# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 05:58:21 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: naphthalene-2,6-diyl bis[dihydrogen (phosphate)]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1ccc2cc(O[P](O)(O)=O)ccc2c1
#
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
 N26  N26  'naphthalene-2,6-diyl bis[dihydrogen (phosphate)]'  ligand  30  20  .  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_N26
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
 N26  O1   O  O2    0  -0.616  -3.7614   0.1816  -0.8688
 N26  C2   C  CR6   0   0.358  -2.4334   0.3136  -0.5178
 N26  C3   C  CR16  0  -0.374  -1.6280  -0.7857  -0.4353
 N26  C4   C  CR66  0   0.121  -0.2605  -0.6268  -0.1181
 N26  C5   C  CR66  0   0.121   0.2553   0.6726   0.1205
 N26  C6   C  CR16  0  -0.307  -0.6162   1.7819   0.0224
 N26  C7   C  CR16  0  -0.315  -1.9359   1.6109  -0.2883
 N26  C16  C  CR16  0  -0.309   0.6126  -1.7356  -0.0235
 N26  C17  C  CR16  0  -0.305   1.9324  -1.5655   0.2858
 N26  C18  C  CR6   0   0.360   2.4282  -0.2683   0.5223
 N26  C19  C  CR16  0  -0.381   1.6228   0.8305   0.4401
 N26  P20  P  P     0   1.441  -4.8419  -0.2440   0.2517
 N26  O2   O  O2    0  -0.616   3.7520  -0.1211   0.8827
 N26  P3   P  P     0   1.440   4.8822  -0.0368  -0.2655
 N26  O4   O  OH1   0  -0.732  -4.8858   0.9552   1.3002
 N26  O5   O  OH1   0  -0.723  -6.1173  -0.1358  -0.6893
 N26  O7   O  O     0  -0.687  -4.5850  -1.5157   0.9464
 N26  O8   O  O     0  -0.688   4.8663  -1.1212  -1.2603
 N26  O9   O  OH1   0  -0.730   4.6889   1.3706  -0.9871
 N26  O10  O  OH1   0  -0.724   6.1167   0.0727   0.7289
 N26  H3   H  HCR6  0   0.277  -2.0220  -1.7759  -0.6261
 N26  H6   H  HCR6  0   0.268  -0.2286   2.7770   0.2002
 N26  H7   H  HCR6  0   0.278  -2.5982   2.4627  -0.3709
 N26  H16  H  HCR6  0   0.268   0.2252  -2.7304  -0.2035
 N26  H17  H  HCR6  0   0.281   2.5959  -2.4161   0.3655
 N26  H19  H  HCR6  0   0.275   2.0160   1.8211   0.6331
 N26  H1   H  HOH1  0   0.500  -5.1697   1.8153   0.9619
 N26  H2   H  HOH1  0   0.510  -6.9017  -0.5849  -0.3455
 N26  H4   H  HOH1  0   0.500   4.7667   2.1533  -0.4248
 N26  H5   H  HOH1  0   0.510   6.9812   0.0425   0.2963

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
 N26  O8   P3   double    1.472  0.020  1.472
 N26  O10  P3   single    1.589  0.020  1.589
 N26  O2   P3   single    1.613  0.020  1.613
 N26  O2   C18  single    1.380  0.020  1.380
 N26  P3   O9   single    1.593  0.020  1.593
 N26  C19  C18  aromatic  1.365  0.020  1.365
 N26  C19  C5   aromatic  1.413  0.020  1.413
 N26  C18  C17  aromatic  1.409  0.020  1.409
 N26  C6   C5   aromatic  1.414  0.020  1.414
 N26  C6   C7   aromatic  1.366  0.020  1.366
 N26  C5   C4   aromatic  1.418  0.020  1.418
 N26  C7   C2   aromatic  1.408  0.020  1.408
 N26  C17  C16  aromatic  1.366  0.020  1.366
 N26  C4   C16  aromatic  1.415  0.020  1.415
 N26  C4   C3   aromatic  1.413  0.020  1.413
 N26  C2   C3   aromatic  1.365  0.020  1.365
 N26  C2   O1   single    1.380  0.020  1.380
 N26  O1   P20  single    1.614  0.020  1.614
 N26  O7   P20  double    1.472  0.020  1.472
 N26  P20  O4   single    1.593  0.020  1.593
 N26  P20  O5   single    1.589  0.020  1.589
 N26  C3   H3   single    0.930  0.020  1.080
 N26  C6   H6   single    0.930  0.020  1.080
 N26  C7   H7   single    0.930  0.020  1.080
 N26  C16  H16  single    0.930  0.020  1.080
 N26  C17  H17  single    0.930  0.020  1.080
 N26  C19  H19  single    0.930  0.020  1.080
 N26  O4   H1   single    0.850  0.020  0.980
 N26  O5   H2   single    0.850  0.020  0.980
 N26  O9   H4   single    0.850  0.020  0.980
 N26  O10  H5   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
 N26  P20  O1   C2   119.53  3.000
 N26  C7   C2   C3   121.57  3.000
 N26  C3   C2   O1   120.40  3.000
 N26  C7   C2   O1   118.01  3.000
 N26  H3   C3   C4   119.65  3.000
 N26  H3   C3   C2   120.74  3.000
 N26  C4   C3   C2   119.60  3.000
 N26  C16  C4   C5   118.85  3.000
 N26  C16  C4   C3   121.62  3.000
 N26  C5   C4   C3   119.53  3.000
 N26  C19  C5   C6   121.63  3.000
 N26  C6   C5   C4   118.88  3.000
 N26  C19  C5   C4   119.49  3.000
 N26  H6   C6   C7   119.88  3.000
 N26  H6   C6   C5   119.27  3.000
 N26  C7   C6   C5   120.85  3.000
 N26  H7   C7   C6   120.66  3.000
 N26  H7   C7   C2   119.77  3.000
 N26  C6   C7   C2   119.57  3.000
 N26  H16  C16  C17  119.86  3.000
 N26  H16  C16  C4   119.23  3.000
 N26  C17  C16  C4   120.92  3.000
 N26  H17  C17  C18  119.72  3.000
 N26  H17  C17  C16  120.75  3.000
 N26  C18  C17  C16  119.52  3.000
 N26  O2   C18  C19  119.73  3.000
 N26  C19  C18  C17  121.57  3.000
 N26  O2   C18  C17  118.67  3.000
 N26  H19  C19  C18  120.75  3.000
 N26  H19  C19  C5   119.59  3.000
 N26  C18  C19  C5   119.65  3.000
 N26  O7   P20  O5   118.59  3.000
 N26  O5   P20  O4   108.44  3.000
 N26  O7   P20  O4   110.15  3.000
 N26  O5   P20  O1    96.21  3.000
 N26  O4   P20  O1   106.07  3.000
 N26  O7   P20  O1   116.03  3.000
 N26  P3   O2   C18  119.45  3.000
 N26  O10  P3   O9   108.47  3.000
 N26  O9   P3   O8   110.09  3.000
 N26  O10  P3   O8   118.83  3.000
 N26  O9   P3   O2   106.47  3.000
 N26  O10  P3   O2    95.88  3.000
 N26  O8   P3   O2   115.79  3.000
 N26  H1   O4   P20  116.57  3.000
 N26  H2   O5   P20  114.14  3.000
 N26  H4   O9   P3   116.23  3.000
 N26  H5   O10  P3   114.35  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
 N26  CONST_01  C5   C6   C7   C2     0.00   0.0  0
 N26  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 N26  CONST_03  C16  C4   C3   C2   180.00   0.0  0
 N26  CONST_04  C19  C5   C4   C3   180.00   0.0  0
 N26  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 N26  CONST_06  C17  C16  C4   C3   180.00   0.0  0
 N26  CONST_07  C6   C7   C2   C3     0.00   0.0  0
 N26  CONST_08  C18  C19  C5   C4     0.00   0.0  0
 N26  CONST_09  C7   C6   C5   C4     0.00   0.0  0
 N26  CONST_10  C18  C17  C16  C4     0.00   0.0  0
 N26  CONST_11  C7   C2   C3   C4     0.00   0.0  0
 N26  CONST_12  C17  C18  C19  C5     0.00   0.0  0
 N26  CONST_13  C17  C16  C4   C5     0.00   0.0  0
 N26  CONST_14  C18  C19  C5   C6   180.00   0.0  0
 N26  CONST_15  C16  C4   C5   C6   180.00   0.0  0
 N26  CONST_16  C19  C5   C6   C7   180.00   0.0  0
 N26  CONST_17  C19  C18  C17  C16    0.00   0.0  0
 N26  CONST_18  C19  C5   C4   C16    0.00   0.0  0
 N26  CONST_19  C6   C7   C2   O1   180.00   0.0  0
 N26  CONST_20  C4   C3   C2   O1   180.00   0.0  0
 N26  CONST_21  O2   C18  C19  C5   180.00   0.0  0
 N26  CONST_22  O2   C18  C17  C16  180.00   0.0  0
 N26  CONST_23  H6   C6   C7   C2   180.00   0.0  0
 N26  CONST_24  H16  C16  C4   C3     0.00   0.0  0
 N26  CONST_25  H7   C7   C2   C3   180.00   0.0  0
 N26  CONST_26  H19  C19  C5   C4   180.00   0.0  0
 N26  CONST_27  H17  C17  C16  C4   180.00   0.0  0
 N26  CONST_28  H3   C3   C4   C5   180.00   0.0  0
 N26  Var_01    O7   P20  O1   C2   -57.36  30.0  3
 N26  Var_02    O8   P3   O2   C18  -52.30  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
 N26  plan-1  O1   0.020
 N26  plan-1  C2   0.020
 N26  plan-1  C3   0.020
 N26  plan-1  C4   0.020
 N26  plan-1  C5   0.020
 N26  plan-1  C6   0.020
 N26  plan-1  C7   0.020
 N26  plan-1  C16  0.020
 N26  plan-1  C17  0.020
 N26  plan-1  C18  0.020
 N26  plan-1  C19  0.020
 N26  plan-1  O2   0.020
 N26  plan-1  H3   0.020
 N26  plan-1  H6   0.020
 N26  plan-1  H7   0.020
 N26  plan-1  H16  0.020
 N26  plan-1  H17  0.020
 N26  plan-1  H19  0.020

