# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 02:56:03 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 4-[4-(1H-indol-3-yl)-3,6-dihydropyridin-1(2H)-yl]-1H-pyrazolo[3,4-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC(=CCN1c2ncnc3[nH]ncc23)c4c[nH]c5ccccc45
#
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
 FZ9  FZ9  4-[4-(1H-indol-3-yl)-3,6-dihydropyridin-1(2H)-yl]-1H-pyrazolo[3,4-d]pyrimidine  ligand  40  24  .  2022-07-25  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_FZ9
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
 FZ9  N01  N  N     0  -0.457  -4.8025  -1.7282   0.4174
 FZ9  C02  C  CR16  0   0.059  -3.9974  -2.1149  -0.5496
 FZ9  N03  N  N     0  -0.499  -2.9522  -1.4749  -1.0615
 FZ9  C04  C  CR6   0   0.538  -2.6074  -0.2713  -0.5888
 FZ9  N05  N  NT    0  -0.473  -1.5730   0.3519  -1.1691
 FZ9  C06  C  CH2   0  -0.364  -1.1136   1.6739  -0.8063
 FZ9  C07  C  CH2   0  -0.503   0.0933   1.5745   0.1095
 FZ9  C08  C  C     0   0.078   1.1207   0.6384  -0.4809
 FZ9  C09  C  CR5   0   0.020   2.4688   0.6982   0.0773
 FZ9  C10  C  CR56  0   0.024   3.5267  -0.2827   0.0307
 FZ9  C11  C  CR16  0  -0.393   3.6556  -1.5778  -0.4896
 FZ9  C12  C  CR16  0  -0.262   4.8471  -2.2578  -0.3267
 FZ9  C13  C  CR16  0  -0.285   5.9299  -1.6785   0.3522
 FZ9  C14  C  CR16  0  -0.301   5.8324  -0.4117   0.8925
 FZ9  C15  C  CR56  0   0.356   4.6267   0.2667   0.7276
 FZ9  N16  N  NR15  0  -0.685   4.2554   1.5009   1.1749
 FZ9  C17  C  CR15  0  -0.077   2.9755   1.7540   0.7978
 FZ9  C18  C  C1    0  -0.376   0.7739  -0.1838  -1.4797
 FZ9  C19  C  CH2   0  -0.320  -0.6208  -0.3475  -2.0080
 FZ9  C20  C  CR56  0  -0.211  -3.3724   0.2607   0.4869
 FZ9  C21  C  CR15  0  -0.129  -3.4070   1.3698   1.3778
 FZ9  N22  N  N     0  -0.238  -4.3938   1.2547   2.2282
 FZ9  N23  N  NR15  0  -0.510  -5.0173   0.1064   1.9379
 FZ9  C24  C  CR56  0   0.526  -4.4432  -0.5400   0.9116
 FZ9  H1   H  HCR6  0   0.253  -4.2125  -3.0812  -0.9948
 FZ9  H2   H  HCH2  0   0.277  -0.8269   2.1837  -1.7299
 FZ9  H3   H  HCH2  0   0.255   0.5157   2.5744   0.2355
 FZ9  H4   H  HCR6  0   0.241   2.8380  -2.0600  -1.0073
 FZ9  H5   H  HCR6  0   0.248   4.9491  -3.2577  -0.7283
 FZ9  H6   H  HCR6  0   0.251   6.8520  -2.2351   0.4588
 FZ9  H7   H  HCR6  0   0.261   6.6589   0.0371   1.4287
 FZ9  H8   H  HNR5  0   0.413   4.8314   2.1298   1.7091
 FZ9  H9   H  HCR5  0   0.288   2.5118   2.6885   1.0697
 FZ9  H10  H  H     0   0.244   1.5140  -0.7973  -1.9767
 FZ9  H11  H  HCH2  0   0.279  -0.8823  -1.4030  -2.0442
 FZ9  H12  H  HCR5  0   0.269  -2.7571   2.2274   1.4432
 FZ9  H13  H  HNR5  0   0.419  -5.8108  -0.1937   2.4826
 FZ9  H14  H  HCH2  0   0.274  -1.9174   2.2631  -0.3773
 FZ9  H15  H  HCH2  0   0.255  -0.1997   1.2372   1.1092
 FZ9  H16  H  HCH2  0   0.255  -0.6876   0.0220  -3.0387

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
 FZ9  C12  C13  aromatic  1.403  0.020  1.403
 FZ9  C12  C11  aromatic  1.382  0.020  1.382
 FZ9  C13  C14  aromatic  1.381  0.020  1.381
 FZ9  C11  C10  aromatic  1.402  0.020  1.402
 FZ9  C14  C15  aromatic  1.393  0.020  1.393
 FZ9  C10  C15  aromatic  1.413  0.020  1.413
 FZ9  C10  C09  aromatic  1.443  0.020  1.443
 FZ9  C15  N16  aromatic  1.364  0.020  1.364
 FZ9  C07  C06  single    1.518  0.020  1.518
 FZ9  C07  C08  single    1.510  0.020  1.510
 FZ9  N22  C21  aromatic  1.308  0.020  1.308
 FZ9  N22  N23  aromatic  1.339  0.020  1.339
 FZ9  C21  C20  aromatic  1.423  0.020  1.423
 FZ9  C06  N05  single    1.446  0.020  1.446
 FZ9  C09  C08  single    1.460  0.020  1.460
 FZ9  C09  C17  aromatic  1.375  0.020  1.375
 FZ9  N16  C17  aromatic  1.358  0.020  1.358
 FZ9  C08  C18  double    1.339  0.020  1.339
 FZ9  N23  C24  aromatic  1.342  0.020  1.342
 FZ9  C20  C24  aromatic  1.403  0.020  1.403
 FZ9  C20  C04  aromatic  1.423  0.020  1.423
 FZ9  N05  C04  single    1.340  0.020  1.340
 FZ9  N05  C19  single    1.449  0.020  1.449
 FZ9  C18  C19  single    1.500  0.020  1.500
 FZ9  C24  N01  aromatic  1.336  0.020  1.336
 FZ9  C04  N03  aromatic  1.338  0.020  1.338
 FZ9  N01  C02  aromatic  1.316  0.020  1.316
 FZ9  N03  C02  aromatic  1.328  0.020  1.328
 FZ9  C02  H1   single    0.930  0.020  1.080
 FZ9  C06  H2   single    0.970  0.020  1.090
 FZ9  C07  H3   single    0.970  0.020  1.090
 FZ9  C11  H4   single    0.930  0.020  1.080
 FZ9  C12  H5   single    0.930  0.020  1.080
 FZ9  C13  H6   single    0.930  0.020  1.080
 FZ9  C14  H7   single    0.930  0.020  1.080
 FZ9  N16  H8   single    0.860  0.020  1.020
 FZ9  C17  H9   single    0.930  0.020  1.080
 FZ9  C18  H10  single    0.930  0.020  1.080
 FZ9  C19  H11  single    0.970  0.020  1.090
 FZ9  C21  H12  single    0.930  0.020  1.080
 FZ9  N23  H13  single    0.860  0.020  1.020
 FZ9  C06  H14  single    0.970  0.020  1.090
 FZ9  C07  H15  single    0.970  0.020  1.090
 FZ9  C19  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
 FZ9  C24  N01  C02  111.63  3.000
 FZ9  H1   C02  N03  115.27  3.000
 FZ9  H1   C02  N01  116.21  3.000
 FZ9  N03  C02  N01  128.52  3.000
 FZ9  C04  N03  C02  120.00  3.000
 FZ9  C20  C04  N05  124.65  3.000
 FZ9  N05  C04  N03  117.66  3.000
 FZ9  C20  C04  N03  117.69  3.000
 FZ9  C19  N05  C06  112.20  3.000
 FZ9  C19  N05  C04  122.25  3.000
 FZ9  C06  N05  C04  124.19  3.000
 FZ9  H14  C06  H2   105.97  3.000
 FZ9  H14  C06  C07  112.70  3.000
 FZ9  H2   C06  C07  109.37  3.000
 FZ9  H14  C06  N05  111.12  3.000
 FZ9  H2   C06  N05  107.32  3.000
 FZ9  C07  C06  N05  110.12  3.000
 FZ9  H15  C07  H3   106.26  3.000
 FZ9  H15  C07  C08  110.36  3.000
 FZ9  H3   C07  C08  110.45  3.000
 FZ9  H15  C07  C06  110.99  3.000
 FZ9  H3   C07  C06  108.48  3.000
 FZ9  C08  C07  C06  110.22  3.000
 FZ9  C18  C08  C09  123.31  3.000
 FZ9  C18  C08  C07  119.73  3.000
 FZ9  C09  C08  C07  116.95  3.000
 FZ9  C17  C09  C10  105.58  3.000
 FZ9  C17  C09  C08  124.89  3.000
 FZ9  C10  C09  C08  129.53  3.000
 FZ9  C15  C10  C11  118.08  3.000
 FZ9  C15  C10  C09  106.88  3.000
 FZ9  C11  C10  C09  135.01  3.000
 FZ9  H4   C11  C12  119.28  3.000
 FZ9  H4   C11  C10  121.35  3.000
 FZ9  C12  C11  C10  119.36  3.000
 FZ9  H5   C12  C13  119.22  3.000
 FZ9  H5   C12  C11  119.49  3.000
 FZ9  C13  C12  C11  121.29  3.000
 FZ9  H6   C13  C14  119.57  3.000
 FZ9  H6   C13  C12  119.52  3.000
 FZ9  C14  C13  C12  120.91  3.000
 FZ9  H7   C14  C15  121.16  3.000
 FZ9  H7   C14  C13  121.35  3.000
 FZ9  C15  C14  C13  117.49  3.000
 FZ9  N16  C15  C14  129.59  3.000
 FZ9  N16  C15  C10  107.55  3.000
 FZ9  C14  C15  C10  122.86  3.000
 FZ9  H8   N16  C17  124.77  3.000
 FZ9  H8   N16  C15  125.71  3.000
 FZ9  C17  N16  C15  109.52  3.000
 FZ9  H9   C17  N16  119.80  3.000
 FZ9  H9   C17  C09  129.73  3.000
 FZ9  N16  C17  C09  110.47  3.000
 FZ9  H10  C18  C19  114.34  3.000
 FZ9  H10  C18  C08  120.89  3.000
 FZ9  C19  C18  C08  124.77  3.000
 FZ9  H16  C19  H11  106.32  3.000
 FZ9  H16  C19  C18  110.53  3.000
 FZ9  H11  C19  C18  109.94  3.000
 FZ9  H16  C19  N05  109.96  3.000
 FZ9  H11  C19  N05  109.24  3.000
 FZ9  C18  C19  N05  110.75  3.000
 FZ9  C24  C20  C21  103.69  3.000
 FZ9  C24  C20  C04  115.20  3.000
 FZ9  C21  C20  C04  141.05  3.000
 FZ9  H12  C21  N22  119.04  3.000
 FZ9  H12  C21  C20  130.04  3.000
 FZ9  N22  C21  C20  110.91  3.000
 FZ9  N23  N22  C21  106.61  3.000
 FZ9  H13  N23  C24  127.34  3.000
 FZ9  H13  N23  N22  120.32  3.000
 FZ9  C24  N23  N22  112.32  3.000
 FZ9  N23  C24  C20  106.45  3.000
 FZ9  C20  C24  N01  126.93  3.000
 FZ9  N23  C24  N01  126.60  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
 FZ9  CONST_01  N22  N23  C24  N01   180.00   0.0  0
 FZ9  CONST_02  C21  C20  C24  N01   180.00   0.0  0
 FZ9  CONST_03  C04  C20  C24  N01     0.00   0.0  0
 FZ9  CONST_04  C04  N03  C02  N01     0.00   0.0  0
 FZ9  CONST_05  N23  C24  N01  C02   180.00   0.0  0
 FZ9  CONST_06  C20  C24  N01  C02     0.00   0.0  0
 FZ9  CONST_07  C20  C04  N03  C02     0.00   0.0  0
 FZ9  CONST_08  C21  C20  C04  N03   180.00   0.0  0
 FZ9  CONST_09  C24  C20  C04  N03     0.00   0.0  0
 FZ9  CONST_10  C24  N01  C02  N03     0.00   0.0  0
 FZ9  CONST_11  N22  C21  C20  C04   180.00   0.0  0
 FZ9  CONST_12  N23  C24  C20  C04   180.00   0.0  0
 FZ9  CONST_13  C12  C11  C10  C09   180.00   0.0  0
 FZ9  CONST_14  C14  C15  C10  C09   180.00   0.0  0
 FZ9  CONST_15  N16  C15  C10  C09     0.00   0.0  0
 FZ9  CONST_16  C15  N16  C17  C09     0.00   0.0  0
 FZ9  CONST_17  C13  C12  C11  C10     0.00   0.0  0
 FZ9  CONST_18  C13  C14  C15  C10     0.00   0.0  0
 FZ9  CONST_19  C17  N16  C15  C10     0.00   0.0  0
 FZ9  CONST_20  N16  C17  C09  C10     0.00   0.0  0
 FZ9  CONST_21  C14  C13  C12  C11     0.00   0.0  0
 FZ9  CONST_22  C14  C15  C10  C11     0.00   0.0  0
 FZ9  CONST_23  N16  C15  C10  C11   180.00   0.0  0
 FZ9  CONST_24  C17  C09  C10  C11   180.00   0.0  0
 FZ9  CONST_25  C15  C14  C13  C12     0.00   0.0  0
 FZ9  CONST_26  C15  C10  C11  C12     0.00   0.0  0
 FZ9  CONST_27  N16  C15  C14  C13   180.00   0.0  0
 FZ9  CONST_28  C17  N16  C15  C14   180.00   0.0  0
 FZ9  CONST_29  C17  C09  C10  C15     0.00   0.0  0
 FZ9  CONST_30  N23  N22  C21  C20     0.00   0.0  0
 FZ9  CONST_31  N22  N23  C24  C20     0.00   0.0  0
 FZ9  CONST_32  C24  N23  N22  C21     0.00   0.0  0
 FZ9  CONST_33  N23  C24  C20  C21     0.00   0.0  0
 FZ9  CONST_34  C24  C20  C21  N22     0.00   0.0  0
 FZ9  CONST_35  N05  C04  N03  C02   180.00   0.0  0
 FZ9  CONST_36  C21  C20  C04  N05     0.00   0.0  0
 FZ9  CONST_37  C24  C20  C04  N05   180.00   0.0  0
 FZ9  CONST_38  C11  C10  C09  C08     0.00   0.0  0
 FZ9  CONST_39  C15  C10  C09  C08   180.00   0.0  0
 FZ9  CONST_40  N16  C17  C09  C08   180.00   0.0  0
 FZ9  CONST_41  H13  N23  C24  N01     0.00   0.0  0
 FZ9  CONST_42  H12  C21  C20  C04     0.00   0.0  0
 FZ9  CONST_43  H1   C02  N03  C04   180.00   0.0  0
 FZ9  CONST_44  H9   C17  C09  C08     0.00   0.0  0
 FZ9  CONST_45  H4   C11  C10  C09     0.00   0.0  0
 FZ9  CONST_46  H8   N16  C17  C09   180.00   0.0  0
 FZ9  CONST_47  H5   C12  C11  C10   180.00   0.0  0
 FZ9  CONST_48  H7   C14  C15  C10   180.00   0.0  0
 FZ9  CONST_49  H6   C13  C12  C11   180.00   0.0  0
 FZ9  Var_01    C06  N05  C04  N03   177.56  30.0  2
 FZ9  Var_02    C07  C06  N05  C04    99.54  30.0  1
 FZ9  Var_03    C18  C19  N05  C04  -122.67  30.0  1
 FZ9  Var_04    C08  C07  C06  N05    49.89  30.0  1
 FZ9  Var_05    C08  C18  C19  N05    -8.38  30.0  1
 FZ9  Var_06    C09  C08  C07  C06   164.25  30.0  1
 FZ9  Var_07    C10  C09  C08  C07   159.51  30.0  2
 FZ9  Var_08    C19  C18  C08  C07    -5.59  30.0  1

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
 FZ9  plan-1  C08  0.020
 FZ9  plan-1  C09  0.020
 FZ9  plan-1  C10  0.020
 FZ9  plan-1  C11  0.020
 FZ9  plan-1  C12  0.020
 FZ9  plan-1  C13  0.020
 FZ9  plan-1  C14  0.020
 FZ9  plan-1  C15  0.020
 FZ9  plan-1  N16  0.020
 FZ9  plan-1  C17  0.020
 FZ9  plan-1  H4   0.020
 FZ9  plan-1  H5   0.020
 FZ9  plan-1  H6   0.020
 FZ9  plan-1  H7   0.020
 FZ9  plan-1  H8   0.020
 FZ9  plan-1  H9   0.020
 FZ9  plan-2  N01  0.020
 FZ9  plan-2  C02  0.020
 FZ9  plan-2  N03  0.020
 FZ9  plan-2  C04  0.020
 FZ9  plan-2  N05  0.020
 FZ9  plan-2  C20  0.020
 FZ9  plan-2  C21  0.020
 FZ9  plan-2  N22  0.020
 FZ9  plan-2  N23  0.020
 FZ9  plan-2  C24  0.020
 FZ9  plan-2  H1   0.020
 FZ9  plan-2  H12  0.020
 FZ9  plan-2  H13  0.020

