# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 19:49:35 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: [(5-bromo-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Br)c2C(=CC(=O)Oc2c1)C[P](O)(O)=O
#
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
 YKG  YKG  '[(5-bromo-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid'  ligand  28  18  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YKG
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
 YKG  C01   C   CH3   0  -0.721   5.2094  -0.1893   0.3856
 YKG  C02   C   CR6   0   0.098   3.7396  -0.2877   0.1230
 YKG  C03   C   CR16  0  -0.255   2.9972   0.8580  -0.1676
 YKG  C04   C   CR6   0  -0.227   1.6336   0.7986  -0.3761
 YKG  C06   C   CR66  0   0.054   0.9125  -0.4141  -0.2785
 YKG  C07   C   CR6   0   0.284  -0.5297  -0.6478  -0.3553
 YKG  C08   C   CH2   0  -0.848  -1.5201   0.4819  -0.2894
 YKG  C13   C   CR16  0  -0.554  -0.9683  -1.9223  -0.4380
 YKG  C14   C   CR6   0   0.559  -0.0965  -3.0658  -0.3470
 YKG  C17   C   CR66  0   0.398   1.7141  -1.5508  -0.0715
 YKG  C18   C   CR16  0  -0.370   3.0826  -1.5006   0.1438
 YKG  O10   O   O     0  -0.704  -4.0163  -0.8041  -0.6214
 YKG  O11   O   OH1   0  -0.741  -3.0907  -0.5739   1.7129
 YKG  O12   O   OH1   0  -0.735  -3.7577   1.5739   0.4363
 YKG  O15   O   O     0  -0.427  -0.4269  -4.2206  -0.4409
 YKG  O16   O   O     0  -0.458   1.1987  -2.7998  -0.0751
 YKG  P09   P   P     0   1.393  -3.2075   0.0784   0.2523
 YKG  BR05  BR  BR    0  -0.016   0.8710   2.4385  -0.9369
 YKG  H1    H   HCH3  0   0.264   5.3905   0.0977   1.4231
 YKG  H2    H   HCH3  0   0.256   5.7113  -1.1393   0.2122
 YKG  H3    H   HCH3  0   0.256   5.6746   0.5674  -0.2449
 YKG  H4    H   HCR6  0   0.283   3.5150   1.8046  -0.2512
 YKG  H5    H   HCH2  0   0.311  -1.1660   1.2474   0.4018
 YKG  H6    H   HCH2  0   0.333  -1.6143   0.9646  -1.2654
 YKG  H7    H   HCR6  0   0.288  -2.0167  -2.1583  -0.5477
 YKG  H8    H   HCR6  0   0.285   3.6212  -2.4237   0.3173
 YKG  H9    H   HOH1  0   0.494  -2.6195  -0.0492   2.3733
 YKG  H10   H   HOH1  0   0.499  -4.7199   1.6313   0.5210

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
 YKG  C01  C02   single    1.496  0.020  1.496
 YKG  O15  C14   double    1.205  0.020  1.205
 YKG  C18  C02   aromatic  1.380  0.020  1.380
 YKG  C18  C17   aromatic  1.386  0.020  1.386
 YKG  O16  C14   single    1.350  0.020  1.350
 YKG  O16  C17   single    1.351  0.020  1.351
 YKG  C02  C03   aromatic  1.396  0.020  1.396
 YKG  C14  C13   single    1.441  0.020  1.441
 YKG  C17  C06   aromatic  1.406  0.020  1.406
 YKG  C03  C04   aromatic  1.381  0.020  1.381
 YKG  C13  C07   double    1.350  0.020  1.350
 YKG  C06  C04   aromatic  1.414  0.020  1.414
 YKG  C06  C07   single    1.463  0.020  1.463
 YKG  C04  BR05  single    1.894  0.020  1.894
 YKG  C07  C08   single    1.504  0.020  1.504
 YKG  C08  P09   single    1.818  0.020  1.818
 YKG  O10  P09   double    1.482  0.020  1.482
 YKG  O12  P09   single    1.604  0.020  1.604
 YKG  P09  O11   single    1.604  0.020  1.604
 YKG  C01  H1    single    0.970  0.020  1.090
 YKG  C01  H2    single    0.970  0.020  1.090
 YKG  C01  H3    single    0.970  0.020  1.090
 YKG  C03  H4    single    0.930  0.020  1.080
 YKG  C08  H5    single    0.970  0.020  1.090
 YKG  C08  H6    single    0.970  0.020  1.090
 YKG  C13  H7    single    0.930  0.020  1.080
 YKG  C18  H8    single    0.930  0.020  1.080
 YKG  O11  H9    single    0.850  0.020  0.980
 YKG  O12  H10   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
 YKG  H3    C01  H2   108.49  3.000
 YKG  H3    C01  H1   107.26  3.000
 YKG  H2    C01  H1   107.72  3.000
 YKG  H3    C01  C02  111.32  3.000
 YKG  H2    C01  C02  111.57  3.000
 YKG  H1    C01  C02  110.31  3.000
 YKG  C18   C02  C03  118.13  3.000
 YKG  C03   C02  C01  120.34  3.000
 YKG  C18   C02  C01  121.53  3.000
 YKG  H4    C03  C04  119.90  3.000
 YKG  H4    C03  C02  118.65  3.000
 YKG  C04   C03  C02  121.43  3.000
 YKG  BR05  C04  C06  123.90  3.000
 YKG  BR05  C04  C03  113.91  3.000
 YKG  C06   C04  C03  122.01  3.000
 YKG  C17   C06  C07  116.14  3.000
 YKG  C07   C06  C04  129.49  3.000
 YKG  C17   C06  C04  114.37  3.000
 YKG  C13   C07  C08  119.86  3.000
 YKG  C08   C07  C06  121.79  3.000
 YKG  C13   C07  C06  118.30  3.000
 YKG  H6    C08  H5   106.50  3.000
 YKG  H6    C08  P09  106.51  3.000
 YKG  H5    C08  P09  105.57  3.000
 YKG  H6    C08  C07  110.45  3.000
 YKG  H5    C08  C07  109.95  3.000
 YKG  P09   C08  C07  117.24  3.000
 YKG  H7    C13  C14  114.85  3.000
 YKG  H7    C13  C07  121.85  3.000
 YKG  C14   C13  C07  123.27  3.000
 YKG  O16   C14  O15  117.89  3.000
 YKG  O16   C14  C13  115.91  3.000
 YKG  O15   C14  C13  126.14  3.000
 YKG  O16   C17  C18  114.23  3.000
 YKG  O16   C17  C06  121.97  3.000
 YKG  C18   C17  C06  123.80  3.000
 YKG  H8    C18  C17  119.02  3.000
 YKG  H8    C18  C02  121.00  3.000
 YKG  C17   C18  C02  119.98  3.000
 YKG  H9    O11  P09  115.92  3.000
 YKG  H10   O12  P09  113.98  3.000
 YKG  C17   O16  C14  123.28  3.000
 YKG  O12   P09  O11  107.44  3.000
 YKG  O11   P09  O10  109.54  3.000
 YKG  O12   P09  O10  115.83  3.000
 YKG  O11   P09  C08  107.10  3.000
 YKG  O12   P09  C08   98.37  3.000
 YKG  O10   P09  C08  117.59  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
 YKG  CONST_01  C06   C17  C18  C02     0.00   0.0  0
 YKG  CONST_02  C06   C04  C03  C02     0.00   0.0  0
 YKG  CONST_03  C17   C18  C02  C03     0.00   0.0  0
 YKG  CONST_04  C17   C06  C04  C03     0.00   0.0  0
 YKG  CONST_05  C18   C02  C03  C04     0.00   0.0  0
 YKG  CONST_06  C18   C17  C06  C04     0.00   0.0  0
 YKG  CONST_07  C17   C18  C02  C01   180.00   0.0  0
 YKG  CONST_08  C04   C03  C02  C01   180.00   0.0  0
 YKG  CONST_09  BR05  C04  C03  C02   180.00   0.0  0
 YKG  CONST_10  BR05  C04  C06  C07     0.00   0.0  0
 YKG  CONST_11  BR05  C04  C06  C17   180.00   0.0  0
 YKG  CONST_12  H8    C18  C02  C03   180.00   0.0  0
 YKG  CONST_13  H4    C03  C04  C06   180.00   0.0  0
 YKG  Var_01    C13   C07  C06  C04   169.99  30.0  1
 YKG  Var_02    C14   C13  C07  C06     5.13  30.0  1
 YKG  Var_03    O16   C14  C13  C07     4.56  30.0  1
 YKG  Var_04    C18   C17  O16  C14  -175.90  30.0  1
 YKG  Var_05    P09   C08  C07  C06  -156.66  30.0  3
 YKG  Var_06    H1    C01  C02  C03    82.55  30.0  2
 YKG  Var_07    O10   P09  C08  C07   -65.58  30.0  3

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
 YKG  plan-1  C13   0.020
 YKG  plan-1  C14   0.020
 YKG  plan-1  O15   0.020
 YKG  plan-1  O16   0.020
 YKG  plan-2  C01   0.020
 YKG  plan-2  C02   0.020
 YKG  plan-2  C03   0.020
 YKG  plan-2  C04   0.020
 YKG  plan-2  C06   0.020
 YKG  plan-2  C07   0.020
 YKG  plan-2  C17   0.020
 YKG  plan-2  C18   0.020
 YKG  plan-2  O16   0.020
 YKG  plan-2  BR05  0.020
 YKG  plan-2  H4    0.020
 YKG  plan-2  H8    0.020

