# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:14:47 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: ~{N}-(1~{H}-indazol-3-yl)-7,7-dimethyl-2-(2-methylpyrazol-3-yl)-5~{H}-furo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nccc1c2nc(Nc3n[nH]c4ccccc34)c5COC(C)(C)c5n2
#
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
 5N4  5N4  ~{N}-(1~{H}-indazol-3-yl)-7,7-dimethyl-2-(2-methylpyrazol-3-yl)-5~{H}-furo[3,4-d]pyrimidin-4-amine  ligand  46  27  .  2022-07-23  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_5N4
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
 5N4  C4   C  CR56  0  -0.131   1.2500  -2.0123  -0.7934
 5N4  C14  C  CH3   0  -0.515  -0.8953   2.7242  -0.2411
 5N4  C5   C  CR6   0   0.529   0.1010  -1.2193  -0.8273
 5N4  C11  C  CR15  0  -0.091   1.9386   3.7781   1.4961
 5N4  C7   C  CR6   0   0.349   1.3086   0.4932   0.0848
 5N4  C9   C  CR5   0   0.372   1.3589   1.8717   0.5693
 5N4  C10  C  CR15  0  -0.493   2.3890   2.4787   1.2652
 5N4  C3   C  CR56  0   0.229   2.3758  -1.4280  -0.2798
 5N4  C2   C  CR5   0   0.197   3.5085  -2.4169  -0.2893
 5N4  N6   N  N     0  -0.474   0.1582   0.0349  -0.3855
 5N4  N8   N  N     0  -0.459   2.4511  -0.1853   0.1704
 5N4  N12  N  N     0  -0.265   0.7340   3.9624   0.9802
 5N4  N13  N  NR5   0  -0.341   0.3894   2.8095   0.4245
 5N4  N15  N  NH1   0  -0.767  -1.0803  -1.6867  -1.2972
 5N4  C16  C  CR5   0   0.397  -2.2612  -0.9475  -1.3082
 5N4  C17  C  CR56  0  -0.102  -2.9381  -0.3604  -0.2028
 5N4  C18  C  CR16  0  -0.296  -2.7139  -0.2498   1.1752
 5N4  C19  C  CR16  0  -0.274  -3.6469   0.4221   1.9303
 5N4  C20  C  CR16  0  -0.263  -4.7952   0.9893   1.3366
 5N4  C21  C  CR16  0  -0.299  -5.0401   0.8897  -0.0136
 5N4  C22  C  CR56  0   0.421  -4.0911   0.1985  -0.7763
 5N4  N23  N  NR15  0  -0.552  -4.0334  -0.0946  -2.0964
 5N4  N25  N  N     0  -0.242  -2.9318  -0.7756  -2.4176
 5N4  C26  C  CH2   0  -0.187   1.5498  -3.4185  -1.1832
 5N4  O27  O  O     0  -0.521   2.9429  -3.5557  -0.9446
 5N4  C28  C  CH3   0  -0.656   3.9174  -2.7804   1.1344
 5N4  H1   H  HCH3  0   0.265  -1.5729   2.0632   0.2929
 5N4  H2   H  HCH3  0   0.260  -1.3069   3.7285  -0.2662
 5N4  H3   H  HCH3  0   0.254  -0.7835   2.3526  -1.2553
 5N4  H4   H  HCR5  0   0.264   2.4383   4.5836   2.0121
 5N4  H5   H  HCR5  0   0.266   3.3217   2.0295   1.5603
 5N4  H6   H  HCH3  0   0.233   5.1093  -1.0123  -0.6301
 5N4  H7   H  HCH3  0   0.243   5.4819  -2.6591  -1.1419
 5N4  H8   H  HCH3  0   0.240   4.3986  -1.6530  -2.1145
 5N4  H9   H  HNH1  0   0.417  -1.0832  -2.5722  -1.7792
 5N4  H10  H  HCR6  0   0.254  -1.8308  -0.6758   1.6322
 5N4  H11  H  HCR6  0   0.257  -3.5030   0.5241   2.9977
 5N4  H12  H  HCR6  0   0.261  -5.5032   1.5161   1.9631
 5N4  H13  H  HCR6  0   0.272  -5.9233   1.3235  -0.4628
 5N4  H14  H  HNR5  0   0.419  -4.7026   0.1337  -2.8127
 5N4  H15  H  HCH2  0   0.236   0.9769  -4.1406  -0.5881
 5N4  H16  H  HCH2  0   0.239   1.3331  -3.6211  -2.2379
 5N4  H17  H  HCH3  0   0.240   3.0692  -3.1630   1.7038
 5N4  H18  H  HCH3  0   0.243   4.6987  -3.5414   1.1259
 5N4  H19  H  HCH3  0   0.233   4.3050  -1.9042   1.6545
 5N4  C1   C  CH3   0  -0.658   4.6938  -1.9061  -1.0958

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
 5N4  C21  C22  aromatic  1.400  0.020  1.400
 5N4  C21  C20  aromatic  1.376  0.020  1.376
 5N4  N23  C22  aromatic  1.353  0.020  1.353
 5N4  N23  N25  aromatic  1.334  0.020  1.334
 5N4  C22  C17  aromatic  1.404  0.020  1.404
 5N4  C20  C19  aromatic  1.412  0.020  1.412
 5N4  N25  C16  aromatic  1.308  0.020  1.308
 5N4  C17  C16  aromatic  1.423  0.020  1.423
 5N4  C17  C18  aromatic  1.401  0.020  1.401
 5N4  C19  C18  aromatic  1.376  0.020  1.376
 5N4  C16  N15  single    1.393  0.020  1.393
 5N4  N15  C5   single    1.354  0.020  1.354
 5N4  C5   N6   aromatic  1.331  0.020  1.331
 5N4  C5   C4   aromatic  1.396  0.020  1.396
 5N4  N6   C7   aromatic  1.325  0.020  1.325
 5N4  C10  C11  aromatic  1.394  0.020  1.394
 5N4  C10  C9   aromatic  1.383  0.020  1.383
 5N4  C11  N12  aromatic  1.323  0.020  1.323
 5N4  C4   C26  single    1.490  0.020  1.490
 5N4  C4   C3   aromatic  1.368  0.020  1.368
 5N4  C7   C9   single    1.462  0.020  1.462
 5N4  C7   N8   aromatic  1.332  0.020  1.332
 5N4  C26  O27  single    1.420  0.020  1.420
 5N4  C9   N13  aromatic  1.357  0.020  1.357
 5N4  N12  N13  aromatic  1.325  0.020  1.325
 5N4  C3   N8   aromatic  1.324  0.020  1.324
 5N4  C3   C2   single    1.504  0.020  1.504
 5N4  N13  C14  single    1.449  0.020  1.449
 5N4  O27  C2   single    1.431  0.020  1.431
 5N4  C2   C1   single    1.522  0.020  1.522
 5N4  C2   C28  single    1.525  0.020  1.525
 5N4  C14  H1   single    0.970  0.020  1.090
 5N4  C14  H2   single    0.970  0.020  1.090
 5N4  C14  H3   single    0.970  0.020  1.090
 5N4  C11  H4   single    0.930  0.020  1.080
 5N4  C10  H5   single    0.930  0.020  1.080
 5N4  C1   H6   single    0.970  0.020  1.090
 5N4  C1   H7   single    0.970  0.020  1.090
 5N4  C1   H8   single    0.970  0.020  1.090
 5N4  N15  H9   single    0.860  0.020  1.020
 5N4  C18  H10  single    0.930  0.020  1.080
 5N4  C19  H11  single    0.930  0.020  1.080
 5N4  C20  H12  single    0.930  0.020  1.080
 5N4  C21  H13  single    0.930  0.020  1.080
 5N4  N23  H14  single    0.860  0.020  1.020
 5N4  C26  H15  single    0.970  0.020  1.090
 5N4  C26  H16  single    0.970  0.020  1.090
 5N4  C28  H17  single    0.970  0.020  1.090
 5N4  C28  H18  single    0.970  0.020  1.090
 5N4  C28  H19  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
 5N4  C26  C4   C3   109.61  3.000
 5N4  C3   C4   C5   116.33  3.000
 5N4  C26  C4   C5   134.05  3.000
 5N4  H3   C14  H2   109.51  3.000
 5N4  H3   C14  H1   108.36  3.000
 5N4  H2   C14  H1   109.74  3.000
 5N4  H3   C14  N13  110.96  3.000
 5N4  H2   C14  N13  106.99  3.000
 5N4  H1   C14  N13  111.27  3.000
 5N4  N15  C5   N6   118.54  3.000
 5N4  N6   C5   C4   119.45  3.000
 5N4  N15  C5   C4   122.01  3.000
 5N4  H4   C11  N12  120.26  3.000
 5N4  H4   C11  C10  128.69  3.000
 5N4  N12  C11  C10  111.05  3.000
 5N4  N8   C7   N6   126.28  3.000
 5N4  N8   C7   C9   115.44  3.000
 5N4  N6   C7   C9   118.27  3.000
 5N4  N13  C9   C10  106.41  3.000
 5N4  N13  C9   C7   126.29  3.000
 5N4  C10  C9   C7   127.30  3.000
 5N4  H5   C10  C9   126.87  3.000
 5N4  H5   C10  C11  128.55  3.000
 5N4  C9   C10  C11  104.57  3.000
 5N4  N8   C3   C2   125.22  3.000
 5N4  C2   C3   C4   109.67  3.000
 5N4  N8   C3   C4   125.11  3.000
 5N4  C28  C2   O27  110.12  3.000
 5N4  C28  C2   C1   111.46  3.000
 5N4  O27  C2   C1   109.41  3.000
 5N4  C28  C2   C3   110.66  3.000
 5N4  C1   C2   C3   111.67  3.000
 5N4  O27  C2   C3   103.22  3.000
 5N4  C7   N6   C5   118.76  3.000
 5N4  C3   N8   C7   114.06  3.000
 5N4  N13  N12  C11  106.20  3.000
 5N4  N12  N13  C9   111.76  3.000
 5N4  N12  N13  C14  118.30  3.000
 5N4  C9   N13  C14  129.93  3.000
 5N4  H9   N15  C16  117.37  3.000
 5N4  H9   N15  C5   118.13  3.000
 5N4  C16  N15  C5   123.98  3.000
 5N4  N25  C16  C17  111.16  3.000
 5N4  C17  C16  N15  128.02  3.000
 5N4  N25  C16  N15  120.74  3.000
 5N4  C22  C17  C18  120.13  3.000
 5N4  C18  C17  C16  136.12  3.000
 5N4  C22  C17  C16  103.75  3.000
 5N4  H10  C18  C19  120.94  3.000
 5N4  H10  C18  C17  121.02  3.000
 5N4  C19  C18  C17  118.04  3.000
 5N4  H11  C19  C20  119.03  3.000
 5N4  H11  C19  C18  119.83  3.000
 5N4  C20  C19  C18  121.14  3.000
 5N4  H12  C20  C21  119.14  3.000
 5N4  H12  C20  C19  118.96  3.000
 5N4  C21  C20  C19  121.90  3.000
 5N4  H13  C21  C22  121.68  3.000
 5N4  H13  C21  C20  121.59  3.000
 5N4  C22  C21  C20  116.73  3.000
 5N4  N23  C22  C21  131.85  3.000
 5N4  N23  C22  C17  106.09  3.000
 5N4  C21  C22  C17  122.06  3.000
 5N4  H14  N23  N25  119.56  3.000
 5N4  H14  N23  C22  128.07  3.000
 5N4  N25  N23  C22  112.37  3.000
 5N4  N23  N25  C16  106.63  3.000
 5N4  H16  C26  H15  107.29  3.000
 5N4  H16  C26  O27  109.75  3.000
 5N4  H15  C26  O27  110.95  3.000
 5N4  H16  C26  C4   112.74  3.000
 5N4  H15  C26  C4   111.98  3.000
 5N4  O27  C26  C4   104.17  3.000
 5N4  C26  O27  C2   112.82  3.000
 5N4  H19  C28  H18  108.05  3.000
 5N4  H19  C28  H17  108.01  3.000
 5N4  H18  C28  H17  108.44  3.000
 5N4  H19  C28  C2   110.44  3.000
 5N4  H18  C28  C2   110.56  3.000
 5N4  H17  C28  C2   111.25  3.000
 5N4  H8   C1   H7   108.44  3.000
 5N4  H8   C1   H6   108.18  3.000
 5N4  H7   C1   H6   107.98  3.000
 5N4  H8   C1   C2   111.23  3.000
 5N4  H7   C1   C2   110.69  3.000
 5N4  H6   C1   C2   110.22  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
 5N4  CONST_01  C7   N6   C5   C4     0.00   0.0  0
 5N4  CONST_02  C7   N8   C3   C4     0.00   0.0  0
 5N4  CONST_03  C9   C7   N6   C5   180.00   0.0  0
 5N4  CONST_04  N8   C7   N6   C5     0.00   0.0  0
 5N4  CONST_05  N8   C3   C4   C5     0.00   0.0  0
 5N4  CONST_06  C7   C9   C10  C11  180.00   0.0  0
 5N4  CONST_07  N13  C9   C10  C11    0.00   0.0  0
 5N4  CONST_08  C9   N13  N12  C11    0.00   0.0  0
 5N4  CONST_09  N12  N13  C9   C7   180.00   0.0  0
 5N4  CONST_10  N12  C11  C10  C9     0.00   0.0  0
 5N4  CONST_11  C3   N8   C7   C9   180.00   0.0  0
 5N4  CONST_12  N13  N12  C11  C10    0.00   0.0  0
 5N4  CONST_13  N6   C7   C9   C10  180.00   0.0  0
 5N4  CONST_14  N8   C7   C9   C10    0.00   0.0  0
 5N4  CONST_15  N12  N13  C9   C10    0.00   0.0  0
 5N4  CONST_16  N6   C5   C4   C3     0.00   0.0  0
 5N4  CONST_17  N6   C7   N8   C3     0.00   0.0  0
 5N4  CONST_18  N13  C9   C7   N6     0.00   0.0  0
 5N4  CONST_19  N13  C9   C7   N8   180.00   0.0  0
 5N4  CONST_20  C22  N23  N25  C16    0.00   0.0  0
 5N4  CONST_21  C21  C22  C17  C16  180.00   0.0  0
 5N4  CONST_22  N23  C22  C17  C16    0.00   0.0  0
 5N4  CONST_23  C19  C18  C17  C16  180.00   0.0  0
 5N4  CONST_24  C20  C21  C22  C17    0.00   0.0  0
 5N4  CONST_25  N25  N23  C22  C17    0.00   0.0  0
 5N4  CONST_26  N23  N25  C16  C17    0.00   0.0  0
 5N4  CONST_27  C20  C19  C18  C17    0.00   0.0  0
 5N4  CONST_28  C21  C22  C17  C18    0.00   0.0  0
 5N4  CONST_29  N23  C22  C17  C18  180.00   0.0  0
 5N4  CONST_30  N25  C16  C17  C18  180.00   0.0  0
 5N4  CONST_31  C21  C20  C19  C18    0.00   0.0  0
 5N4  CONST_32  C22  C21  C20  C19    0.00   0.0  0
 5N4  CONST_33  C22  C17  C18  C19    0.00   0.0  0
 5N4  CONST_34  N23  C22  C21  C20  180.00   0.0  0
 5N4  CONST_35  N25  N23  C22  C21  180.00   0.0  0
 5N4  CONST_36  N25  C16  C17  C22    0.00   0.0  0
 5N4  CONST_37  C10  C9   N13  C14  180.00   0.0  0
 5N4  CONST_38  C7   C9   N13  C14    0.00   0.0  0
 5N4  CONST_39  C11  N12  N13  C14  180.00   0.0  0
 5N4  CONST_40  N15  C5   N6   C7   180.00   0.0  0
 5N4  CONST_41  N15  C5   C4   C3   180.00   0.0  0
 5N4  CONST_42  N23  N25  C16  N15  180.00   0.0  0
 5N4  CONST_43  C22  C17  C16  N15  180.00   0.0  0
 5N4  CONST_44  C18  C17  C16  N15    0.00   0.0  0
 5N4  CONST_45  C26  C4   C5   N15    0.00   0.0  0
 5N4  CONST_46  H5   C10  C9   C7     0.00   0.0  0
 5N4  CONST_47  H4   C11  C10  C9   180.00   0.0  0
 5N4  CONST_48  H14  N23  N25  C16  180.00   0.0  0
 5N4  CONST_49  H10  C18  C17  C16    0.00   0.0  0
 5N4  CONST_50  H13  C21  C22  C17  180.00   0.0  0
 5N4  CONST_51  H11  C19  C18  C17  180.00   0.0  0
 5N4  CONST_52  H12  C20  C19  C18  180.00   0.0  0
 5N4  Var_01    O27  C2   C3   C4     4.35  30.0  1
 5N4  Var_02    O27  C26  C4   C5   177.07  30.0  1
 5N4  Var_03    C16  N15  C5   C4   177.74  30.0  2
 5N4  Var_04    N25  C16  N15  C5   125.17  30.0  2
 5N4  Var_05    H1   C14  N13  C9    68.64  30.0  2
 5N4  Var_06    H6   C1   C2   C3    63.99  30.0  3
 5N4  Var_07    H17  C28  C2   C3    56.12  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
 5N4  plan-1  C14  0.020
 5N4  plan-1  C11  0.020
 5N4  plan-1  C7   0.020
 5N4  plan-1  C9   0.020
 5N4  plan-1  C10  0.020
 5N4  plan-1  N12  0.020
 5N4  plan-1  N13  0.020
 5N4  plan-1  H4   0.020
 5N4  plan-1  H5   0.020
 5N4  plan-2  C4   0.020
 5N4  plan-2  C5   0.020
 5N4  plan-2  C7   0.020
 5N4  plan-2  C9   0.020
 5N4  plan-2  C3   0.020
 5N4  plan-2  C2   0.020
 5N4  plan-2  N6   0.020
 5N4  plan-2  N8   0.020
 5N4  plan-2  N15  0.020
 5N4  plan-2  C26  0.020
 5N4  plan-3  N15  0.020
 5N4  plan-3  C16  0.020
 5N4  plan-3  C17  0.020
 5N4  plan-3  C18  0.020
 5N4  plan-3  C19  0.020
 5N4  plan-3  C20  0.020
 5N4  plan-3  C21  0.020
 5N4  plan-3  C22  0.020
 5N4  plan-3  N23  0.020
 5N4  plan-3  N25  0.020
 5N4  plan-3  H10  0.020
 5N4  plan-3  H11  0.020
 5N4  plan-3  H12  0.020
 5N4  plan-3  H13  0.020
 5N4  plan-3  H14  0.020

