# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:59:43 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 6-[difluoro(phosphono)methyl]naphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2cc(ccc2c1)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
 PIC  PIC  '6-[difluoro(phosphono)methyl]naphthalene-2-carboxylic acid'  ligand  26  20  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PIC
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
 PIC  C1    C  CT     0   0.452  -0.0127   0.7371  -2.6007
 PIC  C2    C  CR6    0  -0.042  -0.2226   0.5349  -1.1347
 PIC  C3    C  CR16   0  -0.276  -1.5153   0.1808  -0.6746
 PIC  C7    C  CR6    0  -0.103   0.1058  -0.0413   3.8930
 PIC  C8    C  CR16   0  -0.295   1.3950   0.3093   3.4262
 PIC  C9    C  CR16   0  -0.309   1.6319   0.5299   2.0976
 PIC  C10   C  CR66   0   0.130   0.5897   0.4173   1.1472
 PIC  C11   C  CR16   0  -0.393   0.8031   0.6409  -0.2325
 PIC  C12   C  C      0   0.399  -0.1364  -0.2881   5.3764
 PIC  C4    C  CR16   0  -0.311  -1.7483  -0.0394   0.6527
 PIC  C5    C  CR66   0   0.131  -0.7060   0.0706   1.6045
 PIC  C6    C  CR16   0  -0.368  -0.9156  -0.1541   2.9831
 PIC  O1    O  OC    -1  -0.594   0.8477  -0.1532   6.1294
 PIC  O2    O  O      0  -0.593  -1.2942  -0.6035   5.7122
 PIC  F1    F  F      0  -0.383  -1.0122   1.5770  -3.0658
 PIC  F2    F  F      0  -0.374   1.1514   1.4540  -2.7945
 PIC  P     P  P      0   1.103   0.0374  -0.8542  -3.6189
 PIC  OP1   O  OP    -1  -0.877   1.2041  -1.6088  -2.9923
 PIC  OP2   O  OP    -1  -0.873  -1.3407  -1.4618  -3.3729
 PIC  OP3   O  O      0  -0.887   0.2772  -0.3600  -5.0433
 PIC  HC3   H  HCR6   0   0.247  -2.3200   0.0735  -1.3868
 PIC  HC8   H  HCR6   0   0.242   2.2016   0.4014   4.1407
 PIC  HC9   H  HCR6   0   0.244   2.6256   0.7970   1.7568
 PIC  HC11  H  HCR6   0   0.244   1.8016   0.9029  -0.5581
 PIC  HC4   H  HCR6   0   0.246  -2.7416  -0.3088   0.9919
 PIC  HC6   H  HCR6   0   0.239  -1.9082  -0.4230   3.3236

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
 PIC  C1   C2    single    1.495  0.020  1.495
 PIC  C1   F1    single    1.386  0.020  1.386
 PIC  C1   F2    single    1.381  0.020  1.381
 PIC  C1   P     single    1.890  0.020  1.890
 PIC  C2   C3    aromatic  1.417  0.020  1.417
 PIC  C2   C11   aromatic  1.370  0.020  1.370
 PIC  C3   C4    aromatic  1.366  0.020  1.366
 PIC  C3   HC3   single    0.930  0.020  1.080
 PIC  C7   C8    aromatic  1.415  0.020  1.415
 PIC  C7   C12   single    1.523  0.020  1.523
 PIC  C7   C6    aromatic  1.373  0.020  1.373
 PIC  C8   C9    aromatic  1.367  0.020  1.367
 PIC  C8   HC8   single    0.930  0.020  1.080
 PIC  C9   C10   aromatic  1.415  0.020  1.415
 PIC  C9   HC9   single    0.930  0.020  1.080
 PIC  C10  C11   aromatic  1.414  0.020  1.414
 PIC  C10  C5    aromatic  1.417  0.020  1.417
 PIC  C11  HC11  single    0.930  0.020  1.080
 PIC  C12  O1    deloc     1.246  0.020  1.246
 PIC  C12  O2    deloc     1.246  0.020  1.246
 PIC  C4   C5    aromatic  1.416  0.020  1.416
 PIC  C4   HC4   single    0.930  0.020  1.080
 PIC  C5   C6    aromatic  1.412  0.020  1.412
 PIC  C6   HC6   single    0.930  0.020  1.080
 PIC  P    OP1   deloc     1.524  0.020  1.524
 PIC  P    OP2   deloc     1.526  0.020  1.526
 PIC  P    OP3   deloc     1.527  0.020  1.527

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
 PIC  P     C1   F2   109.83  3.000
 PIC  P     C1   F1   110.40  3.000
 PIC  F2    C1   F1   104.26  3.000
 PIC  P     C1   C2   114.73  3.000
 PIC  F2    C1   C2   109.04  3.000
 PIC  F1    C1   C2   108.05  3.000
 PIC  C11   C2   C3   119.24  3.000
 PIC  C11   C2   C1   122.02  3.000
 PIC  C3    C2   C1   118.71  3.000
 PIC  HC3   C3   C4   119.86  3.000
 PIC  HC3   C3   C2   119.37  3.000
 PIC  C4    C3   C2   120.76  3.000
 PIC  C6    C7   C12  120.93  3.000
 PIC  C6    C7   C8   118.66  3.000
 PIC  C12   C7   C8   120.41  3.000
 PIC  HC8   C8   C9   119.93  3.000
 PIC  HC8   C8   C7   118.85  3.000
 PIC  C9    C8   C7   121.21  3.000
 PIC  HC9   C9   C10  118.92  3.000
 PIC  HC9   C9   C8   120.27  3.000
 PIC  C10   C9   C8   120.81  3.000
 PIC  C5    C10  C11  119.45  3.000
 PIC  C5    C10  C9   118.43  3.000
 PIC  C11   C10  C9   122.12  3.000
 PIC  HC11  C11  C10  118.10  3.000
 PIC  HC11  C11  C2   120.75  3.000
 PIC  C10   C11  C2   121.15  3.000
 PIC  O2    C12  O1   126.74  3.000
 PIC  O2    C12  C7   116.82  3.000
 PIC  O1    C12  C7   116.44  3.000
 PIC  HC4   C4   C5   118.93  3.000
 PIC  HC4   C4   C3   120.05  3.000
 PIC  C5    C4   C3   121.02  3.000
 PIC  C6    C5   C4   122.31  3.000
 PIC  C6    C5   C10  119.32  3.000
 PIC  C4    C5   C10  118.37  3.000
 PIC  HC6   C6   C5   118.83  3.000
 PIC  HC6   C6   C7   119.60  3.000
 PIC  C5    C6   C7   121.57  3.000
 PIC  OP3   P    OP2  114.91  3.000
 PIC  OP3   P    OP1  115.06  3.000
 PIC  OP2   P    OP1  115.33  3.000
 PIC  OP3   P    C1   103.55  3.000
 PIC  OP2   P    C1   102.97  3.000
 PIC  OP1   P    C1   102.45  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
 PIC  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 PIC  CONST_02  C9    C10  C11  C2   180.00   0.0  0
 PIC  CONST_03  C5    C10  C11  C2     0.00   0.0  0
 PIC  CONST_04  C10   C11  C2   C3     0.00   0.0  0
 PIC  CONST_05  C10   C5   C4   C3     0.00   0.0  0
 PIC  CONST_06  C6    C5   C4   C3   180.00   0.0  0
 PIC  CONST_07  C10   C9   C8   C7     0.00   0.0  0
 PIC  CONST_08  C10   C5   C6   C7     0.00   0.0  0
 PIC  CONST_09  C4    C5   C6   C7   180.00   0.0  0
 PIC  CONST_10  C5    C6   C7   C8     0.00   0.0  0
 PIC  CONST_11  C11   C10  C9   C8   180.00   0.0  0
 PIC  CONST_12  C5    C10  C9   C8     0.00   0.0  0
 PIC  CONST_13  C6    C7   C8   C9     0.00   0.0  0
 PIC  CONST_14  C4    C5   C10  C9   180.00   0.0  0
 PIC  CONST_15  C6    C5   C10  C9     0.00   0.0  0
 PIC  CONST_16  C4    C3   C2   C11    0.00   0.0  0
 PIC  CONST_17  C4    C5   C10  C11    0.00   0.0  0
 PIC  CONST_18  C6    C5   C10  C11  180.00   0.0  0
 PIC  CONST_19  C4    C3   C2   C1   180.00   0.0  0
 PIC  CONST_20  C10   C11  C2   C1   180.00   0.0  0
 PIC  CONST_21  C12   C7   C8   C9   180.00   0.0  0
 PIC  CONST_22  C5    C6   C7   C12  180.00   0.0  0
 PIC  CONST_23  HC4   C4   C3   C2   180.00   0.0  0
 PIC  CONST_24  HC11  C11  C2   C3   180.00   0.0  0
 PIC  CONST_25  HC9   C9   C8   C7   180.00   0.0  0
 PIC  CONST_26  HC6   C6   C7   C8   180.00   0.0  0
 PIC  CONST_27  HC8   C8   C9   C10  180.00   0.0  0
 PIC  CONST_28  HC3   C3   C2   C11  180.00   0.0  0
 PIC  Var_01    F1    C1   C2   C3    49.07  30.0  3
 PIC  Var_02    O1    C12  C7   C8     0.55  30.0  2
 PIC  Var_03    OP1   P    C1   C2   -59.30  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
 PIC  plan-1  C1    0.020
 PIC  plan-1  C2    0.020
 PIC  plan-1  C3    0.020
 PIC  plan-1  C7    0.020
 PIC  plan-1  C8    0.020
 PIC  plan-1  C9    0.020
 PIC  plan-1  C10   0.020
 PIC  plan-1  C11   0.020
 PIC  plan-1  C12   0.020
 PIC  plan-1  C4    0.020
 PIC  plan-1  C5    0.020
 PIC  plan-1  C6    0.020
 PIC  plan-1  HC3   0.020
 PIC  plan-1  HC8   0.020
 PIC  plan-1  HC9   0.020
 PIC  plan-1  HC11  0.020
 PIC  plan-1  HC4   0.020
 PIC  plan-1  HC6   0.020
 PIC  plan-2  C7    0.020
 PIC  plan-2  C12   0.020
 PIC  plan-2  O1    0.020
 PIC  plan-2  O2    0.020

