# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:25:41 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: trifluoro-[hydroxy-[hydroxy-[2-[(4-nitrophenyl)amino]ethoxy]phosphoryl]oxy-phosphoryl]oxy-beryllium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P@](=O)(OCCNc1ccc(cc1)[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
 PNQ  PNQ  trifluoro-[hydroxy-[hydroxy-[2-[(4-nitrophenyl)amino]ethoxy]phosphoryl]oxy-phosphoryl]oxy-beryllium  ligand  36  25  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PNQ
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
 PNQ  BE    BE  BE     0   0.642  35.1065  55.3694  19.4393
 PNQ  F1    F   F      0  -0.619  35.7027  54.2187  18.6951
 PNQ  F2    F   F      0  -0.624  33.8361  55.1245  20.1911
 PNQ  F3    F   F      0  -0.630  35.0497  56.6984  18.5976
 PNQ  PB    P   P      0   1.443  37.3844  56.8545  20.4482
 PNQ  OB1   O   O      0  -0.653  38.7534  56.2580  19.8818
 PNQ  OB2   O   OH1    0  -0.648  36.9750  57.9736  19.4339
 PNQ  OB3   O   OC2    0  -0.725  36.3460  55.8375  20.7464
 PNQ  OA3   O   O2     0  -0.694  37.9092  57.6163  21.7459
 PNQ  PA    P   P      0   1.436  37.8302  59.0741  22.4897
 PNQ  OA1   O   OH1    0  -0.717  38.1792  60.1252  21.3676
 PNQ  OA2   O   O      0  -0.620  36.6218  59.2253  23.3043
 PNQ  OE2   O   O2     0  -0.503  39.2444  59.0595  23.2329
 PNQ  NA3   N   NH1    0  -0.344  40.0816  56.2366  22.9275
 PNQ  CA2   C   CH2    0  -0.392  40.5349  57.1377  23.9645
 PNQ  CA1   C   CH2    0  -0.284  39.4566  58.1398  24.3292
 PNQ  C1    C   C      0   0.263  40.3980  56.3875  21.6954
 PNQ  C6    C   C1     0  -0.136  41.3355  57.3686  21.2307
 PNQ  C5    C   C1     0  -0.231  41.9992  57.1127  20.0940
 PNQ  C4    C   C      0   0.356  41.7721  55.8922  19.3457
 PNQ  C3    C   C1     0  -0.279  40.7553  55.0788  19.6021
 PNQ  C2    C   C1     0  -0.128  39.7995  55.4631  20.6691
 PNQ  N4    N   N      1   0.358  42.6756  55.5824  18.2439
 PNQ  O4A   O   O      0  -0.382  42.9007  54.4261  18.0060
 PNQ  O4B   O   O     -1  -0.214  43.1232  56.5360  17.6538
 PNQ  HOB2  H   HOH1   0   0.480  36.1707  57.6280  18.9016
 PNQ  HOA2  H   HOH1   0   0.498  37.5310  60.2317  20.6535
 PNQ  HNA1  H   HNH1   0   0.511  39.4481  55.4897  23.2001
 PNQ  HA21  H   HCH2   0   0.414  40.7566  56.5336  24.8430
 PNQ  HA22  H   HCH2   0   0.399  41.4669  57.6128  23.6852
 PNQ  HA11  H   HCH2   0   0.250  39.8098  58.7317  25.1725
 PNQ  HA12  H   HCH2   0   0.293  38.5484  57.6375  24.6677
 PNQ  H6    H   H      0   0.401  41.5839  58.2551  21.7955
 PNQ  H5    H   H      0   0.375  42.7503  57.8197  19.7670
 PNQ  H3    H   H      0   0.351  40.5389  54.1876  19.0279
 PNQ  H2    H   H      0   0.354  39.3576  54.5819  21.1350

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
 PNQ  BE   F1    single    1.494  0.020  1.494
 PNQ  BE   F2    single    1.496  0.020  1.496
 PNQ  BE   F3    single    1.574  0.020  1.574
 PNQ  BE   OB3   single    1.861  0.020  1.861
 PNQ  PB   OB1   double    1.597  0.020  1.597
 PNQ  PB   OB2   single    1.565  0.020  1.565
 PNQ  PB   OB3   single    1.484  0.020  1.484
 PNQ  PB   OA3   single    1.594  0.020  1.594
 PNQ  OB2  HOB2  single    0.832  0.020  0.971
 PNQ  OA3  PA    single    1.639  0.020  1.639
 PNQ  PA   OA1   single    1.577  0.020  1.577
 PNQ  PA   OA2   double    1.465  0.020  1.465
 PNQ  PA   OE2   single    1.598  0.020  1.598
 PNQ  OA1  HOA2  single    0.832  0.020  0.971
 PNQ  OE2  CA1   single    1.447  0.020  1.447
 PNQ  NA3  CA2   single    1.447  0.020  1.447
 PNQ  NA3  C1    single    1.281  0.020  1.281
 PNQ  NA3  HNA1  single    0.868  0.020  1.013
 PNQ  CA2  CA1   single    1.517  0.020  1.517
 PNQ  CA2  HA21  single    0.939  0.020  1.096
 PNQ  CA2  HA22  single    0.939  0.020  1.096
 PNQ  CA1  HA11  single    0.939  0.020  1.096
 PNQ  CA1  HA12  single    0.939  0.020  1.096
 PNQ  C1   C6    aromatic  1.434  0.020  1.434
 PNQ  C1   C2    aromatic  1.505  0.020  1.505
 PNQ  C6   C5    aromatic  1.341  0.020  1.341
 PNQ  C6   H6    single    0.929  0.020  1.085
 PNQ  C5   C4    aromatic  1.450  0.020  1.450
 PNQ  C5   H5    single    0.929  0.020  1.085
 PNQ  C4   C3    aromatic  1.327  0.020  1.327
 PNQ  C4   N4    single    1.458  0.020  1.458
 PNQ  C3   C2    aromatic  1.483  0.020  1.483
 PNQ  C3   H3    single    0.929  0.020  1.085
 PNQ  C2   H2    single    0.929  0.020  1.085
 PNQ  N4   O4A   double    1.202  0.020  1.202
 PNQ  N4   O4B   single    1.207  0.020  1.207

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
 PNQ  OB3   BE   F3    100.79  3.000
 PNQ  OB3   BE   F2    104.70  3.000
 PNQ  F3    BE   F2    112.10  3.000
 PNQ  OB3   BE   F1    106.12  3.000
 PNQ  F3    BE   F1    113.47  3.000
 PNQ  F2    BE   F1    117.57  3.000
 PNQ  OA3   PB   OB3   113.23  3.000
 PNQ  OA3   PB   OB2   105.79  3.000
 PNQ  OB3   PB   OB2   115.93  3.000
 PNQ  OA3   PB   OB1   100.67  3.000
 PNQ  OB3   PB   OB1   114.53  3.000
 PNQ  OB2   PB   OB1   105.16  3.000
 PNQ  HOB2  OB2  PB    107.51  3.000
 PNQ  PB    OB3  BE    119.82  3.000
 PNQ  PA    OA3  PB    141.18  3.000
 PNQ  OE2   PA   OA2   118.19  3.000
 PNQ  OE2   PA   OA1    98.12  3.000
 PNQ  OA2   PA   OA1   120.63  3.000
 PNQ  OE2   PA   OA3    99.23  3.000
 PNQ  OA2   PA   OA3   112.58  3.000
 PNQ  OA1   PA   OA3   105.03  3.000
 PNQ  HOA2  OA1  PA    116.69  3.000
 PNQ  CA1   OE2  PA    119.22  3.000
 PNQ  HNA1  NA3  C1    119.89  3.000
 PNQ  HNA1  NA3  CA2   117.43  3.000
 PNQ  C1    NA3  CA2   122.60  3.000
 PNQ  HA22  CA2  HA21  106.04  3.000
 PNQ  HA22  CA2  CA1   112.59  3.000
 PNQ  HA21  CA2  CA1   108.50  3.000
 PNQ  HA22  CA2  NA3   110.99  3.000
 PNQ  HA21  CA2  NA3   107.25  3.000
 PNQ  CA1   CA2  NA3   111.17  3.000
 PNQ  HA12  CA1  HA11  106.24  3.000
 PNQ  HA12  CA1  CA2   111.23  3.000
 PNQ  HA11  CA1  CA2   108.34  3.000
 PNQ  HA12  CA1  OE2   113.92  3.000
 PNQ  HA11  CA1  OE2   106.79  3.000
 PNQ  CA2   CA1  OE2   110.01  3.000
 PNQ  C2    C1   C6    117.32  3.000
 PNQ  C2    C1   NA3   119.03  3.000
 PNQ  C6    C1   NA3   123.61  3.000
 PNQ  H6    C6   C5    119.09  3.000
 PNQ  H6    C6   C1    122.84  3.000
 PNQ  C5    C6   C1    117.88  3.000
 PNQ  H5    C5   C4    120.19  3.000
 PNQ  H5    C5   C6    118.36  3.000
 PNQ  C4    C5   C6    121.38  3.000
 PNQ  N4    C4   C3    119.38  3.000
 PNQ  N4    C4   C5    118.16  3.000
 PNQ  C3    C4   C5    122.43  3.000
 PNQ  H3    C3   C2    117.80  3.000
 PNQ  H3    C3   C4    123.74  3.000
 PNQ  C2    C3   C4    118.29  3.000
 PNQ  H2    C2   C3    111.05  3.000
 PNQ  H2    C2   C1    111.48  3.000
 PNQ  C3    C2   C1    113.16  3.000
 PNQ  O4B   N4   O4A   126.42  3.000
 PNQ  O4B   N4   C4    115.54  3.000
 PNQ  O4A   N4   C4    118.03  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
 PNQ  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 PNQ  CONST_04  C3   C4   C5   C6     0.00   0.0  0
 PNQ  CONST_06  C2   C3   C4   C5     0.00   0.0  0
 PNQ  CONST_09  N4   C4   C5   C6   180.00   0.0  0
 PNQ  CONST_10  N4   C4   C3   C2   180.00   0.0  0
 PNQ  CONST_11  H5   C5   C6   C1   180.00   0.0  0
 PNQ  CONST_14  H6   C6   C5   C4   180.00   0.0  0
 PNQ  Var_01    C6   C1   NA3  CA2    6.68  30.0  2
 PNQ  Var_02    O4A  N4   C4   C5   148.17  30.0  2
 PNQ  Var_03    C1   NA3  CA2  CA1   99.86  30.0  3
 PNQ  Var_04    OB1  PB   OB3  BE   -91.55  30.0  3
 PNQ  Var_05    OA1  PA   OA3  PB   -49.89  30.0  3
 PNQ  Var_06    CA2  CA1  OE2  PA   115.77  30.0  3
 PNQ  Var_07    NA3  CA2  CA1  OE2  -68.81  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
 PNQ  chir_01  PB  OB2  OB3  OA3  both
 PNQ  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
 PNQ  plan-1  NA3  0.020
 PNQ  plan-1  C1   0.020
 PNQ  plan-1  C6   0.020
 PNQ  plan-1  C5   0.020
 PNQ  plan-1  C4   0.020
 PNQ  plan-1  C3   0.020
 PNQ  plan-1  C2   0.020
 PNQ  plan-1  N4   0.020
 PNQ  plan-1  H6   0.020
 PNQ  plan-1  H5   0.020
 PNQ  plan-1  H3   0.020
 PNQ  plan-1  H2   0.020

