# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 13:42:11 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1)c2cc3cccnc3c(n2)c4cccc(c4)[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
 NPV  NPV  '4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid'  ligand  41  28  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NPV
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
 NPV  C4   C  CR6    0  -0.097   4.6638  -0.8522   0.1018
 NPV  C5   C  CR16   0  -0.237   3.4610  -1.5367   0.2550
 NPV  C6   C  CR16   0  -0.267   2.2568  -0.8588   0.2263
 NPV  C7   C  CR6    0   0.062   2.2178   0.5255   0.0425
 NPV  C9   C  CR16   0  -0.233   4.6352   0.5296  -0.0782
 NPV  C10  C  CR6    0   0.261   0.9164   1.2285   0.0008
 NPV  C15  C  CR16   0  -0.070  -3.0419   4.0738  -0.4456
 NPV  C11  C  CR16   0  -0.407   0.8006   2.5825  -0.1971
 NPV  C12  C  CR66   0   0.203  -0.4805   3.1572  -0.2652
 NPV  C13  C  CR16   0  -0.183  -0.6974   4.5340  -0.5046
 NPV  C3   C  C      0   0.534   5.9289  -1.6246   0.1368
 NPV  O1   O  O      0  -0.437   5.9803  -2.8177   0.3178
 NPV  O2   O  OH1    0  -0.593   7.0030  -0.8715  -0.0532
 NPV  C8   C  CR16   0  -0.331   3.4287   1.2051  -0.1064
 NPV  N19  N  N      0  -0.456  -0.1741   0.4500   0.1701
 NPV  C14  C  CR16   0  -0.313  -1.9787   4.9922  -0.5903
 NPV  N16  N  N      0  -0.418  -2.8746   2.7996  -0.2158
 NPV  C17  C  CR66   0   0.131  -1.6147   2.3314  -0.1108
 NPV  C18  C  CR6    0   0.172  -1.3804   0.9461   0.1383
 NPV  C20  C  CR6    0   0.084  -2.4836  -0.0204   0.3425
 NPV  C25  C  CR16   0  -0.316  -2.3610  -1.2862  -0.2202
 NPV  C21  C  CR16   0  -0.255  -3.6025   0.2696   1.1232
 NPV  C22  C  CR16   0  -0.238  -4.5849  -0.6877   1.3308
 NPV  C23  C  CR16   0  -0.273  -4.4792  -1.9440   0.7597
 NPV  C24  C  CR6    0   0.277  -3.3599  -2.2221  -0.0115
 NPV  N26  N  N      1   0.328  -3.2245  -3.5399  -0.6164
 NPV  O27  O  O      0  -0.377  -2.2321  -3.7680  -1.2669
 NPV  O28  O  O     -1  -0.376  -4.1122  -4.3398  -0.4378
 NPV  H5   H  HCR6   0   0.268   3.4615  -2.6092   0.3950
 NPV  H6   H  HCR6   0   0.266   1.3342  -1.4081   0.3465
 NPV  H9   H  HCR6   0   0.271   5.5491   1.0941  -0.1986
 NPV  H15  H  HCR6   0   0.276  -4.0644   4.4246  -0.5295
 NPV  H11  H  HCR6   0   0.280   1.6636   3.2236  -0.3123
 NPV  H13  H  HCR6   0   0.282   0.1484   5.1992  -0.6207
 NPV  HO2  H  HOH1   0   0.489   7.8016  -1.4189  -0.0215
 NPV  H8   H  HCR6   0   0.263   3.4518   2.2769  -0.2471
 NPV  H14  H  HCR6   0   0.285  -2.1938   6.0358  -0.7734
 NPV  H25  H  HCR6   0   0.292  -1.4934  -1.5241  -0.8184
 NPV  H21  H  HCR6   0   0.273  -3.7029   1.2380   1.5899
 NPV  H22  H  HCR6   0   0.281  -5.4410  -0.4533   1.9479
 NPV  H23  H  HCR6   0   0.301  -5.2505  -2.6822   0.9219

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
 NPV  O1   C3   double    1.208  0.020  1.208
 NPV  O2   C3   single    1.325  0.020  1.325
 NPV  C3   C4   single    1.483  0.020  1.483
 NPV  C4   C5   aromatic  1.392  0.020  1.392
 NPV  C4   C9   aromatic  1.394  0.020  1.394
 NPV  C5   C6   aromatic  1.382  0.020  1.382
 NPV  C9   C8   aromatic  1.383  0.020  1.383
 NPV  C6   C7   aromatic  1.397  0.020  1.397
 NPV  C8   C7   aromatic  1.397  0.020  1.397
 NPV  C7   C10  single    1.480  0.020  1.480
 NPV  O28  N26  single    1.208  0.020  1.208
 NPV  C10  N19  aromatic  1.351  0.020  1.351
 NPV  C10  C11  aromatic  1.373  0.020  1.373
 NPV  N19  C18  aromatic  1.305  0.020  1.305
 NPV  N26  O27  double    1.208  0.020  1.208
 NPV  N26  C24  single    1.456  0.020  1.456
 NPV  C11  C12  aromatic  1.406  0.020  1.406
 NPV  C25  C24  aromatic  1.385  0.020  1.385
 NPV  C25  C20  aromatic  1.391  0.020  1.391
 NPV  C24  C23  aromatic  1.387  0.020  1.387
 NPV  C18  C20  single    1.481  0.020  1.481
 NPV  C18  C17  aromatic  1.427  0.020  1.427
 NPV  C12  C17  aromatic  1.411  0.020  1.411
 NPV  C12  C13  aromatic  1.414  0.020  1.414
 NPV  C20  C21  aromatic  1.395  0.020  1.395
 NPV  C17  N16  aromatic  1.348  0.020  1.348
 NPV  C13  C14  aromatic  1.364  0.020  1.364
 NPV  C23  C22  aromatic  1.384  0.020  1.384
 NPV  C21  C22  aromatic  1.387  0.020  1.387
 NPV  N16  C15  aromatic  1.305  0.020  1.305
 NPV  C14  C15  aromatic  1.412  0.020  1.412
 NPV  C5   H5   single    0.930  0.020  1.080
 NPV  C6   H6   single    0.930  0.020  1.080
 NPV  C9   H9   single    0.930  0.020  1.080
 NPV  C15  H15  single    0.930  0.020  1.080
 NPV  C11  H11  single    0.930  0.020  1.080
 NPV  C13  H13  single    0.930  0.020  1.080
 NPV  O2   HO2  single    0.850  0.020  0.980
 NPV  C8   H8   single    0.930  0.020  1.080
 NPV  C14  H14  single    0.930  0.020  1.080
 NPV  C25  H25  single    0.930  0.020  1.080
 NPV  C21  H21  single    0.930  0.020  1.080
 NPV  C22  H22  single    0.930  0.020  1.080
 NPV  C23  H23  single    0.930  0.020  1.080

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
 NPV  C3   C4   C9   122.48  3.000
 NPV  C9   C4   C5   118.94  3.000
 NPV  C3   C4   C5   118.58  3.000
 NPV  H5   C5   C6   119.31  3.000
 NPV  H5   C5   C4   120.08  3.000
 NPV  C6   C5   C4   120.61  3.000
 NPV  H6   C6   C7   119.65  3.000
 NPV  H6   C6   C5   119.49  3.000
 NPV  C7   C6   C5   120.87  3.000
 NPV  C8   C7   C10  121.90  3.000
 NPV  C10  C7   C6   119.93  3.000
 NPV  C8   C7   C6   118.17  3.000
 NPV  H9   C9   C8   118.70  3.000
 NPV  H9   C9   C4   120.98  3.000
 NPV  C8   C9   C4   120.32  3.000
 NPV  N19  C10  C11  121.22  3.000
 NPV  C11  C10  C7   123.14  3.000
 NPV  N19  C10  C7   115.65  3.000
 NPV  H15  C15  N16  116.76  3.000
 NPV  H15  C15  C14  119.44  3.000
 NPV  N16  C15  C14  123.80  3.000
 NPV  H11  C11  C12  118.67  3.000
 NPV  H11  C11  C10  122.19  3.000
 NPV  C12  C11  C10  119.14  3.000
 NPV  C17  C12  C13  117.70  3.000
 NPV  C13  C12  C11  123.10  3.000
 NPV  C17  C12  C11  119.20  3.000
 NPV  H13  C13  C14  121.40  3.000
 NPV  H13  C13  C12  119.78  3.000
 NPV  C14  C13  C12  118.82  3.000
 NPV  O2   C3   O1   123.24  3.000
 NPV  O2   C3   C4   113.08  3.000
 NPV  O1   C3   C4   123.67  3.000
 NPV  HO2  O2   C3   110.02  3.000
 NPV  H8   C8   C9   117.92  3.000
 NPV  H8   C8   C7   120.98  3.000
 NPV  C9   C8   C7   121.10  3.000
 NPV  C18  N19  C10  121.62  3.000
 NPV  H14  C14  C13  121.47  3.000
 NPV  H14  C14  C15  119.69  3.000
 NPV  C13  C14  C15  118.84  3.000
 NPV  C17  N16  C15  118.19  3.000
 NPV  C18  C17  N16  120.28  3.000
 NPV  N16  C17  C12  122.63  3.000
 NPV  C18  C17  C12  117.08  3.000
 NPV  C20  C18  C17  122.37  3.000
 NPV  C17  C18  N19  121.68  3.000
 NPV  C20  C18  N19  115.93  3.000
 NPV  C21  C20  C25  119.10  3.000
 NPV  C21  C20  C18  122.62  3.000
 NPV  C25  C20  C18  118.21  3.000
 NPV  H25  C25  C24  120.93  3.000
 NPV  H25  C25  C20  119.69  3.000
 NPV  C24  C25  C20  119.38  3.000
 NPV  H21  C21  C22  119.23  3.000
 NPV  H21  C21  C20  120.20  3.000
 NPV  C22  C21  C20  120.55  3.000
 NPV  H22  C22  C23  119.53  3.000
 NPV  H22  C22  C21  119.77  3.000
 NPV  C23  C22  C21  120.70  3.000
 NPV  H23  C23  C24  121.52  3.000
 NPV  H23  C23  C22  120.26  3.000
 NPV  C24  C23  C22  118.22  3.000
 NPV  N26  C24  C23  119.16  3.000
 NPV  C23  C24  C25  122.03  3.000
 NPV  N26  C24  C25  118.81  3.000
 NPV  O28  N26  O27  123.92  3.000
 NPV  O27  N26  C24  118.09  3.000
 NPV  O28  N26  C24  117.99  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
 NPV  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 NPV  CONST_02  C7   C8   C9   C4     0.00   0.0  0
 NPV  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 NPV  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 NPV  CONST_05  C10  C7   C6   C5   180.00   0.0  0
 NPV  CONST_06  C9   C4   C5   C6     0.00   0.0  0
 NPV  CONST_07  C9   C8   C7   C6     0.00   0.0  0
 NPV  CONST_08  N19  C10  C7   C6     0.00   0.0  0
 NPV  CONST_09  C11  C10  C7   C6   180.00   0.0  0
 NPV  CONST_10  C18  N19  C10  C7   180.00   0.0  0
 NPV  CONST_11  C12  C11  C10  C7   180.00   0.0  0
 NPV  CONST_12  C10  C7   C8   C9   180.00   0.0  0
 NPV  CONST_13  C20  C18  N19  C10  180.00   0.0  0
 NPV  CONST_14  C17  C18  N19  C10    0.00   0.0  0
 NPV  CONST_15  C17  C12  C11  C10    0.00   0.0  0
 NPV  CONST_16  C13  C12  C11  C10  180.00   0.0  0
 NPV  CONST_17  C18  C17  N16  C15  180.00   0.0  0
 NPV  CONST_18  C12  C17  N16  C15    0.00   0.0  0
 NPV  CONST_19  C12  C13  C14  C15    0.00   0.0  0
 NPV  CONST_20  C8   C7   C10  C11    0.00   0.0  0
 NPV  CONST_21  C18  N19  C10  C11    0.00   0.0  0
 NPV  CONST_22  C18  C17  C12  C11    0.00   0.0  0
 NPV  CONST_23  N16  C17  C12  C11  180.00   0.0  0
 NPV  CONST_24  C14  C13  C12  C11  180.00   0.0  0
 NPV  CONST_25  N19  C10  C11  C12    0.00   0.0  0
 NPV  CONST_26  N19  C18  C17  C12    0.00   0.0  0
 NPV  CONST_27  C20  C18  C17  C12  180.00   0.0  0
 NPV  CONST_28  C18  C17  C12  C13  180.00   0.0  0
 NPV  CONST_29  N16  C17  C12  C13    0.00   0.0  0
 NPV  CONST_30  N16  C15  C14  C13    0.00   0.0  0
 NPV  CONST_31  N19  C10  C7   C8   180.00   0.0  0
 NPV  CONST_34  N16  C17  C18  N19  180.00   0.0  0
 NPV  CONST_35  C17  C12  C13  C14    0.00   0.0  0
 NPV  CONST_36  C17  N16  C15  C14    0.00   0.0  0
 NPV  CONST_37  C20  C18  C17  N16    0.00   0.0  0
 NPV  CONST_40  C24  C25  C20  C18  180.00   0.0  0
 NPV  CONST_41  C22  C21  C20  C18  180.00   0.0  0
 NPV  CONST_42  C23  C24  C25  C20    0.00   0.0  0
 NPV  CONST_43  C23  C22  C21  C20    0.00   0.0  0
 NPV  CONST_44  C22  C23  C24  C25    0.00   0.0  0
 NPV  CONST_45  C22  C21  C20  C25    0.00   0.0  0
 NPV  CONST_46  C24  C25  C20  C21    0.00   0.0  0
 NPV  CONST_47  C24  C23  C22  C21    0.00   0.0  0
 NPV  CONST_48  C3   C4   C5   C6   180.00   0.0  0
 NPV  CONST_49  C8   C9   C4   C3   180.00   0.0  0
 NPV  CONST_50  N26  C24  C25  C20  180.00   0.0  0
 NPV  CONST_51  N26  C24  C23  C22  180.00   0.0  0
 NPV  CONST_52  H6   C6   C5   C4   180.00   0.0  0
 NPV  CONST_53  H8   C8   C9   C4   180.00   0.0  0
 NPV  CONST_54  H9   C9   C4   C5   180.00   0.0  0
 NPV  CONST_55  H5   C5   C6   C7   180.00   0.0  0
 NPV  CONST_56  H11  C11  C10  C7     0.00   0.0  0
 NPV  CONST_57  H13  C13  C14  C15  180.00   0.0  0
 NPV  CONST_58  H14  C14  C13  C12  180.00   0.0  0
 NPV  CONST_59  H15  C15  C14  C13  180.00   0.0  0
 NPV  CONST_60  H25  C25  C20  C18    0.00   0.0  0
 NPV  CONST_61  H21  C21  C20  C18    0.00   0.0  0
 NPV  CONST_62  H22  C22  C21  C20  180.00   0.0  0
 NPV  CONST_63  H23  C23  C24  C25  180.00   0.0  0
 NPV  CONST_64  O28  N26  C24  C25  180.00   0.0  0
 NPV  CONST_65  O27  N26  C24  C25    0.00   0.0  0
 NPV  CONST_66  O28  N26  C24  C23    0.00   0.0  0
 NPV  CONST_67  O27  N26  C24  C23  180.00   0.0  0
 NPV  CONST_68  HO2  O2   C3   C4   180.00   0.0  0
 NPV  Var_01    O1   C3   C4   C5    -1.52  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
 NPV  plan-1  C4   0.020
 NPV  plan-1  C5   0.020
 NPV  plan-1  C6   0.020
 NPV  plan-1  C7   0.020
 NPV  plan-1  C9   0.020
 NPV  plan-1  C10  0.020
 NPV  plan-1  C3   0.020
 NPV  plan-1  C8   0.020
 NPV  plan-1  H5   0.020
 NPV  plan-1  H6   0.020
 NPV  plan-1  H9   0.020
 NPV  plan-1  H8   0.020
 NPV  plan-2  C18  0.020
 NPV  plan-2  C20  0.020
 NPV  plan-2  C25  0.020
 NPV  plan-2  C21  0.020
 NPV  plan-2  C22  0.020
 NPV  plan-2  C23  0.020
 NPV  plan-2  C24  0.020
 NPV  plan-2  N26  0.020
 NPV  plan-2  H25  0.020
 NPV  plan-2  H21  0.020
 NPV  plan-2  H22  0.020
 NPV  plan-2  H23  0.020
 NPV  plan-3  C7   0.020
 NPV  plan-3  C10  0.020
 NPV  plan-3  C15  0.020
 NPV  plan-3  C11  0.020
 NPV  plan-3  C12  0.020
 NPV  plan-3  C13  0.020
 NPV  plan-3  N19  0.020
 NPV  plan-3  C14  0.020
 NPV  plan-3  N16  0.020
 NPV  plan-3  C17  0.020
 NPV  plan-3  C18  0.020
 NPV  plan-3  C20  0.020
 NPV  plan-3  H15  0.020
 NPV  plan-3  H11  0.020
 NPV  plan-3  H13  0.020
 NPV  plan-3  H14  0.020
 NPV  plan-4  C24  0.020
 NPV  plan-4  N26  0.020
 NPV  plan-4  O27  0.020
 NPV  plan-4  O28  0.020
 NPV  plan-5  C4   0.020
 NPV  plan-5  C3   0.020
 NPV  plan-5  O1   0.020
 NPV  plan-5  O2   0.020
 NPV  plan-5  HO2  0.020

