# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 18:42:19 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC[C@@H]([C@@H](O)C1)c2c(O)cc(O)c3C(=O)C=C(Oc23)c4ccccc4Cl
#
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
 F9Z  F9Z  2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one  ligand  48  28  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_F9Z
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
 F9Z  C4   C   CH1   0  -0.416  -1.9899  -0.3495   0.3604
 F9Z  C14  C   CR16  0  -0.298   3.8667  -0.7799   1.2667
 F9Z  C5   C   CR6   0  -0.043  -1.5282   1.0860   0.2509
 F9Z  C6   C   CR6   0   0.319  -2.3883   2.1863   0.1304
 F9Z  C11  C   CR16  0  -0.494   2.5862   1.7315   0.1789
 F9Z  C7   C   CR16  0  -0.462  -1.9237   3.5012   0.0416
 F9Z  C8   C   CR6   0   0.377  -0.5708   3.7656   0.0510
 F9Z  C9   C   CR66  0  -0.339   0.3433   2.6926   0.1517
 F9Z  C10  C   CR6   0   0.521   1.7714   2.9190   0.1246
 F9Z  C12  C   CR6   0   0.393   2.0099   0.5205   0.3091
 F9Z  C13  C   CR6   0   0.105   2.7581  -0.7403   0.4202
 F9Z  N1   N   NT    0  -0.417  -3.8186  -2.5821   0.4561
 F9Z  C3   C   CH2   0  -0.421  -2.8347  -0.6549   1.6032
 F9Z  C1   C   CH3   0  -0.516  -4.2473  -3.9594   0.5497
 F9Z  C2   C   CH2   0  -0.276  -3.1569  -2.1392   1.6675
 F9Z  O1   O   OH1   0  -0.613  -3.7237   2.0709   0.0872
 F9Z  O2   O   OH1   0  -0.631  -0.1406   5.0203  -0.0383
 F9Z  O3   O   O     0  -0.505   2.2554   4.0585   0.0406
 F9Z  C15  C   CR16  0  -0.232   4.6176  -1.9338   1.4120
 F9Z  C16  C   CR16  0  -0.258   4.2653  -3.0752   0.7071
 F9Z  C17  C   CR16  0  -0.195   3.1720  -3.0576  -0.1455
 F9Z  C18  C   CR6   0  -0.102   2.4241  -1.8990  -0.2869
 F9Z  CL1  CL  CL    0  -0.096   1.1044  -1.9164  -1.4034
 F9Z  O4   O   O     0  -0.454   0.6879   0.3598   0.3792
 F9Z  C19  C   CR66  0   0.370  -0.1700   1.3963   0.2532
 F9Z  C20  C   CH1   0   0.096  -2.6959  -0.8739  -0.8921
 F9Z  O5   O   OH1   0  -0.653  -1.8659  -0.6354  -1.9982
 F9Z  C21  C   CH2   0  -0.310  -2.9864  -2.3598  -0.7068
 F9Z  H1   H   HCH1  0   0.270  -1.0964  -0.9696   0.4549
 F9Z  H3   H   HCR6  0   0.291   3.6612   1.8159   0.1068
 F9Z  H4   H   HCR6  0   0.279  -2.6367   4.3115  -0.0423
 F9Z  H6   H   HCH2  0   0.255  -2.2830  -0.3624   2.4982
 F9Z  H7   H   HCH2  0   0.215  -3.7711  -0.0908   1.6215
 F9Z  H8   H   HCH3  0   0.193  -3.4152  -4.6678   0.6845
 F9Z  H9   H   HCH3  0   0.233  -4.9301  -4.0838   1.3916
 F9Z  H10  H   HCH3  0   0.234  -4.7831  -4.2459  -0.3565
 F9Z  H11  H   HCH2  0   0.242  -3.8145  -2.3324   2.5180
 F9Z  H12  H   HCH2  0   0.193  -2.2227  -2.7008   1.8510
 F9Z  H13  H   HOH1  0   0.481  -4.0166   1.1550   0.1232
 F9Z  H14  H   HOH1  0   0.477   0.8472   4.9930  -0.0228
 F9Z  H15  H   HCR6  0   0.274   5.4685  -1.9418   2.0789
 F9Z  H16  H   HCR6  0   0.278   4.8409  -3.9847   0.8138
 F9Z  H17  H   HCR6  0   0.287   2.9037  -3.9418  -0.7074
 F9Z  H18  H   HCH1  0   0.185  -3.6715  -0.3802  -1.0285
 F9Z  H19  H   HOH1  0   0.451  -2.3186  -0.9484  -2.7880
 F9Z  H20  H   HCH2  0   0.193  -2.0260  -2.9049  -0.6463
 F9Z  H21  H   HCH2  0   0.240  -3.5111  -2.7371  -1.5899
 F9Z  H2   H   HCR6  0   0.278   4.1276   0.1052   1.8320

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
 F9Z  C16  C17  aromatic  1.387  0.020  1.387
 F9Z  C16  C15  aromatic  1.387  0.020  1.387
 F9Z  C17  C18  aromatic  1.386  0.020  1.386
 F9Z  C15  C14  aromatic  1.384  0.020  1.384
 F9Z  C18  CL1  single    1.729  0.020  1.729
 F9Z  C18  C13  aromatic  1.398  0.020  1.398
 F9Z  C14  C13  aromatic  1.395  0.020  1.395
 F9Z  C1   N1   single    1.445  0.020  1.445
 F9Z  C13  C12  single    1.470  0.020  1.470
 F9Z  C2   N1   single    1.450  0.020  1.450
 F9Z  C2   C3   single    1.520  0.020  1.520
 F9Z  N1   C21  single    1.447  0.020  1.447
 F9Z  C21  C20  single    1.525  0.020  1.525
 F9Z  C12  O4   single    1.334  0.020  1.334
 F9Z  C12  C11  double    1.347  0.020  1.347
 F9Z  C3   C4   single    1.533  0.020  1.533
 F9Z  O4   C19  single    1.351  0.020  1.351
 F9Z  C4   C20  single    1.530  0.020  1.530
 F9Z  C4   C5   single    1.512  0.020  1.512
 F9Z  C11  C10  single    1.441  0.020  1.441
 F9Z  C20  O5   single    1.403  0.020  1.403
 F9Z  C19  C5   aromatic  1.393  0.020  1.393
 F9Z  C19  C9   aromatic  1.398  0.020  1.398
 F9Z  C5   C6   aromatic  1.402  0.020  1.402
 F9Z  C10  C9   single    1.446  0.020  1.446
 F9Z  C10  O3   double    1.241  0.020  1.241
 F9Z  C9   C8   aromatic  1.413  0.020  1.413
 F9Z  C6   O1   single    1.341  0.020  1.341
 F9Z  C6   C7   aromatic  1.397  0.020  1.397
 F9Z  C8   C7   aromatic  1.378  0.020  1.378
 F9Z  C8   O2   single    1.329  0.020  1.329
 F9Z  C4   H1   single    0.970  0.020  1.090
 F9Z  C14  H2   single    0.930  0.020  1.080
 F9Z  C11  H3   single    0.930  0.020  1.080
 F9Z  C7   H4   single    0.930  0.020  1.080
 F9Z  C3   H6   single    0.970  0.020  1.090
 F9Z  C3   H7   single    0.970  0.020  1.090
 F9Z  C1   H8   single    0.970  0.020  1.090
 F9Z  C1   H9   single    0.970  0.020  1.090
 F9Z  C1   H10  single    0.970  0.020  1.090
 F9Z  C2   H11  single    0.970  0.020  1.090
 F9Z  C2   H12  single    0.970  0.020  1.090
 F9Z  O1   H13  single    0.850  0.020  0.980
 F9Z  O2   H14  single    0.850  0.020  0.980
 F9Z  C15  H15  single    0.930  0.020  1.080
 F9Z  C16  H16  single    0.930  0.020  1.080
 F9Z  C17  H17  single    0.930  0.020  1.080
 F9Z  C20  H18  single    0.970  0.020  1.090
 F9Z  O5   H19  single    0.850  0.020  0.980
 F9Z  C21  H20  single    0.970  0.020  1.090
 F9Z  C21  H21  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
 F9Z  H1   C4   C20  104.70  3.000
 F9Z  H1   C4   C3   105.52  3.000
 F9Z  C20  C4   C3   109.93  3.000
 F9Z  H1   C4   C5   107.20  3.000
 F9Z  C20  C4   C5   114.01  3.000
 F9Z  C3   C4   C5   114.59  3.000
 F9Z  H2   C14  C15  119.74  3.000
 F9Z  H2   C14  C13  119.03  3.000
 F9Z  C15  C14  C13  121.22  3.000
 F9Z  C19  C5   C6   115.06  3.000
 F9Z  C6   C5   C4   124.34  3.000
 F9Z  C19  C5   C4   120.60  3.000
 F9Z  O1   C6   C7   114.21  3.000
 F9Z  C7   C6   C5   122.69  3.000
 F9Z  O1   C6   C5   123.11  3.000
 F9Z  H3   C11  C12  120.14  3.000
 F9Z  H3   C11  C10  119.71  3.000
 F9Z  C12  C11  C10  120.16  3.000
 F9Z  H4   C7   C8   120.22  3.000
 F9Z  H4   C7   C6   119.35  3.000
 F9Z  C8   C7   C6   120.42  3.000
 F9Z  O2   C8   C9   120.80  3.000
 F9Z  O2   C8   C7   119.88  3.000
 F9Z  C9   C8   C7   119.32  3.000
 F9Z  C19  C9   C10  120.60  3.000
 F9Z  C10  C9   C8   121.24  3.000
 F9Z  C19  C9   C8   118.15  3.000
 F9Z  O3   C10  C9   122.01  3.000
 F9Z  O3   C10  C11  122.60  3.000
 F9Z  C9   C10  C11  115.38  3.000
 F9Z  O4   C12  C13  113.40  3.000
 F9Z  O4   C12  C11  122.51  3.000
 F9Z  C13  C12  C11  124.08  3.000
 F9Z  C18  C13  C12  123.43  3.000
 F9Z  C12  C13  C14  118.33  3.000
 F9Z  C18  C13  C14  118.24  3.000
 F9Z  C21  N1   C2   111.23  3.000
 F9Z  C21  N1   C1   111.65  3.000
 F9Z  C2   N1   C1   111.86  3.000
 F9Z  H7   C3   H6   106.32  3.000
 F9Z  H7   C3   C2   108.75  3.000
 F9Z  H6   C3   C2   109.52  3.000
 F9Z  H7   C3   C4   112.49  3.000
 F9Z  H6   C3   C4   109.44  3.000
 F9Z  C2   C3   C4   110.21  3.000
 F9Z  H10  C1   H9   107.67  3.000
 F9Z  H10  C1   H8   107.69  3.000
 F9Z  H9   C1   H8   107.77  3.000
 F9Z  H10  C1   N1   110.00  3.000
 F9Z  H9   C1   N1   110.13  3.000
 F9Z  H8   C1   N1   113.38  3.000
 F9Z  H12  C2   H11  106.83  3.000
 F9Z  H12  C2   C3   108.91  3.000
 F9Z  H11  C2   C3   109.47  3.000
 F9Z  H12  C2   N1   111.67  3.000
 F9Z  H11  C2   N1   108.77  3.000
 F9Z  C3   C2   N1   111.09  3.000
 F9Z  H13  O1   C6   112.57  3.000
 F9Z  H14  O2   C8   107.24  3.000
 F9Z  H15  C15  C16  120.49  3.000
 F9Z  H15  C15  C14  119.86  3.000
 F9Z  C16  C15  C14  119.65  3.000
 F9Z  H16  C16  C17  119.41  3.000
 F9Z  H16  C16  C15  120.44  3.000
 F9Z  C17  C16  C15  120.15  3.000
 F9Z  H17  C17  C18  119.77  3.000
 F9Z  H17  C17  C16  120.31  3.000
 F9Z  C18  C17  C16  119.92  3.000
 F9Z  CL1  C18  C17  117.99  3.000
 F9Z  CL1  C18  C13  121.16  3.000
 F9Z  C17  C18  C13  120.81  3.000
 F9Z  C19  O4   C12  122.14  3.000
 F9Z  O4   C19  C9   119.01  3.000
 F9Z  C9   C19  C5   124.35  3.000
 F9Z  O4   C19  C5   116.63  3.000
 F9Z  H18  C20  C21  106.43  3.000
 F9Z  H18  C20  O5   110.49  3.000
 F9Z  C21  C20  O5   111.96  3.000
 F9Z  H18  C20  C4   110.87  3.000
 F9Z  O5   C20  C4   108.30  3.000
 F9Z  C21  C20  C4   108.80  3.000
 F9Z  H19  O5   C20  108.26  3.000
 F9Z  H21  C21  H20  106.89  3.000
 F9Z  H21  C21  C20  109.22  3.000
 F9Z  H20  C21  C20  108.75  3.000
 F9Z  H21  C21  N1   108.65  3.000
 F9Z  H20  C21  N1   112.31  3.000
 F9Z  C20  C21  N1   110.91  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
 F9Z  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 F9Z  CONST_02  C17  C18  C13  C14     0.00   0.0  0
 F9Z  CONST_03  C8   C9   C19  C5      0.00   0.0  0
 F9Z  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 F9Z  CONST_05  C9   C19  C5   C6      0.00   0.0  0
 F9Z  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 F9Z  CONST_07  C19  C5   C6   C7      0.00   0.0  0
 F9Z  CONST_08  C19  C9   C8   C7      0.00   0.0  0
 F9Z  CONST_09  C16  C17  C18  C13     0.00   0.0  0
 F9Z  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 F9Z  CONST_11  C18  C17  C16  C15     0.00   0.0  0
 F9Z  CONST_12  C18  C13  C14  C15     0.00   0.0  0
 F9Z  CONST_13  O4   C19  C5   C4      0.00   0.0  0
 F9Z  CONST_14  C9   C19  C5   C4    180.00   0.0  0
 F9Z  CONST_15  C7   C6   C5   C4    180.00   0.0  0
 F9Z  CONST_16  C17  C18  C13  C12   180.00   0.0  0
 F9Z  CONST_17  C15  C14  C13  C12   180.00   0.0  0
 F9Z  CONST_18  O1   C6   C5   C4      0.00   0.0  0
 F9Z  CONST_19  CL1  C18  C13  C14   180.00   0.0  0
 F9Z  CONST_20  O2   C8   C7   C6    180.00   0.0  0
 F9Z  CONST_21  O1   C6   C7   C8    180.00   0.0  0
 F9Z  CONST_22  O2   C8   C9   C10     0.00   0.0  0
 F9Z  CONST_23  CL1  C18  C13  C12     0.00   0.0  0
 F9Z  CONST_24  C19  C5   C6   O1    180.00   0.0  0
 F9Z  CONST_25  C19  C9   C8   O2    180.00   0.0  0
 F9Z  CONST_26  CL1  C18  C17  C16   180.00   0.0  0
 F9Z  CONST_27  H16  C16  C15  C14   180.00   0.0  0
 F9Z  CONST_28  H4   C7   C6   C5    180.00   0.0  0
 F9Z  CONST_29  H2   C14  C13  C12     0.00   0.0  0
 F9Z  CONST_30  H17  C17  C18  C13   180.00   0.0  0
 F9Z  CONST_31  H15  C15  C14  C13   180.00   0.0  0
 F9Z  Var_01    N1   C2   C3   C4    -56.03  30.0  1
 F9Z  Var_02    O4   C12  C13  C14  -134.26  30.0  2
 F9Z  Var_03    C19  C9   C10  C11     1.30  30.0  1
 F9Z  Var_04    C12  C11  C10  C9     -2.94  30.0  1
 F9Z  Var_05    C13  C12  C11  C10  -177.79  30.0  1
 F9Z  Var_06    C21  N1   C2   C3     59.91  30.0  1
 F9Z  Var_07    C20  C21  N1   C2    -61.74  30.0  1
 F9Z  Var_08    H8   C1   N1   C2    -62.11  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
 F9Z  chir_01  C4   C3  C20  C5   negativ
 F9Z  chir_02  C20  O5  C4   C21  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
 F9Z  plan-1  C14  0.020
 F9Z  plan-1  C12  0.020
 F9Z  plan-1  C13  0.020
 F9Z  plan-1  C15  0.020
 F9Z  plan-1  C16  0.020
 F9Z  plan-1  C17  0.020
 F9Z  plan-1  C18  0.020
 F9Z  plan-1  CL1  0.020
 F9Z  plan-1  H15  0.020
 F9Z  plan-1  H16  0.020
 F9Z  plan-1  H17  0.020
 F9Z  plan-1  H2   0.020
 F9Z  plan-2  C4   0.020
 F9Z  plan-2  C5   0.020
 F9Z  plan-2  C6   0.020
 F9Z  plan-2  C7   0.020
 F9Z  plan-2  C8   0.020
 F9Z  plan-2  C9   0.020
 F9Z  plan-2  C10  0.020
 F9Z  plan-2  O1   0.020
 F9Z  plan-2  O2   0.020
 F9Z  plan-2  O4   0.020
 F9Z  plan-2  C19  0.020
 F9Z  plan-2  H4   0.020
 F9Z  plan-3  C11  0.020
 F9Z  plan-3  C9   0.020
 F9Z  plan-3  C10  0.020
 F9Z  plan-3  O3   0.020

