# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:15:11 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  30  19  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.440  -1.6072   3.6135  -0.2272
 XJE  C03  C  CR6    0   0.352  -1.6919   1.2394  -0.0980
 XJE  C04  C  CR16   0  -0.444  -3.0685   1.2756   0.0638
 XJE  C05  C  CR6    0   0.114  -3.8193   0.1038   0.1729
 XJE  C06  C  CH3    0  -0.726  -5.3073   0.1854   0.3284
 XJE  C07  C  CR16   0  -0.411  -3.1754  -1.1147   0.1013
 XJE  C08  C  CR66   0   0.404  -1.7951  -1.1469  -0.0557
 XJE  C10  C  CR6    0   0.540   0.0568  -2.6133  -0.3549
 XJE  C12  C  CR16   0  -0.587   0.9086  -1.4645  -0.3533
 XJE  C13  C  CR6    0   0.300   0.4526  -0.1931  -0.2081
 XJE  C14  C  CH2    0  -0.817   1.4468   0.9254  -0.1333
 XJE  C19  C  CR66   0  -0.162  -0.9929  -0.0008  -0.1180
 XJE  O02  O  O2     0  -0.456  -0.9698   2.3519  -0.2654
 XJE  O09  O  O      0  -0.471  -1.2657  -2.3865  -0.1468
 XJE  O11  O  O      0  -0.461   0.3946  -3.7687  -0.4910
 XJE  O16  O  OP    -1  -0.896   3.0093  -0.0400   1.8770
 XJE  O17  O  O      0  -0.891   3.8275  -0.3961  -0.5347
 XJE  O18  O  OP    -1  -0.896   3.8146   1.9623   0.4769
 XJE  P15  P  P      0   1.184   3.1881   0.5621   0.4826
 XJE  H1   H  HCH3   0   0.264  -0.8226   4.3517  -0.3711
 XJE  H2   H  HCH3   0   0.232  -2.3451   3.7220  -1.0254
 XJE  H3   H  HCH3   0   0.233  -2.0935   3.7966   0.7339
 XJE  H4   H  HCR6   0   0.280  -3.5921   2.2214   0.0982
 XJE  H5   H  HCH3   0   0.255  -5.7756   0.5128  -0.6017
 XJE  H6   H  HCH3   0   0.249  -5.7370  -0.7787   0.5951
 XJE  H7   H  HCH3   0   0.250  -5.5845   0.9066   1.0975
 XJE  H8   H  HCR6   0   0.265  -3.7283  -2.0435   0.1624
 XJE  H9   H  HCR6   0   0.273   1.9711  -1.6403  -0.4580
 XJE  H10  H  HCH2   0   0.232   1.5186   1.3776  -1.1300
 XJE  H11  H  HCH2   0   0.229   1.0559   1.7167   0.5032

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    1.498  0.020  1.498
 XJE  C01  O02  single    1.414  0.020  1.414
 XJE  C04  C05  aromatic  1.396  0.020  1.396
 XJE  C04  C03  aromatic  1.387  0.020  1.387
 XJE  C05  C07  aromatic  1.380  0.020  1.380
 XJE  O02  C03  single    1.337  0.020  1.337
 XJE  O17  P15  deloc     1.537  0.020  1.537
 XJE  C03  C19  aromatic  1.424  0.020  1.424
 XJE  C07  C08  aromatic  1.390  0.020  1.390
 XJE  O18  P15  deloc     1.534  0.020  1.534
 XJE  C19  C08  aromatic  1.400  0.020  1.400
 XJE  C19  C13  single    1.461  0.020  1.461
 XJE  P15  C14  single    1.882  0.020  1.882
 XJE  P15  O16  deloc     1.529  0.020  1.529
 XJE  C08  O09  single    1.351  0.020  1.351
 XJE  C14  C13  single    1.498  0.020  1.498
 XJE  C13  C12  double    1.359  0.020  1.359
 XJE  O09  C10  single    1.358  0.020  1.358
 XJE  C12  C10  single    1.430  0.020  1.430
 XJE  C10  O11  double    1.211  0.020  1.211
 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

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   108.99  3.000
 XJE  H3   C01  H1   108.90  3.000
 XJE  H2   C01  H1   108.87  3.000
 XJE  H3   C01  O02  111.96  3.000
 XJE  H2   C01  O02  111.92  3.000
 XJE  H1   C01  O02  106.08  3.000
 XJE  O02  C03  C19  117.25  3.000
 XJE  C19  C03  C04  120.79  3.000
 XJE  O02  C03  C04  121.95  3.000
 XJE  H4   C04  C05  118.11  3.000
 XJE  H4   C04  C03  120.47  3.000
 XJE  C05  C04  C03  121.41  3.000
 XJE  C07  C05  C06  121.12  3.000
 XJE  C07  C05  C04  119.09  3.000
 XJE  C06  C05  C04  119.77  3.000
 XJE  H7   C06  H6   108.22  3.000
 XJE  H7   C06  H5   107.07  3.000
 XJE  H6   C06  H5   107.76  3.000
 XJE  H7   C06  C05  111.21  3.000
 XJE  H6   C06  C05  111.67  3.000
 XJE  H5   C06  C05  110.73  3.000
 XJE  H8   C07  C08  119.58  3.000
 XJE  H8   C07  C05  121.08  3.000
 XJE  C08  C07  C05  119.33  3.000
 XJE  O09  C08  C19  121.57  3.000
 XJE  O09  C08  C07  114.72  3.000
 XJE  C19  C08  C07  123.71  3.000
 XJE  O11  C10  O09  116.63  3.000
 XJE  O11  C10  C12  126.88  3.000
 XJE  O09  C10  C12  116.47  3.000
 XJE  H9   C12  C13  119.47  3.000
 XJE  H9   C12  C10  117.02  3.000
 XJE  C13  C12  C10  123.50  3.000
 XJE  C19  C13  C14  123.72  3.000
 XJE  C14  C13  C12  118.77  3.000
 XJE  C19  C13  C12  117.51  3.000
 XJE  H11  C14  H10  104.79  3.000
 XJE  H11  C14  P15  106.34  3.000
 XJE  H10  C14  P15  108.44  3.000
 XJE  H11  C14  C13  109.49  3.000
 XJE  H10  C14  C13  107.81  3.000
 XJE  P15  C14  C13  119.08  3.000
 XJE  C13  C19  C08  117.50  3.000
 XJE  C13  C19  C03  126.96  3.000
 XJE  C08  C19  C03  115.53  3.000
 XJE  C03  O02  C01  119.71  3.000
 XJE  C10  O09  C08  123.05  3.000
 XJE  O18  P15  O17  113.38  3.000
 XJE  O18  P15  O16  114.23  3.000
 XJE  O17  P15  O16  114.00  3.000
 XJE  O16  P15  C14  105.43  3.000
 XJE  O18  P15  C14  101.56  3.000
 XJE  O17  P15  C14  106.77  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  -173.26  30.0  1
 XJE  Var_02    C12  C10  O09  C08     5.62  30.0  1
 XJE  Var_03    C19  C08  O09  C10    -2.62  30.0  1
 XJE  Var_04    C19  C13  C12  C10    -3.21  30.0  1
 XJE  Var_05    O09  C10  C12  C13    -2.57  30.0  1
 XJE  Var_06    C04  C03  O02  C01     2.50  30.0  2
 XJE  Var_07    P15  C14  C13  C12   -25.74  30.0  2
 XJE  Var_08    H5   C06  C05  C04    71.07  30.0  2
 XJE  Var_09    O17  P15  C14  C13    64.31  30.0  3
 XJE  Var_10    H1   C01  O02  C03   179.19  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

