# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 12:40:58 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: N~1~-[2-(1H-indazol-5-yl)pyrido[3,4-d]pyrimidin-4-yl]-2-methylpropane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(N)CNc1nc(nc2cnccc12)c3ccc4[nH]ncc4c3
#
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
 3J7  3J7  N~1~-[2-(1H-indazol-5-yl)pyrido[3,4-d]pyrimidin-4-yl]-2-methylpropane-1,2-diamine  ligand  44  25  .  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_3J7
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
 3J7  C1    C  CR16  0  -0.084   3.0029  -3.8185  -0.1690
 3J7  C2    C  CR16  0  -0.367   3.0308  -2.4460  -0.1909
 3J7  C3    C  CR16  0  -0.111   0.7247  -3.8882  -0.0729
 3J7  C11   C  CR16  0  -0.294  -2.0067   1.5002   0.0272
 3J7  C12   C  CR56  0   0.419  -4.3674   1.4001   0.1163
 3J7  C13   C  CR56  0  -0.055  -4.3223  -0.0055   0.1035
 3J7  C14   C  CR15  0  -0.126  -5.6892  -0.3964   0.1531
 3J7  C15   C  CH2   0  -0.229   2.6489   1.9289  -0.2996
 3J7  C16   C  CT    0   0.003   4.0187   2.5290   0.0408
 3J7  C17   C  CH3   0  -0.646   3.9618   4.0361  -0.2137
 3J7  C18   C  CH3   0  -0.638   4.3626   2.2666   1.5058
 3J7  N1    N  N     0  -0.387   1.8635  -4.5304  -0.1120
 3J7  C4    C  CR66  0   0.164   0.6224  -2.4782  -0.0870
 3J7  C5    C  CR66  0   0.046   1.8170  -1.7479  -0.1524
 3J7  C6    C  CR6   0   0.562   1.6602  -0.3114  -0.1689
 3J7  N2    N  N     0  -0.508   0.4555   0.2214  -0.1133
 3J7  C7    C  CR6   0   0.392  -0.6162  -0.5870  -0.0444
 3J7  N3    N  N     0  -0.496  -0.5976  -1.8965  -0.0337
 3J7  C8    C  CR6   0  -0.040  -1.9334   0.0845   0.0143
 3J7  C9    C  CR16  0  -0.365  -3.0943  -0.6673   0.0529
 3J7  C10   C  CR16  0  -0.273  -3.2020   2.1744   0.0783
 3J7  N4    N  N     0  -0.225  -6.4701   0.6520   0.1911
 3J7  N5    N  NR15  0  -0.546  -5.6760   1.7276   0.1683
 3J7  N6    N  NH1   0  -0.664   2.7190   0.4889  -0.2304
 3J7  N7    N  NH2   0  -0.792   5.0096   1.8433  -0.7892
 3J7  H1    H  HCR6  0   0.271   3.9245  -4.3866  -0.1976
 3J7  H2    H  HCR6  0   0.269   3.9863  -1.9398  -0.2372
 3J7  H3    H  HCR6  0   0.269  -0.1879  -4.4745  -0.0253
 3J7  H4    H  HCR6  0   0.265  -1.0858   2.0653  -0.0048
 3J7  H5    H  HCR5  0   0.270  -6.1032  -1.3934   0.1616
 3J7  H6    H  HCH2  0   0.251   1.8940   2.2980   0.3949
 3J7  H7    H  HCH2  0   0.240   2.3403   2.2462  -1.3036
 3J7  H8    H  HCH3  0   0.224   3.1936   4.5168   0.3954
 3J7  H9    H  HCH3  0   0.233   4.9190   4.5007   0.0304
 3J7  H10   H  HCH3  0   0.228   3.7409   4.2502  -1.2613
 3J7  H11   H  HCH3  0   0.231   4.3827   1.2004   1.7339
 3J7  H12   H  HCH3  0   0.231   5.3451   2.6770   1.7466
 3J7  H13   H  HCH3  0   0.228   3.6366   2.7410   2.1669
 3J7  H14   H  HCR6  0   0.255  -3.0457  -1.7478   0.0429
 3J7  H15   H  HCR6  0   0.271  -3.2355   3.2555   0.0881
 3J7  H17   H  HNH1  0   0.403   3.6391   0.1149  -0.4226
 3J7  H18   H  HNH2  0   0.348   4.9035   2.1221  -1.7586
 3J7  H19   H  HNH2  0   0.353   5.9435   2.1275  -0.5185
 3J7  H191  H  HNR5  0   0.418  -6.0829   2.6484   0.1957

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
 3J7  C1   N1    aromatic  1.345  0.020  1.345
 3J7  C1   C2    aromatic  1.373  0.020  1.373
 3J7  C1   H1    single    0.930  0.020  1.080
 3J7  C2   C5    aromatic  1.401  0.020  1.401
 3J7  C2   H2    single    0.930  0.020  1.080
 3J7  C3   C4    aromatic  1.414  0.020  1.414
 3J7  C3   H3    single    0.930  0.020  1.080
 3J7  C11  C10   aromatic  1.373  0.020  1.373
 3J7  C11  H4    single    0.930  0.020  1.080
 3J7  C12  N5    aromatic  1.350  0.020  1.350
 3J7  C13  C12   aromatic  1.406  0.020  1.406
 3J7  C13  C14   aromatic  1.423  0.020  1.423
 3J7  C14  N4    aromatic  1.308  0.020  1.308
 3J7  C14  H5    single    0.930  0.020  1.080
 3J7  C15  C16   single    1.534  0.020  1.534
 3J7  C15  H6    single    0.970  0.020  1.090
 3J7  C15  H7    single    0.970  0.020  1.090
 3J7  C16  C17   single    1.530  0.020  1.530
 3J7  C16  C18   single    1.528  0.020  1.528
 3J7  C17  H8    single    0.970  0.020  1.090
 3J7  C17  H9    single    0.970  0.020  1.090
 3J7  C17  H10   single    0.970  0.020  1.090
 3J7  C18  H11   single    0.970  0.020  1.090
 3J7  C18  H12   single    0.970  0.020  1.090
 3J7  C18  H13   single    0.970  0.020  1.090
 3J7  N1   C3    aromatic  1.308  0.020  1.308
 3J7  C4   N3    aromatic  1.353  0.020  1.353
 3J7  C5   C4    aromatic  1.402  0.020  1.402
 3J7  C5   C6    aromatic  1.445  0.020  1.445
 3J7  C6   N2    aromatic  1.318  0.020  1.318
 3J7  N2   C7    aromatic  1.344  0.020  1.344
 3J7  C7   C8    single    1.480  0.020  1.480
 3J7  N3   C7    aromatic  1.310  0.020  1.310
 3J7  C8   C11   aromatic  1.418  0.020  1.418
 3J7  C8   C9    aromatic  1.384  0.020  1.384
 3J7  C9   C13   aromatic  1.396  0.020  1.396
 3J7  C9   H14   single    0.930  0.020  1.080
 3J7  C10  C12   aromatic  1.400  0.020  1.400
 3J7  C10  H15   single    0.930  0.020  1.080
 3J7  N5   N4    aromatic  1.337  0.020  1.337
 3J7  N6   C6    single    1.329  0.020  1.329
 3J7  N6   C15   single    1.443  0.020  1.443
 3J7  N6   H17   single    0.860  0.020  1.020
 3J7  N7   C16   single    1.463  0.020  1.463
 3J7  N7   H18   single    0.890  0.020  1.040
 3J7  N7   H19   single    0.890  0.020  1.040
 3J7  N5   H191  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
 3J7  H1    C1   N1   116.38  3.000
 3J7  H1    C1   C2   120.44  3.000
 3J7  N1    C1   C2   123.17  3.000
 3J7  H2    C2   C5   122.22  3.000
 3J7  H2    C2   C1   119.08  3.000
 3J7  C5    C2   C1   118.69  3.000
 3J7  H3    C3   C4   118.56  3.000
 3J7  H3    C3   N1   117.90  3.000
 3J7  C4    C3   N1   123.53  3.000
 3J7  H4    C11  C10  119.08  3.000
 3J7  H4    C11  C8   118.54  3.000
 3J7  C10   C11  C8   122.38  3.000
 3J7  N5    C12  C10  132.37  3.000
 3J7  C10   C12  C13  121.73  3.000
 3J7  N5    C12  C13  105.90  3.000
 3J7  C9    C13  C14  135.75  3.000
 3J7  C9    C13  C12  120.16  3.000
 3J7  C14   C13  C12  104.09  3.000
 3J7  H5    C14  N4   120.74  3.000
 3J7  H5    C14  C13  128.50  3.000
 3J7  N4    C14  C13  110.76  3.000
 3J7  H7    C15  H6   106.87  3.000
 3J7  H7    C15  N6   110.25  3.000
 3J7  H6    C15  N6   109.93  3.000
 3J7  N6    C15  C16  109.65  3.000
 3J7  H7    C15  C16  109.95  3.000
 3J7  H6    C15  C16  110.16  3.000
 3J7  N7    C16  C18  108.13  3.000
 3J7  N7    C16  C17  113.11  3.000
 3J7  C18   C16  C17  109.71  3.000
 3J7  N7    C16  C15  107.19  3.000
 3J7  C18   C16  C15  110.29  3.000
 3J7  C17   C16  C15  108.38  3.000
 3J7  H10   C17  H9   107.97  3.000
 3J7  H10   C17  H8   107.85  3.000
 3J7  H9    C17  H8   107.75  3.000
 3J7  H10   C17  C16  111.12  3.000
 3J7  H9    C17  C16  110.46  3.000
 3J7  H8    C17  C16  111.54  3.000
 3J7  H13   C18  H12  107.57  3.000
 3J7  H13   C18  H11  108.11  3.000
 3J7  H12   C18  H11  107.75  3.000
 3J7  H13   C18  C16  110.90  3.000
 3J7  H12   C18  C16  110.46  3.000
 3J7  H11   C18  C16  111.88  3.000
 3J7  C3    N1   C1   118.62  3.000
 3J7  N3    C4   C5   123.13  3.000
 3J7  C5    C4   C3   117.28  3.000
 3J7  N3    C4   C3   119.59  3.000
 3J7  C6    C5   C4   115.21  3.000
 3J7  C6    C5   C2   126.09  3.000
 3J7  C4    C5   C2   118.70  3.000
 3J7  N6    C6   N2   119.13  3.000
 3J7  N6    C6   C5   120.85  3.000
 3J7  N2    C6   C5   120.02  3.000
 3J7  C7    N2   C6   119.19  3.000
 3J7  C8    C7   N3   117.78  3.000
 3J7  N3    C7   N2   126.18  3.000
 3J7  C8    C7   N2   116.03  3.000
 3J7  C7    N3   C4   116.26  3.000
 3J7  C9    C8   C7   120.10  3.000
 3J7  C9    C8   C11  119.93  3.000
 3J7  C7    C8   C11  119.97  3.000
 3J7  H14   C9   C8   120.32  3.000
 3J7  H14   C9   C13  120.89  3.000
 3J7  C8    C9   C13  118.79  3.000
 3J7  H15   C10  C12  121.80  3.000
 3J7  H15   C10  C11  121.19  3.000
 3J7  C12   C10  C11  117.01  3.000
 3J7  N5    N4   C14  106.84  3.000
 3J7  H191  N5   N4   119.67  3.000
 3J7  H191  N5   C12  127.92  3.000
 3J7  N4    N5   C12  112.41  3.000
 3J7  H17   N6   C6   120.72  3.000
 3J7  H17   N6   C15  113.83  3.000
 3J7  C6    N6   C15  124.36  3.000
 3J7  H19   N7   H18  105.95  3.000
 3J7  H19   N7   C16  109.95  3.000
 3J7  H18   N7   C16  110.03  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
 3J7  CONST_01  C4    C3   N1   C1     0.00   0.0  0
 3J7  CONST_02  C4    C5   C2   C1     0.00   0.0  0
 3J7  CONST_03  C6    C5   C2   C1   180.00   0.0  0
 3J7  CONST_04  C3    N1   C1   C2     0.00   0.0  0
 3J7  CONST_05  C3    C4   C5   C2     0.00   0.0  0
 3J7  CONST_06  N3    C4   C5   C2   180.00   0.0  0
 3J7  CONST_07  N2    C6   C5   C2   180.00   0.0  0
 3J7  CONST_08  C7    N3   C4   C3   180.00   0.0  0
 3J7  CONST_09  C6    C5   C4   C3   180.00   0.0  0
 3J7  CONST_10  N5    C12  C10  C11  180.00   0.0  0
 3J7  CONST_11  C13   C12  C10  C11    0.00   0.0  0
 3J7  CONST_12  N2    C7   C8   C11    0.00   0.0  0
 3J7  CONST_13  N3    C7   C8   C11  180.00   0.0  0
 3J7  CONST_14  C13   C9   C8   C11    0.00   0.0  0
 3J7  CONST_15  C14   N4   N5   C12    0.00   0.0  0
 3J7  CONST_16  N4    C14  C13  C12    0.00   0.0  0
 3J7  CONST_17  C8    C9   C13  C12    0.00   0.0  0
 3J7  CONST_18  C8    C11  C10  C12    0.00   0.0  0
 3J7  CONST_19  N4    N5   C12  C13    0.00   0.0  0
 3J7  CONST_20  N5    N4   C14  C13    0.00   0.0  0
 3J7  CONST_21  C7    C8   C9   C13  180.00   0.0  0
 3J7  CONST_22  N5    C12  C13  C14    0.00   0.0  0
 3J7  CONST_23  C10   C12  C13  C14  180.00   0.0  0
 3J7  CONST_24  C8    C9   C13  C14  180.00   0.0  0
 3J7  CONST_25  C5    C2   C1   N1     0.00   0.0  0
 3J7  CONST_26  N3    C4   C3   N1   180.00   0.0  0
 3J7  CONST_27  C5    C4   C3   N1     0.00   0.0  0
 3J7  CONST_28  N2    C7   N3   C4     0.00   0.0  0
 3J7  CONST_29  C8    C7   N3   C4   180.00   0.0  0
 3J7  CONST_30  N2    C6   C5   C4     0.00   0.0  0
 3J7  CONST_31  C7    N3   C4   C5     0.00   0.0  0
 3J7  CONST_32  C7    N2   C6   C5     0.00   0.0  0
 3J7  CONST_33  N3    C4   C5   C6     0.00   0.0  0
 3J7  CONST_34  C8    C7   N2   C6   180.00   0.0  0
 3J7  CONST_35  N3    C7   N2   C6     0.00   0.0  0
 3J7  CONST_36  C9    C8   C7   N2   180.00   0.0  0
 3J7  CONST_37  C10   C11  C8   C7   180.00   0.0  0
 3J7  CONST_38  C9    C8   C7   N3     0.00   0.0  0
 3J7  CONST_39  C10   C11  C8   C9     0.00   0.0  0
 3J7  CONST_40  N5    C12  C13  C9   180.00   0.0  0
 3J7  CONST_41  C10   C12  C13  C9     0.00   0.0  0
 3J7  CONST_42  N4    C14  C13  C9   180.00   0.0  0
 3J7  CONST_43  N4    N5   C12  C10  180.00   0.0  0
 3J7  CONST_44  N6    C6   C5   C2     0.00   0.0  0
 3J7  CONST_45  N6    C6   C5   C4   180.00   0.0  0
 3J7  CONST_46  N6    C6   N2   C7   180.00   0.0  0
 3J7  CONST_47  H3    C3   N1   C1   180.00   0.0  0
 3J7  CONST_48  H1    C1   N1   C3   180.00   0.0  0
 3J7  CONST_49  H14   C9   C8   C11  180.00   0.0  0
 3J7  CONST_50  H5    C14  C13  C12  180.00   0.0  0
 3J7  CONST_51  H4    C11  C10  C12  180.00   0.0  0
 3J7  CONST_52  H191  N5   C12  C13  180.00   0.0  0
 3J7  CONST_53  H15   C10  C12  C13  180.00   0.0  0
 3J7  CONST_54  H2    C2   C1   N1   180.00   0.0  0
 3J7  CONST_55  C5    C6   N6   C15  180.00   0.0  0
 3J7  CONST_56  N2    C6   N6   C15    0.00   0.0  0
 3J7  CONST_57  H17   N6   C6   C5     0.00   0.0  0
 3J7  Var_01    C6    N6   C15  C16  164.00  30.0  1
 3J7  Var_02    N6    C15  C16  C17  172.87  30.0  2
 3J7  Var_03    H8    C17  C16  C15   59.49  30.0  3
 3J7  Var_04    H11   C18  C16  C15   58.96  30.0  3
 3J7  Var_05    H18   N7   C16  C15   70.52  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
 3J7  plan-1  C11   0.020
 3J7  plan-1  C12   0.020
 3J7  plan-1  C13   0.020
 3J7  plan-1  C14   0.020
 3J7  plan-1  C7    0.020
 3J7  plan-1  C8    0.020
 3J7  plan-1  C9    0.020
 3J7  plan-1  C10   0.020
 3J7  plan-1  N4    0.020
 3J7  plan-1  N5    0.020
 3J7  plan-1  H4    0.020
 3J7  plan-1  H5    0.020
 3J7  plan-1  H14   0.020
 3J7  plan-1  H15   0.020
 3J7  plan-1  H191  0.020
 3J7  plan-2  C1    0.020
 3J7  plan-2  C2    0.020
 3J7  plan-2  C3    0.020
 3J7  plan-2  N1    0.020
 3J7  plan-2  C4    0.020
 3J7  plan-2  C5    0.020
 3J7  plan-2  C6    0.020
 3J7  plan-2  N2    0.020
 3J7  plan-2  C7    0.020
 3J7  plan-2  N3    0.020
 3J7  plan-2  C8    0.020
 3J7  plan-2  N6    0.020
 3J7  plan-2  H1    0.020
 3J7  plan-2  H2    0.020
 3J7  plan-2  H3    0.020
 3J7  plan-3  C15   0.020
 3J7  plan-3  C6    0.020
 3J7  plan-3  N6    0.020
 3J7  plan-3  H17   0.020

