# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 22:02:57 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 6-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-4-oxidanylidene-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CCC(=O)CCC(O)=O)c1O
#
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
 5NJ  5NJ  '6-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-4-oxidanylidene-hexanoic acid'  ligand  41  23  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5NJ
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
 5NJ  OA   O  O     0  -0.444   6.0561   0.7457   1.8788
 5NJ  CA   C  C     0   0.556   6.0819   1.0624   0.7155
 5NJ  OB   O  OH1   0  -0.596   7.1053   1.7044   0.1614
 5NJ  CB   C  CH2   0  -0.582   4.9928   0.7925  -0.2850
 5NJ  CG   C  CH2   0  -0.555   3.7950   0.0928   0.3263
 5NJ  CD   C  C     0   0.416   2.6988  -0.1997  -0.6672
 5NJ  OE   O  O     0  -0.405   2.8148   0.0331  -1.8485
 5NJ  CF   C  CH2   0  -0.557   1.4455  -0.8074  -0.0887
 5NJ  C4A  C  CH2   0  -0.530   0.4058  -1.1993  -1.1367
 5NJ  C4   C  CR6   0   0.107  -0.8393  -1.7297  -0.4830
 5NJ  C3   C  CR6   0   0.247  -0.9364  -3.0745  -0.1384
 5NJ  O3   O  OH1   0  -0.620   0.1115  -3.8713  -0.4276
 5NJ  C2   C  CR6   0   0.128  -2.0898  -3.5569   0.4922
 5NJ  C2A  C  CH3   0  -0.787  -2.2110  -5.0054   0.8625
 5NJ  N1   N  N     0  -0.411  -3.0985  -2.7498   0.7807
 5NJ  C6   C  CR16  0  -0.133  -3.0181  -1.4617   0.4694
 5NJ  C5   C  CR6   0  -0.086  -1.9161  -0.9008  -0.1582
 5NJ  C5A  C  CH2   0  -0.210  -1.8548   0.5585  -0.5133
 5NJ  O4P  O  O2    0  -0.590  -2.9550   1.2389   0.0797
 5NJ  P    P  P     0   1.465  -3.1049   2.8179  -0.1212
 5NJ  O3P  O  O     0  -0.707  -3.0891   3.3075  -1.5112
 5NJ  O1P  O  OH1   0  -0.728  -4.4474   2.9827   0.7179
 5NJ  O2P  O  OH1   0  -0.742  -1.9185   3.5023   0.7007
 5NJ  H1   H  HOH1  0   0.480   7.7923   1.8667   0.8251
 5NJ  H2   H  HCH2  0   0.287   4.7013   1.7443  -0.7365
 5NJ  H3   H  HCH2  0   0.289   5.4185   0.1988  -1.0984
 5NJ  H4   H  HCH2  0   0.282   4.0877  -0.8594   0.7796
 5NJ  H6   H  HCH2  0   0.285   1.7304  -1.6730   0.5167
 5NJ  H7   H  HCH2  0   0.262   0.1709  -0.3389  -1.7646
 5NJ  H8   H  HOH1  0   0.484  -0.0555  -4.7819  -0.1616
 5NJ  H9   H  HCH3  0   0.258  -1.4529  -5.3070   1.5902
 5NJ  H10  H  HCH3  0   0.272  -3.1856  -5.1929   1.3065
 5NJ  H11  H  HCH3  0   0.255  -2.1134  -5.6626  -0.0054
 5NJ  H12  H  HCR6  0   0.258  -3.8744  -0.8563   0.7382
 5NJ  H13  H  HCH2  0   0.253  -0.9144   0.9924  -0.1587
 5NJ  H14  H  HCH2  0   0.264  -1.8808   0.6819  -1.6006
 5NJ  H15  H  HOH1  0   0.505  -4.8235   3.8729   0.6859
 5NJ  H16  H  HOH1  0   0.497  -1.8825   3.2929   1.6437
 5NJ  H17  H  HCH2  0   0.279   3.3695   0.6805   1.1448
 5NJ  H5   H  HCH2  0   0.282   1.0261  -0.0898   0.6248
 5NJ  H18  H  HCH2  0   0.273   0.8292  -1.9472  -1.8072

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
 5NJ  OE   CD   double    1.210  0.020  1.210
 5NJ  OA   CA   double    1.206  0.020  1.206
 5NJ  CB   CA   single    1.503  0.020  1.503
 5NJ  CB   CG   single    1.516  0.020  1.516
 5NJ  CA   OB   single    1.329  0.020  1.329
 5NJ  CD   CG   single    1.508  0.020  1.508
 5NJ  CD   CF   single    1.508  0.020  1.508
 5NJ  O3   C3   single    1.348  0.020  1.348
 5NJ  CF   C4A  single    1.527  0.020  1.527
 5NJ  C4A  C4   single    1.503  0.020  1.503
 5NJ  C3   C4   aromatic  1.392  0.020  1.392
 5NJ  C3   C2   aromatic  1.400  0.020  1.400
 5NJ  C2A  C2   single    1.500  0.020  1.500
 5NJ  C4   C5   aromatic  1.397  0.020  1.397
 5NJ  C2   N1   aromatic  1.324  0.020  1.324
 5NJ  O3P  P    double    1.474  0.020  1.474
 5NJ  C5   C5A  single    1.503  0.020  1.503
 5NJ  C5   C6   aromatic  1.387  0.020  1.387
 5NJ  N1   C6   aromatic  1.328  0.020  1.328
 5NJ  O4P  C5A  single    1.423  0.020  1.423
 5NJ  O4P  P    single    1.599  0.020  1.599
 5NJ  P    O1P  single    1.592  0.020  1.592
 5NJ  P    O2P  single    1.597  0.020  1.597
 5NJ  OB   H1   single    0.850  0.020  0.980
 5NJ  CB   H2   single    0.970  0.020  1.090
 5NJ  CB   H3   single    0.970  0.020  1.090
 5NJ  CG   H4   single    0.970  0.020  1.090
 5NJ  CF   H6   single    0.970  0.020  1.090
 5NJ  C4A  H7   single    0.970  0.020  1.090
 5NJ  O3   H8   single    0.850  0.020  0.980
 5NJ  C2A  H9   single    0.970  0.020  1.090
 5NJ  C2A  H10  single    0.970  0.020  1.090
 5NJ  C2A  H11  single    0.970  0.020  1.090
 5NJ  C6   H12  single    0.930  0.020  1.080
 5NJ  C5A  H13  single    0.970  0.020  1.090
 5NJ  C5A  H14  single    0.970  0.020  1.090
 5NJ  O1P  H15  single    0.850  0.020  0.980
 5NJ  O2P  H16  single    0.850  0.020  0.980
 5NJ  CG   H17  single    0.970  0.020  1.090
 5NJ  CF   H5   single    0.970  0.020  1.090
 5NJ  C4A  H18  single    0.970  0.020  1.090

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
 5NJ  CB   CA   OB   111.53  3.000
 5NJ  OB   CA   OA   123.06  3.000
 5NJ  CB   CA   OA   125.41  3.000
 5NJ  H1   OB   CA   109.96  3.000
 5NJ  H3   CB   H2   105.63  3.000
 5NJ  H3   CB   CG   110.91  3.000
 5NJ  H2   CB   CG   110.96  3.000
 5NJ  H3   CB   CA   108.09  3.000
 5NJ  H2   CB   CA   108.17  3.000
 5NJ  CG   CB   CA   112.76  3.000
 5NJ  H17  CG   H4   105.16  3.000
 5NJ  H17  CG   CD   108.33  3.000
 5NJ  H4   CG   CD   107.37  3.000
 5NJ  H17  CG   CB   111.17  3.000
 5NJ  H4   CG   CB   110.93  3.000
 5NJ  CD   CG   CB   113.47  3.000
 5NJ  CF   CD   OE   122.13  3.000
 5NJ  CF   CD   CG   115.44  3.000
 5NJ  OE   CD   CG   122.43  3.000
 5NJ  H5   CF   H6   104.93  3.000
 5NJ  H5   CF   C4A  110.76  3.000
 5NJ  H6   CF   C4A  110.73  3.000
 5NJ  H5   CF   CD   107.70  3.000
 5NJ  H6   CF   CD   108.34  3.000
 5NJ  C4A  CF   CD   113.94  3.000
 5NJ  H18  C4A  H7   105.71  3.000
 5NJ  H18  C4A  C4   110.31  3.000
 5NJ  H7   C4A  C4   110.51  3.000
 5NJ  H18  C4A  CF   109.50  3.000
 5NJ  H7   C4A  CF   109.83  3.000
 5NJ  C4   C4A  CF   110.86  3.000
 5NJ  C5   C4   C3   117.51  3.000
 5NJ  C5   C4   C4A  122.02  3.000
 5NJ  C3   C4   C4A  120.44  3.000
 5NJ  C2   C3   O3   122.23  3.000
 5NJ  C2   C3   C4   120.13  3.000
 5NJ  O3   C3   C4   117.64  3.000
 5NJ  H8   O3   C3   111.39  3.000
 5NJ  N1   C2   C2A  118.25  3.000
 5NJ  N1   C2   C3   121.05  3.000
 5NJ  C2A  C2   C3   120.70  3.000
 5NJ  H11  C2A  H10  107.49  3.000
 5NJ  H11  C2A  H9   107.50  3.000
 5NJ  H10  C2A  H9   107.59  3.000
 5NJ  H11  C2A  C2   112.17  3.000
 5NJ  H10  C2A  C2   109.87  3.000
 5NJ  H9   C2A  C2   112.01  3.000
 5NJ  C6   N1   C2   119.63  3.000
 5NJ  H12  C6   C5   120.98  3.000
 5NJ  H12  C6   N1   115.88  3.000
 5NJ  C5   C6   N1   123.13  3.000
 5NJ  C5A  C5   C6   122.14  3.000
 5NJ  C6   C5   C4   118.54  3.000
 5NJ  C5A  C5   C4   119.32  3.000
 5NJ  H14  C5A  H13  107.31  3.000
 5NJ  H14  C5A  O4P  109.97  3.000
 5NJ  H13  C5A  O4P  109.86  3.000
 5NJ  H14  C5A  C5   110.07  3.000
 5NJ  H13  C5A  C5   110.08  3.000
 5NJ  O4P  C5A  C5   109.53  3.000
 5NJ  P    O4P  C5A  119.50  3.000
 5NJ  O2P  P    O1P  108.11  3.000
 5NJ  O2P  P    O3P  109.57  3.000
 5NJ  O1P  P    O3P  118.15  3.000
 5NJ  O2P  P    O4P  106.79  3.000
 5NJ  O1P  P    O4P   96.61  3.000
 5NJ  O3P  P    O4P  116.46  3.000
 5NJ  H15  O1P  P    113.95  3.000
 5NJ  H16  O2P  P    115.90  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
 5NJ  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 5NJ  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 5NJ  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 5NJ  CONST_04  C6   N1   C2   C3      0.00   0.0  0
 5NJ  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 5NJ  CONST_06  C5   C6   N1   C2      0.00   0.0  0
 5NJ  CONST_07  C2   C3   C4   C4A   180.00   0.0  0
 5NJ  CONST_08  C6   C5   C4   C4A   180.00   0.0  0
 5NJ  CONST_09  C2A  C2   C3   C4    180.00   0.0  0
 5NJ  CONST_10  C5A  C5   C4   C3    180.00   0.0  0
 5NJ  CONST_11  C5   C4   C3   O3    180.00   0.0  0
 5NJ  CONST_12  N1   C2   C3   O3    180.00   0.0  0
 5NJ  CONST_13  C6   N1   C2   C2A   180.00   0.0  0
 5NJ  CONST_14  C5A  C5   C6   N1    180.00   0.0  0
 5NJ  CONST_15  H12  C6   C5   C4    180.00   0.0  0
 5NJ  CONST_16  H1   OB   CA   OA      0.00   0.0  0
 5NJ  Var_01    C3   C4   C4A  CF    -86.10  30.0  2
 5NJ  Var_02    O4P  C5A  C5   C4   -171.50  30.0  2
 5NJ  Var_03    H9   C2A  C2   C3     62.54  30.0  2
 5NJ  Var_04    C4   C4A  CF   CD   -177.06  30.0  3
 5NJ  Var_05    CG   CB   CA   OA      1.59  30.0  3
 5NJ  Var_06    CD   CG   CB   CA   -179.35  30.0  3
 5NJ  Var_07    OE   CD   CG   CB      4.30  30.0  2
 5NJ  Var_08    C4A  CF   CD   CG   -175.06  30.0  3
 5NJ  Var_09    O3P  P    O4P  C5A    53.65  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
 5NJ  plan-1  C4A  0.020
 5NJ  plan-1  C4   0.020
 5NJ  plan-1  C3   0.020
 5NJ  plan-1  O3   0.020
 5NJ  plan-1  C2   0.020
 5NJ  plan-1  C2A  0.020
 5NJ  plan-1  N1   0.020
 5NJ  plan-1  C6   0.020
 5NJ  plan-1  C5   0.020
 5NJ  plan-1  C5A  0.020
 5NJ  plan-1  H12  0.020
 5NJ  plan-2  CG   0.020
 5NJ  plan-2  CD   0.020
 5NJ  plan-2  OE   0.020
 5NJ  plan-2  CF   0.020
 5NJ  plan-3  OA   0.020
 5NJ  plan-3  CA   0.020
 5NJ  plan-3  OB   0.020
 5NJ  plan-3  CB   0.020
 5NJ  plan-3  H1   0.020

