# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:44:07 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 4-nitrophenyl hydrogen (R)-methylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 PNP  PNP  '4-nitrophenyl hydrogen (R)-methylphosphonate'  ligand  21  14  .  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_PNP
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
 PNP  C1   C  CR6    0   0.413  -0.0104  -0.5747   0.4737
 PNP  C2   C  CR16   0  -0.332   1.2034  -0.5018  -0.2119
 PNP  C3   C  CR16   0  -0.262   1.2210  -0.3261  -1.5813
 PNP  C4   C  CR6    0   0.233   0.0171  -0.2092  -2.2659
 PNP  C5   C  CR16   0  -0.263  -1.2004  -0.2689  -1.5981
 PNP  C6   C  CR16   0  -0.332  -1.2095  -0.4441  -0.2287
 PNP  CM   C  CH3    0  -0.950  -0.0642  -0.3774   4.3925
 PNP  N    N  N      1   0.328   0.0318  -0.0237  -3.7007
 PNP  O1N  O  O      0  -0.389  -1.0283   0.0722  -4.2771
 PNP  O2N  O  O     -1  -0.389   1.1038   0.0281  -4.2607
 PNP  P    P  P      0   1.237   0.0353   0.5578   2.8440
 PNP  O1P  O  O2     0  -0.643  -0.0266  -0.7919   1.7977
 PNP  O2P  O  O      0  -0.779  -1.2124   1.3573   2.6075
 PNP  O3P  O  OP    -1  -0.779   1.3845   1.1922   2.6723
 PNP  H2   H  HCR6   0   0.278   2.1323  -0.6008   0.3325
 PNP  H3   H  HCR6   0   0.295   2.1661  -0.2780  -2.1025
 PNP  H5   H  HCR6   0   0.295  -2.1349  -0.1753  -2.1321
 PNP  H6   H  HCR6   0   0.277  -2.1496  -0.4977   0.3030
 PNP  HM1  H  HCH3   0   0.255  -0.0383   0.3214   5.2292
 PNP  HM2  H  HCH3   0   0.252  -0.9923  -0.9443   4.4590
 PNP  HM3  H  HCH3   0   0.252   0.7744  -1.0641   4.5040

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
 PNP  C1  C2   aromatic  1.396  0.020  1.396
 PNP  C1  C6   aromatic  1.396  0.020  1.396
 PNP  C1  O1P  single    1.342  0.020  1.342
 PNP  C2  C3   aromatic  1.381  0.020  1.381
 PNP  C2  H2   single    0.930  0.020  1.080
 PNP  C3  C4   aromatic  1.390  0.020  1.390
 PNP  C3  H3   single    0.930  0.020  1.080
 PNP  C4  C5   aromatic  1.390  0.020  1.390
 PNP  C4  N    single    1.447  0.020  1.447
 PNP  C5  C6   aromatic  1.381  0.020  1.381
 PNP  C5  H5   single    0.930  0.020  1.080
 PNP  C6  H6   single    0.930  0.020  1.080
 PNP  CM  P    single    1.812  0.020  1.812
 PNP  CM  HM1  single    0.970  0.020  1.090
 PNP  CM  HM2  single    0.970  0.020  1.090
 PNP  CM  HM3  single    0.970  0.020  1.090
 PNP  N   O1N  double    1.211  0.020  1.211
 PNP  N   O2N  single    1.211  0.020  1.211
 PNP  P   O1P  single    1.709  0.020  1.709
 PNP  P   O2P  deloc     1.501  0.020  1.501
 PNP  P   O3P  deloc     1.501  0.020  1.501

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
 PNP  O1P  C1   C6   120.09  3.000
 PNP  O1P  C1   C2   120.23  3.000
 PNP  C6   C1   C2   119.67  3.000
 PNP  H2   C2   C3   120.00  3.000
 PNP  H2   C2   C1   119.67  3.000
 PNP  C3   C2   C1   120.32  3.000
 PNP  H3   C3   C4   121.09  3.000
 PNP  H3   C3   C2   119.69  3.000
 PNP  C4   C3   C2   119.22  3.000
 PNP  N    C4   C5   119.40  3.000
 PNP  N    C4   C3   119.37  3.000
 PNP  C5   C4   C3   121.23  3.000
 PNP  H5   C5   C6   119.70  3.000
 PNP  H5   C5   C4   121.10  3.000
 PNP  C6   C5   C4   119.20  3.000
 PNP  H6   C6   C5   119.98  3.000
 PNP  H6   C6   C1   119.66  3.000
 PNP  C5   C6   C1   120.35  3.000
 PNP  HM3  CM   HM2  108.75  3.000
 PNP  HM3  CM   HM1  107.88  3.000
 PNP  HM2  CM   HM1  107.87  3.000
 PNP  HM3  CM   P    111.75  3.000
 PNP  HM2  CM   P    111.57  3.000
 PNP  HM1  CM   P    108.88  3.000
 PNP  O2N  N    O1N  123.50  3.000
 PNP  O2N  N    C4   118.25  3.000
 PNP  O1N  N    C4   118.26  3.000
 PNP  O3P  P    O2P  120.28  3.000
 PNP  O3P  P    O1P  107.24  3.000
 PNP  O2P  P    O1P  107.11  3.000
 PNP  O3P  P    CM   111.43  3.000
 PNP  O2P  P    CM   111.35  3.000
 PNP  O1P  P    CM    96.52  3.000
 PNP  P    O1P  C1   118.42  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
 PNP  CONST_01  C4   C3  C2   C1     0.00   0.0  0
 PNP  CONST_02  C4   C5  C6   C1     0.00   0.0  0
 PNP  CONST_03  C5   C6  C1   C2     0.00   0.0  0
 PNP  CONST_04  C5   C4  C3   C2     0.00   0.0  0
 PNP  CONST_05  C6   C1  C2   C3     0.00   0.0  0
 PNP  CONST_06  C6   C5  C4   C3     0.00   0.0  0
 PNP  CONST_07  N    C4  C3   C2   180.00   0.0  0
 PNP  CONST_08  O1P  C1  C2   C3   180.00   0.0  0
 PNP  CONST_09  O1P  C1  C6   C5   180.00   0.0  0
 PNP  CONST_10  N    C4  C5   C6   180.00   0.0  0
 PNP  CONST_11  H3   C3  C2   C1   180.00   0.0  0
 PNP  CONST_12  H5   C5  C6   C1   180.00   0.0  0
 PNP  CONST_13  H6   C6  C1   C2   180.00   0.0  0
 PNP  CONST_14  H2   C2  C3   C4   180.00   0.0  0
 PNP  CONST_15  O1N  N   C4   C3   180.00   0.0  0
 PNP  CONST_16  O2N  N   C4   C3     0.00   0.0  0
 PNP  CONST_17  O1N  N   C4   C5     0.00   0.0  0
 PNP  CONST_18  O2N  N   C4   C5   180.00   0.0  0
 PNP  Var_01    CM   P   O1P  C1   178.50  30.0  2
 PNP  Var_02    HM1  CM  P    O1P  179.93  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
 PNP  plan-1  C1   0.020
 PNP  plan-1  C2   0.020
 PNP  plan-1  C3   0.020
 PNP  plan-1  C4   0.020
 PNP  plan-1  C5   0.020
 PNP  plan-1  C6   0.020
 PNP  plan-1  N    0.020
 PNP  plan-1  O1P  0.020
 PNP  plan-1  H2   0.020
 PNP  plan-1  H3   0.020
 PNP  plan-1  H5   0.020
 PNP  plan-1  H6   0.020
 PNP  plan-2  C4   0.020
 PNP  plan-2  N    0.020
 PNP  plan-2  O1N  0.020
 PNP  plan-2  O2N  0.020

