# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:05:09 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-nitrophenyl (4-carboxybutyl)phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC[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
 NPE  NPE  '4-nitrophenyl (4-carboxybutyl)phosphonate'  ligand  32  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPE
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
 NPE  C1    C  CR6    0   0.233  -4.7192   0.1028   0.1667
 NPE  N1    N  N      1   0.328  -6.1485  -0.0455   0.0006
 NPE  O1N   O  O     -1  -0.389  -6.7041  -0.9451   0.5902
 NPE  O2N   O  O      0  -0.389  -6.7261   0.7367  -0.7206
 NPE  C2    C  CR16   0  -0.263  -4.0348  -0.7724   1.0021
 NPE  C3    C  CR16   0  -0.332  -2.6707  -0.6271   1.1587
 NPE  C4    C  CR6    0   0.414  -1.9896   0.3956   0.4958
 NPE  C5    C  CR16   0  -0.331  -2.6908   1.2563  -0.3503
 NPE  C6    C  CR16   0  -0.262  -4.0553   1.1192  -0.5104
 NPE  O3P   O  O2     0  -0.643  -0.6710   0.5603   0.6829
 NPE  P     P  P      0   1.261   0.3996  -0.2752  -0.3565
 NPE  O1P   O  O      0  -0.781   0.1804   0.2636  -1.7415
 NPE  O2P   O  OP    -1  -0.781   0.2226  -1.7417  -0.0858
 NPE  C7    C  CH2    0  -0.720   1.9465   0.3515   0.3611
 NPE  C8    C  CH2    0  -0.429   3.1643  -0.2810  -0.3112
 NPE  C9    C  CH2    0  -0.395   4.4848   0.2486   0.2351
 NPE  C10   C  CH2    0  -0.582   5.6870  -0.4024  -0.4286
 NPE  C11   C  C      0   0.410   7.0700   0.0638   0.0588
 NPE  O1    O  O      0  -0.610   7.1120   0.9097   0.9738
 NPE  O2    O  OC    -1  -0.635   8.0536  -0.4564  -0.5106
 NPE  H2    H  HCR6   0   0.295  -4.5513  -1.5650   1.5234
 NPE  H3    H  HCR6   0   0.277  -2.1267  -1.2986   1.8085
 NPE  H5    H  HCR6   0   0.277  -2.1622   2.0446  -0.8680
 NPE  H6    H  HCR6   0   0.295  -4.5879   1.7972  -1.1613
 NPE  H71   H  HCH2   0   0.243   1.9665   0.1420   1.4342
 NPE  H72   H  HCH2   0   0.243   1.9829   1.4388   0.2490
 NPE  H81   H  HCH2   0   0.214   3.1209  -0.1033  -1.3905
 NPE  H82   H  HCH2   0   0.215   3.1271  -1.3671  -0.1820
 NPE  H91   H  HCH2   0   0.202   4.5206   0.0834   1.3158
 NPE  H92   H  HCH2   0   0.202   4.5232   1.3332   0.0964
 NPE  H101  H  HCH2   0   0.216   5.6354  -0.2476  -1.5128
 NPE  H102  H  HCH2   0   0.217   5.6300  -1.4900  -0.2999

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
 NPE  C1   N1    single    1.447  0.020  1.447
 NPE  C1   C2    aromatic  1.390  0.020  1.390
 NPE  C1   C6    aromatic  1.390  0.020  1.390
 NPE  N1   O1N   single    1.211  0.020  1.211
 NPE  N1   O2N   double    1.211  0.020  1.211
 NPE  C2   C3    aromatic  1.381  0.020  1.381
 NPE  C2   H2    single    0.930  0.020  1.080
 NPE  C3   C4    aromatic  1.396  0.020  1.396
 NPE  C3   H3    single    0.930  0.020  1.080
 NPE  C4   C5    aromatic  1.396  0.020  1.396
 NPE  C4   O3P   single    1.342  0.020  1.342
 NPE  C5   C6    aromatic  1.381  0.020  1.381
 NPE  C5   H5    single    0.930  0.020  1.080
 NPE  C6   H6    single    0.930  0.020  1.080
 NPE  O3P  P     single    1.710  0.020  1.710
 NPE  P    O1P   deloc     1.502  0.020  1.502
 NPE  P    O2P   deloc     1.502  0.020  1.502
 NPE  P    C7    single    1.817  0.020  1.817
 NPE  C7   C8    single    1.528  0.020  1.528
 NPE  C7   H71   single    0.970  0.020  1.090
 NPE  C7   H72   single    0.970  0.020  1.090
 NPE  C8   C9    single    1.524  0.020  1.524
 NPE  C8   H81   single    0.970  0.020  1.090
 NPE  C8   H82   single    0.970  0.020  1.090
 NPE  C9   C10   single    1.520  0.020  1.520
 NPE  C9   H91   single    0.970  0.020  1.090
 NPE  C9   H92   single    0.970  0.020  1.090
 NPE  C10  C11   single    1.539  0.020  1.539
 NPE  C10  H101  single    0.970  0.020  1.090
 NPE  C10  H102  single    0.970  0.020  1.090
 NPE  C11  O1    deloc     1.247  0.020  1.247
 NPE  C11  O2    deloc     1.250  0.020  1.250

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
 NPE  C6    C1   C2    121.19  3.000
 NPE  C6    C1   N1    119.40  3.000
 NPE  C2    C1   N1    119.41  3.000
 NPE  O2N   N1   O1N   123.46  3.000
 NPE  O2N   N1   C1    118.27  3.000
 NPE  O1N   N1   C1    118.27  3.000
 NPE  H2    C2   C3    119.67  3.000
 NPE  H2    C2   C1    121.10  3.000
 NPE  C3    C2   C1    119.23  3.000
 NPE  H3    C3   C4    119.66  3.000
 NPE  H3    C3   C2    119.99  3.000
 NPE  C4    C3   C2    120.35  3.000
 NPE  O3P   C4   C5    120.16  3.000
 NPE  O3P   C4   C3    120.20  3.000
 NPE  C5    C4   C3    119.63  3.000
 NPE  H5    C5   C6    120.01  3.000
 NPE  H5    C5   C4    119.62  3.000
 NPE  C6    C5   C4    120.36  3.000
 NPE  H6    C6   C5    119.65  3.000
 NPE  H6    C6   C1    121.13  3.000
 NPE  C5    C6   C1    119.22  3.000
 NPE  P     O3P  C4    118.06  3.000
 NPE  C7    P    O2P   111.47  3.000
 NPE  C7    P    O1P   111.39  3.000
 NPE  O2P   P    O1P   119.95  3.000
 NPE  C7    P    O3P    97.15  3.000
 NPE  O2P   P    O3P   107.08  3.000
 NPE  O1P   P    O3P   107.08  3.000
 NPE  H72   C7   H71   106.89  3.000
 NPE  H72   C7   C8    109.87  3.000
 NPE  H71   C7   C8    109.75  3.000
 NPE  H72   C7   P     109.31  3.000
 NPE  H71   C7   P     109.70  3.000
 NPE  C8    C7   P     111.22  3.000
 NPE  H82   C8   H81   106.03  3.000
 NPE  H82   C8   C9    109.40  3.000
 NPE  H81   C8   C9    109.35  3.000
 NPE  H82   C8   C7    109.38  3.000
 NPE  H81   C8   C7    109.57  3.000
 NPE  C9    C8   C7    112.89  3.000
 NPE  H92   C9   H91   105.89  3.000
 NPE  H92   C9   C10   109.97  3.000
 NPE  H91   C9   C10   109.93  3.000
 NPE  H92   C9   C8    109.24  3.000
 NPE  H91   C9   C8    109.27  3.000
 NPE  C10   C9   C8    112.34  3.000
 NPE  H102  C10  H101  104.69  3.000
 NPE  H102  C10  C11   108.06  3.000
 NPE  H101  C10  C11   108.22  3.000
 NPE  H102  C10  C9    109.42  3.000
 NPE  H101  C10  C9    109.52  3.000
 NPE  C11   C10  C9    116.29  3.000
 NPE  O2    C11  O1    126.17  3.000
 NPE  O2    C11  C10   115.91  3.000
 NPE  O1    C11  C10   117.92  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
 NPE  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 NPE  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 NPE  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 NPE  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 NPE  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 NPE  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 NPE  CONST_07  C3   C2   C1   N1    180.00   0.0  0
 NPE  CONST_08  C5   C6   C1   N1    180.00   0.0  0
 NPE  CONST_09  O3P  C4   C3   C2    180.00   0.0  0
 NPE  CONST_10  O3P  C4   C5   C6    180.00   0.0  0
 NPE  CONST_11  H3   C3   C2   C1    180.00   0.0  0
 NPE  CONST_12  H5   C5   C6   C1    180.00   0.0  0
 NPE  CONST_13  H6   C6   C1   C2    180.00   0.0  0
 NPE  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 NPE  CONST_15  C2   C1   N1   O1N     0.00   0.0  0
 NPE  CONST_16  C6   C1   N1   O1N   180.00   0.0  0
 NPE  CONST_17  C2   C1   N1   O2N   180.00   0.0  0
 NPE  CONST_18  C6   C1   N1   O2N     0.00   0.0  0
 NPE  Var_01    O1P  P    O3P  C4     64.28  30.0  3
 NPE  Var_02    C8   C7   P    O3P   176.79  30.0  3
 NPE  Var_03    C9   C8   C7   P     178.34  30.0  3
 NPE  Var_04    C10  C9   C8   C7    179.21  30.0  3
 NPE  Var_05    C11  C10  C9   C8   -179.83  30.0  3
 NPE  Var_06    O1   C11  C10  C9      1.59  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
 NPE  plan-1  C1   0.020
 NPE  plan-1  N1   0.020
 NPE  plan-1  C2   0.020
 NPE  plan-1  C3   0.020
 NPE  plan-1  C4   0.020
 NPE  plan-1  C5   0.020
 NPE  plan-1  C6   0.020
 NPE  plan-1  O3P  0.020
 NPE  plan-1  H2   0.020
 NPE  plan-1  H3   0.020
 NPE  plan-1  H5   0.020
 NPE  plan-1  H6   0.020
 NPE  plan-2  C1   0.020
 NPE  plan-2  N1   0.020
 NPE  plan-2  O1N  0.020
 NPE  plan-2  O2N  0.020
 NPE  plan-3  C10  0.020
 NPE  plan-3  C11  0.020
 NPE  plan-3  O1   0.020
 NPE  plan-3  O2   0.020

