# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:03:55 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: [naphthalene-2,7-diylbis(difluoromethanediyl)]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)C(F)(F)c1ccc2ccc(cc2c1)C(F)(F)[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
 FNP  FNP  '[naphthalene-2,7-diylbis(difluoromethanediyl)]bis(phosphonic acid)'  ligand  30  24  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FNP
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
 FNP  C1   C  CT     0   0.454  -0.3913   0.7350   3.6354
 FNP  C2   C  CR6    0  -0.041   0.4403  -0.5320  -2.3830
 FNP  C3   C  CR16   0  -0.286   1.8507  -0.4117  -2.3742
 FNP  C4   C  CR16   0  -0.309   2.5203  -0.1282  -1.2170
 FNP  C5   C  CR66   0   0.093   1.8224   0.0734  -0.0045
 FNP  C6   C  CR16   0  -0.309   2.4760   0.3653   1.2150
 FNP  C7   C  CR16   0  -0.280   1.7634   0.5678   2.3627
 FNP  C8   C  CR6    0  -0.041   0.3481   0.5055   2.3569
 FNP  C9   C  CR16   0  -0.395  -0.3033   0.2046   1.1899
 FNP  C10  C  CR66   0   0.166   0.4093  -0.0177  -0.0120
 FNP  C11  C  CR16   0  -0.388  -0.2564  -0.3228  -1.2215
 FNP  F1   F  F      0  -0.374  -1.6848   1.1186   3.3427
 FNP  F2   F  F      0  -0.383   0.1627   1.8444   4.2551
 FNP  P1   P  P      0   1.101  -0.4043  -0.7297   4.8271
 FNP  OP1  O  O      0  -0.888  -1.1706  -0.1993   6.0367
 FNP  OP2  O  OP    -1  -0.874   1.0814  -0.9799   5.0691
 FNP  OP3  O  OP    -1  -0.878  -1.1256  -1.8075   4.0265
 FNP  F3   F  F      0  -0.381   0.4792  -1.7713  -4.3600
 FNP  F4   F  F      0  -0.375  -1.4543  -1.4642  -3.3917
 FNP  P2   P  P      0   1.100  -0.5712   0.6826  -4.7590
 FNP  OP4  O  O      0  -0.888  -1.2854   0.1043  -5.9783
 FNP  OP5  O  OP    -1  -0.877  -1.4351   1.5663  -3.8668
 FNP  OP6  O  OP    -1  -0.875   0.8395   1.1992  -5.0249
 FNP  HC3  H  HCR6   0   0.246   2.4057  -0.5475  -3.2913
 FNP  HC4  H  HCR6   0   0.247   3.6012  -0.0502  -1.2212
 FNP  HC6  H  HCR6   0   0.247   3.5580   0.4230   1.2305
 FNP  HC7  H  HCR6   0   0.246   2.2848   0.7761   3.2857
 FNP  HC9  H  HCR6   0   0.243  -1.3834   0.1390   1.1595
 FNP  H11  H  HCR6   0   0.242  -1.3366  -0.3915  -1.2044
 FNP  C12  C  CT     0   0.456  -0.2608  -0.8268  -3.6690

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
 FNP  C1   C8   single    1.495  0.020  1.495
 FNP  C1   F1   single    1.381  0.020  1.381
 FNP  C1   F2   single    1.386  0.020  1.386
 FNP  C1   P1   single    1.888  0.020  1.888
 FNP  C2   C3   aromatic  1.416  0.020  1.416
 FNP  C2   C11  aromatic  1.370  0.020  1.370
 FNP  C2   C12  single    1.494  0.020  1.494
 FNP  C3   C4   aromatic  1.367  0.020  1.367
 FNP  C3   HC3  single    0.930  0.020  1.080
 FNP  C4   C5   aromatic  1.413  0.020  1.413
 FNP  C4   HC4  single    0.930  0.020  1.080
 FNP  C5   C6   aromatic  1.414  0.020  1.414
 FNP  C5   C10  aromatic  1.416  0.020  1.416
 FNP  C6   C7   aromatic  1.366  0.020  1.366
 FNP  C6   HC6  single    0.930  0.020  1.080
 FNP  C7   C8   aromatic  1.417  0.020  1.417
 FNP  C7   HC7  single    0.930  0.020  1.080
 FNP  C8   C9   aromatic  1.370  0.020  1.370
 FNP  C9   C10  aromatic  1.415  0.020  1.415
 FNP  C9   HC9  single    0.930  0.020  1.080
 FNP  C10  C11  aromatic  1.414  0.020  1.414
 FNP  C11  H11  single    0.930  0.020  1.080
 FNP  C12  F3   single    1.385  0.020  1.385
 FNP  C12  F4   single    1.381  0.020  1.381
 FNP  C12  P2   single    1.887  0.020  1.887
 FNP  P1   OP1  deloc     1.527  0.020  1.527
 FNP  P1   OP2  deloc     1.526  0.020  1.526
 FNP  P1   OP3  deloc     1.524  0.020  1.524
 FNP  P2   OP4  deloc     1.527  0.020  1.527
 FNP  P2   OP5  deloc     1.524  0.020  1.524
 FNP  P2   OP6  deloc     1.526  0.020  1.526

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
 FNP  P1   C1   F2   109.96  3.000
 FNP  P1   C1   F1   110.05  3.000
 FNP  F2   C1   F1   104.30  3.000
 FNP  P1   C1   C8   115.10  3.000
 FNP  F2   C1   C8   107.91  3.000
 FNP  F1   C1   C8   108.95  3.000
 FNP  C12  C2   C11  121.40  3.000
 FNP  C12  C2   C3   119.32  3.000
 FNP  C11  C2   C3   119.23  3.000
 FNP  HC3  C3   C4   119.54  3.000
 FNP  HC3  C3   C2   119.72  3.000
 FNP  C4   C3   C2   120.74  3.000
 FNP  HC4  C4   C5   119.05  3.000
 FNP  HC4  C4   C3   120.03  3.000
 FNP  C5   C4   C3   120.93  3.000
 FNP  C10  C5   C6   118.63  3.000
 FNP  C10  C5   C4   118.62  3.000
 FNP  C6   C5   C4   122.75  3.000
 FNP  HC6  C6   C7   120.06  3.000
 FNP  HC6  C6   C5   119.00  3.000
 FNP  C7   C6   C5   120.94  3.000
 FNP  HC7  C7   C8   119.62  3.000
 FNP  HC7  C7   C6   119.64  3.000
 FNP  C8   C7   C6   120.74  3.000
 FNP  C9   C8   C7   119.23  3.000
 FNP  C9   C8   C1   121.81  3.000
 FNP  C7   C8   C1   118.94  3.000
 FNP  HC9  C9   C10  117.98  3.000
 FNP  HC9  C9   C8   120.78  3.000
 FNP  C10  C9   C8   121.24  3.000
 FNP  C11  C10  C9   121.56  3.000
 FNP  C11  C10  C5   119.23  3.000
 FNP  C9   C10  C5   119.21  3.000
 FNP  H11  C11  C10  118.03  3.000
 FNP  H11  C11  C2   120.73  3.000
 FNP  C10  C11  C2   121.23  3.000
 FNP  OP3  P1   OP2  115.35  3.000
 FNP  OP3  P1   OP1  115.10  3.000
 FNP  OP2  P1   OP1  114.83  3.000
 FNP  OP3  P1   C1   102.73  3.000
 FNP  OP2  P1   C1   102.74  3.000
 FNP  OP1  P1   C1   103.53  3.000
 FNP  OP6  P2   OP5  115.45  3.000
 FNP  OP6  P2   OP4  114.93  3.000
 FNP  OP5  P2   OP4  114.95  3.000
 FNP  OP6  P2   C12  102.67  3.000
 FNP  OP5  P2   C12  102.64  3.000
 FNP  OP4  P2   C12  103.61  3.000
 FNP  P2   C12  F4   110.06  3.000
 FNP  P2   C12  F3   110.19  3.000
 FNP  F4   C12  F3   104.31  3.000
 FNP  P2   C12  C2   114.61  3.000
 FNP  F4   C12  C2   108.89  3.000
 FNP  F3   C12  C2   108.26  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
 FNP  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 FNP  CONST_02  C5   C10  C11  C2      0.00   0.0  0
 FNP  CONST_03  C9   C10  C11  C2    180.00   0.0  0
 FNP  CONST_04  C10  C11  C2   C3      0.00   0.0  0
 FNP  CONST_05  C6   C5   C4   C3    180.00   0.0  0
 FNP  CONST_06  C10  C5   C4   C3      0.00   0.0  0
 FNP  CONST_07  C11  C2   C3   C4      0.00   0.0  0
 FNP  CONST_08  C7   C6   C5   C4    180.00   0.0  0
 FNP  CONST_09  C9   C10  C5   C4    180.00   0.0  0
 FNP  CONST_10  C11  C10  C5   C4      0.00   0.0  0
 FNP  CONST_11  C8   C7   C6   C5      0.00   0.0  0
 FNP  CONST_12  C8   C9   C10  C5      0.00   0.0  0
 FNP  CONST_13  C9   C10  C5   C6      0.00   0.0  0
 FNP  CONST_14  C11  C10  C5   C6    180.00   0.0  0
 FNP  CONST_15  C9   C8   C7   C6      0.00   0.0  0
 FNP  CONST_16  C10  C5   C6   C7      0.00   0.0  0
 FNP  CONST_17  C10  C9   C8   C7      0.00   0.0  0
 FNP  CONST_18  C11  C10  C9   C8    180.00   0.0  0
 FNP  CONST_19  C6   C7   C8   C1    180.00   0.0  0
 FNP  CONST_20  C10  C9   C8   C1    180.00   0.0  0
 FNP  CONST_21  C12  C2   C3   C4    180.00   0.0  0
 FNP  CONST_22  C12  C2   C11  C10   180.00   0.0  0
 FNP  CONST_23  HC4  C4   C3   C2    180.00   0.0  0
 FNP  CONST_24  H11  C11  C2   C3    180.00   0.0  0
 FNP  CONST_25  HC6  C6   C5   C4      0.00   0.0  0
 FNP  CONST_26  HC3  C3   C4   C5    180.00   0.0  0
 FNP  CONST_27  HC7  C7   C6   C5    180.00   0.0  0
 FNP  CONST_28  HC9  C9   C10  C5    180.00   0.0  0
 FNP  Var_01    F3   C12  C2   C3     41.01  30.0  2
 FNP  Var_02    F1   C1   C8   C7    158.02  30.0  3
 FNP  Var_03    OP4  P2   C12  C2   -179.96  30.0  3
 FNP  Var_04    OP1  P1   C1   C8    178.07  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
 FNP  plan-1  C1   0.020
 FNP  plan-1  C2   0.020
 FNP  plan-1  C3   0.020
 FNP  plan-1  C4   0.020
 FNP  plan-1  C5   0.020
 FNP  plan-1  C6   0.020
 FNP  plan-1  C7   0.020
 FNP  plan-1  C8   0.020
 FNP  plan-1  C9   0.020
 FNP  plan-1  C10  0.020
 FNP  plan-1  C11  0.020
 FNP  plan-1  HC3  0.020
 FNP  plan-1  HC4  0.020
 FNP  plan-1  HC6  0.020
 FNP  plan-1  HC7  0.020
 FNP  plan-1  HC9  0.020
 FNP  plan-1  H11  0.020
 FNP  plan-1  C12  0.020

