# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 09:02:32 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  29  20  .  2021-08-20  2021-08-20  
;
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   0.551  -0.0660   0.7758  -2.5971
 PIC  C2    C  CR6   0  -0.114  -0.2853   0.5656  -1.1320
 PIC  C3    C  CR16  0  -0.289  -1.5897   0.2850  -0.6596
 PIC  C7    C  CR6   0  -0.083   0.1238  -0.0545   3.8495
 PIC  C8    C  CR16  0  -0.264   1.4276   0.2265   3.3722
 PIC  C9    C  CR16  0  -0.295   1.6419   0.4393   2.0410
 PIC  C10   C  CR66  0   0.146   0.5719   0.3880   1.1177
 PIC  C11   C  CR16  0  -0.344   0.7719   0.6097  -0.2615
 PIC  C12   C  C     0   0.541  -0.1525  -0.2907   5.2901
 PIC  C4    C  CR16  0  -0.288  -1.8033   0.0620   0.6704
 PIC  C5    C  CR66  0   0.141  -0.7329   0.1081   1.5929
 PIC  C6    C  CR16  0  -0.322  -0.9295  -0.1130   2.9712
 PIC  O1    O  OH1   0  -0.592   0.9267  -0.1633   6.0470
 PIC  O2    O  O     0  -0.435  -1.2430  -0.5667   5.7290
 PIC  F1    F  F     0  -0.332  -1.1245   1.4324  -3.1471
 PIC  F2    F  F     0  -0.326   1.0345   1.5414  -2.8203
 PIC  P     P  P     0   1.314   0.1511  -0.7780  -3.5946
 PIC  OP1   O  OH1   0  -0.733   1.3740  -1.4266  -2.8071
 PIC  OP2   O  OH1   0  -0.733  -1.1532  -1.6432  -3.2763
 PIC  OP3   O  O     0  -0.683   0.2976  -0.5291  -5.0415
 PIC  HC3   H  HCR6  0   0.281  -2.4276   0.2554  -1.3424
 PIC  HC8   H  HCR6  0   0.272   2.2626   0.2727   4.0563
 PIC  HC9   H  HCR6  0   0.268   2.6401   0.6531   1.6805
 PIC  HC11  H  HCR6  0   0.274   1.7758   0.8184  -0.6073
 PIC  HC4   H  HCR6  0   0.271  -2.8025  -0.1491   1.0294
 PIC  HC6   H  HCR6  0   0.271  -1.9283  -0.3278   3.3291
 PIC  HO1   H  HOH1  0   0.490   0.7025  -0.3237   6.9758
 PIC  HOP1  H  HOH1  0   0.511   1.8759  -2.0927  -3.2997
 PIC  HOP2  H  HOH1  0   0.503  -1.1721  -2.1194  -2.4350

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    1.496  0.020  1.496
 PIC  C1   F1    single    1.362  0.020  1.362
 PIC  C1   F2    single    1.359  0.020  1.359
 PIC  C1   P     single    1.859  0.020  1.859
 PIC  C2   C3    aromatic  1.415  0.020  1.415
 PIC  C2   C11   aromatic  1.370  0.020  1.370
 PIC  C3   C4    aromatic  1.365  0.020  1.365
 PIC  C3   HC3   single    0.930  0.020  1.080
 PIC  C7   C8    aromatic  1.417  0.020  1.417
 PIC  C7   C12   single    1.486  0.020  1.486
 PIC  C7   C6    aromatic  1.373  0.020  1.373
 PIC  C8   C9    aromatic  1.365  0.020  1.365
 PIC  C8   HC8   single    0.930  0.020  1.080
 PIC  C9   C10   aromatic  1.414  0.020  1.414
 PIC  C9   HC9   single    0.930  0.020  1.080
 PIC  C10  C11   aromatic  1.411  0.020  1.411
 PIC  C10  C5    aromatic  1.417  0.020  1.417
 PIC  C11  HC11  single    0.930  0.020  1.080
 PIC  C12  O1    single    1.324  0.020  1.324
 PIC  C12  O2    double    1.207  0.020  1.207
 PIC  C4   C5    aromatic  1.414  0.020  1.414
 PIC  C4   HC4   single    0.930  0.020  1.080
 PIC  C5   C6    aromatic  1.410  0.020  1.410
 PIC  C6   HC6   single    0.930  0.020  1.080
 PIC  O1   HO1   single    0.850  0.020  0.980
 PIC  P    OP1   single    1.593  0.020  1.593
 PIC  P    OP2   single    1.597  0.020  1.597
 PIC  P    OP3   double    1.475  0.020  1.475
 PIC  OP1  HOP1  single    0.850  0.020  0.980
 PIC  OP2  HOP2  single    0.850  0.020  0.980

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   106.74  3.000
 PIC  P     C1   F1   106.09  3.000
 PIC  F2    C1   F1   106.94  3.000
 PIC  P     C1   C2   115.16  3.000
 PIC  F2    C1   C2   111.01  3.000
 PIC  F1    C1   C2   110.45  3.000
 PIC  C11   C2   C3   120.36  3.000
 PIC  C11   C2   C1   120.30  3.000
 PIC  C3    C2   C1   119.32  3.000
 PIC  HC3   C3   C4   119.31  3.000
 PIC  HC3   C3   C2   120.58  3.000
 PIC  C4    C3   C2   120.11  3.000
 PIC  C6    C7   C12  118.10  3.000
 PIC  C6    C7   C8   119.94  3.000
 PIC  C12   C7   C8   121.97  3.000
 PIC  HC8   C8   C9   119.30  3.000
 PIC  HC8   C8   C7   120.43  3.000
 PIC  C9    C8   C7   120.27  3.000
 PIC  HC9   C9   C10  119.17  3.000
 PIC  HC9   C9   C8   120.02  3.000
 PIC  C10   C9   C8   120.81  3.000
 PIC  C5    C10  C11  119.30  3.000
 PIC  C5    C10  C9   119.02  3.000
 PIC  C11   C10  C9   121.68  3.000
 PIC  HC11  C11  C10  118.30  3.000
 PIC  HC11  C11  C2   121.26  3.000
 PIC  C10   C11  C2   120.43  3.000
 PIC  O2    C12  O1   123.38  3.000
 PIC  O2    C12  C7   123.83  3.000
 PIC  O1    C12  C7   112.79  3.000
 PIC  HC4   C4   C5   119.26  3.000
 PIC  HC4   C4   C3   119.95  3.000
 PIC  C5    C4   C3   120.79  3.000
 PIC  C6    C5   C4   121.82  3.000
 PIC  C6    C5   C10  119.17  3.000
 PIC  C4    C5   C10  119.01  3.000
 PIC  HC6   C6   C5   118.88  3.000
 PIC  HC6   C6   C7   120.33  3.000
 PIC  C5    C6   C7   120.79  3.000
 PIC  HO1   O1   C12  110.08  3.000
 PIC  OP3   P    OP2  111.59  3.000
 PIC  OP3   P    OP1  118.51  3.000
 PIC  OP2   P    OP1  107.93  3.000
 PIC  OP3   P    C1   113.38  3.000
 PIC  OP2   P    C1   104.50  3.000
 PIC  OP1   P    C1    99.48  3.000
 PIC  HOP1  OP1  P    115.25  3.000
 PIC  HOP2  OP2  P    117.14  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  CONST_29  HO1   O1   C12  C7   180.00   0.0  0
 PIC  Var_01    F1    C1   C2   C3    36.46  30.0  2
 PIC  Var_02    O1    C12  C7   C8     2.15  30.0  2
 PIC  Var_03    OP1   P    C1   C2   -56.03  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
 PIC  plan-2  HO1   0.020

