7   C  CR56  0   0.357  -2.2414  -0.6953   0.4243
 GQ5  C9   C  CR6   0   0.328   0.0877  -1.1121   0.3545
 GQ5  N1   N  NR15  0  -0.683  -3.4762  -0.1129   0.3586
 GQ5  C2   C  CH2   0  -0.483  -7.8829   1.6161  -1.1699
 GQ5  N2   N  NH1   0  -0.758   1.3885  -0.6518   0.0635
 GQ5  C10  C  C     0   0.518   2.5003  -0.8798   0.8044
 GQ5  C4   C  CH2   0  -0.272  -6.3161  -0.1439  -1.5030
 GQ5  N3   N  N     0  -0.235   8.2090   0.5828  -0.1721
 GQ5  N5   N  N     0  -0.483  -3.8463  -2.1959   1.0307
 GQ5  C6   C  CR5   0   0.430  -4.3873  -1.0477   0.7298
 GQ5  O    O  O     0  -0.470   2.5145  -1.6247   1.7711
 GQ5  C11  C  CR6   0  -0.052   3.7359  -0.1770   0.3485
 GQ5  C18  C  CR16  0  -0.302   3.6983   1.0325  -0.3886
 GQ5  C17  C  CR16  0  -0.288   4.8391   1.6802  -0.7956
 GQ5  C16  C  CR56  0   0.462   6.0621   1.0908  -0.4538
 GQ5  N4   N  NR5   0  -0.391   7.3403   1.4606  -0.6896
 GQ5  C15  C  CH3   0  -0.522   7.8122   2.5715  -1.4769
 GQ5  C14  C  CR15  0  -0.110   7.5149  -0.3554   0.4174
 GQ5  C13  C  CR56  0  -0.079   6.1235  -0.1053   0.2843
 GQ5  C12  C  CR16  0  -0.345   4.9504  -0.7361   0.6989
 GQ5  C8   C  CR16  0  -0.391  -0.9622  -0.2212   0.1749
 GQ5  C19  C  CR16  0  -0.297  -0.1462  -2.4359   0.7668
 GQ5  C20  C  CR16  0  -0.341  -1.4275  -2.8880   1.0234
 GQ5  C21  C  CR56  0   0.128  -2.4941  -2.0087   0.8547
 GQ5  C5   C  CH2   0  -0.371  -5.8352  -0.6960   0.8193
 GQ5  N    N  NR5   0  -0.452  -6.1740   0.3243  -0.1370
 GQ5  C1   C  CR15  0  -0.034  -7.3595   1.1193   0.1954
 GQ5  C    C  CH3   0  -0.662  -7.0131   2.2422   1.1582
 GQ5  C3   C  CH2   0  -0.451  -6.8912   1.0731  -2.2044
 GQ5  H1   H  HNR5  0   0.411  -3.7135   0.8236   0.0684
 GQ5  H3   H  HCH2  0   0.239  -7.9605   2.7038  -1.2038
 GQ5  H4   H  HNH1  0   0.415   1.4642  -0.0360  -0.7299
 GQ5  H5   H  HCH2  0   0.236  -5.3559  -0.4650  -1.9139
 GQ5  H6   H  HCH2  0   0.197  -7.0093  -0.9985  -1.5786
 GQ5  H8   H  HCR6  0   0.258   2.7498   1.4998  -0.6212
 GQ5  H9   H  HCR6  0   0.281   4.7803   2.6082  -1.3479
 GQ5  H10  H  HCH3  0   0.258   8.0162   2.2696  -2.5040
 GQ5  H11  H  HCH3  0   0.260   7.0615   3.3573  -1.4842
 GQ5  H12  H  HCH3  0   0.268   8.7218   2.9666  -1.0324
 GQ5  H13  H  HCR5  0   0.274   8.0067  -1.1744   0.9197
 GQ5  H14  H  HCR6  0   0.263   4.9910  -1.6519   1.2741
 GQ5  H15  H  HCR6  0   0.276  -0.7814   0.7995  -0.1385
 GQ5  H16  H  HCR6  0   0.261   0.6835  -3.1182   0.8709
 GQ5  H17  H  HCR6  0   0.256  -1.5952  -3.9096   1.3392
 GQ5  H18  H  HCH2  0   0.237  -6.4340  -1.6135   0.7186
 GQ5  H19  H  HCH2  0   0.275  -6.0234  -0.3167   1.8290
 GQ5  H21  H  HCR5  0   0.212  -8.1274   0.4840   0.6620
 GQ5  H22  H  HCH3  0   0.224  -7.9087   2.7994   1.4366
 GQ5  H23  H  HCH3  0   0.224  -6.5646   1.8653   2.0799
 GQ5  H24  H  HCH3  0   0.220  -6.3077   2.9356   0.6975
 GQ5  H25  H  HCH2  0   0.236  -7.3601   0.8286  -3.1571
 GQ5  H26  H  HCH2  0   0.229  -6.0975   1.7969  -2.3979
 GQ5  H2   H  HCH2  0   0.236  -8.8817   1.2192  -1.3549

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
 GQ5  C3   C4   single    1.518  0.020  1.518
 GQ5  C3   C2   single    1.532  0.020  1.532
 GQ5  C4   N    single    1.451  0.020  1.451
 GQ5  C2   C1   single    1.544  0.020  1.544
 GQ5  C1   N    single    1.466  0.020  1.466
 GQ5  C1   C    single    1.519  0.020  1.519
 GQ5  N5   C21  aromatic  1.376  0.020  1.376
 GQ5  N5   C6   aromatic  1.304  0.020  1.304
 GQ5  N    C5   single    1.439  0.020  1.439
 GQ5  C20  C21  aromatic  1.393  0.020  1.393
 GQ5  C20  C19  aromatic  1.383  0.020  1.383
 GQ5  C5   C6   single    1.493  0.020  1.493
 GQ5  C21  C7   aromatic  1.405  0.020  1.405
 GQ5  C6   N1   aromatic  1.357  0.020  1.357
 GQ5  C19  C9   aromatic  1.406  0.020  1.406
 GQ5  C7   N1   aromatic  1.367  0.020  1.367
 GQ5  C7   C8   aromatic  1.387  0.020  1.387
 GQ5  C9   C8   aromatic  1.389  0.020  1.389
 GQ5  C9   N2   single    1.410  0.020  1.410
 GQ5  N2   C10  single    1.355  0.020  1.355
 GQ5  C10  O    double    1.220  0.020  1.220
 GQ5  C10  C11  single    1.493  0.020  1.493
 GQ5  C12  C11  aromatic  1.382  0.020  1.382
 GQ5  C12  C13  aromatic  1.395  0.020  1.395
 GQ5  C11  C18  aromatic  1.417  0.020  1.417
 GQ5  C14  C13  aromatic  1.420  0.020  1.420
 GQ5  C14  N3   aromatic  1.307  0.020  1.307
 GQ5  C13  C16  aromatic  1.407  0.020  1.407
 GQ5  N3   N4   aromatic  1.339  0.020  1.339
 GQ5  C18  C17  aromatic  1.374  0.020  1.374
 GQ5  C16  C17  aromatic  1.400  0.020  1.400
 GQ5  C16  N4   aromatic  1.351  0.020  1.351
 GQ5  N4   C15  single    1.441  0.020  1.441
 GQ5  N1   H1   single    0.860  0.020  1.020
 GQ5  C2   H2   single    0.970  0.020  1.090
 GQ5  C2   H3   single    0.970  0.020  1.090
 GQ5  N2   H4   single    0.860  0.020  1.020
 GQ5  C4   H5   single    0.970  0.020  1.090
 GQ5  C4   H6   single    0.970  0.020  1.090
 GQ5  C18  H8   single    0.930  0.020  1.080
 GQ5  C17  H9   single    0.930  0.020  1.080
 GQ5  C15  H10  single    0.970  0.020  1.090
 GQ5  C15  H11  single    0.970  0.020  1.090
 GQ5  C15  H12  single    0.970  0.020  1.090
 GQ5  C14  H13  single    0.930  0.020  1.080
 GQ5  C12  H14  single    0.930  0.020  1.080
 GQ5  C8   H15  single    0.930  0.020  1.080
 GQ5  C19  H16  single    0.930  0.020  1.080
 GQ5  C20  H17  single    0.930  0.020  1.080
 GQ5  C5   H18  single    0.970  0.020  1.090
 GQ5  C5   H19  single    0.970  0.020  1.090
 GQ5  C1   H21  single    0.970  0.020  1.090
 GQ5  C    H22  single    0.970  0.020  1.090
 GQ5  C    H23  single    0.970  0.020  1.090
 GQ5  C    H24  single    0.970  0.020  1.090
 GQ5  C3   H25  single    0.970  0.020  1.090
 GQ5  C3   H26  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
 GQ5  C21  C7   C8   122.72  3.000
 GQ5  C8   C7   N1   132.76  3.000
 GQ5  C21  C7   N1   104.51  3.000
 GQ5  C19  C9   C8   121.07  3.000
 GQ5  C8   C9   N2   117.47  3.000
 GQ5  C19  C9   N2   121.42  3.000
 GQ5  H1   N1   C6   124.07  3.000
 GQ5  H1   N1   C7   128.46  3.000
 GQ5  C6   N1   C7   107.45  3.000
 GQ5  H3   C2   H2   107.00  3.000
 GQ5  H3   C2   C3   112.23  3.000
 GQ5  H2   C2   C3   110.44  3.000
 GQ5  H3   C2   C1   111.86  3.000
 GQ5  H2   C2   C1   110.08  3.000
 GQ5  C3   C2   C1   105.28  3.000
 GQ5  H4   N2   C10  118.15  3.000
 GQ5  H4   N2   C9   115.56  3.000
 GQ5  C10  N2   C9   126.08  3.000
 GQ5  C11  C10  O    121.31  3.000
 GQ5  C11  C10  N2   115.65  3.000
 GQ5  O    C10  N2   123.03  3.000
 GQ5  H6   C4   H5   107.39  3.000
 GQ5  H6   C4   C3   110.58  3.000
 GQ5  H5   C4   C3   113.26  3.000
 GQ5  H6   C4   N    112.09  3.000
 GQ5  H5   C4   N    111.27  3.000
 GQ5  C3   C4   N    102.32  3.000
 GQ5  C14  N3   N4   107.47  3.000
 GQ5  C21  N5   C6   104.97  3.000
 GQ5  C5   C6   N5   126.57  3.000
 GQ5  C5   C6   N1   120.36  3.000
 GQ5  N5   C6   N1   113.01  3.000
 GQ5  C12  C11  C18  120.03  3.000
 GQ5  C18  C11  C10  122.60  3.000
 GQ5  C12  C11  C10  117.35  3.000
 GQ5  H8   C18  C17  117.41  3.000
 GQ5  H8   C18  C11  120.23  3.000
 GQ5  C17  C18  C11  122.32  3.000
 GQ5  H9   C17  C16  122.24  3.000
 GQ5  H9   C17  C18  120.71  3.000
 GQ5  C16  C17  C18  117.04  3.000
 GQ5  C13  C16  N4   106.43  3.000
 GQ5  N4   C16  C17  131.95  3.000
 GQ5  C13  C16  C17  121.61  3.000
 GQ5  C15  N4   C16  128.02  3.000
 GQ5  C15  N4   N3   120.27  3.000
 GQ5  C16  N4   N3   111.52  3.000
 GQ5  H12  C15  H11  108.55  3.000
 GQ5  H12  C15  H10  109.24  3.000
 GQ5  H11  C15  H10  108.86  3.000
 GQ5  H12  C15  N4   109.32  3.000
 GQ5  H11  C15  N4   109.56  3.000
 GQ5  H10  C15  N4   111.26  3.000
 GQ5  H13  C14  C13  128.60  3.000
 GQ5  H13  C14  N3   120.82  3.000
 GQ5  C13  C14  N3   110.58  3.000
 GQ5  C12  C13  C14  135.77  3.000
 GQ5  C14  C13  C16  103.99  3.000
 GQ5  C12  C13  C16  120.24  3.000
 GQ5  H14  C12  C13  120.60  3.000
 GQ5  H14  C12  C11  120.66  3.000
 GQ5  C13  C12  C11  118.73  3.000
 GQ5  H15  C8   C9   121.06  3.000
 GQ5  H15  C8   C7   121.89  3.000
 GQ5  C9   C8   C7   117.06  3.000
 GQ5  H16  C19  C20  119.19  3.000
 GQ5  H16  C19  C9   119.71  3.000
 GQ5  C20  C19  C9   121.09  3.000
 GQ5  H17  C20  C21  120.84  3.000
 GQ5  H17  C20  C19  120.42  3.000
 GQ5  C21  C20  C19  118.74  3.000
 GQ5  C20  C21  N5   130.62  3.000
 GQ5  C20  C21  C7   119.31  3.000
 GQ5  N5   C21  C7   110.06  3.000
 GQ5  H19  C5   H18  106.25  3.000
 GQ5  H19  C5   N    109.07  3.000
 GQ5  H18  C5   N    113.73  3.000
 GQ5  H19  C5   C6   107.67  3.000
 GQ5  H18  C5   C6   109.02  3.000
 GQ5  N    C5   C6   110.83  3.000
 GQ5  C1   N    C5   115.11  3.000
 GQ5  C5   N    C4   114.83  3.000
 GQ5  C1   N    C4   108.02  3.000
 GQ5  H21  C1   C    108.49  3.000
 GQ5  H21  C1   N    110.33  3.000
 GQ5  C    C1   N    111.12  3.000
 GQ5  H21  C1   C2   108.91  3.000
 GQ5  C    C1   C2   113.56  3.000
 GQ5  N    C1   C2   104.37  3.000
 GQ5  H24  C    H23  108.07  3.000
 GQ5  H24  C    H22  108.29  3.000
 GQ5  H23  C    H22  107.34  3.000
 GQ5  H24  C    C1   110.46  3.000
 GQ5  H23  C    C1   111.92  3.000
 GQ5  H22  C    C1   110.61  3.000
 GQ5  H26  C3   H25  107.87  3.000
 GQ5  H26  C3   C4   109.76  3.000
 GQ5  H25  C3   C4   112.78  3.000
 GQ5  H26  C3   C2   110.81  3.000
 GQ5  H25  C3   C2   113.04  3.000
 GQ5  C4   C3   C2   102.55  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
 GQ5  CONST_01  C6   N5   C21  C7      0.00   0.0  0
 GQ5  CONST_02  C19  C20  C21  C7      0.00   0.0  0
 GQ5  CONST_03  N5   C6   N1   C7      0.00   0.0  0
 GQ5  CONST_04  C19  C9   C8   C7      0.00   0.0  0
 GQ5  CONST_05  C21  C20  C19  C9      0.00   0.0  0
 GQ5  CONST_06  C21  C7   C8   C9      0.00   0.0  0
 GQ5  CONST_07  N1   C7   C8   C9    180.00   0.0  0
 GQ5  CONST_08  C21  N5   C6   N1      0.00   0.0  0
 GQ5  CONST_09  N5   C21  C7   N1      0.00   0.0  0
 GQ5  CONST_10  C20  C21  C7   N1    180.00   0.0  0
 GQ5  CONST_11  C12  C13  C14  N3    180.00   0.0  0
 GQ5  CONST_12  C16  C13  C14  N3      0.00   0.0  0
 GQ5  CONST_13  C13  C16  N4   N3      0.00   0.0  0
 GQ5  CONST_14  C17  C16  N4   N3    180.00   0.0  0
 GQ5  CONST_15  C19  C20  C21  N5    180.00   0.0  0
 GQ5  CONST_16  C8   C7   C21  N5    180.00   0.0  0
 GQ5  CONST_17  C20  C21  N5   C6    180.00   0.0  0
 GQ5  CONST_18  C21  C7   N1   C6      0.00   0.0  0
 GQ5  CONST_19  C8   C7   N1   C6    180.00   0.0  0
 GQ5  CONST_20  C14  C13  C12  C11   180.00   0.0  0
 GQ5  CONST_21  C16  C13  C12  C11     0.00   0.0  0
 GQ5  CONST_22  C16  C17  C18  C11     0.00   0.0  0
 GQ5  CONST_23  C13  C12  C11  C18     0.00   0.0  0
 GQ5  CONST_24  C13  C16  C17  C18     0.00   0.0  0
 GQ5  CONST_25  N4   C16  C17  C18   180.00   0.0  0
 GQ5  CONST_26  C12  C11  C18  C17     0.00   0.0  0
 GQ5  CONST_27  C12  C13  C16  C17     0.00   0.0  0
 GQ5  CONST_28  C14  C13  C16  C17   180.00   0.0  0
 GQ5  CONST_29  C14  N3   N4   C16     0.00   0.0  0
 GQ5  CONST_30  C13  C14  N3   N4      0.00   0.0  0
 GQ5  CONST_31  C12  C13  C16  N4    180.00   0.0  0
 GQ5  CONST_32  C14  C13  C16  N4      0.00   0.0  0
 GQ5  CONST_33  C20  C21  C7   C8      0.00   0.0  0
 GQ5  CONST_34  C20  C19  C9   C8      0.00   0.0  0
 GQ5  CONST_35  C5   C6   N1   C7    180.00   0.0  0
 GQ5  CONST_36  N2   C9   C8   C7    180.00   0.0  0
 GQ5  CONST_37  C20  C19  C9   N2    180.00   0.0  0
 GQ5  CONST_38  C13  C12  C11  C10   180.00   0.0  0
 GQ5  CONST_39  C17  C18  C11  C10   180.00   0.0  0
 GQ5  CONST_40  C15  N4   C16  C17     0.00   0.0  0
 GQ5  CONST_41  C14  N3   N4   C15   180.00   0.0  0
 GQ5  CONST_42  C13  C16  N4   C15   180.00   0.0  0
 GQ5  CONST_43  C5   C6   N5   C21   180.00   0.0  0
 GQ5  CONST_44  H17  C20  C21  C7    180.00   0.0  0
 GQ5  CONST_45  H15  C8   C7   N1      0.00   0.0  0
 GQ5  CONST_46  H1   N1   C6   N5    180.00   0.0  0
 GQ5  CONST_47  H9   C17  C18  C11   180.00   0.0  0
 GQ5  CONST_48  H14  C12  C11  C18   180.00   0.0  0
 GQ5  CONST_49  H13  C14  C13  C16   180.00   0.0  0
 GQ5  CONST_50  H8   C18  C17  C16   180.00   0.0  0
 GQ5  CONST_51  H16  C19  C9   C8    180.00   0.0  0
 GQ5  CONST_52  C11  C10  N2   C9    180.00   0.0  0
 GQ5  CONST_56  O    C10  N2   C9      0.00   0.0  0
 GQ5  Var_01    N    C4   C3   C2    -39.78  30.0  1
 GQ5  Var_02    C1   C2   C3   C4     25.17  30.0  1
 GQ5  Var_03    C3   C4   N    C1     40.86  30.0  1
 GQ5  Var_04    N    C5   C6   N1     30.92  30.0  1
 GQ5  Var_05    C6   C5   N    C4     77.28  30.0  3
 GQ5  Var_06    C12  C11  C10  N2   -155.49  30.0  2
 GQ5  Var_07    H10  C15  N4   N3     81.31  30.0  2

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
 GQ5  chir_01  C1  C2  N  C  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
 GQ5  plan-1  C7   0.020
 GQ5  plan-1  C9   0.020
 GQ5  plan-1  N1   0.020
 GQ5  plan-1  N2   0.020
 GQ5  plan-1  N5   0.020
 GQ5  plan-1  C6   0.020
 GQ5  plan-1  C8   0.020
 GQ5  plan-1  C19  0.020
 GQ5  plan-1  C20  0.020
 GQ5  plan-1  C21  0.020
 GQ5  plan-1  C5   0.020
 GQ5  plan-1  H1   0.020
 GQ5  plan-1  H15  0.020
 GQ5  plan-1  H16  0.020
 GQ5  plan-1  H17  0.020
 GQ5  plan-2  C10  0.020
 GQ5  plan-2  N3   0.020
 GQ5  plan-2  C11  0.020
 GQ5  plan-2  C18  0.020
 GQ5  plan-2  C17  0.020
 GQ5  plan-2  C16  0.020
 GQ5  plan-2  N4   0.020
 GQ5  plan-2  C15  0.020
 GQ5  plan-2  C14  0.020
 GQ5  plan-2  C13  0.020
 GQ5  plan-2  C12  0.020
 GQ5  plan-2  H8   0.020
 GQ5  plan-2  H9   0.020
 GQ5  plan-2  H13  0.020
 GQ5  plan-2  H14  0.020
 GQ5  plan-3  C9   0.020
 GQ5  plan-3  N2   0.020
 GQ5  plan-3  C10  0.020
 GQ5  plan-3  O    0.020
 GQ5  plan-3  C11  0.020
 GQ5  plan-3  H4   0.020

