# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:08:15 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: trifluoro-[hydroxy-[hydroxy-[2-[methyl-(2-nitrophenyl)amino]ethoxy]phosphoryl]oxy-phosphoryl]oxy-beryllium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCO[P@](O)(=O)O[P@@](O)(=O)O[Be-](F)(F)F)c1ccccc1[N+]([O-])=O
#
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
 NMQ  NMQ  trifluoro-[hydroxy-[hydroxy-[2-[methyl-(2-nitrophenyl)amino]ethoxy]phosphoryl]oxy-phosphoryl]oxy-beryllium  ligand  39  26  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NMQ
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
 NMQ  BE    BE  BE    -1   0.495  -0.8879   2.3485   4.7468
 NMQ  F1    F   F      0  -0.604  -0.1217   3.5646   4.4645
 NMQ  F2    F   F      0  -0.604  -1.0080   1.8352   6.1145
 NMQ  F3    F   F      0  -0.542   1.1803   0.9228   3.6264
 NMQ  PB    P   P      0   1.550  -0.1653   0.4606   2.7608
 NMQ  OB1   O   O      0  -0.327   0.6168   1.0423   1.4745
 NMQ  OB2   O   OH1    0  -0.632   0.0157  -1.0760   3.1805
 NMQ  OB3   O   OC2    0  -0.625  -1.1638   1.3099   3.5511
 NMQ  OA3   O   O2     0  -0.532  -1.3472   0.0067   1.5826
 NMQ  PA    P   P      0   1.410  -1.4575  -1.2683   0.6426
 NMQ  OA1   O   OH1    0  -0.687  -0.0017  -1.6648   0.1188
 NMQ  OA2   O   O      0  -0.733  -2.1235  -2.4495   1.2221
 NMQ  OE2   O   O2     0  -0.565  -2.2183  -0.5641  -0.5712
 NMQ  NA3   N   NT     0  -0.388  -0.6873   0.1514  -2.8967
 NMQ  CA2   C   CH2    0  -0.350  -2.0843  -0.2754  -2.9478
 NMQ  CA1   C   CH2    0  -0.226  -2.4162  -1.2289  -1.8227
 NMQ  C1    C   CR6    0   0.259   0.0319  -0.0242  -4.0971
 NMQ  C6    C   CR16   0  -0.240  -0.4832   0.3880  -5.3264
 NMQ  C5    C   CR16   0  -0.201   0.2108   0.1926  -6.5080
 NMQ  C4    C   CR16   0  -0.284   1.4493  -0.4364  -6.4993
 NMQ  C3    C   CR16   0  -0.241   1.9804  -0.8780  -5.3027
 NMQ  C2    C   CR6    0   0.148   1.2808  -0.6556  -4.1230
 NMQ  N2    N   N      1   0.305   1.8757  -1.1638  -2.9048
 NMQ  O2A   O   O     -1  -0.367   2.4023  -2.2487  -2.9482
 NMQ  O2B   O   O      0  -0.377   1.8293  -0.4745  -1.9076
 NMQ  CA3   C   CH3    0  -0.536  -0.5028   1.4868  -2.3340
 NMQ  HOB2  H   HOH1   0   0.512   0.7542  -1.2267   3.7855
 NMQ  HOA2  H   HOH1   0   0.496   0.4624  -1.0284  -0.4455
 NMQ  HA21  H   HCH2   0   0.272  -2.7641   0.5838  -2.9291
 NMQ  HA22  H   HCH2   0   0.256  -2.2892  -0.8117  -3.8763
 NMQ  HA11  H   HCH2   0   0.294  -3.4594  -1.5421  -1.8932
 NMQ  HA12  H   HCH2   0   0.290  -1.7894  -2.1202  -1.9050
 NMQ  H6    H   HCR6   0   0.269  -1.4513   0.8732  -5.3483
 NMQ  H5    H   HCR6   0   0.284  -0.2165   0.5344  -7.4413
 NMQ  H4    H   HCR6   0   0.243   1.9966  -0.5885  -7.4191
 NMQ  H3    H   HCR6   0   0.296   2.9372  -1.3816  -5.2846
 NMQ  HA31  H   HCH3   0   0.277   0.5549   1.7356  -2.2931
 NMQ  HA32  H   HCH3   0   0.226  -1.0129   2.2575  -2.9252
 NMQ  HA33  H   HCH3   0   0.178  -0.8932   1.5238  -1.3193

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
 NMQ  BE   F1    single    1.465  0.020  1.465
 NMQ  BE   F2    single    1.466  0.020  1.466
 NMQ  BE   F3    single    2.751  0.020  2.751
 NMQ  BE   OB3   single    1.608  0.020  1.608
 NMQ  PB   OB1   double    1.614  0.020  1.614
 NMQ  PB   OB2   single    1.603  0.020  1.603
 NMQ  PB   OB3   single    1.531  0.020  1.531
 NMQ  PB   OA3   single    1.729  0.020  1.729
 NMQ  OB2  HOB2  single    0.850  0.020  0.980
 NMQ  OA3  PA    single    1.588  0.020  1.588
 NMQ  PA   OA1   single    1.597  0.020  1.597
 NMQ  PA   OA2   double    1.475  0.020  1.475
 NMQ  PA   OE2   single    1.596  0.020  1.596
 NMQ  OA1  HOA2  single    0.850  0.020  0.980
 NMQ  OE2  CA1   single    1.431  0.020  1.431
 NMQ  NA3  CA2   single    1.462  0.020  1.462
 NMQ  NA3  C1    single    1.410  0.020  1.410
 NMQ  NA3  CA3   single    1.461  0.020  1.461
 NMQ  CA2  CA1   single    1.512  0.020  1.512
 NMQ  CA2  HA21  single    0.970  0.020  1.090
 NMQ  CA2  HA22  single    0.970  0.020  1.090
 NMQ  CA1  HA11  single    0.970  0.020  1.090
 NMQ  CA1  HA12  single    0.970  0.020  1.090
 NMQ  C1   C6    aromatic  1.395  0.020  1.395
 NMQ  C1   C2    aromatic  1.400  0.020  1.400
 NMQ  C6   C5    aromatic  1.384  0.020  1.384
 NMQ  C6   H6    single    0.930  0.020  1.080
 NMQ  C5   C4    aromatic  1.389  0.020  1.389
 NMQ  C5   H5    single    0.930  0.020  1.080
 NMQ  C4   C3    aromatic  1.382  0.020  1.382
 NMQ  C4   H4    single    0.930  0.020  1.080
 NMQ  C3   C2    aromatic  1.389  0.020  1.389
 NMQ  C3   H3    single    0.930  0.020  1.080
 NMQ  C2   N2    single    1.448  0.020  1.448
 NMQ  N2   O2A   single    1.207  0.020  1.207
 NMQ  N2   O2B   double    1.213  0.020  1.213
 NMQ  CA3  HA31  single    0.970  0.020  1.090
 NMQ  CA3  HA32  single    0.970  0.020  1.090
 NMQ  CA3  HA33  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
 NMQ  OB3   BE   F3     59.42  3.000
 NMQ  OB3   BE   F2    116.98  3.000
 NMQ  F3    BE   F2    105.08  3.000
 NMQ  OB3   BE   F1    118.87  3.000
 NMQ  F3    BE   F1     87.63  3.000
 NMQ  F2    BE   F1    120.89  3.000
 NMQ  OA3   PB   OB3    92.95  3.000
 NMQ  OA3   PB   OB2    90.23  3.000
 NMQ  OB3   PB   OB2   118.05  3.000
 NMQ  OA3   PB   OB1    83.27  3.000
 NMQ  OB3   PB   OB1   121.85  3.000
 NMQ  OB2   PB   OB1   119.96  3.000
 NMQ  HOB2  OB2  PB    113.55  3.000
 NMQ  PB    OB3  BE    129.09  3.000
 NMQ  PA    OA3  PB    131.41  3.000
 NMQ  OE2   PA   OA2   115.91  3.000
 NMQ  OE2   PA   OA1   107.13  3.000
 NMQ  OA2   PA   OA1   109.98  3.000
 NMQ  OE2   PA   OA3    97.41  3.000
 NMQ  OA2   PA   OA3   116.23  3.000
 NMQ  OA1   PA   OA3   109.28  3.000
 NMQ  HOA2  OA1  PA    117.68  3.000
 NMQ  CA1   OE2  PA    121.74  3.000
 NMQ  CA3   NA3  C1    112.16  3.000
 NMQ  CA3   NA3  CA2   113.65  3.000
 NMQ  C1    NA3  CA2   114.91  3.000
 NMQ  HA22  CA2  HA21  106.46  3.000
 NMQ  HA22  CA2  CA1   106.38  3.000
 NMQ  HA21  CA2  CA1   110.23  3.000
 NMQ  HA22  CA2  NA3   110.64  3.000
 NMQ  HA21  CA2  NA3   111.31  3.000
 NMQ  CA1   CA2  NA3   111.59  3.000
 NMQ  HA12  CA1  HA11  108.02  3.000
 NMQ  HA12  CA1  CA2   109.42  3.000
 NMQ  HA11  CA1  CA2   110.04  3.000
 NMQ  HA12  CA1  OE2   111.44  3.000
 NMQ  HA11  CA1  OE2   108.78  3.000
 NMQ  CA2   CA1  OE2   109.12  3.000
 NMQ  C2    C1   C6    116.51  3.000
 NMQ  C2    C1   NA3   121.80  3.000
 NMQ  C6    C1   NA3   121.66  3.000
 NMQ  H6    C6   C5    119.61  3.000
 NMQ  H6    C6   C1    118.70  3.000
 NMQ  C5    C6   C1    121.69  3.000
 NMQ  H5    C5   C4    120.04  3.000
 NMQ  H5    C5   C6    119.59  3.000
 NMQ  C4    C5   C6    120.37  3.000
 NMQ  H4    C4   C3    119.82  3.000
 NMQ  H4    C4   C5    120.65  3.000
 NMQ  C3    C4   C5    119.53  3.000
 NMQ  H3    C3   C2    120.39  3.000
 NMQ  H3    C3   C4    120.23  3.000
 NMQ  C2    C3   C4    119.38  3.000
 NMQ  N2    C2   C3    116.83  3.000
 NMQ  N2    C2   C1    120.62  3.000
 NMQ  C3    C2   C1    122.49  3.000
 NMQ  O2B   N2   O2A   123.85  3.000
 NMQ  O2B   N2   C2    118.45  3.000
 NMQ  O2A   N2   C2    117.69  3.000
 NMQ  HA33  CA3  HA32  108.17  3.000
 NMQ  HA33  CA3  HA31  107.83  3.000
 NMQ  HA32  CA3  HA31  108.16  3.000
 NMQ  HA33  CA3  NA3   110.19  3.000
 NMQ  HA32  CA3  NA3   112.08  3.000
 NMQ  HA31  CA3  NA3   110.27  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
 NMQ  CONST_01  C4    C5   C6   C1      0.00   0.0  0
 NMQ  CONST_02  C4    C3   C2   C1      0.00   0.0  0
 NMQ  CONST_03  C3    C2   C1   C6      0.00   0.0  0
 NMQ  CONST_04  C3    C4   C5   C6      0.00   0.0  0
 NMQ  CONST_05  C2    C1   C6   C5      0.00   0.0  0
 NMQ  CONST_06  C2    C3   C4   C5      0.00   0.0  0
 NMQ  CONST_07  C5    C6   C1   NA3   180.00   0.0  0
 NMQ  CONST_08  C3    C2   C1   NA3   180.00   0.0  0
 NMQ  CONST_09  N2    C2   C1   C6    180.00   0.0  0
 NMQ  CONST_10  N2    C2   C3   C4    180.00   0.0  0
 NMQ  CONST_11  H5    C5   C6   C1    180.00   0.0  0
 NMQ  CONST_12  H3    C3   C2   C1    180.00   0.0  0
 NMQ  CONST_13  H4    C4   C5   C6    180.00   0.0  0
 NMQ  CONST_14  H6    C6   C5   C4    180.00   0.0  0
 NMQ  Var_01    C6    C1   NA3  CA2    47.79  30.0  2
 NMQ  Var_02    O2A   N2   C2   C1    137.18  30.0  2
 NMQ  Var_03    C1    NA3  CA2  CA1   127.38  30.0  3
 NMQ  Var_04    HA31  CA3  NA3  C1    -49.32  30.0  3
 NMQ  Var_05    OB1   PB   OB3  BE    -85.13  30.0  3
 NMQ  Var_06    OA1   PA   OA3  PB    -38.66  30.0  3
 NMQ  Var_07    CA2   CA1  OE2  PA   -134.91  30.0  3
 NMQ  Var_08    NA3   CA2  CA1  OE2    61.52  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
 NMQ  chir_01  PB  OB2  OB3  OA3  both
 NMQ  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
 NMQ  plan-1  NA3  0.020
 NMQ  plan-1  C1   0.020
 NMQ  plan-1  C6   0.020
 NMQ  plan-1  C5   0.020
 NMQ  plan-1  C4   0.020
 NMQ  plan-1  C3   0.020
 NMQ  plan-1  C2   0.020
 NMQ  plan-1  N2   0.020
 NMQ  plan-1  H6   0.020
 NMQ  plan-1  H5   0.020
 NMQ  plan-1  H4   0.020
 NMQ  plan-1  H3   0.020

