# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:20:23 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 7-{[(1R,2S)-2-aminocyclohexyl]amino}-5-(1H-indol-7-ylamino)pyrido[4,3-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCCC[C@H]1Nc2cc3N=CNC(=O)c3c(Nc4cccc5cc[nH]c45)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
 2X6  2X6  7-{[(1R,2S)-2-aminocyclohexyl]amino}-5-(1H-indol-7-ylamino)pyrido[4,3-d]pyrimidin-4(3H)-one  ligand  52  29  .  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_2X6
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
 2X6  C1   C  CH2   0  -0.435  -4.4780   2.7805  -0.3227
 2X6  C2   C  CH2   0  -0.438  -5.0589   2.3514  -1.6638
 2X6  C3   C  CH2   0  -0.429  -4.3876   1.0790  -2.1641
 2X6  C11  C  CR16  0   0.153  -0.1777  -4.8441  -0.2234
 2X6  C12  C  CR6   0   0.519   0.7110  -0.8468   0.2699
 2X6  C13  C  CR6   0   0.332   2.4108   0.9265   0.5917
 2X6  C14  C  CR16  0  -0.330   1.7773   1.8698   1.3846
 2X6  C15  C  CR16  0  -0.273   2.3168   3.1548   1.5527
 2X6  C16  C  CR16  0  -0.361   3.4993   3.5343   0.9526
 2X6  C17  C  CR56  0   0.052   4.1650   2.6019   0.1469
 2X6  C18  C  CR56  0   0.276   3.6056   1.3191  -0.0278
 2X6  C19  C  CR15  0  -0.031   5.4864   1.4086  -1.2185
 2X6  C20  C  CR15  0  -0.412   5.3684   2.6315  -0.6251
 2X6  C10  C  CR6   0   0.593   1.5641  -3.2049   0.0169
 2X6  N2   N  NR16  0  -0.659   1.1276  -4.5053  -0.1486
 2X6  N3   N  N     0  -0.469  -1.1557  -4.0170  -0.1645
 2X6  C8   C  CR66  0   0.383  -0.8417  -2.6833  -0.0137
 2X6  C7   C  CR16  0  -0.537  -1.8763  -1.7641   0.0315
 2X6  C9   C  CR66  0  -0.339   0.4980  -2.2490   0.0939
 2X6  N6   N  N     0  -0.519  -0.2796   0.0169   0.2931
 2X6  C6   C  CR6   0   0.524  -1.5483  -0.4083   0.1664
 2X6  C5   C  CH1   0  -0.091  -3.9058   0.3717   0.2290
 2X6  C4   C  CH2   0  -0.448  -4.4883  -0.0337  -1.1291
 2X6  C    C  CH1   0  -0.100  -4.5690   1.6676   0.7188
 2X6  N    N  NH2   0  -0.799  -3.9438   2.1071   1.9565
 2X6  N5   N  NR15  0  -0.680   4.4320   0.6178  -0.8594
 2X6  H1   H  HCH2  0   0.216  -3.4335   3.0842  -0.4523
 2X6  H2   H  HCH2  0   0.235  -5.0061   3.6616   0.0536
 2X6  H3   H  HCH2  0   0.212  -6.1347   2.1758  -1.5571
 2X6  H4   H  HCH2  0   0.232  -4.9478   3.1565  -2.3934
 2X6  H5   H  HCH2  0   0.232  -4.8429   0.7512  -3.1013
 2X6  H6   H  HCH2  0   0.216  -3.3355   1.2827  -2.3854
 2X6  H7   H  HCR6  0   0.301  -0.3726  -5.9030  -0.3426
 2X6  H8   H  HCR6  0   0.259   0.8537   1.6168   1.8818
 2X6  H9   H  HCR6  0   0.246   1.7855   3.8567   2.1824
 2X6  H10  H  HCR6  0   0.244   3.9011   4.5289   1.0990
 2X6  H11  H  HCR5  0   0.281   6.2486   1.0313  -1.8809
 2X6  H12  H  HCR5  0   0.249   6.0549   3.4567  -0.7257
 2X6  H13  H  HNR6  0   0.433   1.8261  -5.2337  -0.2115
 2X6  H14  H  HCR6  0   0.268  -2.8958  -2.1125  -0.0380
 2X6  H15  H  HNH1  0   0.380  -2.1342   1.4608   0.5182
 2X6  H16  H  HCH1  0   0.249  -4.1351  -0.4175   0.9586
 2X6  H17  H  HCH2  0   0.225  -5.5391  -0.2996  -0.9768
 2X6  H18  H  HCH2  0   0.243  -3.9980  -0.9371  -1.4953
 2X6  H19  H  HCH1  0   0.221  -5.6342   1.4214   0.8470
 2X6  H20  H  HNH2  0   0.350  -4.4054   2.9473   2.2832
 2X6  H21  H  HNH2  0   0.346  -4.0865   1.4131   2.6812
 2X6  H23  H  HNH1  0   0.416   2.6887  -1.1165   0.3638
 2X6  H24  H  HNR5  0   0.405   4.2742  -0.3108  -1.2130
 2X6  N1   N  NH1   0  -0.648  -2.4713   0.5697   0.1839
 2X6  N4   N  NH1   0  -0.800   1.9804  -0.3916   0.4094
 2X6  O    O  O     0  -0.495   2.7705  -2.9710   0.0824

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
 2X6  C3   C4   single    1.523  0.020  1.523
 2X6  C3   C2   single    1.523  0.020  1.523
 2X6  C4   C5   single    1.532  0.020  1.532
 2X6  C2   C1   single    1.523  0.020  1.523
 2X6  C5   N1   single    1.449  0.020  1.449
 2X6  C5   C    single    1.536  0.020  1.536
 2X6  N1   C6   single    1.345  0.020  1.345
 2X6  C1   C    single    1.527  0.020  1.527
 2X6  C    N    single    1.455  0.020  1.455
 2X6  C6   N6   aromatic  1.344  0.020  1.344
 2X6  C6   C7   aromatic  1.401  0.020  1.401
 2X6  C15  C14  aromatic  1.404  0.020  1.404
 2X6  C15  C16  aromatic  1.379  0.020  1.379
 2X6  N6   C12  aromatic  1.315  0.020  1.315
 2X6  C7   C8   aromatic  1.385  0.020  1.385
 2X6  C14  C13  aromatic  1.386  0.020  1.386
 2X6  C16  C17  aromatic  1.401  0.020  1.401
 2X6  C12  N4   single    1.356  0.020  1.356
 2X6  C12  C9   aromatic  1.429  0.020  1.429
 2X6  C8   C9   aromatic  1.412  0.020  1.412
 2X6  C8   N3   single    1.378  0.020  1.378
 2X6  C13  N4   single    1.398  0.020  1.398
 2X6  C13  C18  aromatic  1.402  0.020  1.402
 2X6  C17  C18  aromatic  1.410  0.020  1.410
 2X6  C17  C20  aromatic  1.430  0.020  1.430
 2X6  C9   C10  single    1.434  0.020  1.434
 2X6  N3   C11  double    1.282  0.020  1.282
 2X6  C18  N5   aromatic  1.366  0.020  1.366
 2X6  C20  C19  aromatic  1.364  0.020  1.364
 2X6  C11  N2   single    1.351  0.020  1.351
 2X6  C10  N2   single    1.382  0.020  1.382
 2X6  C10  O    double    1.231  0.020  1.231
 2X6  N5   C19  aromatic  1.366  0.020  1.366
 2X6  C1   H1   single    0.970  0.020  1.090
 2X6  C1   H2   single    0.970  0.020  1.090
 2X6  C2   H3   single    0.970  0.020  1.090
 2X6  C2   H4   single    0.970  0.020  1.090
 2X6  C3   H5   single    0.970  0.020  1.090
 2X6  C3   H6   single    0.970  0.020  1.090
 2X6  C11  H7   single    0.930  0.020  1.080
 2X6  C14  H8   single    0.930  0.020  1.080
 2X6  C15  H9   single    0.930  0.020  1.080
 2X6  C16  H10  single    0.930  0.020  1.080
 2X6  C19  H11  single    0.930  0.020  1.080
 2X6  C20  H12  single    0.930  0.020  1.080
 2X6  N2   H13  single    0.860  0.020  1.020
 2X6  C7   H14  single    0.930  0.020  1.080
 2X6  N1   H15  single    0.890  0.020  1.040
 2X6  C5   H16  single    0.970  0.020  1.090
 2X6  C4   H17  single    0.970  0.020  1.090
 2X6  C4   H18  single    0.970  0.020  1.090
 2X6  C    H19  single    0.970  0.020  1.090
 2X6  N    H20  single    0.890  0.020  1.040
 2X6  N    H21  single    0.890  0.020  1.040
 2X6  N4   H23  single    0.860  0.020  1.020
 2X6  N5   H24  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
 2X6  H2   C1   H1   106.12  3.000
 2X6  H2   C1   C    108.88  3.000
 2X6  H1   C1   C    109.85  3.000
 2X6  H2   C1   C2   110.22  3.000
 2X6  H1   C1   C2   109.73  3.000
 2X6  C    C1   C2   111.87  3.000
 2X6  H4   C2   H3   106.45  3.000
 2X6  H4   C2   C3   110.58  3.000
 2X6  H3   C2   C3   109.33  3.000
 2X6  H4   C2   C1   109.98  3.000
 2X6  H3   C2   C1   109.51  3.000
 2X6  C3   C2   C1   110.88  3.000
 2X6  H6   C3   H5   106.45  3.000
 2X6  H6   C3   C4   109.69  3.000
 2X6  H5   C3   C4   109.65  3.000
 2X6  H6   C3   C2   109.55  3.000
 2X6  H5   C3   C2   110.41  3.000
 2X6  C4   C3   C2   110.97  3.000
 2X6  H7   C11  N3   119.89  3.000
 2X6  H7   C11  N2   115.16  3.000
 2X6  N3   C11  N2   124.95  3.000
 2X6  N4   C12  N6   118.89  3.000
 2X6  N4   C12  C9   118.79  3.000
 2X6  N6   C12  C9   122.32  3.000
 2X6  N4   C13  C18  117.94  3.000
 2X6  C18  C13  C14  116.86  3.000
 2X6  N4   C13  C14  125.14  3.000
 2X6  H8   C14  C15  119.24  3.000
 2X6  H8   C14  C13  119.69  3.000
 2X6  C15  C14  C13  121.07  3.000
 2X6  H9   C15  C16  119.71  3.000
 2X6  H9   C15  C14  118.33  3.000
 2X6  C16  C15  C14  121.96  3.000
 2X6  H10  C16  C17  120.86  3.000
 2X6  H10  C16  C15  120.80  3.000
 2X6  C17  C16  C15  118.33  3.000
 2X6  C20  C17  C18  106.60  3.000
 2X6  C20  C17  C16  134.17  3.000
 2X6  C18  C17  C16  119.23  3.000
 2X6  N5   C18  C17  107.60  3.000
 2X6  N5   C18  C13  129.85  3.000
 2X6  C17  C18  C13  122.55  3.000
 2X6  H11  C19  N5   120.31  3.000
 2X6  H11  C19  C20  129.95  3.000
 2X6  N5   C19  C20  109.74  3.000
 2X6  H12  C20  C19  126.18  3.000
 2X6  H12  C20  C17  127.02  3.000
 2X6  C19  C20  C17  106.80  3.000
 2X6  C9   C10  N2   113.52  3.000
 2X6  N2   C10  O    119.67  3.000
 2X6  C9   C10  O    126.82  3.000
 2X6  H13  N2   C10  117.86  3.000
 2X6  H13  N2   C11  118.91  3.000
 2X6  C10  N2   C11  123.23  3.000
 2X6  C8   N3   C11  117.09  3.000
 2X6  C9   C8   C7   120.14  3.000
 2X6  C9   C8   N3   121.46  3.000
 2X6  C7   C8   N3   118.40  3.000
 2X6  H14  C7   C6   122.64  3.000
 2X6  H14  C7   C8   119.29  3.000
 2X6  C6   C7   C8   118.07  3.000
 2X6  C8   C9   C10  119.74  3.000
 2X6  C10  C9   C12  123.36  3.000
 2X6  C8   C9   C12  116.90  3.000
 2X6  C6   N6   C12  120.12  3.000
 2X6  N1   C6   N6   114.62  3.000
 2X6  N6   C6   C7   122.41  3.000
 2X6  N1   C6   C7   122.97  3.000
 2X6  H16  C5   C    107.71  3.000
 2X6  H16  C5   C4   108.61  3.000
 2X6  C    C5   C4   109.98  3.000
 2X6  H16  C5   N1   108.99  3.000
 2X6  C    C5   N1   108.79  3.000
 2X6  C4   C5   N1   112.64  3.000
 2X6  H18  C4   H17  106.08  3.000
 2X6  H18  C4   C5   110.22  3.000
 2X6  H17  C4   C5   107.82  3.000
 2X6  H18  C4   C3   110.31  3.000
 2X6  H17  C4   C3   109.60  3.000
 2X6  C5   C4   C3   112.58  3.000
 2X6  H19  C    N    112.60  3.000
 2X6  H19  C    C5   105.44  3.000
 2X6  N    C    C5   109.92  3.000
 2X6  H19  C    C1   107.46  3.000
 2X6  N    C    C1   109.54  3.000
 2X6  C5   C    C1   111.83  3.000
 2X6  H21  N    H20  105.86  3.000
 2X6  H21  N    C    109.94  3.000
 2X6  H20  N    C    109.22  3.000
 2X6  H24  N5   C19  124.26  3.000
 2X6  H24  N5   C18  126.36  3.000
 2X6  C19  N5   C18  109.25  3.000
 2X6  H15  N1   C5   116.16  3.000
 2X6  H15  N1   C6   114.64  3.000
 2X6  C5   N1   C6   125.49  3.000
 2X6  H23  N4   C13  117.67  3.000
 2X6  H23  N4   C12  114.15  3.000
 2X6  C13  N4   C12  128.17  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
 2X6  CONST_01  C7   C6   N6   C12    0.00   0.0  0
 2X6  CONST_02  C7   C8   C9   C12    0.00   0.0  0
 2X6  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 2X6  CONST_04  C16  C17  C18  C13    0.00   0.0  0
 2X6  CONST_05  C20  C17  C18  C13  180.00   0.0  0
 2X6  CONST_06  C19  N5   C18  C13  180.00   0.0  0
 2X6  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 2X6  CONST_08  C17  C18  C13  C14    0.00   0.0  0
 2X6  CONST_09  N5   C18  C13  C14  180.00   0.0  0
 2X6  CONST_10  C18  C13  C14  C15    0.00   0.0  0
 2X6  CONST_11  C18  C17  C16  C15    0.00   0.0  0
 2X6  CONST_12  C20  C17  C16  C15  180.00   0.0  0
 2X6  CONST_13  N5   C18  C17  C16  180.00   0.0  0
 2X6  CONST_14  C19  C20  C17  C16  180.00   0.0  0
 2X6  CONST_15  C19  N5   C18  C17    0.00   0.0  0
 2X6  CONST_16  N5   C19  C20  C17    0.00   0.0  0
 2X6  CONST_17  C19  C20  C17  C18    0.00   0.0  0
 2X6  CONST_18  C20  C19  N5   C18    0.00   0.0  0
 2X6  CONST_19  N5   C18  C17  C20    0.00   0.0  0
 2X6  CONST_20  N6   C6   C7   C8     0.00   0.0  0
 2X6  CONST_21  N6   C12  C9   C8     0.00   0.0  0
 2X6  CONST_22  C6   N6   C12  C9     0.00   0.0  0
 2X6  CONST_23  C6   C7   C8   C9     0.00   0.0  0
 2X6  CONST_24  C9   C10  N2   C11    0.00   0.0  0
 2X6  CONST_25  N3   C11  N2   C10    0.00   0.0  0
 2X6  CONST_26  C8   N3   C11  N2     0.00   0.0  0
 2X6  CONST_27  N1   C6   N6   C12  180.00   0.0  0
 2X6  CONST_28  N4   C13  C14  C15  180.00   0.0  0
 2X6  CONST_29  N4   C13  C18  C17  180.00   0.0  0
 2X6  CONST_30  N4   C12  C9   C10    0.00   0.0  0
 2X6  CONST_31  N1   C6   C7   C8   180.00   0.0  0
 2X6  CONST_32  N4   C12  C9   C8   180.00   0.0  0
 2X6  CONST_33  N4   C12  N6   C6   180.00   0.0  0
 2X6  CONST_34  N5   C18  C13  N4     0.00   0.0  0
 2X6  CONST_35  C5   N1   C6   C7     0.00   0.0  0
 2X6  CONST_36  C5   N1   C6   N6   180.00   0.0  0
 2X6  CONST_37  O    C10  N2   C11  180.00   0.0  0
 2X6  CONST_38  H9   C15  C14  C13  180.00   0.0  0
 2X6  CONST_39  H24  N5   C18  C13    0.00   0.0  0
 2X6  CONST_40  H10  C16  C15  C14  180.00   0.0  0
 2X6  CONST_41  H8   C14  C15  C16  180.00   0.0  0
 2X6  CONST_42  H12  C20  C17  C16    0.00   0.0  0
 2X6  CONST_43  H11  C19  C20  C17  180.00   0.0  0
 2X6  CONST_44  H14  C7   C8   N3     0.00   0.0  0
 2X6  CONST_45  H7   C11  N2   C10  180.00   0.0  0
 2X6  CONST_46  H13  N2   C11  N3   180.00   0.0  0
 2X6  CONST_47  H15  N1   C6   C7   180.00   0.0  0
 2X6  Var_01    C4   C3   C2   C1    55.44  30.0  1
 2X6  Var_02    C5   C4   C3   C2   -56.01  30.0  1
 2X6  Var_03    C    C1   C2   C3   -55.48  30.0  1
 2X6  Var_04    C14  C13  N4   C12   39.47  30.0  3
 2X6  Var_05    N6   C12  N4   C13    0.46  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
 2X6  chir_01  C5  C4  N1  C   negativ
 2X6  chir_02  C   N   C1  C5  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
 2X6  plan-1  C13  0.020
 2X6  plan-1  C14  0.020
 2X6  plan-1  C15  0.020
 2X6  plan-1  C16  0.020
 2X6  plan-1  C17  0.020
 2X6  plan-1  C18  0.020
 2X6  plan-1  C19  0.020
 2X6  plan-1  C20  0.020
 2X6  plan-1  N5   0.020
 2X6  plan-1  H8   0.020
 2X6  plan-1  H9   0.020
 2X6  plan-1  H10  0.020
 2X6  plan-1  H11  0.020
 2X6  plan-1  H12  0.020
 2X6  plan-1  H24  0.020
 2X6  plan-1  N4   0.020
 2X6  plan-2  C11  0.020
 2X6  plan-2  C12  0.020
 2X6  plan-2  C10  0.020
 2X6  plan-2  N2   0.020
 2X6  plan-2  N3   0.020
 2X6  plan-2  C8   0.020
 2X6  plan-2  C7   0.020
 2X6  plan-2  C9   0.020
 2X6  plan-2  N6   0.020
 2X6  plan-2  C6   0.020
 2X6  plan-2  H7   0.020
 2X6  plan-2  H13  0.020
 2X6  plan-2  H14  0.020
 2X6  plan-2  N1   0.020
 2X6  plan-2  N4   0.020
 2X6  plan-2  O    0.020
 2X6  plan-3  C6   0.020
 2X6  plan-3  C5   0.020
 2X6  plan-3  H15  0.020
 2X6  plan-3  N1   0.020

