# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:58:21 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-(2-chlorophenyl)-5,7-dihydroxy-8-[(3S,4R)-3-hydroxy-1-methylpiperidin-4-yl]-4H-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
 CPB  CPB  2-(2-chlorophenyl)-5,7-dihydroxy-8-[(3S,4R)-3-hydroxy-1-methylpiperidin-4-yl]-4H-chromen-4-one  ligand  48  28  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CPB
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
 CPB  C1    C   CH3   0  -0.516   5.4732   0.2890  -1.3270
 CPB  N1    N   NT    0  -0.398   4.0407   0.1491  -1.2125
 CPB  C16   C   CH2   0  -0.282   3.3722   1.4338  -1.2635
 CPB  C15   C   CH2   0  -0.418   1.8826   1.2782  -1.0012
 CPB  C14   C   CH1   0  -0.335   1.2788   0.3391  -2.0499
 CPB  C13   C   CH1   0   0.085   2.0250  -0.9992  -2.0805
 CPB  C12   C   CH2   0  -0.315   3.5226  -0.7482  -2.2217
 CPB  C8    C   CR6   0  -0.079  -0.2225   0.1411  -2.0532
 CPB  C9    C   CR66  0   0.373  -1.0185  -0.0564  -0.9253
 CPB  O1    O   O     0  -0.456  -0.3762   0.0141   0.2578
 CPB  C2    C   CR6   0   0.387  -0.9893  -0.2015   1.4256
 CPB  C3    C   CR16  0  -0.503  -2.3000  -0.4785   1.4952
 CPB  C4    C   CR6   0   0.469  -3.1269  -0.5207   0.3031
 CPB  O4    O   OC    0  -0.446  -4.3296  -0.7418   0.3780
 CPB  C10   C   CR66  0  -0.287  -2.4044  -0.2984  -0.9505
 CPB  C5    C   CR6   0   0.363  -3.0234  -0.3449  -2.2178
 CPB  O5    O   OH1   0  -0.598  -4.3360  -0.5793  -2.2917
 CPB  C6    C   CR16  0  -0.547  -2.2703  -0.1554  -3.3587
 CPB  C7    C   CR6   0   0.367  -0.8980   0.0770  -3.2764
 CPB  O7    O   OH1   0  -0.617  -0.1784   0.2415  -4.3942
 CPB  C21   C   CR6   0   0.102  -0.0380  -0.1634   2.5496
 CPB  C22   C   CR6   0  -0.118  -0.2985   0.4629   3.7704
 CPB  CL1   CL  CL    0  -0.116  -1.7531   1.3637   4.0394
 CPB  C23   C   CR16  0  -0.191   0.6263   0.4305   4.8042
 CPB  C24   C   CR16  0  -0.259   1.8332  -0.2271   4.6306
 CPB  C25   C   CR16  0  -0.237   2.1232  -0.8349   3.4175
 CPB  C26   C   CR16  0  -0.304   1.1991  -0.7954   2.3886
 CPB  O3    O   OH1   0  -0.656   1.6963  -1.7377  -0.9270
 CPB  H11   H   HCH3  0   0.231   5.8509   0.9387  -0.5357
 CPB  H12   H   HCH3  0   0.230   5.9568  -0.6834  -1.2180
 CPB  H13   H   HCH3  0   0.188   5.7941   0.7156  -2.2911
 CPB  H161  H   HCH2  0   0.234   3.8097   2.0859  -0.5032
 CPB  H162  H   HCH2  0   0.180   3.5329   1.9352  -2.2370
 CPB  H151  H   HCH2  0   0.247   1.7523   0.9140   0.0142
 CPB  H152  H   HCH2  0   0.228   1.4018   2.2572  -1.0631
 CPB  H141  H   HCH1  0   0.252   1.5229   0.8036  -3.0091
 CPB  H131  H   HCH1  0   0.212   1.7088  -1.5428  -2.9821
 CPB  H121  H   HCH2  0   0.189   3.7026  -0.3635  -3.2433
 CPB  H122  H   HCH2  0   0.238   4.0601  -1.7005  -2.1612
 CPB  H31   H   HCR6  0   0.273  -2.7637  -0.6859   2.4481
 CPB  HO5   H   HOH1  0   0.480  -4.6120  -0.5963  -3.2164
 CPB  H61   H   HCR6  0   0.288  -2.7497  -0.1974  -4.3317
 CPB  HO7   H   HOH1  0   0.485  -0.7420   0.1934  -5.1753
 CPB  H231  H   HCR6  0   0.286   0.4047   0.9272   5.7389
 CPB  H241  H   HCR6  0   0.276   2.5468  -0.2526   5.4429
 CPB  H251  H   HCR6  0   0.269   3.0676  -1.3412   3.2710
 CPB  H261  H   HCR6  0   0.299   1.4340  -1.2625   1.4408
 CPB  HO3   H   HOH1  0   0.449   2.1868  -2.5653  -0.9506

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
 CPB  C1   N1    single    1.444  0.020  1.444
 CPB  C1   H11   single    0.970  0.020  1.090
 CPB  C1   H12   single    0.970  0.020  1.090
 CPB  C1   H13   single    0.970  0.020  1.090
 CPB  N1   C16   single    1.449  0.020  1.449
 CPB  N1   C12   single    1.446  0.020  1.446
 CPB  C16  C15   single    1.521  0.020  1.521
 CPB  C16  H161  single    0.970  0.020  1.090
 CPB  C16  H162  single    0.970  0.020  1.090
 CPB  C15  C14   single    1.532  0.020  1.532
 CPB  C15  H151  single    0.970  0.020  1.090
 CPB  C15  H152  single    0.970  0.020  1.090
 CPB  C14  C13   single    1.533  0.020  1.533
 CPB  C14  C8    single    1.514  0.020  1.514
 CPB  C14  H141  single    0.970  0.020  1.090
 CPB  C13  C12   single    1.525  0.020  1.525
 CPB  C13  O3    single    1.408  0.020  1.408
 CPB  C13  H131  single    0.970  0.020  1.090
 CPB  C12  H121  single    0.970  0.020  1.090
 CPB  C12  H122  single    0.970  0.020  1.090
 CPB  C8   C9    aromatic  1.395  0.020  1.395
 CPB  C8   C7    aromatic  1.399  0.020  1.399
 CPB  C9   O1    aromatic  1.348  0.020  1.348
 CPB  C9   C10   aromatic  1.407  0.020  1.407
 CPB  O1   C2    aromatic  1.337  0.020  1.337
 CPB  C2   C3    aromatic  1.341  0.020  1.341
 CPB  C2   C21   single    1.473  0.020  1.473
 CPB  C3   C4    aromatic  1.451  0.020  1.451
 CPB  C3   H31   single    0.930  0.020  1.080
 CPB  C4   O4    double    1.225  0.020  1.225
 CPB  C4   C10   aromatic  1.464  0.020  1.464
 CPB  C10  C5    aromatic  1.411  0.020  1.411
 CPB  C5   O5    single    1.335  0.020  1.335
 CPB  C5   C6    aromatic  1.380  0.020  1.380
 CPB  O5   HO5   single    0.850  0.020  0.980
 CPB  C6   C7    aromatic  1.394  0.020  1.394
 CPB  C6   H61   single    0.930  0.020  1.080
 CPB  C7   O7    single    1.340  0.020  1.340
 CPB  O7   HO7   single    0.850  0.020  0.980
 CPB  C21  C22   aromatic  1.397  0.020  1.397
 CPB  C21  C26   aromatic  1.399  0.020  1.399
 CPB  C22  CL1   single    1.732  0.020  1.732
 CPB  C22  C23   aromatic  1.388  0.020  1.388
 CPB  C23  C24   aromatic  1.385  0.020  1.385
 CPB  C23  H231  single    0.930  0.020  1.080
 CPB  C24  C25   aromatic  1.388  0.020  1.388
 CPB  C24  H241  single    0.930  0.020  1.080
 CPB  C25  C26   aromatic  1.384  0.020  1.384
 CPB  C25  H251  single    0.930  0.020  1.080
 CPB  C26  H261  single    0.930  0.020  1.080
 CPB  O3   HO3   single    0.850  0.020  0.980

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
 CPB  H13   C1   H12   107.65  3.000
 CPB  H13   C1   H11   107.65  3.000
 CPB  H12   C1   H11   107.74  3.000
 CPB  H13   C1   N1    113.31  3.000
 CPB  H12   C1   N1    110.20  3.000
 CPB  H11   C1   N1    110.09  3.000
 CPB  C12   N1   C16   111.11  3.000
 CPB  C12   N1   C1    111.11  3.000
 CPB  C16   N1   C1    111.65  3.000
 CPB  H162  C16  H161  106.47  3.000
 CPB  H162  C16  C15   109.89  3.000
 CPB  H161  C16  C15   109.46  3.000
 CPB  H162  C16  N1    111.45  3.000
 CPB  H161  C16  N1    108.65  3.000
 CPB  C15   C16  N1    110.80  3.000
 CPB  H152  C15  H151  107.49  3.000
 CPB  H152  C15  C14   109.71  3.000
 CPB  H151  C15  C14   112.77  3.000
 CPB  H152  C15  C16   109.25  3.000
 CPB  H151  C15  C16   108.23  3.000
 CPB  C14   C15  C16   109.32  3.000
 CPB  H141  C14  C8    105.96  3.000
 CPB  H141  C14  C13   104.17  3.000
 CPB  C8    C14  C13   111.62  3.000
 CPB  H141  C14  C15   104.61  3.000
 CPB  C8    C14  C15   118.19  3.000
 CPB  C13   C14  C15   110.92  3.000
 CPB  H131  C13  O3    110.20  3.000
 CPB  H131  C13  C12   106.73  3.000
 CPB  O3    C13  C12   113.03  3.000
 CPB  H131  C13  C14   107.95  3.000
 CPB  O3    C13  C14   109.14  3.000
 CPB  C12   C13  C14   109.65  3.000
 CPB  H122  C12  H121  105.87  3.000
 CPB  H122  C12  C13   109.49  3.000
 CPB  H121  C12  C13   107.61  3.000
 CPB  H122  C12  N1    108.97  3.000
 CPB  H121  C12  N1    111.74  3.000
 CPB  C13   C12  N1    112.91  3.000
 CPB  C7    C8   C9    115.16  3.000
 CPB  C7    C8   C14   119.12  3.000
 CPB  C9    C8   C14   125.63  3.000
 CPB  C10   C9   O1    119.60  3.000
 CPB  C10   C9   C8    124.89  3.000
 CPB  O1    C9   C8    115.50  3.000
 CPB  C2    O1   C9    122.67  3.000
 CPB  C21   C2   C3    126.64  3.000
 CPB  C21   C2   O1    111.49  3.000
 CPB  C3    C2   O1    121.79  3.000
 CPB  H31   C3   C4    118.33  3.000
 CPB  H31   C3   C2    120.33  3.000
 CPB  C4    C3   C2    121.34  3.000
 CPB  C10   C4   O4    124.35  3.000
 CPB  C10   C4   C3    114.69  3.000
 CPB  O4    C4   C3    120.95  3.000
 CPB  C5    C10  C4    123.20  3.000
 CPB  C5    C10  C9    116.99  3.000
 CPB  C4    C10  C9    119.80  3.000
 CPB  C6    C5   O5    120.98  3.000
 CPB  C6    C5   C10   119.90  3.000
 CPB  O5    C5   C10   119.12  3.000
 CPB  HO5   O5   C5    109.71  3.000
 CPB  H61   C6   C7    119.61  3.000
 CPB  H61   C6   C5    119.65  3.000
 CPB  C7    C6   C5    120.74  3.000
 CPB  O7    C7   C6    120.00  3.000
 CPB  O7    C7   C8    117.69  3.000
 CPB  C6    C7   C8    122.31  3.000
 CPB  HO7   O7   C7    110.84  3.000
 CPB  C26   C21  C22   117.92  3.000
 CPB  C26   C21  C2    118.15  3.000
 CPB  C22   C21  C2    123.93  3.000
 CPB  C23   C22  CL1   117.14  3.000
 CPB  C23   C22  C21   121.10  3.000
 CPB  CL1   C22  C21   121.71  3.000
 CPB  H231  C23  C24   120.33  3.000
 CPB  H231  C23  C22   119.78  3.000
 CPB  C24   C23  C22   119.89  3.000
 CPB  H241  C24  C25   120.56  3.000
 CPB  H241  C24  C23   119.47  3.000
 CPB  C25   C24  C23   119.97  3.000
 CPB  H251  C25  C26   119.73  3.000
 CPB  H251  C25  C24   120.40  3.000
 CPB  C26   C25  C24   119.87  3.000
 CPB  H261  C26  C25   119.60  3.000
 CPB  H261  C26  C21   119.20  3.000
 CPB  C25   C26  C21   121.21  3.000
 CPB  HO3   O3   C13   108.17  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
 CPB  CONST_01  C2    O1   C9   C8   180.00   0.0  0
 CPB  CONST_02  C4    C10  C9   C8   180.00   0.0  0
 CPB  CONST_03  C5    C10  C9   C8     0.00   0.0  0
 CPB  CONST_04  C5    C6   C7   C8     0.00   0.0  0
 CPB  CONST_05  C6    C7   C8   C9     0.00   0.0  0
 CPB  CONST_06  C3    C2   O1   C9     0.00   0.0  0
 CPB  CONST_07  C21   C2   O1   C9   180.00   0.0  0
 CPB  CONST_08  C3    C4   C10  C9     0.00   0.0  0
 CPB  CONST_09  C6    C5   C10  C9     0.00   0.0  0
 CPB  CONST_10  C7    C8   C9   O1   180.00   0.0  0
 CPB  CONST_11  C4    C10  C9   O1     0.00   0.0  0
 CPB  CONST_12  C5    C10  C9   O1   180.00   0.0  0
 CPB  CONST_13  C4    C3   C2   O1     0.00   0.0  0
 CPB  CONST_16  C10   C9   O1   C2     0.00   0.0  0
 CPB  CONST_17  C10   C4   C3   C2     0.00   0.0  0
 CPB  CONST_18  C23   C22  C21  C2   180.00   0.0  0
 CPB  CONST_19  C25   C26  C21  C2   180.00   0.0  0
 CPB  CONST_22  C5    C10  C4   C3   180.00   0.0  0
 CPB  CONST_23  C21   C2   C3   C4   180.00   0.0  0
 CPB  CONST_24  C6    C5   C10  C4   180.00   0.0  0
 CPB  CONST_25  C7    C8   C9   C10    0.00   0.0  0
 CPB  CONST_26  C7    C6   C5   C10    0.00   0.0  0
 CPB  CONST_27  C24   C23  C22  C21    0.00   0.0  0
 CPB  CONST_28  C24   C25  C26  C21    0.00   0.0  0
 CPB  CONST_29  C25   C26  C21  C22    0.00   0.0  0
 CPB  CONST_30  C25   C24  C23  C22    0.00   0.0  0
 CPB  CONST_31  C26   C21  C22  C23    0.00   0.0  0
 CPB  CONST_32  C26   C25  C24  C23    0.00   0.0  0
 CPB  CONST_33  O1    C9   C8   C14    0.00   0.0  0
 CPB  CONST_34  C10   C9   C8   C14  180.00   0.0  0
 CPB  CONST_35  C6    C7   C8   C14  180.00   0.0  0
 CPB  CONST_36  O7    C7   C8   C14    0.00   0.0  0
 CPB  CONST_37  O7    C7   C8   C9   180.00   0.0  0
 CPB  CONST_38  O4    C4   C10  C9   180.00   0.0  0
 CPB  CONST_39  O5    C5   C10  C9   180.00   0.0  0
 CPB  CONST_40  O4    C4   C3   C2   180.00   0.0  0
 CPB  CONST_41  CL1   C22  C21  C2     0.00   0.0  0
 CPB  CONST_42  O5    C5   C10  C4     0.00   0.0  0
 CPB  CONST_43  C5    C10  C4   O4     0.00   0.0  0
 CPB  CONST_44  O7    C7   C6   C5   180.00   0.0  0
 CPB  CONST_45  C7    C6   C5   O5   180.00   0.0  0
 CPB  CONST_46  C26   C21  C22  CL1  180.00   0.0  0
 CPB  CONST_47  C24   C23  C22  CL1  180.00   0.0  0
 CPB  CONST_48  H61   C6   C7   C8   180.00   0.0  0
 CPB  CONST_49  H31   C3   C2   O1   180.00   0.0  0
 CPB  CONST_50  H261  C26  C21  C2     0.00   0.0  0
 CPB  CONST_51  H231  C23  C22  C21  180.00   0.0  0
 CPB  CONST_52  H251  C25  C26  C21  180.00   0.0  0
 CPB  CONST_53  H241  C24  C23  C22  180.00   0.0  0
 CPB  Var_01    C14   C15  C16  N1   -58.94  30.0  1
 CPB  Var_02    C13   C12  N1   C16  -58.89  30.0  1
 CPB  Var_03    C12   N1   C16  C15   61.06  30.0  1
 CPB  Var_04    H11   C1   N1   C16   57.47  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
 CPB  chir_01  C14  C15  C13  C8   negativ
 CPB  chir_02  C13  O3   C14  C12  negativ

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
 CPB  plan-1  C2    0.020
 CPB  plan-1  C21   0.020
 CPB  plan-1  C22   0.020
 CPB  plan-1  CL1   0.020
 CPB  plan-1  C23   0.020
 CPB  plan-1  C24   0.020
 CPB  plan-1  C25   0.020
 CPB  plan-1  C26   0.020
 CPB  plan-1  H231  0.020
 CPB  plan-1  H241  0.020
 CPB  plan-1  H251  0.020
 CPB  plan-1  H261  0.020
 CPB  plan-2  C14   0.020
 CPB  plan-2  C8    0.020
 CPB  plan-2  C9    0.020
 CPB  plan-2  O1    0.020
 CPB  plan-2  C4    0.020
 CPB  plan-2  C10   0.020
 CPB  plan-2  C5    0.020
 CPB  plan-2  O5    0.020
 CPB  plan-2  C6    0.020
 CPB  plan-2  C7    0.020
 CPB  plan-2  O7    0.020
 CPB  plan-2  H61   0.020
 CPB  plan-3  C3    0.020
 CPB  plan-3  C4    0.020
 CPB  plan-3  O4    0.020
 CPB  plan-3  C10   0.020

