# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 13:25:00 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 7-methyl-4-oxidanylidene-1~{H}-1,8-naphthyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2C(=O)C(=CNc2n1)C(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
 SJN  SJN  '7-methyl-4-oxidanylidene-1~{H}-1,8-naphthyridine-3-carboxylic acid'  ligand  22  15  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SJN
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
 SJN  C10  C  CR6    0  -0.363   8.5253  -23.4340  37.9930
 SJN  N12  N  NR16   0  -0.667   7.0749  -23.3067  36.0871
 SJN  C13  C  C      0   0.394   9.8912  -23.9072  38.4846
 SJN  C01  C  CH3    0  -0.730   2.8738  -21.1894  35.8961
 SJN  C02  C  CR6    0   0.251   4.0901  -21.5692  36.6804
 SJN  N03  N  N      0  -0.453   5.0363  -22.2505  36.0610
 SJN  C04  C  CR66   0   0.480   6.1212  -22.5980  36.7530
 SJN  C05  C  CR66   0  -0.206   6.3381  -22.2955  38.0994
 SJN  C06  C  CR16   0  -0.164   5.3229  -21.5724  38.7347
 SJN  C07  C  CR16   0  -0.333   4.2005  -21.2059  38.0332
 SJN  C08  C  CR6    0   0.393   7.5599  -22.7176  38.8125
 SJN  O09  O  O      0  -0.452   7.6749  -22.4796  40.0120
 SJN  C11  C  CR16   0   0.016   8.2095  -23.7038  36.6952
 SJN  O14  O  O      0  -0.600  10.3992  -24.8527  37.8465
 SJN  O15  O  OC    -1  -0.580  10.3948  -23.2992  39.4435
 SJN  H2   H  HCH3   0   0.253   2.9436  -21.5424  34.8700
 SJN  H3   H  HCH3   0   0.256   1.9756  -21.6115  36.3495
 SJN  H4   H  HCH3   0   0.256   2.7437  -20.1063  35.8843
 SJN  H5   H  HCR6   0   0.268   5.4312  -21.3069  39.7781
 SJN  H6   H  HCR6   0   0.263   3.4055  -20.6461  38.5076
 SJN  H7   H  HCR6   0   0.302   8.8887  -24.2667  36.0711
 SJN  H1   H  HNR6   0   0.416   6.9139  -23.5330  35.1165

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
 SJN  C01  C02  single    1.496  0.020  1.496
 SJN  N12  C11  single    1.347  0.020  1.347
 SJN  N12  C04  single    1.362  0.020  1.362
 SJN  N03  C02  aromatic  1.320  0.020  1.320
 SJN  N03  C04  aromatic  1.333  0.020  1.333
 SJN  C11  C10  double    1.363  0.020  1.363
 SJN  C02  C07  aromatic  1.405  0.020  1.405
 SJN  C04  C05  aromatic  1.397  0.020  1.397
 SJN  O14  C13  deloc     1.249  0.020  1.249
 SJN  C07  C06  aromatic  1.373  0.020  1.373
 SJN  C10  C13  single    1.527  0.020  1.527
 SJN  C10  C08  single    1.455  0.020  1.455
 SJN  C05  C06  aromatic  1.399  0.020  1.399
 SJN  C05  C08  single    1.476  0.020  1.476
 SJN  C13  O15  deloc     1.242  0.020  1.242
 SJN  C08  O09  double    1.228  0.020  1.228
 SJN  C01  H2   single    0.970  0.020  1.090
 SJN  C01  H3   single    0.970  0.020  1.090
 SJN  C01  H4   single    0.970  0.020  1.090
 SJN  C06  H5   single    0.930  0.020  1.080
 SJN  C07  H6   single    0.930  0.020  1.080
 SJN  C11  H7   single    0.930  0.020  1.080
 SJN  N12  H1   single    0.860  0.020  1.020

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
 SJN  C11  C10  C08  118.70  3.000
 SJN  C08  C10  C13  124.39  3.000
 SJN  C11  C10  C13  116.91  3.000
 SJN  H1   N12  C11  120.15  3.000
 SJN  H1   N12  C04  118.36  3.000
 SJN  C11  N12  C04  121.50  3.000
 SJN  O15  C13  O14  126.89  3.000
 SJN  O15  C13  C10  117.36  3.000
 SJN  O14  C13  C10  115.73  3.000
 SJN  H4   C01  H3   106.88  3.000
 SJN  H4   C01  H2   108.65  3.000
 SJN  H3   C01  H2   108.63  3.000
 SJN  H4   C01  C02  110.76  3.000
 SJN  H3   C01  C02  110.68  3.000
 SJN  H2   C01  C02  111.11  3.000
 SJN  C07  C02  N03  121.93  3.000
 SJN  C07  C02  C01  120.19  3.000
 SJN  N03  C02  C01  117.88  3.000
 SJN  C04  N03  C02  118.31  3.000
 SJN  C05  C04  N03  124.77  3.000
 SJN  C05  C04  N12  118.37  3.000
 SJN  N03  C04  N12  116.86  3.000
 SJN  C08  C05  C06  121.94  3.000
 SJN  C08  C05  C04  122.15  3.000
 SJN  C06  C05  C04  115.91  3.000
 SJN  H5   C06  C07  120.58  3.000
 SJN  H5   C06  C05  119.48  3.000
 SJN  C07  C06  C05  119.94  3.000
 SJN  H6   C07  C06  120.98  3.000
 SJN  H6   C07  C02  119.88  3.000
 SJN  C06  C07  C02  119.14  3.000
 SJN  O09  C08  C05  119.59  3.000
 SJN  O09  C08  C10  125.69  3.000
 SJN  C05  C08  C10  114.70  3.000
 SJN  H7   C11  N12  114.97  3.000
 SJN  H7   C11  C10  120.51  3.000
 SJN  N12  C11  C10  124.52  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
 SJN  CONST_01  C05  C04  N03  C02    0.00   0.0  0
 SJN  CONST_02  C05  C06  C07  C02    0.00   0.0  0
 SJN  CONST_03  C06  C07  C02  N03    0.00   0.0  0
 SJN  CONST_04  C06  C05  C04  N03    0.00   0.0  0
 SJN  CONST_05  C07  C02  N03  C04    0.00   0.0  0
 SJN  CONST_06  C07  C06  C05  C04    0.00   0.0  0
 SJN  CONST_07  C04  N03  C02  C01  180.00   0.0  0
 SJN  CONST_08  C06  C07  C02  C01  180.00   0.0  0
 SJN  CONST_09  H5   C06  C07  C02  180.00   0.0  0
 SJN  CONST_10  H6   C07  C02  N03  180.00   0.0  0
 SJN  Var_01    O14  C13  C10  C08  157.23  30.0  2
 SJN  Var_02    H2   C01  C02  N03   -0.24  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
 SJN  plan-1  C10  0.020
 SJN  plan-1  N12  0.020
 SJN  plan-1  C13  0.020
 SJN  plan-1  C01  0.020
 SJN  plan-1  C02  0.020
 SJN  plan-1  N03  0.020
 SJN  plan-1  C04  0.020
 SJN  plan-1  C05  0.020
 SJN  plan-1  C06  0.020
 SJN  plan-1  C07  0.020
 SJN  plan-1  C08  0.020
 SJN  plan-1  O09  0.020
 SJN  plan-1  C11  0.020
 SJN  plan-1  H5   0.020
 SJN  plan-1  H6   0.020
 SJN  plan-1  H7   0.020
 SJN  plan-1  H1   0.020
 SJN  plan-2  C10  0.020
 SJN  plan-2  C13  0.020
 SJN  plan-2  O14  0.020
 SJN  plan-2  O15  0.020

