# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 03:44:36 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 4-nitrophenyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1ccc(cc1)[N+]([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
 4NP  4NP  '4-nitrophenyl dihydrogen phosphate'  ligand  18  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4NP
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
 4NP  P    P  P      0   1.181   2.9316  -0.2943   0.2150
 4NP  O1   O  O2     0  -0.552   1.6789   0.4308  -0.8466
 4NP  O2   O  O      0  -0.813   2.4420   0.1131   1.5914
 4NP  O3   O  OP    -1  -0.938   4.1517   0.4243  -0.3120
 4NP  O4   O  OP    -1  -0.883   2.8355  -1.7769  -0.0997
 4NP  C1   C  CR6    0   0.378   0.3950   0.2736  -0.5892
 4NP  C2   C  CR16   0  -0.222  -0.1988  -0.9671  -0.3004
 4NP  C3   C  CR16   0  -0.261  -1.5518  -1.0602  -0.0715
 4NP  C4   C  CR6    0   0.160  -2.3523   0.0772  -0.1406
 4NP  C5   C  CR16   0  -0.130  -1.7926   1.3180  -0.4330
 4NP  C6   C  CR16   0  -0.395  -0.4333   1.4113  -0.6432
 4NP  N    N  N      1   0.271  -3.7686  -0.0364   0.0814
 4NP  O5   O  O     -1  -0.335  -4.4614   0.9439  -0.0913
 4NP  O6   O  O      0  -0.470  -4.2134  -1.1035   0.4532
 4NP  H21  H  HCR6   0   0.246   0.4280  -1.8455  -0.2414
 4NP  H31  H  HCR6   0   0.264  -1.9788  -2.0266   0.1520
 4NP  H51  H  HCR6   0   0.274  -2.4037   2.2085  -0.4869
 4NP  H61  H  HCR6   0   0.225   0.0060   2.3703  -0.8783

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
 4NP  P   O1   single    1.795  0.020  1.795
 4NP  P   O2   deloc     1.517  0.020  1.517
 4NP  P   O3   deloc     1.511  0.020  1.511
 4NP  P   O4   deloc     1.519  0.020  1.519
 4NP  O1  C1   single    1.319  0.020  1.319
 4NP  C1  C2   aromatic  1.405  0.020  1.405
 4NP  C1  C6   aromatic  1.408  0.020  1.408
 4NP  C2  C3   aromatic  1.375  0.020  1.375
 4NP  C2  H21  single    0.930  0.020  1.080
 4NP  C3  C4   aromatic  1.393  0.020  1.393
 4NP  C3  H31  single    0.930  0.020  1.080
 4NP  C4  C5   aromatic  1.392  0.020  1.392
 4NP  C4  N    single    1.438  0.020  1.438
 4NP  C5  C6   aromatic  1.379  0.020  1.379
 4NP  C5  H51  single    0.930  0.020  1.080
 4NP  C6  H61  single    0.930  0.020  1.080
 4NP  N   O5   single    1.213  0.020  1.213
 4NP  N   O6   double    1.214  0.020  1.214

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
 4NP  O4   P   O3  116.31  3.000
 4NP  O4   P   O2  115.46  3.000
 4NP  O3   P   O2  116.71  3.000
 4NP  O4   P   O1  103.16  3.000
 4NP  O3   P   O1   99.50  3.000
 4NP  O2   P   O1  101.71  3.000
 4NP  C1   O1  P   121.05  3.000
 4NP  C6   C1  C2  118.20  3.000
 4NP  C6   C1  O1  117.96  3.000
 4NP  C2   C1  O1  123.82  3.000
 4NP  H21  C2  C3  120.43  3.000
 4NP  H21  C2  C1  118.93  3.000
 4NP  C3   C2  C1  120.63  3.000
 4NP  H31  C3  C4  120.92  3.000
 4NP  H31  C3  C2  118.95  3.000
 4NP  C4   C3  C2  120.13  3.000
 4NP  N    C4  C5  119.92  3.000
 4NP  N    C4  C3  119.60  3.000
 4NP  C5   C4  C3  120.48  3.000
 4NP  H51  C5  C6  119.59  3.000
 4NP  H51  C5  C4  121.14  3.000
 4NP  C6   C5  C4  119.26  3.000
 4NP  H61  C6  C5  119.61  3.000
 4NP  H61  C6  C1  119.09  3.000
 4NP  C5   C6  C1  121.29  3.000
 4NP  O6   N   O5  123.00  3.000
 4NP  O6   N   C4  118.52  3.000
 4NP  O5   N   C4  118.47  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
 4NP  CONST_01  C4   C3  C2  C1    0.00   0.0  0
 4NP  CONST_02  C4   C5  C6  C1    0.00   0.0  0
 4NP  CONST_03  C5   C6  C1  C2    0.00   0.0  0
 4NP  CONST_04  C5   C4  C3  C2    0.00   0.0  0
 4NP  CONST_05  C6   C1  C2  C3    0.00   0.0  0
 4NP  CONST_06  C6   C5  C4  C3    0.00   0.0  0
 4NP  CONST_07  C3   C2  C1  O1  180.00   0.0  0
 4NP  CONST_08  C5   C6  C1  O1  180.00   0.0  0
 4NP  CONST_09  N    C4  C3  C2  180.00   0.0  0
 4NP  CONST_10  N    C4  C5  C6  180.00   0.0  0
 4NP  CONST_11  H31  C3  C2  C1  180.00   0.0  0
 4NP  CONST_12  H51  C5  C6  C1  180.00   0.0  0
 4NP  CONST_13  H61  C6  C1  C2  180.00   0.0  0
 4NP  CONST_14  H21  C2  C3  C4  180.00   0.0  0
 4NP  CONST_15  O5   N   C4  C3  180.00   0.0  0
 4NP  CONST_16  O6   N   C4  C3    0.00   0.0  0
 4NP  CONST_17  O5   N   C4  C5    0.00   0.0  0
 4NP  CONST_18  O6   N   C4  C5  180.00   0.0  0
 4NP  Var_01    C2   C1  O1  P   -48.63  30.0  2

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
 4NP  plan-1  O1   0.020
 4NP  plan-1  C1   0.020
 4NP  plan-1  C2   0.020
 4NP  plan-1  C3   0.020
 4NP  plan-1  C4   0.020
 4NP  plan-1  C5   0.020
 4NP  plan-1  C6   0.020
 4NP  plan-1  N    0.020
 4NP  plan-1  H21  0.020
 4NP  plan-1  H31  0.020
 4NP  plan-1  H51  0.020
 4NP  plan-1  H61  0.020
 4NP  plan-2  C4   0.020
 4NP  plan-2  N    0.020
 4NP  plan-2  O5   0.020
 4NP  plan-2  O6   0.020

