# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:53:31 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-cyclopropyl-4-(furan-2-yl)-1H-pyrazolo[3,4-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC1c2n[nH]c3nccc(c4occc4)c23
#
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
 Z2M  Z2M  3-cyclopropyl-4-(furan-2-yl)-1H-pyrazolo[3,4-b]pyridine  ligand  28  17  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Z2M
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
 Z2M  C     C  CR15  0  -0.003   3.3886   0.3085   0.2706
 Z2M  N     N  N     0  -0.247  -1.9813  -1.8183  -0.1811
 Z2M  O     O  O     0  -0.398   2.0656   0.1227   0.4127
 Z2M  C1    C  CR5   0   0.320   1.4384   1.1932  -0.1159
 Z2M  N1    N  NR15  0  -0.520  -2.8524  -0.8211  -0.0102
 Z2M  C2    C  CR6   0   0.111  -0.0093   1.2457  -0.0636
 Z2M  N2    N  N     0  -0.430  -2.8490   1.5563   0.1323
 Z2M  C3    C  CR56  0  -0.105  -0.8604   0.1238  -0.0818
 Z2M  C4    C  CR5   0   0.193  -0.7778  -1.3002  -0.2273
 Z2M  C5    C  CR56  0   0.526  -2.2439   0.3785   0.0306
 Z2M  C6    C  CR16  0  -0.057  -2.0240   2.5865   0.1129
 Z2M  C7    C  CR16  0  -0.428  -0.6324   2.4852   0.0224
 Z2M  C8    C  CH1   0  -0.357   0.4049  -2.1575  -0.4326
 Z2M  C9    C  CH2   0  -0.464   0.9870  -2.9357   0.7133
 Z2M  C10   C  CH2   0  -0.484   0.2717  -3.6486  -0.3899
 Z2M  C11   C  CR15  0  -0.373   2.3618   2.0724  -0.5970
 Z2M  C12   C  CR15  0  -0.327   3.6347   1.4901  -0.3468
 Z2M  H     H  HCR5  0   0.282   4.0309  -0.4686   0.6522
 Z2M  H6    H  HCR6  0   0.268  -2.4746   3.5693   0.1912
 Z2M  H7    H  HCR6  0   0.269  -0.0430   3.3910   0.0572
 Z2M  H8    H  HCH1  0   0.266   1.1230  -1.7642  -1.1416
 Z2M  H9    H  HCH2  0   0.249   2.0649  -3.0145   0.7721
 Z2M  H9A   H  HCH2  0   0.247   0.4898  -2.8593   1.6723
 Z2M  H10   H  HCH2  0   0.250  -0.7033  -4.0665  -0.1784
 Z2M  H10A  H  HCH2  0   0.254   0.8592  -4.2191  -1.0974
 Z2M  H11   H  HCR5  0   0.272   2.1566   3.0103  -1.0876
 Z2M  H12   H  HCR5  0   0.271   4.6016   1.8963  -0.5935
 Z2M  HN1   H  HNR5  0   0.416  -3.8414  -1.0093   0.0254

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
 Z2M  C    O     aromatic  1.344  0.020  1.344
 Z2M  C    C12   aromatic  1.356  0.020  1.356
 Z2M  N    N1    aromatic  1.335  0.020  1.335
 Z2M  N    C4    aromatic  1.311  0.020  1.311
 Z2M  O    C1    aromatic  1.349  0.020  1.349
 Z2M  C1   C2    single    1.450  0.020  1.450
 Z2M  C1   C11   aromatic  1.363  0.020  1.363
 Z2M  N1   C5    aromatic  1.346  0.020  1.346
 Z2M  C2   C3    aromatic  1.408  0.020  1.408
 Z2M  C2   C7    aromatic  1.390  0.020  1.390
 Z2M  N2   C5    aromatic  1.328  0.020  1.328
 Z2M  N2   C6    aromatic  1.320  0.020  1.320
 Z2M  C3   C4    aromatic  1.434  0.020  1.434
 Z2M  C3   C5    aromatic  1.411  0.020  1.411
 Z2M  C4   C8    single    1.475  0.020  1.475
 Z2M  C6   C7    aromatic  1.398  0.020  1.398
 Z2M  C8   C9    single    1.502  0.020  1.502
 Z2M  C8   C10   single    1.498  0.020  1.498
 Z2M  C9   C10   single    1.496  0.020  1.496
 Z2M  C11  C12   aromatic  1.422  0.020  1.422
 Z2M  C    H     single    0.930  0.020  1.080
 Z2M  N1   HN1   single    0.860  0.020  1.020
 Z2M  C6   H6    single    0.930  0.020  1.080
 Z2M  C7   H7    single    0.930  0.020  1.080
 Z2M  C8   H8    single    0.970  0.020  1.090
 Z2M  C9   H9    single    0.970  0.020  1.090
 Z2M  C9   H9A   single    0.970  0.020  1.090
 Z2M  C10  H10   single    0.970  0.020  1.090
 Z2M  C10  H10A  single    0.970  0.020  1.090
 Z2M  C11  H11   single    0.930  0.020  1.080
 Z2M  C12  H12   single    0.930  0.020  1.080

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
 Z2M  H     C    C12  132.95  3.000
 Z2M  H     C    O    116.72  3.000
 Z2M  C12   C    O    110.33  3.000
 Z2M  C4    N    N1   107.96  3.000
 Z2M  C1    O    C    107.86  3.000
 Z2M  C11   C1   C2   131.76  3.000
 Z2M  C11   C1   O    109.60  3.000
 Z2M  C2    C1   O    118.62  3.000
 Z2M  HN1   N1   C5   127.54  3.000
 Z2M  HN1   N1   N    120.37  3.000
 Z2M  C5    N1   N    112.01  3.000
 Z2M  C7    C2   C3   116.12  3.000
 Z2M  C7    C2   C1   118.83  3.000
 Z2M  C3    C2   C1   125.05  3.000
 Z2M  C6    N2   C5   113.97  3.000
 Z2M  C5    C3   C4   104.11  3.000
 Z2M  C5    C3   C2   116.60  3.000
 Z2M  C4    C3   C2   139.26  3.000
 Z2M  C8    C4   C3   129.61  3.000
 Z2M  C8    C4   N    120.74  3.000
 Z2M  C3    C4   N    109.63  3.000
 Z2M  C3    C5   N2   127.79  3.000
 Z2M  C3    C5   N1   106.26  3.000
 Z2M  N2    C5   N1   125.94  3.000
 Z2M  H6    C6   C7   118.96  3.000
 Z2M  H6    C6   N2   116.53  3.000
 Z2M  C7    C6   N2   124.51  3.000
 Z2M  H7    C7   C6   118.67  3.000
 Z2M  H7    C7   C2   120.31  3.000
 Z2M  C6    C7   C2   120.98  3.000
 Z2M  H8    C8   C10  116.05  3.000
 Z2M  H8    C8   C9   115.50  3.000
 Z2M  C10   C8   C9    59.81  3.000
 Z2M  H8    C8   C4   114.30  3.000
 Z2M  C10   C8   C4   120.23  3.000
 Z2M  C9    C8   C4   120.37  3.000
 Z2M  H9A   C9   H9   114.47  3.000
 Z2M  H9A   C9   C10  117.86  3.000
 Z2M  H9    C9   C10  118.79  3.000
 Z2M  H9A   C9   C8   117.45  3.000
 Z2M  H9    C9   C8   117.71  3.000
 Z2M  C10   C9   C8    59.94  3.000
 Z2M  H10A  C10  H10  114.42  3.000
 Z2M  H10A  C10  C9   118.29  3.000
 Z2M  H10   C10  C9   118.10  3.000
 Z2M  H10A  C10  C8   117.26  3.000
 Z2M  H10   C10  C8   118.06  3.000
 Z2M  C9    C10  C8    60.26  3.000
 Z2M  H11   C11  C12  127.35  3.000
 Z2M  H11   C11  C1   126.37  3.000
 Z2M  C12   C11  C1   106.28  3.000
 Z2M  H12   C12  C11  127.49  3.000
 Z2M  H12   C12  C    126.57  3.000
 Z2M  C11   C12  C    105.94  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
 Z2M  CONST_01  C2   C1   O    C   180.00   0.0  0
 Z2M  CONST_02  C11  C1   O    C     0.00   0.0  0
 Z2M  CONST_03  C1   C11  C12  C     0.00   0.0  0
 Z2M  CONST_04  N2   C5   N1   N   180.00   0.0  0
 Z2M  CONST_05  C3   C5   N1   N     0.00   0.0  0
 Z2M  CONST_06  C2   C3   C4   N   180.00   0.0  0
 Z2M  CONST_07  C5   C3   C4   N     0.00   0.0  0
 Z2M  CONST_08  C11  C12  C    O     0.00   0.0  0
 Z2M  CONST_11  C12  C11  C1   O     0.00   0.0  0
 Z2M  CONST_12  C12  C    O    C1    0.00   0.0  0
 Z2M  CONST_13  C4   C3   C2   C1    0.00   0.0  0
 Z2M  CONST_14  C5   C3   C2   C1  180.00   0.0  0
 Z2M  CONST_15  C6   C7   C2   C1  180.00   0.0  0
 Z2M  CONST_16  C3   C4   N    N1    0.00   0.0  0
 Z2M  CONST_17  C6   N2   C5   N1  180.00   0.0  0
 Z2M  CONST_18  C2   C3   C5   N1  180.00   0.0  0
 Z2M  CONST_19  C4   C3   C5   N1    0.00   0.0  0
 Z2M  CONST_20  C12  C11  C1   C2  180.00   0.0  0
 Z2M  CONST_21  N2   C5   C3   C2    0.00   0.0  0
 Z2M  CONST_22  N2   C6   C7   C2    0.00   0.0  0
 Z2M  CONST_23  C4   C3   C5   N2  180.00   0.0  0
 Z2M  CONST_25  C6   C7   C2   C3    0.00   0.0  0
 Z2M  CONST_26  C6   N2   C5   C3    0.00   0.0  0
 Z2M  CONST_27  C5   N1   N    C4    0.00   0.0  0
 Z2M  CONST_28  C7   C2   C3   C4  180.00   0.0  0
 Z2M  CONST_29  C7   C6   N2   C5    0.00   0.0  0
 Z2M  CONST_30  C7   C2   C3   C5    0.00   0.0  0
 Z2M  CONST_32  C8   C4   N    N1  180.00   0.0  0
 Z2M  CONST_33  C8   C4   C3   C2    0.00   0.0  0
 Z2M  CONST_34  C8   C4   C3   C5  180.00   0.0  0
 Z2M  CONST_35  H11  C11  C12  C   180.00   0.0  0
 Z2M  CONST_36  H12  C12  C    O   180.00   0.0  0
 Z2M  CONST_37  H    C    O    C1  180.00   0.0  0
 Z2M  CONST_38  H7   C7   C2   C1    0.00   0.0  0
 Z2M  CONST_39  H6   C6   C7   C2  180.00   0.0  0
 Z2M  CONST_40  HN1  N1   C5   N2    0.00   0.0  0
 Z2M  Var_01    C9   C8   C4   N   -79.57  30.0  2
 Z2M  Var_02    C10  C9   C8   C4  109.52  30.0  1

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
 Z2M  chir_01  C8  C4  C9  C10  both

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
 Z2M  plan-1  C    0.020
 Z2M  plan-1  O    0.020
 Z2M  plan-1  C1   0.020
 Z2M  plan-1  C2   0.020
 Z2M  plan-1  C11  0.020
 Z2M  plan-1  C12  0.020
 Z2M  plan-1  H    0.020
 Z2M  plan-1  H11  0.020
 Z2M  plan-1  H12  0.020
 Z2M  plan-2  N    0.020
 Z2M  plan-2  C1   0.020
 Z2M  plan-2  N1   0.020
 Z2M  plan-2  C2   0.020
 Z2M  plan-2  N2   0.020
 Z2M  plan-2  C3   0.020
 Z2M  plan-2  C4   0.020
 Z2M  plan-2  C5   0.020
 Z2M  plan-2  C6   0.020
 Z2M  plan-2  C7   0.020
 Z2M  plan-2  C8   0.020
 Z2M  plan-2  H6   0.020
 Z2M  plan-2  H7   0.020
 Z2M  plan-2  HN1  0.020

