# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 00:50:20 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C=C(C(O)=O)C(=O)c2ccc(C)nc12
#
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
 NIX  NIX  '1-ethyl-7-methyl-4-oxo-1,4-dihydro-1,8-naphthyridine-3-carboxylic acid'  ligand  29  17  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NIX
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
 NIX  N1    N  NR6   0  -0.515   0.3795   8.7821   3.5697
 NIX  C2    C  CR16  0   0.069   1.6905   8.6691   3.3582
 NIX  C3    C  CR6   0  -0.366   2.2868   8.5477   2.1279
 NIX  C4    C  CR6   0   0.427   1.4697   8.5406   0.9291
 NIX  O4    O  OC    0  -0.441   1.8843   8.4368  -0.2186
 NIX  C4A   C  CR66  0  -0.171   0.0298   8.6725   1.1986
 NIX  C5    C  CR16  0  -0.158  -0.9010   8.6820   0.1549
 NIX  C6    C  CR16  0  -0.333  -2.2391   8.8089   0.4325
 NIX  C7    C  CR6   0   0.258  -2.6472   8.9269   1.7698
 NIX  N8    N  N     0  -0.457  -1.7784   8.9162   2.7646
 NIX  C8A   C  CR66  0   0.511  -0.4858   8.7933   2.4906
 NIX  C9    C  CH3   0  -0.730  -4.0952   9.0766   2.1103
 NIX  C1E   C  CH2   0  -0.318  -0.1301   8.9477   4.9367
 NIX  C2E   C  CH3   0  -0.665  -0.4082  10.3978   5.2820
 NIX  C1L   C  C     0   0.535   3.7554   8.4296   2.1483
 NIX  O1L   O  O     0  -0.460   4.4107   8.4235   3.1690
 NIX  O2L   O  OH1   0  -0.584   4.3109   8.3323   0.9508
 NIX  H2    H  HCR6  0   0.323   2.3029   8.6742   4.2497
 NIX  H5    H  HCR6  0   0.277  -0.5550   8.5881  -0.8657
 NIX  H6    H  HCR6  0   0.273  -2.9743   8.8189  -0.3604
 NIX  H91   H  HCH3  0   0.259  -4.6779   8.2508   1.6997
 NIX  H92   H  HCH3  0   0.260  -4.4966   9.9949   1.6784
 NIX  H93   H  HCH3  0   0.256  -4.2398   9.1073   3.1874
 NIX  HE11  H  HCH2  0   0.269   0.6235   8.5326   5.6033
 NIX  HE21  H  HCH2  0   0.274  -1.0263   8.3417   5.0402
 NIX  HE12  H  HCH3  0   0.243  -1.1828  10.8185   4.6434
 NIX  HE22  H  HCH3  0   0.237   0.4912  11.0064   5.1880
 NIX  HE32  H  HCH3  0   0.246  -0.7511  10.4620   6.3142
 NIX  H2L1  H  HOH1  0   0.480   5.2715   8.2646   1.0584

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
 NIX  N1   C2    aromatic  1.333  0.020  1.333
 NIX  N1   C8A   aromatic  1.383  0.020  1.383
 NIX  N1   C1E   single    1.468  0.020  1.468
 NIX  C2   C3    aromatic  1.373  0.020  1.373
 NIX  C2   H2    single    0.930  0.020  1.080
 NIX  C3   C4    aromatic  1.451  0.020  1.451
 NIX  C3   C1L   single    1.473  0.020  1.473
 NIX  C4   O4    double    1.225  0.020  1.225
 NIX  C4   C4A   aromatic  1.471  0.020  1.471
 NIX  C4A  C5    aromatic  1.398  0.020  1.398
 NIX  C4A  C8A   aromatic  1.396  0.020  1.396
 NIX  C5   C6    aromatic  1.372  0.020  1.372
 NIX  C5   H5    single    0.930  0.020  1.080
 NIX  C6   C7    aromatic  1.403  0.020  1.403
 NIX  C6   H6    single    0.930  0.020  1.080
 NIX  C7   N8    aromatic  1.321  0.020  1.321
 NIX  C7   C9    single    1.495  0.020  1.495
 NIX  N8   C8A   aromatic  1.327  0.020  1.327
 NIX  C9   H91   single    0.970  0.020  1.090
 NIX  C9   H92   single    0.970  0.020  1.090
 NIX  C9   H93   single    0.970  0.020  1.090
 NIX  C1E  C2E   single    1.516  0.020  1.516
 NIX  C1E  HE11  single    0.970  0.020  1.090
 NIX  C1E  HE21  single    0.970  0.020  1.090
 NIX  C2E  HE12  single    0.970  0.020  1.090
 NIX  C2E  HE22  single    0.970  0.020  1.090
 NIX  C2E  HE32  single    0.970  0.020  1.090
 NIX  C1L  O1L   double    1.213  0.020  1.213
 NIX  C1L  O2L   single    1.324  0.020  1.324
 NIX  O2L  H2L1  single    0.850  0.020  0.980

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
 NIX  C1E   N1   C8A   120.55  3.000
 NIX  C1E   N1   C2    119.92  3.000
 NIX  C8A   N1   C2    119.48  3.000
 NIX  H2    C2   C3    119.56  3.000
 NIX  H2    C2   N1    115.20  3.000
 NIX  C3    C2   N1    125.24  3.000
 NIX  C1L   C3   C4    124.92  3.000
 NIX  C1L   C3   C2    115.32  3.000
 NIX  C4    C3   C2    119.76  3.000
 NIX  C4A   C4   O4    120.71  3.000
 NIX  C4A   C4   C3    113.55  3.000
 NIX  O4    C4   C3    125.74  3.000
 NIX  C8A   C4A  C5    116.38  3.000
 NIX  C8A   C4A  C4    122.60  3.000
 NIX  C5    C4A  C4    121.03  3.000
 NIX  H5    C5   C6    120.71  3.000
 NIX  H5    C5   C4A   119.39  3.000
 NIX  C6    C5   C4A   119.90  3.000
 NIX  H6    C6   C7    120.02  3.000
 NIX  H6    C6   C5    121.02  3.000
 NIX  C7    C6   C5    118.96  3.000
 NIX  C9    C7   N8    117.80  3.000
 NIX  C9    C7   C6    120.48  3.000
 NIX  N8    C7   C6    121.72  3.000
 NIX  C8A   N8   C7    119.07  3.000
 NIX  N8    C8A  C4A   123.97  3.000
 NIX  N8    C8A  N1    116.68  3.000
 NIX  C4A   C8A  N1    119.35  3.000
 NIX  H93   C9   H92   108.62  3.000
 NIX  H93   C9   H91   108.86  3.000
 NIX  H92   C9   H91   106.95  3.000
 NIX  H93   C9   C7    110.93  3.000
 NIX  H92   C9   C7    110.51  3.000
 NIX  H91   C9   C7    110.84  3.000
 NIX  HE21  C1E  HE11  107.46  3.000
 NIX  HE21  C1E  C2E   111.12  3.000
 NIX  HE11  C1E  C2E   110.63  3.000
 NIX  HE21  C1E  N1    108.18  3.000
 NIX  HE11  C1E  N1    106.67  3.000
 NIX  C2E   C1E  N1    112.54  3.000
 NIX  HE32  C2E  HE22  107.97  3.000
 NIX  HE32  C2E  HE12  108.00  3.000
 NIX  HE22  C2E  HE12  108.72  3.000
 NIX  HE32  C2E  C1E   109.25  3.000
 NIX  HE22  C2E  C1E   111.28  3.000
 NIX  HE12  C2E  C1E   111.50  3.000
 NIX  O2L   C1L  O1L   122.29  3.000
 NIX  O2L   C1L  C3    114.30  3.000
 NIX  O1L   C1L  C3    123.41  3.000
 NIX  H2L1  O2L  C1L   108.70  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
 NIX  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 NIX  CONST_02  C4    C4A  C8A  N1     0.00   0.0  0
 NIX  CONST_03  C5    C4A  C8A  N1   180.00   0.0  0
 NIX  CONST_04  C7    N8   C8A  N1   180.00   0.0  0
 NIX  CONST_05  C4A   C8A  N1   C2     0.00   0.0  0
 NIX  CONST_06  N8    C8A  N1   C2   180.00   0.0  0
 NIX  CONST_07  C4A   C4   C3   C2     0.00   0.0  0
 NIX  CONST_08  C8A   N1   C2   C3     0.00   0.0  0
 NIX  CONST_09  C5    C4A  C4   C3   180.00   0.0  0
 NIX  CONST_10  C8A   C4A  C4   C3     0.00   0.0  0
 NIX  CONST_11  C6    C5   C4A  C4   180.00   0.0  0
 NIX  CONST_12  N8    C8A  C4A  C4   180.00   0.0  0
 NIX  CONST_13  C7    C6   C5   C4A    0.00   0.0  0
 NIX  CONST_14  C7    N8   C8A  C4A    0.00   0.0  0
 NIX  CONST_15  N8    C8A  C4A  C5     0.00   0.0  0
 NIX  CONST_16  N8    C7   C6   C5     0.00   0.0  0
 NIX  CONST_17  C8A   C4A  C5   C6     0.00   0.0  0
 NIX  CONST_18  C8A   N8   C7   C6     0.00   0.0  0
 NIX  CONST_19  C1L   C3   C2   N1   180.00   0.0  0
 NIX  CONST_20  O4    C4   C3   C2   180.00   0.0  0
 NIX  CONST_21  C1E   N1   C2   C3   180.00   0.0  0
 NIX  CONST_22  C5    C4A  C4   O4     0.00   0.0  0
 NIX  CONST_23  C8A   C4A  C4   O4   180.00   0.0  0
 NIX  CONST_24  C1L   C3   C4   C4A  180.00   0.0  0
 NIX  CONST_25  C1E   N1   C8A  C4A  180.00   0.0  0
 NIX  CONST_26  C9    C7   C6   C5   180.00   0.0  0
 NIX  CONST_27  C1E   N1   C8A  N8     0.00   0.0  0
 NIX  CONST_28  C9    C7   N8   C8A  180.00   0.0  0
 NIX  CONST_29  H2    C2   C3   C4   180.00   0.0  0
 NIX  CONST_30  H5    C5   C4A  C4     0.00   0.0  0
 NIX  CONST_31  H6    C6   C5   C4A  180.00   0.0  0
 NIX  CONST_32  H2L1  O2L  C1L  C3   180.00   0.0  0
 NIX  Var_01    C2E   C1E  N1   C2    97.64  30.0  2
 NIX  Var_02    O1L   C1L  C3   C2     0.75  30.0  2
 NIX  Var_03    H91   C9   C7   C6    56.25  30.0  2
 NIX  Var_04    HE12  C2E  C1E  N1    62.55  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
 NIX  plan-1  N1    0.020
 NIX  plan-1  C2    0.020
 NIX  plan-1  C3    0.020
 NIX  plan-1  C4    0.020
 NIX  plan-1  O4    0.020
 NIX  plan-1  C4A   0.020
 NIX  plan-1  C5    0.020
 NIX  plan-1  C6    0.020
 NIX  plan-1  C7    0.020
 NIX  plan-1  N8    0.020
 NIX  plan-1  C8A   0.020
 NIX  plan-1  C9    0.020
 NIX  plan-1  C1E   0.020
 NIX  plan-1  C1L   0.020
 NIX  plan-1  H2    0.020
 NIX  plan-1  H5    0.020
 NIX  plan-1  H6    0.020
 NIX  plan-2  C3    0.020
 NIX  plan-2  C1L   0.020
 NIX  plan-2  O1L   0.020
 NIX  plan-2  O2L   0.020
 NIX  plan-2  H2L1  0.020

