# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 10:59:16 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-2H-indazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)[C@@H]2CCNC[C@H]2COc3ccc4n[nH]cc4c3
#
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
 ZSO  ZSO  5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-2H-indazole  ligand  44  24  .  2022-07-22  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_ZSO
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
 ZSO  F    F  F     0  -0.319   3.9099  -4.3241   0.4686
 ZSO  C    C  CR6   0   0.506   3.6080  -3.0325   0.2459
 ZSO  C5   C  CR16  0  -0.395   3.3807  -2.6096  -1.0476
 ZSO  C4   C  CR16  0  -0.311   3.0671  -1.2732  -1.2606
 ZSO  C3   C  CR6   0   0.162   2.9812  -0.3673  -0.2075
 ZSO  C2   C  CR16  0  -0.296   3.2217  -0.8371   1.0831
 ZSO  C1   C  CR16  0  -0.395   3.5347  -2.1672   1.3210
 ZSO  C6   C  CH1   0  -0.327   2.6466   1.0811  -0.4636
 ZSO  C10  C  CH1   0  -0.282   1.3270   1.5239   0.1933
 ZSO  C9   C  CH2   0  -0.290   1.0828   3.0117  -0.0975
 ZSO  N    N  NH1   0  -0.577   2.1770   3.8892   0.2748
 ZSO  C8   C  CH2   0  -0.319   3.4362   3.4660  -0.3129
 ZSO  C7   C  CH2   0  -0.420   3.7839   2.0097  -0.0252
 ZSO  C11  C  CH2   0  -0.158   0.1771   0.6663  -0.3028
 ZSO  O    O  O2    0  -0.486  -1.0050   1.0798   0.3588
 ZSO  C12  C  CR6   0   0.390  -2.1805   0.4736   0.0727
 ZSO  C18  C  CR16  0  -0.444  -3.2838   0.9074   0.7641
 ZSO  C17  C  CR56  0  -0.083  -4.5240   0.2966   0.4864
 ZSO  C15  C  CR56  0   0.226  -4.6315  -0.7394  -0.4826
 ZSO  C14  C  CR16  0  -0.277  -3.4830  -1.1680  -1.1802
 ZSO  C13  C  CR16  0  -0.379  -2.2872  -0.5666  -0.9004
 ZSO  C16  C  CR15  0  -0.029  -5.8261   0.4504   0.9566
 ZSO  N2   N  NR15  0  -0.399  -6.5570  -0.4424   0.2795
 ZSO  N1   N  N     0  -0.315  -5.8919  -1.1785  -0.5925
 ZSO  H1   H  HCR6  0   0.277   3.4442  -3.3051  -1.8742
 ZSO  H2   H  HCR6  0   0.259   2.8821  -0.9342  -2.2728
 ZSO  H3   H  HCR6  0   0.258   3.1690  -0.1600   1.9270
 ZSO  H4   H  HCR6  0   0.277   3.7199  -2.5234   2.3259
 ZSO  H5   H  HCH1  0   0.238   2.5240   1.2029  -1.5481
 ZSO  H6   H  HCH1  0   0.233   1.4188   1.3945   1.2800
 ZSO  H7   H  HCH2  0   0.211   0.9001   3.1303  -1.1731
 ZSO  H8   H  HCH2  0   0.244   0.1805   3.3516   0.4122
 ZSO  H9   H  HNH1  0   0.339   2.2677   3.8942   1.2843
 ZSO  H11  H  HCH2  0   0.217   3.3703   3.6112  -1.3970
 ZSO  H12  H  HCH2  0   0.238   4.2314   4.1236   0.0440
 ZSO  H13  H  HCH2  0   0.220   3.9715   1.8853   1.0468
 ZSO  H14  H  HCH2  0   0.236   4.7061   1.7304  -0.5414
 ZSO  H15  H  HCH2  0   0.215   0.0751   0.7801  -1.3906
 ZSO  H16  H  HCH2  0   0.235   0.3733  -0.3921  -0.1003
 ZSO  H17  H  HCR6  0   0.255  -3.1967   1.6992   1.4978
 ZSO  H18  H  HCR6  0   0.264  -3.5421  -1.9538  -1.9218
 ZSO  H19  H  HCR6  0   0.279  -1.4100  -0.8971  -1.4396
 ZSO  H20  H  HCR5  0   0.293  -6.2623   1.1044   1.6931
 ZSO  H21  H  HNR5  0   0.430  -7.5501  -0.5880   0.3869

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
 ZSO  C1   C2   aromatic  1.387  0.020  1.387
 ZSO  C1   C    aromatic  1.382  0.020  1.382
 ZSO  F    C    single    1.345  0.020  1.345
 ZSO  C2   C3   aromatic  1.394  0.020  1.394
 ZSO  C14  C13  aromatic  1.367  0.020  1.367
 ZSO  C14  C15  aromatic  1.410  0.020  1.410
 ZSO  C    C5   aromatic  1.380  0.020  1.380
 ZSO  C13  C12  aromatic  1.428  0.020  1.428
 ZSO  C15  N1   aromatic  1.339  0.020  1.339
 ZSO  C15  C17  aromatic  1.423  0.020  1.423
 ZSO  N1   N2   aromatic  1.321  0.020  1.321
 ZSO  C3   C6   single    1.508  0.020  1.508
 ZSO  C3   C4   aromatic  1.392  0.020  1.392
 ZSO  C12  O    single    1.353  0.020  1.353
 ZSO  C12  C18  aromatic  1.372  0.020  1.372
 ZSO  C5   C4   aromatic  1.389  0.020  1.389
 ZSO  O    C11  single    1.416  0.020  1.416
 ZSO  C6   C7   single    1.532  0.020  1.532
 ZSO  C6   C10  single    1.539  0.020  1.539
 ZSO  C7   C8   single    1.525  0.020  1.525
 ZSO  C17  C18  aromatic  1.410  0.020  1.410
 ZSO  C17  C16  aromatic  1.393  0.020  1.393
 ZSO  N2   C16  aromatic  1.338  0.020  1.338
 ZSO  C8   N    single    1.453  0.020  1.453
 ZSO  C11  C10  single    1.518  0.020  1.518
 ZSO  C10  C9   single    1.535  0.020  1.535
 ZSO  C9   N    single    1.451  0.020  1.451
 ZSO  C5   H1   single    0.930  0.020  1.080
 ZSO  C4   H2   single    0.930  0.020  1.080
 ZSO  C2   H3   single    0.930  0.020  1.080
 ZSO  C1   H4   single    0.930  0.020  1.080
 ZSO  C6   H5   single    0.970  0.020  1.090
 ZSO  C10  H6   single    0.970  0.020  1.090
 ZSO  C9   H7   single    0.970  0.020  1.090
 ZSO  C9   H8   single    0.970  0.020  1.090
 ZSO  N    H9   single    0.890  0.020  1.040
 ZSO  C8   H11  single    0.970  0.020  1.090
 ZSO  C8   H12  single    0.970  0.020  1.090
 ZSO  C7   H13  single    0.970  0.020  1.090
 ZSO  C7   H14  single    0.970  0.020  1.090
 ZSO  C11  H15  single    0.970  0.020  1.090
 ZSO  C11  H16  single    0.970  0.020  1.090
 ZSO  C18  H17  single    0.930  0.020  1.080
 ZSO  C14  H18  single    0.930  0.020  1.080
 ZSO  C13  H19  single    0.930  0.020  1.080
 ZSO  C16  H20  single    0.930  0.020  1.080
 ZSO  N2   H21  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
 ZSO  C1   C    C5   121.91  3.000
 ZSO  C5   C    F    119.12  3.000
 ZSO  C1   C    F    118.97  3.000
 ZSO  H1   C5   C4   120.96  3.000
 ZSO  H1   C5   C    120.62  3.000
 ZSO  C4   C5   C    118.41  3.000
 ZSO  H2   C4   C3   119.51  3.000
 ZSO  H2   C4   C5   118.88  3.000
 ZSO  C3   C4   C5   121.61  3.000
 ZSO  C6   C3   C2   121.26  3.000
 ZSO  C6   C3   C4   120.68  3.000
 ZSO  C2   C3   C4   118.06  3.000
 ZSO  H3   C2   C1   118.48  3.000
 ZSO  H3   C2   C3   120.14  3.000
 ZSO  C1   C2   C3   121.38  3.000
 ZSO  H4   C1   C2   120.90  3.000
 ZSO  H4   C1   C    120.48  3.000
 ZSO  C2   C1   C    118.62  3.000
 ZSO  H5   C6   C7   107.35  3.000
 ZSO  H5   C6   C10  107.09  3.000
 ZSO  C7   C6   C10  109.87  3.000
 ZSO  H5   C6   C3   107.39  3.000
 ZSO  C10  C6   C3   113.20  3.000
 ZSO  C7   C6   C3   111.63  3.000
 ZSO  H6   C10  C11  108.68  3.000
 ZSO  H6   C10  C9   108.35  3.000
 ZSO  C11  C10  C9   111.41  3.000
 ZSO  H6   C10  C6   108.47  3.000
 ZSO  C9   C10  C6   109.53  3.000
 ZSO  C11  C10  C6   110.33  3.000
 ZSO  H8   C9   H7   106.66  3.000
 ZSO  H8   C9   N    108.39  3.000
 ZSO  H7   C9   N    108.15  3.000
 ZSO  H8   C9   C10  110.18  3.000
 ZSO  H7   C9   C10  108.47  3.000
 ZSO  N    C9   C10  114.67  3.000
 ZSO  H9   N    C8   109.08  3.000
 ZSO  H9   N    C9   109.03  3.000
 ZSO  C8   N    C9   111.94  3.000
 ZSO  H12  C8   H11  106.70  3.000
 ZSO  H12  C8   C7   110.33  3.000
 ZSO  H11  C8   C7   109.09  3.000
 ZSO  H12  C8   N    108.88  3.000
 ZSO  H11  C8   N    108.03  3.000
 ZSO  C7   C8   N    113.55  3.000
 ZSO  H14  C7   H13  106.77  3.000
 ZSO  H14  C7   C8   110.32  3.000
 ZSO  H13  C7   C8   109.40  3.000
 ZSO  H14  C7   C6   109.65  3.000
 ZSO  H13  C7   C6   109.78  3.000
 ZSO  C8   C7   C6   110.83  3.000
 ZSO  H16  C11  H15  107.44  3.000
 ZSO  H16  C11  O    110.19  3.000
 ZSO  H15  C11  O    110.78  3.000
 ZSO  H16  C11  C10  110.48  3.000
 ZSO  H15  C11  C10  109.61  3.000
 ZSO  O    C11  C10  108.34  3.000
 ZSO  C12  O    C11  119.71  3.000
 ZSO  C13  C12  C18  120.89  3.000
 ZSO  C18  C12  O    116.76  3.000
 ZSO  C13  C12  O    122.35  3.000
 ZSO  H17  C18  C17  121.40  3.000
 ZSO  H17  C18  C12  120.51  3.000
 ZSO  C17  C18  C12  118.09  3.000
 ZSO  C16  C17  C15  103.87  3.000
 ZSO  C16  C17  C18  135.06  3.000
 ZSO  C15  C17  C18  121.07  3.000
 ZSO  N1   C15  C14  128.76  3.000
 ZSO  N1   C15  C17  111.46  3.000
 ZSO  C14  C15  C17  119.78  3.000
 ZSO  H18  C14  C13  120.48  3.000
 ZSO  H18  C14  C15  121.01  3.000
 ZSO  C13  C14  C15  118.51  3.000
 ZSO  H19  C13  C14  118.23  3.000
 ZSO  H19  C13  C12  120.11  3.000
 ZSO  C14  C13  C12  121.66  3.000
 ZSO  H20  C16  N2   122.00  3.000
 ZSO  H20  C16  C17  132.56  3.000
 ZSO  N2   C16  C17  105.43  3.000
 ZSO  H21  N2   N1   119.03  3.000
 ZSO  H21  N2   C16  125.44  3.000
 ZSO  N1   N2   C16  115.53  3.000
 ZSO  N2   N1   C15  103.71  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
 ZSO  CONST_01  C3   C2   C1   C      0.00   0.0  0
 ZSO  CONST_02  C3   C4   C5   C      0.00   0.0  0
 ZSO  CONST_03  C2   C1   C    C5     0.00   0.0  0
 ZSO  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 ZSO  CONST_05  C1   C2   C3   C4     0.00   0.0  0
 ZSO  CONST_06  C1   C    C5   C4     0.00   0.0  0
 ZSO  CONST_07  C15  C14  C13  C12    0.00   0.0  0
 ZSO  CONST_08  C15  C17  C18  C12    0.00   0.0  0
 ZSO  CONST_09  C16  C17  C18  C12  180.00   0.0  0
 ZSO  CONST_10  C14  C13  C12  C18    0.00   0.0  0
 ZSO  CONST_11  C14  C15  C17  C18    0.00   0.0  0
 ZSO  CONST_12  N1   C15  C17  C18  180.00   0.0  0
 ZSO  CONST_13  N2   C16  C17  C18  180.00   0.0  0
 ZSO  CONST_14  C13  C14  C15  C17    0.00   0.0  0
 ZSO  CONST_15  N2   N1   C15  C17    0.00   0.0  0
 ZSO  CONST_16  C13  C12  C18  C17    0.00   0.0  0
 ZSO  CONST_17  N1   N2   C16  C17    0.00   0.0  0
 ZSO  CONST_18  C16  N2   N1   C15    0.00   0.0  0
 ZSO  CONST_19  N2   C16  C17  C15    0.00   0.0  0
 ZSO  CONST_20  N2   N1   C15  C14  180.00   0.0  0
 ZSO  CONST_21  C16  C17  C15  C14  180.00   0.0  0
 ZSO  CONST_22  N1   C15  C14  C13  180.00   0.0  0
 ZSO  CONST_23  N1   C15  C17  C16    0.00   0.0  0
 ZSO  CONST_24  C6   C3   C4   C5   180.00   0.0  0
 ZSO  CONST_25  C6   C3   C2   C1   180.00   0.0  0
 ZSO  CONST_26  C2   C1   C    F    180.00   0.0  0
 ZSO  CONST_27  C4   C5   C    F    180.00   0.0  0
 ZSO  CONST_28  C14  C13  C12  O    180.00   0.0  0
 ZSO  CONST_29  C17  C18  C12  O    180.00   0.0  0
 ZSO  CONST_30  H3   C2   C1   C    180.00   0.0  0
 ZSO  CONST_31  H2   C4   C5   C    180.00   0.0  0
 ZSO  CONST_32  H4   C1   C    C5   180.00   0.0  0
 ZSO  CONST_33  H1   C5   C4   C3   180.00   0.0  0
 ZSO  CONST_34  H18  C14  C13  C12  180.00   0.0  0
 ZSO  CONST_35  H19  C13  C12  C18  180.00   0.0  0
 ZSO  CONST_36  H20  C16  C17  C18    0.00   0.0  0
 ZSO  CONST_37  H21  N2   C16  C17  180.00   0.0  0
 ZSO  CONST_38  H17  C18  C17  C15  180.00   0.0  0
 ZSO  Var_01    N    C8   C7   C6    54.86  30.0  1
 ZSO  Var_02    C8   N    C9   C10   53.66  30.0  1
 ZSO  Var_03    C7   C8   N    C9   -53.44  30.0  1
 ZSO  Var_04    C13  C12  O    C11   -1.14  30.0  1
 ZSO  Var_05    H15  C11  O    C12   58.90  30.0  3

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
 ZSO  chir_01  C6   C3  C7   C10  positiv
 ZSO  chir_02  C10  C6  C11  C9   positiv

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
 ZSO  plan-1  F    0.020
 ZSO  plan-1  C    0.020
 ZSO  plan-1  C5   0.020
 ZSO  plan-1  C4   0.020
 ZSO  plan-1  C3   0.020
 ZSO  plan-1  C2   0.020
 ZSO  plan-1  C1   0.020
 ZSO  plan-1  C6   0.020
 ZSO  plan-1  H1   0.020
 ZSO  plan-1  H2   0.020
 ZSO  plan-1  H3   0.020
 ZSO  plan-1  H4   0.020
 ZSO  plan-2  O    0.020
 ZSO  plan-2  C12  0.020
 ZSO  plan-2  C18  0.020
 ZSO  plan-2  C17  0.020
 ZSO  plan-2  C15  0.020
 ZSO  plan-2  C14  0.020
 ZSO  plan-2  C13  0.020
 ZSO  plan-2  C16  0.020
 ZSO  plan-2  N2   0.020
 ZSO  plan-2  N1   0.020
 ZSO  plan-2  H17  0.020
 ZSO  plan-2  H18  0.020
 ZSO  plan-2  H19  0.020
 ZSO  plan-2  H20  0.020
 ZSO  plan-2  H21  0.020

