# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 04:48:56 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: (2~{S})-8-methoxy-5,7-bis(oxidanyl)-2-phenyl-2,3-dihydrochromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(O)cc(O)c2C(=O)C[C@H](Oc12)c3ccccc3
#
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
 CU5  CU5  (2~{S})-8-methoxy-5,7-bis(oxidanyl)-2-phenyl-2,3-dihydrochromen-4-one  ligand  35  21  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CU5
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
 CU5  C10   C  C     0   0.454  -0.5301   2.1152   0.4666
 CU5  C15   C  CH3   0  -0.408  -0.9792  -3.3602   0.6848
 CU5  C17   C  CR16  0  -0.313   3.6292   0.4679  -1.1671
 CU5  C20   C  CR16  0  -0.240   4.4044  -0.9454   1.0882
 CU5  C21   C  CR16  0  -0.292   3.0799  -0.5657   0.9303
 CU5  C01   C  CH2   0  -0.593   0.9286   1.7675   0.5533
 CU5  C02   C  CH1   0  -0.043   1.2631   0.6015  -0.3630
 CU5  O03   O  O2    0  -0.467   0.4118  -0.5111  -0.0892
 CU5  C04   C  CR6   0   0.377  -0.9043  -0.2729  -0.0564
 CU5  C05   C  CR6   0   0.139  -1.7425  -1.3589  -0.2440
 CU5  C06   C  CR6   0   0.329  -3.1292  -1.1518  -0.2021
 CU5  C07   C  CR16  0  -0.519  -3.6688   0.1165  -0.0041
 CU5  C08   C  CR6   0   0.391  -2.8247   1.1987   0.1826
 CU5  C09   C  CR6   0  -0.335  -1.4215   1.0208   0.1653
 CU5  O11   O  O     0  -0.465  -0.9339   3.2572   0.6858
 CU5  O12   O  OH1   0  -0.626  -3.3592   2.3975   0.3903
 CU5  O13   O  OH1   0  -0.601  -3.8923  -2.2292  -0.3834
 CU5  O14   O  O2    0  -0.481  -1.2418  -2.5982  -0.4871
 CU5  C16   C  CR6   0   0.104   2.6840   0.1433  -0.2016
 CU5  C18   C  CR16  0  -0.239   4.9578   0.0954  -1.0054
 CU5  C19   C  CR16  0  -0.262   5.3471  -0.6140   0.1217
 CU5  H151  H  HCH3  0   0.239  -0.6111  -4.3320   0.3610
 CU5  H152  H  HCH3  0   0.222  -0.2173  -2.8895   1.3114
 CU5  H153  H  HCH3  0   0.222  -1.8822  -3.5092   1.2818
 CU5  H201  H  HCR6  0   0.259   4.7029  -1.4990   1.9688
 CU5  H211  H  HCR6  0   0.256   2.3551  -0.8252   1.6922
 CU5  H011  H  HCH2  0   0.297   1.5375   2.6340   0.2928
 CU5  H012  H  HCH2  0   0.298   1.1536   1.5124   1.5955
 CU5  H021  H  HCH1  0   0.273   1.0967   0.9108  -1.4025
 CU5  H071  H  HCR6  0   0.286  -4.7428   0.2601   0.0132
 CU5  H121  H  HOH1  0   0.477  -2.6217   3.0332   0.5395
 CU5  H131  H  HOH1  0   0.485  -4.8272  -1.9945  -0.3448
 CU5  H181  H  HCR6  0   0.259   5.6856   0.3548  -1.7631
 CU5  H191  H  HCR6  0   0.260   6.3803  -0.9102   0.2479
 CU5  H171  H  HCR6  0   0.257   3.3263   1.0141  -2.0528

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
 CU5  O12  C08   single    1.329  0.020  1.329
 CU5  O11  C10   double    1.231  0.020  1.231
 CU5  C08  C07   aromatic  1.385  0.020  1.385
 CU5  C08  C09   aromatic  1.415  0.020  1.415
 CU5  C07  C06   aromatic  1.392  0.020  1.392
 CU5  C10  C09   single    1.443  0.020  1.443
 CU5  C10  C01   single    1.502  0.020  1.502
 CU5  C09  C04   aromatic  1.411  0.020  1.411
 CU5  C18  C19   aromatic  1.387  0.020  1.387
 CU5  C18  C17   aromatic  1.389  0.020  1.389
 CU5  C19  C20   aromatic  1.390  0.020  1.390
 CU5  C06  O13   single    1.333  0.020  1.333
 CU5  C06  C05   aromatic  1.403  0.020  1.403
 CU5  C17  C16   aromatic  1.390  0.020  1.390
 CU5  C20  C21   aromatic  1.387  0.020  1.387
 CU5  C01  C02   single    1.520  0.020  1.520
 CU5  C04  C05   aromatic  1.385  0.020  1.385
 CU5  C04  O03   single    1.338  0.020  1.338
 CU5  C05  O14   single    1.359  0.020  1.359
 CU5  C16  C21   aromatic  1.393  0.020  1.393
 CU5  C16  C02   single    1.502  0.020  1.502
 CU5  C02  O03   single    1.427  0.020  1.427
 CU5  O14  C15   single    1.422  0.020  1.422
 CU5  C15  H151  single    0.970  0.020  1.090
 CU5  C15  H152  single    0.970  0.020  1.090
 CU5  C15  H153  single    0.970  0.020  1.090
 CU5  C17  H171  single    0.930  0.020  1.080
 CU5  C20  H201  single    0.930  0.020  1.080
 CU5  C21  H211  single    0.930  0.020  1.080
 CU5  C01  H011  single    0.970  0.020  1.090
 CU5  C01  H012  single    0.970  0.020  1.090
 CU5  C02  H021  single    0.970  0.020  1.090
 CU5  C07  H071  single    0.930  0.020  1.080
 CU5  O12  H121  single    0.850  0.020  0.980
 CU5  O13  H131  single    0.850  0.020  0.980
 CU5  C18  H181  single    0.930  0.020  1.080
 CU5  C19  H191  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
 CU5  O11   C10  C09   122.55  3.000
 CU5  C09   C10  C01   115.87  3.000
 CU5  O11   C10  C01   121.53  3.000
 CU5  H153  C15  H152  108.76  3.000
 CU5  H153  C15  H151  108.68  3.000
 CU5  H152  C15  H151  108.62  3.000
 CU5  H153  C15  O14   111.76  3.000
 CU5  H152  C15  O14   111.74  3.000
 CU5  H151  C15  O14   107.20  3.000
 CU5  H171  C17  C18   119.83  3.000
 CU5  H171  C17  C16   119.70  3.000
 CU5  C18   C17  C16   120.46  3.000
 CU5  H201  C20  C19   120.04  3.000
 CU5  H201  C20  C21   119.74  3.000
 CU5  C19   C20  C21   120.22  3.000
 CU5  H211  C21  C16   120.22  3.000
 CU5  H211  C21  C20   119.57  3.000
 CU5  C16   C21  C20   120.21  3.000
 CU5  H012  C01  H011  107.30  3.000
 CU5  H012  C01  C02   110.45  3.000
 CU5  H011  C01  C02   110.03  3.000
 CU5  H012  C01  C10   107.94  3.000
 CU5  H011  C01  C10   110.15  3.000
 CU5  C02   C01  C10   110.88  3.000
 CU5  H021  C02  C16   109.35  3.000
 CU5  H021  C02  O03   108.12  3.000
 CU5  C16   C02  O03   107.81  3.000
 CU5  H021  C02  C01   108.75  3.000
 CU5  O03   C02  C01   110.55  3.000
 CU5  C16   C02  C01   112.17  3.000
 CU5  C04   O03  C02   116.91  3.000
 CU5  C09   C04  C05   121.24  3.000
 CU5  C05   C04  O03   116.91  3.000
 CU5  C09   C04  O03   121.85  3.000
 CU5  O14   C05  C06   120.28  3.000
 CU5  O14   C05  C04   121.11  3.000
 CU5  C06   C05  C04   118.60  3.000
 CU5  O13   C06  C07   122.26  3.000
 CU5  O13   C06  C05   116.27  3.000
 CU5  C07   C06  C05   121.45  3.000
 CU5  H071  C07  C08   119.89  3.000
 CU5  H071  C07  C06   120.47  3.000
 CU5  C08   C07  C06   119.65  3.000
 CU5  O12   C08  C09   120.95  3.000
 CU5  C09   C08  C07   120.31  3.000
 CU5  O12   C08  C07   118.74  3.000
 CU5  C08   C09  C04   118.74  3.000
 CU5  C04   C09  C10   120.12  3.000
 CU5  C08   C09  C10   120.98  3.000
 CU5  H121  O12  C08   107.74  3.000
 CU5  H131  O13  C06   110.66  3.000
 CU5  C05   O14  C15   114.16  3.000
 CU5  C02   C16  C21   120.76  3.000
 CU5  C02   C16  C17   119.84  3.000
 CU5  C21   C16  C17   119.35  3.000
 CU5  H181  C18  C19   120.17  3.000
 CU5  H181  C18  C17   119.83  3.000
 CU5  C19   C18  C17   119.99  3.000
 CU5  H191  C19  C18   120.17  3.000
 CU5  H191  C19  C20   120.07  3.000
 CU5  C18   C19  C20   119.76  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
 CU5  CONST_01  C20   C19  C18  C17    0.00   0.0  0
 CU5  CONST_02  C20   C21  C16  C17    0.00   0.0  0
 CU5  CONST_03  C18   C19  C20  C21    0.00   0.0  0
 CU5  CONST_04  C18   C17  C16  C21    0.00   0.0  0
 CU5  CONST_05  C07   C08  C09  C04    0.00   0.0  0
 CU5  CONST_06  C07   C06  C05  C04    0.00   0.0  0
 CU5  CONST_07  C08   C07  C06  C05    0.00   0.0  0
 CU5  CONST_08  C08   C09  C04  C05    0.00   0.0  0
 CU5  CONST_09  C09   C08  C07  C06    0.00   0.0  0
 CU5  CONST_10  C09   C04  C05  C06    0.00   0.0  0
 CU5  CONST_11  C19   C18  C17  C16    0.00   0.0  0
 CU5  CONST_12  C19   C20  C21  C16    0.00   0.0  0
 CU5  CONST_13  C02   C16  C21  C20  180.00   0.0  0
 CU5  CONST_14  C18   C17  C16  C02  180.00   0.0  0
 CU5  CONST_15  O12   C08  C09  C10    0.00   0.0  0
 CU5  CONST_16  O14   C05  C04  O03    0.00   0.0  0
 CU5  CONST_17  O12   C08  C09  C04  180.00   0.0  0
 CU5  CONST_18  O13   C06  C05  C04  180.00   0.0  0
 CU5  CONST_19  O12   C08  C07  C06  180.00   0.0  0
 CU5  CONST_20  O14   C05  C06  C07  180.00   0.0  0
 CU5  CONST_21  O13   C06  C07  C08  180.00   0.0  0
 CU5  CONST_22  O14   C05  C04  C09  180.00   0.0  0
 CU5  CONST_23  H191  C19  C18  C17  180.00   0.0  0
 CU5  CONST_24  H211  C21  C16  C17  180.00   0.0  0
 CU5  CONST_25  H181  C18  C19  C20  180.00   0.0  0
 CU5  CONST_26  H171  C17  C16  C21  180.00   0.0  0
 CU5  CONST_27  H071  C07  C06  C05  180.00   0.0  0
 CU5  CONST_28  H201  C20  C21  C16  180.00   0.0  0
 CU5  Var_01    C08   C09  C10  C01  173.96  30.0  1
 CU5  Var_02    C09   C10  C01  C02   30.14  30.0  1
 CU5  Var_03    C09   C04  O03  C02  -21.47  30.0  1
 CU5  Var_04    C06   C05  O14  C15  -92.23  30.0  2
 CU5  Var_05    H151  C15  O14  C05  178.52  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
 CU5  chir_01  C02  C01  C16  O03  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
 CU5  plan-1  C17   0.020
 CU5  plan-1  C20   0.020
 CU5  plan-1  C21   0.020
 CU5  plan-1  C02   0.020
 CU5  plan-1  C16   0.020
 CU5  plan-1  C18   0.020
 CU5  plan-1  C19   0.020
 CU5  plan-1  H201  0.020
 CU5  plan-1  H211  0.020
 CU5  plan-1  H181  0.020
 CU5  plan-1  H191  0.020
 CU5  plan-1  H171  0.020
 CU5  plan-2  C10   0.020
 CU5  plan-2  O03   0.020
 CU5  plan-2  C04   0.020
 CU5  plan-2  C05   0.020
 CU5  plan-2  C06   0.020
 CU5  plan-2  C07   0.020
 CU5  plan-2  C08   0.020
 CU5  plan-2  C09   0.020
 CU5  plan-2  O12   0.020
 CU5  plan-2  O13   0.020
 CU5  plan-2  O14   0.020
 CU5  plan-2  H071  0.020
 CU5  plan-3  C10   0.020
 CU5  plan-3  C01   0.020
 CU5  plan-3  C09   0.020
 CU5  plan-3  O11   0.020

