# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:23:56 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  20  14  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   1.404   2.7674   0.1364   0.4025
 4NP  O1   O  O2     0  -0.525   1.7370  -0.0813  -0.8276
 4NP  O2   O  O      0  -0.727   2.5763   1.3628   1.1873
 4NP  O3   O  OH1    0  -0.741   4.0941  -0.0438  -0.4505
 4NP  O4   O  OH1    0  -0.682   2.5969  -1.1539   1.3243
 4NP  C1   C  CR6    0   0.373   0.3874  -0.0531  -0.6010
 4NP  C2   C  CR16   0  -0.331  -0.3224  -1.2422  -0.6879
 4NP  C3   C  CR16   0  -0.258  -1.6885  -1.2390  -0.4819
 4NP  C4   C  CR6    0   0.231  -2.3235  -0.0392  -0.1952
 4NP  C5   C  CR16   0  -0.269  -1.6217   1.1550  -0.1225
 4NP  C6   C  CR16   0  -0.279  -0.2546   1.1464  -0.3226
 4NP  N    N  N      1   0.342  -3.7545  -0.0374   0.0328
 4NP  O5   O  O     -1  -0.292  -4.3193   1.0273   0.1317
 4NP  O6   O  O      0  -0.420  -4.3221  -1.0978   0.1168
 4NP  HO3  H  HOH1   0   0.502   4.8937   0.2463   0.0036
 4NP  HO4  H  HOH1   0   0.499   2.8833  -1.9945   0.9510
 4NP  H21  H  HCR6   0   0.292   0.1844  -2.1664  -0.9264
 4NP  H31  H  HCR6   0   0.302  -2.2393  -2.1648  -0.5490
 4NP  H51  H  HCR6   0   0.302  -2.1168   2.0887   0.0971
 4NP  H61  H  HCR6   0   0.278   0.3027   2.0702  -0.2719

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    1.619  0.020  1.619
 4NP  P   O2   double    1.468  0.020  1.468
 4NP  P   O3   single    1.587  0.020  1.587
 4NP  P   O4   single    1.595  0.020  1.595
 4NP  O1  C1   single    1.369  0.020  1.369
 4NP  O3  HO3  single    0.850  0.020  0.980
 4NP  O4  HO4  single    0.850  0.020  0.980
 4NP  C1  C2   aromatic  1.388  0.020  1.388
 4NP  C1  C6   aromatic  1.389  0.020  1.389
 4NP  C2  C3   aromatic  1.382  0.020  1.382
 4NP  C2  H21  single    0.930  0.020  1.080
 4NP  C3  C4   aromatic  1.387  0.020  1.387
 4NP  C3  H31  single    0.930  0.020  1.080
 4NP  C4  C5   aromatic  1.387  0.020  1.387
 4NP  C4  N    single    1.449  0.020  1.449
 4NP  C5  C6   aromatic  1.382  0.020  1.382
 4NP  C5  H51  single    0.930  0.020  1.080
 4NP  C6  H61  single    0.930  0.020  1.080
 4NP  N   O5   single    1.209  0.020  1.209
 4NP  N   O6   double    1.206  0.020  1.206

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  107.94  3.000
 4NP  O4   P   O2  110.67  3.000
 4NP  O3   P   O2  119.39  3.000
 4NP  O4   P   O1  105.20  3.000
 4NP  O3   P   O1   96.22  3.000
 4NP  O2   P   O1  115.81  3.000
 4NP  C1   O1  P   119.93  3.000
 4NP  HO3  O3  P   113.94  3.000
 4NP  HO4  O4  P   116.76  3.000
 4NP  C6   C1  C2  121.08  3.000
 4NP  C6   C1  O1  120.45  3.000
 4NP  C2   C1  O1  118.45  3.000
 4NP  H21  C2  C3  119.90  3.000
 4NP  H21  C2  C1  120.46  3.000
 4NP  C3   C2  C1  119.64  3.000
 4NP  H31  C3  C4  121.40  3.000
 4NP  H31  C3  C2  119.57  3.000
 4NP  C4   C3  C2  119.03  3.000
 4NP  N    C4  C5  119.36  3.000
 4NP  N    C4  C3  119.05  3.000
 4NP  C5   C4  C3  121.59  3.000
 4NP  H51  C5  C6  119.25  3.000
 4NP  H51  C5  C4  121.56  3.000
 4NP  C6   C5  C4  119.18  3.000
 4NP  H61  C6  C5  119.89  3.000
 4NP  H61  C6  C1  120.64  3.000
 4NP  C5   C6  C1  119.46  3.000
 4NP  O6   N   O5  123.28  3.000
 4NP  O6   N   C4  118.34  3.000
 4NP  O5   N   C4  118.37  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   -109.20  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

