# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 00:46:35 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: benzene-1,2,3,4-tetrayl tetrakis[dihydrogen (phosphate)]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1ccc(O[P](O)(O)=O)c(O[P](O)(O)=O)c1O[P](O)(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
 GVF  GVF  'benzene-1,2,3,4-tetrayl tetrakis[dihydrogen (phosphate)]'  ligand  28  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GVF
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
 GVF  OAE  O  OP    -1  -0.907   0.8198  -3.5441   3.6850
 GVF  PAH  P  P      0   1.209   0.7907  -2.4477   4.7410
 GVF  OAG  O  OP    -1  -0.899   1.7517  -2.6360   5.9075
 GVF  OAI  O  O      0  -0.901  -0.6091  -2.0287   5.1789
 GVF  OAM  O  O2     0  -0.652   1.4204  -1.0477   3.9525
 GVF  CAL  C  CR6    0   0.203   1.5727  -1.0125   2.6168
 GVF  CAP  C  CR6    0   0.212   2.7773  -1.4407   2.0429
 GVF  OAQ  O  O2     0  -0.652   3.7515  -1.9253   2.8314
 GVF  PAT  P  P      0   1.211   5.0869  -0.9523   3.3252
 GVF  OAS  O  OP    -1  -0.892   4.8466  -0.6978   4.8078
 GVF  OAY  O  OP    -1  -0.909   6.2716  -1.8748   3.0570
 GVF  OAU  O  O      0  -0.907   5.0143   0.2978   2.4589
 GVF  CAO  C  CR6    0   0.262   2.9592  -1.3919   0.6480
 GVF  OAR  O  O2     0  -0.648   4.1417  -1.8093   0.1495
 GVF  PAW  P  P      0   1.216   4.2700  -2.7448  -1.2864
 GVF  OAV  O  OP    -1  -0.899   3.9798  -1.7799  -2.4345
 GVF  OAZ  O  OP    -1  -0.892   5.7263  -3.1793  -1.1962
 GVF  OAX  O  O      0  -0.901   3.2492  -3.8613  -1.1245
 GVF  CAN  C  CR16   0  -0.411   1.9192  -0.9177  -0.1434
 GVF  CAJ  C  CR16   0  -0.413   0.7244  -0.4868   0.4260
 GVF  CAK  C  CR6    0   0.251   0.5290  -0.5342   1.8019
 GVF  OAF  O  O2     0  -0.646  -0.6235  -0.1639   2.4002
 GVF  PAC  P  P      0   1.214  -1.5047   1.2337   1.9275
 GVF  OAB  O  OP    -1  -0.897  -2.1656   0.8754   0.5979
 GVF  OAA  O  OP    -1  -0.890  -2.4775   1.3486   3.0921
 GVF  OAD  O  O      0  -0.903  -0.4635   2.3404   1.8382
 GVF  HAN  H  HCR6   0   0.219   2.0553  -0.8732  -1.2158
 GVF  HAJ  H  HCR6   0   0.221  -0.0801  -0.1327  -0.2054

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
 GVF  OAE  PAH  deloc     1.523  0.020  1.523
 GVF  PAH  OAG  deloc     1.523  0.020  1.523
 GVF  PAH  OAI  deloc     1.525  0.020  1.525
 GVF  PAH  OAM  single    1.726  0.020  1.726
 GVF  OAM  CAL  single    1.345  0.020  1.345
 GVF  CAL  CAP  aromatic  1.401  0.020  1.401
 GVF  CAP  OAQ  single    1.344  0.020  1.344
 GVF  OAQ  PAT  single    1.724  0.020  1.724
 GVF  PAT  OAS  deloc     1.523  0.020  1.523
 GVF  PAT  OAY  deloc     1.525  0.020  1.525
 GVF  PAT  OAU  deloc     1.523  0.020  1.523
 GVF  CAP  CAO  aromatic  1.408  0.020  1.408
 GVF  CAO  OAR  single    1.350  0.020  1.350
 GVF  OAR  PAW  single    1.719  0.020  1.719
 GVF  PAW  OAV  deloc     1.528  0.020  1.528
 GVF  PAW  OAZ  deloc     1.522  0.020  1.522
 GVF  PAW  OAX  deloc     1.521  0.020  1.521
 GVF  CAO  CAN  aromatic  1.390  0.020  1.390
 GVF  CAN  CAJ  aromatic  1.392  0.020  1.392
 GVF  CAL  CAK  aromatic  1.408  0.020  1.408
 GVF  CAJ  CAK  aromatic  1.390  0.020  1.390
 GVF  CAK  OAF  single    1.350  0.020  1.350
 GVF  OAF  PAC  single    1.719  0.020  1.719
 GVF  PAC  OAB  deloc     1.527  0.020  1.527
 GVF  PAC  OAA  deloc     1.522  0.020  1.522
 GVF  PAC  OAD  deloc     1.522  0.020  1.522
 GVF  CAN  HAN  single    0.930  0.020  1.080
 GVF  CAJ  HAJ  single    0.930  0.020  1.080

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
 GVF  OAM  PAH  OAI  104.08  3.000
 GVF  OAM  PAH  OAG  102.71  3.000
 GVF  OAI  PAH  OAG  113.15  3.000
 GVF  OAM  PAH  OAE  105.09  3.000
 GVF  OAI  PAH  OAE  114.49  3.000
 GVF  OAG  PAH  OAE  115.48  3.000
 GVF  CAL  OAM  PAH  121.09  3.000
 GVF  CAK  CAL  CAP  120.26  3.000
 GVF  CAK  CAL  OAM  119.99  3.000
 GVF  CAP  CAL  OAM  119.74  3.000
 GVF  CAO  CAP  OAQ  120.03  3.000
 GVF  CAO  CAP  CAL  120.42  3.000
 GVF  OAQ  CAP  CAL  119.54  3.000
 GVF  PAT  OAQ  CAP  121.73  3.000
 GVF  OAU  PAT  OAY  115.69  3.000
 GVF  OAU  PAT  OAS  114.14  3.000
 GVF  OAY  PAT  OAS  113.25  3.000
 GVF  OAU  PAT  OAQ  105.27  3.000
 GVF  OAY  PAT  OAQ  102.11  3.000
 GVF  OAS  PAT  OAQ  104.53  3.000
 GVF  CAN  CAO  OAR  123.42  3.000
 GVF  CAN  CAO  CAP  118.64  3.000
 GVF  OAR  CAO  CAP  117.94  3.000
 GVF  PAW  OAR  CAO  122.85  3.000
 GVF  OAX  PAW  OAZ  115.22  3.000
 GVF  OAX  PAW  OAV  114.58  3.000
 GVF  OAZ  PAW  OAV  113.99  3.000
 GVF  OAX  PAW  OAR  105.10  3.000
 GVF  OAZ  PAW  OAR  100.21  3.000
 GVF  OAV  PAW  OAR  105.66  3.000
 GVF  HAN  CAN  CAJ  120.05  3.000
 GVF  HAN  CAN  CAO  118.96  3.000
 GVF  CAJ  CAN  CAO  120.99  3.000
 GVF  HAJ  CAJ  CAK  118.95  3.000
 GVF  HAJ  CAJ  CAN  120.05  3.000
 GVF  CAK  CAJ  CAN  120.99  3.000
 GVF  OAF  CAK  CAJ  123.30  3.000
 GVF  OAF  CAK  CAL  117.99  3.000
 GVF  CAJ  CAK  CAL  118.70  3.000
 GVF  PAC  OAF  CAK  122.60  3.000
 GVF  OAD  PAC  OAA  115.29  3.000
 GVF  OAD  PAC  OAB  114.55  3.000
 GVF  OAA  PAC  OAB  114.03  3.000
 GVF  OAD  PAC  OAF  104.87  3.000
 GVF  OAA  PAC  OAF  100.30  3.000
 GVF  OAB  PAC  OAF  105.70  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
 GVF  CONST_01  CAN  CAO  CAP  CAL    0.00   0.0  0
 GVF  CONST_02  CAN  CAJ  CAK  CAL    0.00   0.0  0
 GVF  CONST_03  CAJ  CAK  CAL  CAP    0.00   0.0  0
 GVF  CONST_04  CAJ  CAN  CAO  CAP    0.00   0.0  0
 GVF  CONST_05  CAK  CAL  CAP  CAO    0.00   0.0  0
 GVF  CONST_06  CAK  CAJ  CAN  CAO    0.00   0.0  0
 GVF  CONST_07  CAO  CAP  CAL  OAM  180.00   0.0  0
 GVF  CONST_08  CAJ  CAK  CAL  OAM  180.00   0.0  0
 GVF  CONST_09  OAR  CAO  CAP  CAL  180.00   0.0  0
 GVF  CONST_10  OAF  CAK  CAL  CAP  180.00   0.0  0
 GVF  CONST_11  CAK  CAL  CAP  OAQ  180.00   0.0  0
 GVF  CONST_12  CAN  CAO  CAP  OAQ  180.00   0.0  0
 GVF  CONST_13  CAJ  CAN  CAO  OAR  180.00   0.0  0
 GVF  CONST_14  OAF  CAK  CAJ  CAN  180.00   0.0  0
 GVF  CONST_15  HAJ  CAJ  CAK  CAL  180.00   0.0  0
 GVF  CONST_16  HAN  CAN  CAO  CAP  180.00   0.0  0
 GVF  Var_01    CAP  CAL  OAM  PAH  -89.75  30.0  2
 GVF  Var_02    CAO  CAP  OAQ  PAT   82.27  30.0  2
 GVF  Var_03    CAN  CAO  OAR  PAW  -40.55  30.0  2
 GVF  Var_04    OAS  PAT  OAQ  CAP  108.75  30.0  3
 GVF  Var_05    OAV  PAW  OAR  CAO   73.43  30.0  3
 GVF  Var_06    OAB  PAC  OAF  CAK   73.78  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
 GVF  plan-1  OAM  0.020
 GVF  plan-1  CAL  0.020
 GVF  plan-1  CAP  0.020
 GVF  plan-1  OAQ  0.020
 GVF  plan-1  CAO  0.020
 GVF  plan-1  OAR  0.020
 GVF  plan-1  CAN  0.020
 GVF  plan-1  CAJ  0.020
 GVF  plan-1  CAK  0.020
 GVF  plan-1  OAF  0.020
 GVF  plan-1  HAN  0.020
 GVF  plan-1  HAJ  0.020

