# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:52:55 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: ~{N}-(7-chloranyl-1~{H}-indazol-3-yl)-7,7-dimethyl-2-(1~{H}-pyrazol-4-yl)-5~{H}-furo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)OCc2c(Nc3n[nH]c4c(Cl)cccc34)nc(nc12)c5c[nH]nc5
#
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
 5N3  5N3  ~{N}-(7-chloranyl-1~{H}-indazol-3-yl)-7,7-dimethyl-2-(1~{H}-pyrazol-4-yl)-5~{H}-furo[3,4-d]pyrimidin-4-amine  ligand  43  27  .  2022-03-10  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5N3
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
 5N3  C4   C   CR56  0  -0.170   1.9784  -1.5101  -0.0987
 5N3  C14  C   CR15  0  -0.090   3.6443   3.3378  -0.0361
 5N3  C5   C   CR6   0   0.534   0.8747  -0.6488  -0.0952
 5N3  C7   C   CR6   0   0.332   2.3129   1.1252  -0.0688
 5N3  C9   C   CR5   0  -0.189   2.4615   2.5704  -0.0513
 5N3  C10  C   CR15  0   0.036   1.4479   3.5100  -0.0446
 5N3  C3   C   CR56  0   0.224   3.2094  -0.9160  -0.0879
 5N3  C2   C   CR5   0   0.198   4.2824  -1.9684  -0.0973
 5N3  N6   N   N     0  -0.464   1.0646   0.6616  -0.0797
 5N3  N8   N   N     0  -0.460   3.4235   0.3923  -0.0731
 5N3  N11  N   NR15  0  -0.424   2.0479   4.7033  -0.0269
 5N3  N13  N   N     0  -0.262   3.3782   4.6273  -0.0212
 5N3  N15  N   NH1   0  -0.774  -0.3885  -1.1524  -0.1061
 5N3  C16  C   CR5   0   0.473  -1.5983  -0.4867  -0.0972
 5N3  C17  C   CR56  0  -0.174  -2.8527  -1.1652   0.0181
 5N3  C18  C   CR16  0  -0.312  -3.2684  -2.4937   0.1520
 5N3  C19  C   CR16  0  -0.280  -4.6195  -2.7444   0.2356
 5N3  C20  C   CR16  0  -0.244  -5.5631  -1.6992   0.1888
 5N3  C21  C   CR6   0  -0.111  -5.1603  -0.3926   0.0588
 5N3  C22  C   CR56  0   0.548  -3.7916  -0.1243  -0.0275
 5N3  N23  N   NR15  0  -0.558  -3.0932   1.0179  -0.1554
 5N3  N25  N   N     0  -0.241  -1.7659   0.8054  -0.2006
 5N3  CL   CL  CL    0  -0.105  -6.2867   0.9147  -0.0005
 5N3  C27  C   CH2   0  -0.190   2.1380  -2.9919  -0.1142
 5N3  O28  O   O     0  -0.522   3.5431  -3.1927  -0.1010
 5N3  C29  C   CH3   0  -0.656   5.1446  -1.8912   1.1563
 5N3  H1   H   HCR5  0   0.259   4.6643   2.9859  -0.0354
 5N3  H2   H   HCR5  0   0.294   0.3764   3.3956  -0.0531
 5N3  H3   H   HCH3  0   0.232   5.6769  -0.9292  -1.3772
 5N3  H4   H   HCH3  0   0.242   5.8646  -2.6837  -1.3892
 5N3  H5   H   HCH3  0   0.239   4.5182  -1.9291  -2.2568
 5N3  H6   H   HNR5  0   0.426   1.5995   5.6059  -0.0169
 5N3  H7   H   HNH1  0   0.427  -0.4633  -2.1571  -0.0993
 5N3  H8   H   HCR6  0   0.262  -2.5565  -3.3081   0.1932
 5N3  H9   H   HCR6  0   0.269  -4.9760  -3.7595   0.3418
 5N3  H10  H   HCR6  0   0.284  -6.6178  -1.9293   0.2586
 5N3  H11  H   HNR5  0   0.418  -3.4433   1.9598  -0.2118
 5N3  H12  H   HCH2  0   0.236   1.6783  -3.4708   0.7589
 5N3  H13  H   HCH2  0   0.236   1.6947  -3.4483  -1.0076
 5N3  H14  H   HCH3  0   0.239   4.5377  -1.9501   2.0607
 5N3  H15  H   HCH3  0   0.242   5.8706  -2.7053   1.1726
 5N3  H16  H   HCH3  0   0.232   5.6939  -0.9498   1.1778
 5N3  C1   C   CH3   0  -0.656   5.1337  -1.8742  -1.3580

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
 5N3  CL   C21  single    1.727  0.020  1.727
 5N3  C21  C22  aromatic  1.397  0.020  1.397
 5N3  C21  C20  aromatic  1.373  0.020  1.373
 5N3  N23  C22  aromatic  1.345  0.020  1.345
 5N3  N23  N25  aromatic  1.345  0.020  1.345
 5N3  C22  C17  aromatic  1.403  0.020  1.403
 5N3  C20  C19  aromatic  1.409  0.020  1.409
 5N3  N25  C16  aromatic  1.307  0.020  1.307
 5N3  C17  C16  aromatic  1.431  0.020  1.431
 5N3  C17  C18  aromatic  1.398  0.020  1.398
 5N3  C19  C18  aromatic  1.377  0.020  1.377
 5N3  C16  N15  single    1.381  0.020  1.381
 5N3  N15  C5   single    1.360  0.020  1.360
 5N3  C5   N6   aromatic  1.324  0.020  1.324
 5N3  C5   C4   aromatic  1.400  0.020  1.400
 5N3  N6   C7   aromatic  1.332  0.020  1.332
 5N3  C14  N13  aromatic  1.317  0.020  1.317
 5N3  C14  C9   aromatic  1.410  0.020  1.410
 5N3  C4   C27  single    1.490  0.020  1.490
 5N3  C4   C3   aromatic  1.367  0.020  1.367
 5N3  C27  O28  single    1.419  0.020  1.419
 5N3  N13  N11  aromatic  1.332  0.020  1.332
 5N3  C7   C9   single    1.453  0.020  1.453
 5N3  C7   N8   aromatic  1.331  0.020  1.331
 5N3  C9   C10  aromatic  1.382  0.020  1.382
 5N3  C3   N8   aromatic  1.326  0.020  1.326
 5N3  C3   C2   single    1.503  0.020  1.503
 5N3  O28  C2   single    1.430  0.020  1.430
 5N3  N11  C10  aromatic  1.336  0.020  1.336
 5N3  C2   C1   single    1.524  0.020  1.524
 5N3  C2   C29  single    1.523  0.020  1.523
 5N3  C14  H1   single    0.930  0.020  1.080
 5N3  C10  H2   single    0.930  0.020  1.080
 5N3  C1   H3   single    0.970  0.020  1.090
 5N3  C1   H4   single    0.970  0.020  1.090
 5N3  C1   H5   single    0.970  0.020  1.090
 5N3  N11  H6   single    0.860  0.020  1.020
 5N3  N15  H7   single    0.860  0.020  1.020
 5N3  C18  H8   single    0.930  0.020  1.080
 5N3  C19  H9   single    0.930  0.020  1.080
 5N3  C20  H10  single    0.930  0.020  1.080
 5N3  N23  H11  single    0.860  0.020  1.020
 5N3  C27  H12  single    0.970  0.020  1.090
 5N3  C27  H13  single    0.970  0.020  1.090
 5N3  C29  H14  single    0.970  0.020  1.090
 5N3  C29  H15  single    0.970  0.020  1.090
 5N3  C29  H16  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
 5N3  C27  C4   C3   109.62  3.000
 5N3  C3   C4   C5   116.26  3.000
 5N3  C27  C4   C5   134.11  3.000
 5N3  H1   C14  N13  120.70  3.000
 5N3  H1   C14  C9   127.99  3.000
 5N3  N13  C14  C9   111.32  3.000
 5N3  N15  C5   N6   119.99  3.000
 5N3  N6   C5   C4   119.72  3.000
 5N3  N15  C5   C4   120.29  3.000
 5N3  N8   C7   N6   126.20  3.000
 5N3  N8   C7   C9   117.55  3.000
 5N3  N6   C7   C9   116.25  3.000
 5N3  C10  C9   C7   126.96  3.000
 5N3  C10  C9   C14  104.19  3.000
 5N3  C7   C9   C14  128.85  3.000
 5N3  H2   C10  N11  122.79  3.000
 5N3  H2   C10  C9   131.07  3.000
 5N3  N11  C10  C9   106.14  3.000
 5N3  N8   C3   C2   125.15  3.000
 5N3  C2   C3   C4   109.79  3.000
 5N3  N8   C3   C4   125.06  3.000
 5N3  C29  C2   O28  109.76  3.000
 5N3  C29  C2   C1   111.19  3.000
 5N3  O28  C2   C1   109.84  3.000
 5N3  C29  C2   C3   111.31  3.000
 5N3  C1   C2   C3   111.14  3.000
 5N3  O28  C2   C3   103.32  3.000
 5N3  C7   N6   C5   118.62  3.000
 5N3  C3   N8   C7   114.13  3.000
 5N3  H6   N11  N13  119.68  3.000
 5N3  H6   N11  C10  126.89  3.000
 5N3  N13  N11  C10  113.43  3.000
 5N3  N11  N13  C14  104.93  3.000
 5N3  H7   N15  C16  114.56  3.000
 5N3  H7   N15  C5   115.99  3.000
 5N3  C16  N15  C5   129.44  3.000
 5N3  N25  C16  C17  111.27  3.000
 5N3  C17  C16  N15  122.68  3.000
 5N3  N25  C16  N15  126.04  3.000
 5N3  C22  C17  C18  120.60  3.000
 5N3  C18  C17  C16  135.96  3.000
 5N3  C22  C17  C16  103.44  3.000
 5N3  H8   C18  C19  120.40  3.000
 5N3  H8   C18  C17  121.52  3.000
 5N3  C19  C18  C17  118.07  3.000
 5N3  H9   C19  C20  118.61  3.000
 5N3  H9   C19  C18  120.04  3.000
 5N3  C20  C19  C18  121.34  3.000
 5N3  H10  C20  C21  119.63  3.000
 5N3  H10  C20  C19  119.54  3.000
 5N3  C21  C20  C19  120.83  3.000
 5N3  CL   C21  C22  119.43  3.000
 5N3  C22  C21  C20  118.41  3.000
 5N3  CL   C21  C20  122.16  3.000
 5N3  N23  C22  C21  132.66  3.000
 5N3  N23  C22  C17  106.60  3.000
 5N3  C21  C22  C17  120.74  3.000
 5N3  H11  N23  N25  119.29  3.000
 5N3  H11  N23  C22  128.28  3.000
 5N3  N25  N23  C22  112.43  3.000
 5N3  N23  N25  C16  106.26  3.000
 5N3  H13  C27  H12  107.30  3.000
 5N3  H13  C27  O28  110.41  3.000
 5N3  H12  C27  O28  110.23  3.000
 5N3  H13  C27  C4   112.26  3.000
 5N3  H12  C27  C4   112.40  3.000
 5N3  O28  C27  C4   104.27  3.000
 5N3  C27  O28  C2   113.00  3.000
 5N3  H16  C29  H15  107.99  3.000
 5N3  H16  C29  H14  108.10  3.000
 5N3  H15  C29  H14  108.52  3.000
 5N3  H16  C29  C2   110.19  3.000
 5N3  H15  C29  C2   110.55  3.000
 5N3  H14  C29  C2   111.38  3.000
 5N3  H5   C1   H4   108.49  3.000
 5N3  H5   C1   H3   108.08  3.000
 5N3  H4   C1   H3   107.99  3.000
 5N3  H5   C1   C2   111.30  3.000
 5N3  H4   C1   C2   110.61  3.000
 5N3  H3   C1   C2   110.27  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
 5N3  CONST_01  C7   N6   C5   C4      0.00   0.0  0
 5N3  CONST_02  C7   N8   C3   C4      0.00   0.0  0
 5N3  CONST_03  C10  N11  N13  C14     0.00   0.0  0
 5N3  CONST_04  N6   C7   C9   C14   180.00   0.0  0
 5N3  CONST_05  N8   C7   C9   C14     0.00   0.0  0
 5N3  CONST_06  N11  C10  C9   C14     0.00   0.0  0
 5N3  CONST_07  C9   C7   N6   C5    180.00   0.0  0
 5N3  CONST_08  N8   C7   N6   C5      0.00   0.0  0
 5N3  CONST_09  N8   C3   C4   C5      0.00   0.0  0
 5N3  CONST_10  N13  C14  C9   C7    180.00   0.0  0
 5N3  CONST_11  N11  C10  C9   C7    180.00   0.0  0
 5N3  CONST_12  N11  N13  C14  C9      0.00   0.0  0
 5N3  CONST_13  C3   N8   C7   C9    180.00   0.0  0
 5N3  CONST_14  N13  N11  C10  C9      0.00   0.0  0
 5N3  CONST_15  N13  C14  C9   C10     0.00   0.0  0
 5N3  CONST_16  N6   C7   C9   C10     0.00   0.0  0
 5N3  CONST_17  N8   C7   C9   C10   180.00   0.0  0
 5N3  CONST_18  N6   C5   C4   C3      0.00   0.0  0
 5N3  CONST_19  N6   C7   N8   C3      0.00   0.0  0
 5N3  CONST_20  C22  N23  N25  C16     0.00   0.0  0
 5N3  CONST_21  C21  C22  C17  C16   180.00   0.0  0
 5N3  CONST_22  N23  C22  C17  C16     0.00   0.0  0
 5N3  CONST_23  C19  C18  C17  C16   180.00   0.0  0
 5N3  CONST_24  C20  C21  C22  C17     0.00   0.0  0
 5N3  CONST_25  N25  N23  C22  C17     0.00   0.0  0
 5N3  CONST_26  N23  N25  C16  C17     0.00   0.0  0
 5N3  CONST_27  C20  C19  C18  C17     0.00   0.0  0
 5N3  CONST_28  C21  C22  C17  C18     0.00   0.0  0
 5N3  CONST_29  N23  C22  C17  C18   180.00   0.0  0
 5N3  CONST_30  N25  C16  C17  C18   180.00   0.0  0
 5N3  CONST_31  C21  C20  C19  C18     0.00   0.0  0
 5N3  CONST_32  C22  C21  C20  C19     0.00   0.0  0
 5N3  CONST_33  C22  C17  C18  C19     0.00   0.0  0
 5N3  CONST_34  N23  C22  C21  C20   180.00   0.0  0
 5N3  CONST_35  N25  N23  C22  C21   180.00   0.0  0
 5N3  CONST_36  N25  C16  C17  C22     0.00   0.0  0
 5N3  CONST_37  N15  C5   N6   C7    180.00   0.0  0
 5N3  CONST_38  N15  C5   C4   C3    180.00   0.0  0
 5N3  CONST_39  N23  N25  C16  N15   180.00   0.0  0
 5N3  CONST_40  C22  C17  C16  N15   180.00   0.0  0
 5N3  CONST_41  C18  C17  C16  N15     0.00   0.0  0
 5N3  CONST_42  C27  C4   C5   N15     0.00   0.0  0
 5N3  CONST_43  CL   C21  C22  C17   180.00   0.0  0
 5N3  CONST_44  CL   C21  C20  C19   180.00   0.0  0
 5N3  CONST_45  CL   C21  C22  N23     0.00   0.0  0
 5N3  CONST_46  H6   N11  N13  C14   180.00   0.0  0
 5N3  CONST_47  H2   C10  C9   C14   180.00   0.0  0
 5N3  CONST_48  H1   C14  C9   C7      0.00   0.0  0
 5N3  CONST_49  H11  N23  N25  C16   180.00   0.0  0
 5N3  CONST_50  H8   C18  C17  C16     0.00   0.0  0
 5N3  CONST_51  H9   C19  C18  C17   180.00   0.0  0
 5N3  CONST_52  H10  C20  C19  C18   180.00   0.0  0
 5N3  Var_01    O28  C2   C3   C4     -0.54  30.0  1
 5N3  Var_02    O28  C27  C4   C5   -179.68  30.0  1
 5N3  Var_03    C16  N15  C5   C4    179.58  30.0  1
 5N3  Var_04    N25  C16  N15  C5      6.77  30.0  1
 5N3  Var_05    H3   C1   C2   C3     64.54  30.0  3
 5N3  Var_06    H14  C29  C2   C3     55.04  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
 5N3  plan-1  C14  0.020
 5N3  plan-1  C7   0.020
 5N3  plan-1  C9   0.020
 5N3  plan-1  C10  0.020
 5N3  plan-1  N11  0.020
 5N3  plan-1  N13  0.020
 5N3  plan-1  H1   0.020
 5N3  plan-1  H2   0.020
 5N3  plan-1  H6   0.020
 5N3  plan-2  C4   0.020
 5N3  plan-2  C5   0.020
 5N3  plan-2  C7   0.020
 5N3  plan-2  C9   0.020
 5N3  plan-2  C3   0.020
 5N3  plan-2  C2   0.020
 5N3  plan-2  N6   0.020
 5N3  plan-2  N8   0.020
 5N3  plan-2  N15  0.020
 5N3  plan-2  C27  0.020
 5N3  plan-3  N15  0.020
 5N3  plan-3  C16  0.020
 5N3  plan-3  C17  0.020
 5N3  plan-3  C18  0.020
 5N3  plan-3  C19  0.020
 5N3  plan-3  C20  0.020
 5N3  plan-3  C21  0.020
 5N3  plan-3  C22  0.020
 5N3  plan-3  N23  0.020
 5N3  plan-3  N25  0.020
 5N3  plan-3  CL   0.020
 5N3  plan-3  H8   0.020
 5N3  plan-3  H9   0.020
 5N3  plan-3  H10  0.020
 5N3  plan-3  H11  0.020

