# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun  3 01:37:14 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: [(5-methoxy-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(C)cc2OC(=O)C=C(C[P](O)(O)=O)c12
#
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
 XJE  XJE  '[(5-methoxy-7-methyl-2-oxo-2H-1-benzopyran-4-yl)methyl]phosphonic acid'  ligand  32  19  .  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_XJE
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
 XJE  C01  C  CH3   0  -0.433  -1.5307   3.5950  -0.2949
 XJE  C03  C  CR6   0   0.414  -1.6658   1.2212  -0.1137
 XJE  C04  C  CR16  0  -0.467  -3.0423   1.2739   0.0544
 XJE  C05  C  CR6   0   0.043  -3.8095   0.1136   0.1656
 XJE  C06  C  CH3   0  -0.674  -5.2983   0.2125   0.3126
 XJE  C07  C  CR16  0  -0.432  -3.1842  -1.1158   0.0943
 XJE  C08  C  CR66  0   0.515  -1.8093  -1.1676  -0.0435
 XJE  C10  C  CR6   0   0.534   0.0283  -2.6742  -0.2341
 XJE  C12  C  CR16  0  -0.443   0.8940  -1.5315  -0.3105
 XJE  C13  C  CR6   0   0.152   0.4468  -0.2557  -0.2292
 XJE  C14  C  CH2   0  -0.820   1.4230   0.8900  -0.2105
 XJE  C19  C  CR66  0  -0.128  -0.9889  -0.0337  -0.1252
 XJE  O02  O  O2    0  -0.492  -0.9182   2.3174  -0.2688
 XJE  O09  O  O     0  -0.542  -1.2930  -2.4232  -0.0940
 XJE  O11  O  O     0  -0.425   0.3830  -3.8293  -0.2646
 XJE  O16  O  OH1   0  -0.790   3.1947  -0.2333   1.5515
 XJE  O17  O  O     0  -0.721   3.9357  -0.2754  -0.8563
 XJE  O18  O  OH1   0  -0.725   3.6836   2.0113   0.3767
 XJE  P15  P  P     0   1.392   3.1656   0.5133   0.1287
 XJE  H1   H  HCH3  0   0.293  -0.7289   4.3119  -0.4516
 XJE  H2   H  HCH3  0   0.234  -2.2492   3.6799  -1.1130
 XJE  H3   H  HCH3  0   0.217  -2.0317   3.8192   0.6496
 XJE  H4   H  HCR6  0   0.273  -3.5528   2.2269   0.1048
 XJE  H5   H  HCH3  0   0.270  -5.7572   0.4699  -0.6452
 XJE  H6   H  HCH3  0   0.252  -5.7319  -0.7280   0.6492
 XJE  H7   H  HCH3  0   0.264  -5.5749   0.9934   1.0218
 XJE  H8   H  HCR6  0   0.274  -3.7521  -2.0341   0.1667
 XJE  H9   H  HCR6  0   0.309   1.9431  -1.7579  -0.4280
 XJE  H10  H  HCH2  0   0.337   1.3839   1.4195  -1.1647
 XJE  H11  H  HCH2  0   0.343   1.1239   1.6192   0.5431
 XJE  H12  H  HOH1  0   0.462   2.7609   0.2317   2.2780
 XJE  H13  H  HOH1  0   0.512   4.6454   2.1043   0.3009

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
 XJE  C06  C05  single    1.499  0.020  1.499
 XJE  C01  O02  single    1.417  0.020  1.417
 XJE  C04  C05  aromatic  1.395  0.020  1.395
 XJE  C04  C03  aromatic  1.388  0.020  1.388
 XJE  C05  C07  aromatic  1.381  0.020  1.381
 XJE  O02  C03  single    1.336  0.020  1.336
 XJE  O17  P15  double    1.478  0.020  1.478
 XJE  C03  C19  aromatic  1.426  0.020  1.426
 XJE  C07  C08  aromatic  1.383  0.020  1.383
 XJE  O18  P15  single    1.604  0.020  1.604
 XJE  C19  C08  aromatic  1.402  0.020  1.402
 XJE  C19  C13  single    1.456  0.020  1.456
 XJE  P15  C14  single    1.815  0.020  1.815
 XJE  P15  O16  single    1.607  0.020  1.607
 XJE  C08  O09  single    1.359  0.020  1.359
 XJE  C14  C13  single    1.505  0.020  1.505
 XJE  C13  C12  double    1.354  0.020  1.354
 XJE  O09  C10  single    1.352  0.020  1.352
 XJE  C12  C10  single    1.436  0.020  1.436
 XJE  C10  O11  double    1.209  0.020  1.209
 XJE  C01  H1   single    0.970  0.020  1.090
 XJE  C01  H2   single    0.970  0.020  1.090
 XJE  C01  H3   single    0.970  0.020  1.090
 XJE  C04  H4   single    0.930  0.020  1.080
 XJE  C06  H5   single    0.970  0.020  1.090
 XJE  C06  H6   single    0.970  0.020  1.090
 XJE  C06  H7   single    0.970  0.020  1.090
 XJE  C07  H8   single    0.930  0.020  1.080
 XJE  C12  H9   single    0.930  0.020  1.080
 XJE  C14  H10  single    0.970  0.020  1.090
 XJE  C14  H11  single    0.970  0.020  1.090
 XJE  O16  H12  single    0.850  0.020  0.980
 XJE  O18  H13  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
 XJE  H3   C01  H2   109.27  3.000
 XJE  H3   C01  H1   109.12  3.000
 XJE  H2   C01  H1   109.03  3.000
 XJE  H3   C01  O02  111.55  3.000
 XJE  H2   C01  O02  111.61  3.000
 XJE  H1   C01  O02  106.17  3.000
 XJE  O02  C03  C19  117.10  3.000
 XJE  C19  C03  C04  120.36  3.000
 XJE  O02  C03  C04  122.54  3.000
 XJE  H4   C04  C05  117.98  3.000
 XJE  H4   C04  C03  120.47  3.000
 XJE  C05  C04  C03  121.56  3.000
 XJE  C07  C05  C06  120.89  3.000
 XJE  C07  C05  C04  119.15  3.000
 XJE  C06  C05  C04  119.93  3.000
 XJE  H7   C06  H6   108.44  3.000
 XJE  H7   C06  H5   107.15  3.000
 XJE  H6   C06  H5   107.89  3.000
 XJE  H7   C06  C05  111.28  3.000
 XJE  H6   C06  C05  111.64  3.000
 XJE  H5   C06  C05  110.28  3.000
 XJE  H8   C07  C08  119.78  3.000
 XJE  H8   C07  C05  120.95  3.000
 XJE  C08  C07  C05  119.25  3.000
 XJE  O09  C08  C19  121.53  3.000
 XJE  O09  C08  C07  114.60  3.000
 XJE  C19  C08  C07  123.88  3.000
 XJE  O11  C10  O09  117.83  3.000
 XJE  O11  C10  C12  125.61  3.000
 XJE  O09  C10  C12  116.55  3.000
 XJE  H9   C12  C13  121.66  3.000
 XJE  H9   C12  C10  115.14  3.000
 XJE  C13  C12  C10  123.20  3.000
 XJE  C19  C13  C14  121.49  3.000
 XJE  C14  C13  C12  120.24  3.000
 XJE  C19  C13  C12  118.25  3.000
 XJE  H11  C14  H10  105.65  3.000
 XJE  H11  C14  P15  105.85  3.000
 XJE  H10  C14  P15  107.36  3.000
 XJE  H11  C14  C13  109.86  3.000
 XJE  H10  C14  C13  109.57  3.000
 XJE  P15  C14  C13  117.84  3.000
 XJE  C13  C19  C08  117.24  3.000
 XJE  C13  C19  C03  127.06  3.000
 XJE  C08  C19  C03  115.69  3.000
 XJE  C03  O02  C01  120.00  3.000
 XJE  C10  O09  C08  123.15  3.000
 XJE  H12  O16  P15  115.74  3.000
 XJE  H13  O18  P15  113.45  3.000
 XJE  O18  P15  O17  115.65  3.000
 XJE  O18  P15  O16  106.92  3.000
 XJE  O17  P15  O16  109.43  3.000
 XJE  O16  P15  C14  106.22  3.000
 XJE  O18  P15  C14   98.34  3.000
 XJE  O17  P15  C14  119.11  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
 XJE  CONST_01  C07  C05  C04  C03     0.00   0.0  0
 XJE  CONST_02  C07  C08  C19  C03     0.00   0.0  0
 XJE  CONST_03  C08  C07  C05  C04     0.00   0.0  0
 XJE  CONST_04  C08  C19  C03  C04     0.00   0.0  0
 XJE  CONST_05  C19  C03  C04  C05     0.00   0.0  0
 XJE  CONST_06  C19  C08  C07  C05     0.00   0.0  0
 XJE  CONST_07  C06  C05  C04  C03   180.00   0.0  0
 XJE  CONST_08  O02  C03  C04  C05   180.00   0.0  0
 XJE  CONST_09  C08  C07  C05  C06   180.00   0.0  0
 XJE  CONST_10  O02  C03  C19  C08   180.00   0.0  0
 XJE  CONST_11  O02  C03  C19  C13     0.00   0.0  0
 XJE  CONST_12  H8   C07  C05  C04   180.00   0.0  0
 XJE  CONST_13  H4   C04  C05  C07   180.00   0.0  0
 XJE  Var_01    C12  C13  C19  C03  -175.77  30.0  1
 XJE  Var_02    C12  C10  O09  C08     0.90  30.0  1
 XJE  Var_03    C19  C08  O09  C10    -0.48  30.0  1
 XJE  Var_04    C19  C13  C12  C10    -3.12  30.0  1
 XJE  Var_05    O09  C10  C12  C13     1.00  30.0  1
 XJE  Var_06    C04  C03  O02  C01    -1.37  30.0  2
 XJE  Var_07    P15  C14  C13  C12   -15.39  30.0  2
 XJE  Var_08    H5   C06  C05  C04    75.20  30.0  2
 XJE  Var_09    O17  P15  C14  C13    66.85  30.0  3
 XJE  Var_10    H1   C01  O02  C03  -178.77  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
 XJE  plan-1  C10  0.020
 XJE  plan-1  C12  0.020
 XJE  plan-1  O09  0.020
 XJE  plan-1  O11  0.020
 XJE  plan-2  C03  0.020
 XJE  plan-2  C04  0.020
 XJE  plan-2  C05  0.020
 XJE  plan-2  C06  0.020
 XJE  plan-2  C07  0.020
 XJE  plan-2  C08  0.020
 XJE  plan-2  C13  0.020
 XJE  plan-2  C19  0.020
 XJE  plan-2  O02  0.020
 XJE  plan-2  O09  0.020
 XJE  plan-2  H4   0.020
 XJE  plan-2  H8   0.020

