# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:04:11 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   0.733  33.3267  59.3614  21.4609
 DAE  F1    F   F      0  -0.606  32.2800  59.5316  22.5046
 DAE  F2    F   F      0  -0.573  32.7654  58.4659  20.2250
 DAE  F3    F   F      0  -0.604  34.0777  60.5462  20.9687
 DAE  PB    P   P      0   1.530  34.7069  56.8186  21.7347
 DAE  OB1   O   O      0  -0.326  34.1972  55.9798  22.9958
 DAE  OB2   O   OH1    0  -0.754  33.9415  56.4711  20.4459
 DAE  OB3   O   OC2    0  -0.656  34.6042  58.2468  22.1897
 DAE  OA3   O   O2     0  -0.673  36.2091  56.2949  21.5549
 DAE  PA    P   P      0   1.494  37.1255  56.4770  20.2119
 DAE  OA1   O   OH1    0  -0.706  36.9557  55.0654  19.5288
 DAE  OA2   O   O      0  -0.673  36.7994  57.6922  19.4529
 DAE  OE2   O   O2     0  -0.571  38.5766  56.3693  20.8391
 DAE  NA3   N   NH1    0  -0.667  41.3471  56.8399  20.6196
 DAE  CA2   C   CH2    0  -0.314  40.6089  57.1404  21.8267
 DAE  CA1   C   CH2    0  -0.218  39.1831  57.4984  21.4937
 DAE  C1    C   CR6    0   0.443  42.6650  56.6648  20.5600
 DAE  C6    C   CR16   0  -0.371  43.4567  56.8252  21.7286
 DAE  C5    C   CR16   0  -0.241  44.8122  56.6713  21.7197
 DAE  C4    C   CR6    0   0.246  45.4687  56.3397  20.5287
 DAE  C3    C   CR16   0  -0.341  44.7544  56.1680  19.3670
 DAE  C2    C   CR6    0   0.215  43.3763  56.3234  19.3686
 DAE  N4    N   N      1   0.324  46.8975  56.1719  20.5152
 DAE  O4A   O   O      0  -0.389  47.4357  55.8879  19.4681
 DAE  O4B   O   O     -1  -0.387  47.4948  56.3246  21.5577
 DAE  N2    N   N      1   0.352  42.7103  56.1192  18.1101
 DAE  O2A   O   O      0  -0.412  41.4954  56.1986  18.0722
 DAE  O2B   O   O     -1  -0.378  43.3753  55.8741  17.1312
 DAE  HOB2  H   HOH1   0   0.540  33.3076  57.3390  20.2202
 DAE  HOA2  H   HOH1   0   0.518  36.9123  55.0876  18.5621
 DAE  HNA1  H   HNH1   0   0.418  40.8260  56.6351  19.7811
 DAE  HA21  H   HCH2   0   0.275  40.6396  56.2993  22.5252
 DAE  HA22  H   HCH2   0   0.276  41.0363  58.0068  22.3358
 DAE  HA11  H   HCH2   0   0.269  39.1503  58.3713  20.8391
 DAE  HA12  H   HCH2   0   0.280  38.6516  57.7306  22.4176
 DAE  H6    H   HCR6   0   0.309  42.9784  57.0746  22.6635
 DAE  H5    H   HCR6   0   0.310  45.3624  56.8078  22.6394
 DAE  H3    H   HCR6   0   0.330  45.2585  55.9086  18.4482

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    1.626  0.020  1.626
 DAE  BE   F3    single    1.487  0.020  1.487
 DAE  BE   OB3   single    1.845  0.020  1.845
 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    1.601  0.020  1.601
 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    1.585  0.020  1.585
 DAE  OA1  HOA2  single    0.850  0.020  0.980
 DAE  OE2  CA1   single    1.439  0.020  1.439
 DAE  NA3  CA2   single    1.446  0.020  1.446
 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    1.439  0.020  1.439
 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    105.22  3.000
 DAE  OB3   BE   F2    101.92  3.000
 DAE  F3    BE   F2    111.20  3.000
 DAE  OB3   BE   F1    106.20  3.000
 DAE  F3    BE   F1    119.77  3.000
 DAE  F2    BE   F1    110.69  3.000
 DAE  OA3   PB   OB3   114.15  3.000
 DAE  OA3   PB   OB2   107.39  3.000
 DAE  OB3   PB   OB2   115.74  3.000
 DAE  OA3   PB   OB1   102.48  3.000
 DAE  OB3   PB   OB1   103.78  3.000
 DAE  OB2   PB   OB1   112.57  3.000
 DAE  HOB2  OB2  PB    106.31  3.000
 DAE  PB    OB3  BE    120.13  3.000
 DAE  PA    OA3  PB    125.54  3.000
 DAE  OE2   PA   OA2   117.64  3.000
 DAE  OE2   PA   OA1   102.07  3.000
 DAE  OA2   PA   OA1   119.51  3.000
 DAE  OE2   PA   OA3   100.40  3.000
 DAE  OA2   PA   OA3   113.07  3.000
 DAE  OA1   PA   OA3   101.28  3.000
 DAE  HOA2  OA1  PA    114.63  3.000
 DAE  CA1   OE2  PA    120.84  3.000
 DAE  HNA1  NA3  C1    116.60  3.000
 DAE  HNA1  NA3  CA2   118.20  3.000
 DAE  C1    NA3  CA2   124.75  3.000
 DAE  HA22  CA2  HA21  107.54  3.000
 DAE  HA22  CA2  CA1   106.55  3.000
 DAE  HA21  CA2  CA1   110.50  3.000
 DAE  HA22  CA2  NA3   110.75  3.000
 DAE  HA21  CA2  NA3   111.03  3.000
 DAE  CA1   CA2  NA3   110.35  3.000
 DAE  HA12  CA1  HA11  108.84  3.000
 DAE  HA12  CA1  CA2   108.92  3.000
 DAE  HA11  CA1  CA2   110.54  3.000
 DAE  HA12  CA1  OE2   110.30  3.000
 DAE  HA11  CA1  OE2   110.00  3.000
 DAE  CA2   CA1  OE2   108.23  3.000
 DAE  C2    C1   C6    115.81  3.000
 DAE  C2    C1   NA3   124.17  3.000
 DAE  C6    C1   NA3   120.01  3.000
 DAE  H6    C6   C5    118.17  3.000
 DAE  H6    C6   C1    119.45  3.000
 DAE  C5    C6   C1    122.38  3.000
 DAE  H5    C5   C4    121.02  3.000
 DAE  H5    C5   C6    119.09  3.000
 DAE  C4    C5   C6    119.89  3.000
 DAE  N4    C4   C3    119.58  3.000
 DAE  N4    C4   C5    120.10  3.000
 DAE  C3    C4   C5    120.33  3.000
 DAE  H3    C3   C2    119.47  3.000
 DAE  H3    C3   C4    120.44  3.000
 DAE  C2    C3   C4    120.09  3.000
 DAE  N2    C2   C3    116.30  3.000
 DAE  N2    C2   C1    122.20  3.000
 DAE  C3    C2   C1    121.49  3.000
 DAE  O4B   N4   O4A   123.69  3.000
 DAE  O4B   N4   C4    117.84  3.000
 DAE  O4A   N4   C4    118.47  3.000
 DAE  O2B   N2   O2A   122.47  3.000
 DAE  O2B   N2   C2    118.86  3.000
 DAE  O2A   N2   C2    118.67  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    -2.63  30.0  2
 DAE  Var_02    O2A  N2   C2   C1     -2.41  30.0  2
 DAE  Var_03    O4A  N4   C4   C5   -179.84  30.0  2
 DAE  Var_04    C1   NA3  CA2  CA1   170.56  30.0  3
 DAE  Var_05    OB1  PB   OB3  BE   -110.08  30.0  3
 DAE  Var_06    OA1  PA   OA3  PB    -99.14  30.0  3
 DAE  Var_07    CA2  CA1  OE2  PA   -173.05  30.0  3
 DAE  Var_08    NA3  CA2  CA1  OE2    60.66  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

