# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 21:00:37 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: [[2-[(2,4-dinitrophenyl)amino]ethoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-trifluoro-beryllium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P@](=O)(OCCNc1ccc(cc1[N+]([O-])=O)[N+]([O-])=O)O[P@@](O)(=O)O[Be-](F)(F)F
#
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
 DAE  DAE  '[[2-[(2,4-dinitrophenyl)amino]ethoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-trifluoro-beryllium'  ligand  38  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DAE
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
 DAE  BE    BE  BE    -1   0.734  33.3756  59.2503  21.7253
 DAE  F1    F   F      0  -0.606  32.5302  59.4781  22.9285
 DAE  F2    F   F      0  -0.574  32.6198  58.2922  20.6536
 DAE  F3    F   F      0  -0.605  34.0225  60.4079  21.0534
 DAE  PB    P   P      0   1.529  34.8338  56.7351  21.8482
 DAE  OB1   O   O      0  -0.328  34.5255  55.9124  23.1833
 DAE  OB2   O   OH1    0  -0.752  33.8973  56.3447  20.6910
 DAE  OB3   O   OC2    0  -0.655  34.7680  58.1697  22.2876
 DAE  OA3   O   O2     0  -0.674  36.3037  56.2292  21.4678
 DAE  PA    P   P      0   1.495  37.0710  56.4875  20.0465
 DAE  OA1   O   OH1    0  -0.705  36.9525  55.0575  19.3916
 DAE  OA2   O   O      0  -0.672  36.5620  57.6622  19.3251
 DAE  OE2   O   O2     0  -0.570  38.5782  56.5165  20.5329
 DAE  NA3   N   NH1    0  -0.666  41.3563  57.0218  20.4107
 DAE  CA2   C   CH2    0  -0.315  40.5493  57.3891  21.5536
 DAE  CA1   C   CH2    0  -0.222  39.1373  57.6999  21.1295
 DAE  C1    C   CR6    0   0.442  42.6576  56.7488  20.4687
 DAE  C6    C   CR16   0  -0.371  43.3476  56.8569  21.7062
 DAE  C5    C   CR16   0  -0.241  44.6811  56.5956  21.8248
 DAE  C4    C   CR6    0   0.246  45.4180  56.2038  20.7008
 DAE  C3    C   CR16   0  -0.341  44.8036  56.0808  19.4771
 DAE  C2    C   CR6    0   0.216  43.4481  56.3444  19.3492
 DAE  N4    N   N      1   0.323  46.8243  55.9267  20.8204
 DAE  O4A   O   O      0  -0.389  47.4334  55.5916  19.8287
 DAE  O4B   O   O     -1  -0.387  47.3331  56.0429  21.9134
 DAE  N2    N   N      1   0.352  42.8889  56.1855  18.0340
 DAE  O2A   O   O      0  -0.412  41.6997  56.3959  17.8757
 DAE  O2B   O   O     -1  -0.379  43.6142  55.8482  17.1279
 DAE  HOB2  H   HOH1   0   0.538  33.2077  57.1839  20.5597
 DAE  HOA2  H   HOH1   0   0.518  36.9296  55.0556  18.4240
 DAE  HNA1  H   HNH1   0   0.420  40.9007  56.8881  19.5213
 DAE  HA21  H   HCH2   0   0.274  40.5485  56.5929  22.3034
 DAE  HA22  H   HCH2   0   0.276  40.9418  58.2899  22.0321
 DAE  HA11  H   HCH2   0   0.271  39.1161  58.5214  20.4112
 DAE  HA12  H   HCH2   0   0.277  38.5676  57.9928  22.0134
 DAE  H6    H   HCR6   0   0.310  42.8053  57.1536  22.5910
 DAE  H5    H   HCR6   0   0.310  45.1512  56.6957  22.7925
 DAE  H3    H   HCR6   0   0.330  45.3695  55.7791  18.6085

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
 DAE  BE   F1    single    1.488  0.020  1.488
 DAE  BE   F2    single    1.624  0.020  1.624
 DAE  BE   F3    single    1.487  0.020  1.487
 DAE  BE   OB3   single    1.850  0.020  1.850
 DAE  PB   OB1   double    1.598  0.020  1.598
 DAE  PB   OB2   single    1.539  0.020  1.539
 DAE  PB   OB3   single    1.502  0.020  1.502
 DAE  PB   OA3   single    1.600  0.020  1.600
 DAE  OB2  HOB2  single    0.850  0.020  0.980
 DAE  OA3  PA    single    1.636  0.020  1.636
 DAE  PA   OA1   single    1.577  0.020  1.577
 DAE  PA   OA2   double    1.469  0.020  1.469
 DAE  PA   OE2   single    1.584  0.020  1.584
 DAE  OA1  HOA2  single    0.850  0.020  0.980
 DAE  OE2  CA1   single    1.438  0.020  1.438
 DAE  NA3  CA2   single    1.447  0.020  1.447
 DAE  NA3  C1    single    1.331  0.020  1.331
 DAE  NA3  HNA1  single    0.860  0.020  1.020
 DAE  CA2  CA1   single    1.507  0.020  1.507
 DAE  CA2  HA21  single    0.970  0.020  1.090
 DAE  CA2  HA22  single    0.970  0.020  1.090
 DAE  CA1  HA11  single    0.970  0.020  1.090
 DAE  CA1  HA12  single    0.970  0.020  1.090
 DAE  C1   C6    aromatic  1.421  0.020  1.421
 DAE  C1   C2    aromatic  1.429  0.020  1.429
 DAE  C6   C5    aromatic  1.364  0.020  1.364
 DAE  C6   H6    single    0.930  0.020  1.080
 DAE  C5   C4    aromatic  1.400  0.020  1.400
 DAE  C5   H5    single    0.930  0.020  1.080
 DAE  C4   C3    aromatic  1.375  0.020  1.375
 DAE  C4   N4    single    1.438  0.020  1.438
 DAE  C3   C2    aromatic  1.387  0.020  1.387
 DAE  C3   H3    single    0.930  0.020  1.080
 DAE  C2   N2    single    1.438  0.020  1.438
 DAE  N4   O4A   double    1.211  0.020  1.211
 DAE  N4   O4B   single    1.211  0.020  1.211
 DAE  N2   O2A   double    1.218  0.020  1.218
 DAE  N2   O2B   single    1.209  0.020  1.209

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
 DAE  OB3   BE   F3    105.35  3.000
 DAE  OB3   BE   F2    101.90  3.000
 DAE  F3    BE   F2    111.32  3.000
 DAE  OB3   BE   F1    105.74  3.000
 DAE  F3    BE   F1    119.56  3.000
 DAE  F2    BE   F1    111.07  3.000
 DAE  OA3   PB   OB3   114.31  3.000
 DAE  OA3   PB   OB2   107.46  3.000
 DAE  OB3   PB   OB2   115.83  3.000
 DAE  OA3   PB   OB1   102.30  3.000
 DAE  OB3   PB   OB1   103.81  3.000
 DAE  OB2   PB   OB1   112.34  3.000
 DAE  HOB2  OB2  PB    106.21  3.000
 DAE  PB    OB3  BE    120.13  3.000
 DAE  PA    OA3  PB    125.97  3.000
 DAE  OE2   PA   OA2   117.76  3.000
 DAE  OE2   PA   OA1   102.45  3.000
 DAE  OA2   PA   OA1   119.67  3.000
 DAE  OE2   PA   OA3   100.51  3.000
 DAE  OA2   PA   OA3   112.97  3.000
 DAE  OA1   PA   OA3   100.51  3.000
 DAE  HOA2  OA1  PA    114.75  3.000
 DAE  CA1   OE2  PA    120.82  3.000
 DAE  HNA1  NA3  C1    116.95  3.000
 DAE  HNA1  NA3  CA2   118.59  3.000
 DAE  C1    NA3  CA2   124.27  3.000
 DAE  HA22  CA2  HA21  107.47  3.000
 DAE  HA22  CA2  CA1   106.84  3.000
 DAE  HA21  CA2  CA1   110.03  3.000
 DAE  HA22  CA2  NA3   110.78  3.000
 DAE  HA21  CA2  NA3   110.93  3.000
 DAE  CA1   CA2  NA3   110.66  3.000
 DAE  HA12  CA1  HA11  108.71  3.000
 DAE  HA12  CA1  CA2   108.45  3.000
 DAE  HA11  CA1  CA2   111.02  3.000
 DAE  HA12  CA1  OE2   110.72  3.000
 DAE  HA11  CA1  OE2   109.80  3.000
 DAE  CA2   CA1  OE2   108.13  3.000
 DAE  C2    C1   C6    115.79  3.000
 DAE  C2    C1   NA3   124.39  3.000
 DAE  C6    C1   NA3   119.81  3.000
 DAE  H6    C6   C5    118.20  3.000
 DAE  H6    C6   C1    119.39  3.000
 DAE  C5    C6   C1    122.41  3.000
 DAE  H5    C5   C4    121.06  3.000
 DAE  H5    C5   C6    119.05  3.000
 DAE  C4    C5   C6    119.89  3.000
 DAE  N4    C4   C3    119.59  3.000
 DAE  N4    C4   C5    120.11  3.000
 DAE  C3    C4   C5    120.30  3.000
 DAE  H3    C3   C2    119.42  3.000
 DAE  H3    C3   C4    120.46  3.000
 DAE  C2    C3   C4    120.12  3.000
 DAE  N2    C2   C3    116.32  3.000
 DAE  N2    C2   C1    122.19  3.000
 DAE  C3    C2   C1    121.49  3.000
 DAE  O4B   N4   O4A   123.66  3.000
 DAE  O4B   N4   C4    117.86  3.000
 DAE  O4A   N4   C4    118.48  3.000
 DAE  O2B   N2   O2A   122.46  3.000
 DAE  O2B   N2   C2    118.89  3.000
 DAE  O2A   N2   C2    118.65  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
 DAE  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 DAE  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 DAE  CONST_03  C3   C2   C1   C6      0.00   0.0  0
 DAE  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 DAE  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 DAE  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 DAE  CONST_07  C5   C6   C1   NA3   180.00   0.0  0
 DAE  CONST_08  C3   C2   C1   NA3   180.00   0.0  0
 DAE  CONST_09  N2   C2   C1   C6    180.00   0.0  0
 DAE  CONST_10  N4   C4   C5   C6    180.00   0.0  0
 DAE  CONST_11  N2   C2   C3   C4    180.00   0.0  0
 DAE  CONST_12  N4   C4   C3   C2    180.00   0.0  0
 DAE  CONST_13  H5   C5   C6   C1    180.00   0.0  0
 DAE  CONST_14  H3   C3   C2   C1    180.00   0.0  0
 DAE  CONST_15  H6   C6   C5   C4    180.00   0.0  0
 DAE  Var_01    C6   C1   NA3  CA2    -2.25  30.0  2
 DAE  Var_02    O2A  N2   C2   C1     -0.46  30.0  2
 DAE  Var_03    O4A  N4   C4   C5   -179.91  30.0  2
 DAE  Var_04    C1   NA3  CA2  CA1   177.05  30.0  3
 DAE  Var_05    OB1  PB   OB3  BE   -110.16  30.0  3
 DAE  Var_06    OA1  PA   OA3  PB   -105.24  30.0  3
 DAE  Var_07    CA2  CA1  OE2  PA    176.81  30.0  3
 DAE  Var_08    NA3  CA2  CA1  OE2    61.11  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
 DAE  chir_01  PB  OB2  OB3  OA3  both
 DAE  chir_02  PA  OA1  OA2  OE2  both

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
 DAE  plan-1  NA3  0.020
 DAE  plan-1  C1   0.020
 DAE  plan-1  C6   0.020
 DAE  plan-1  C5   0.020
 DAE  plan-1  C4   0.020
 DAE  plan-1  C3   0.020
 DAE  plan-1  C2   0.020
 DAE  plan-1  N4   0.020
 DAE  plan-1  N2   0.020
 DAE  plan-1  H6   0.020
 DAE  plan-1  H5   0.020
 DAE  plan-1  H3   0.020

