# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:04:10 2021
#   Inital geometry file: a 45 line input string
#   Ligand name: 1,8-naphthyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1cnc2ncccc2c1
#
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
 W3P  W3P  '1,8-naphthyridine        '  ligand  16  10  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W3P
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
 W3P  N1  N  N     0  -0.406  -5.0696  14.9905  -1.5022
 W3P  C4  C  CR16  0  -0.326  -3.0177  15.1288  -0.2590
 W3P  C5  C  CR16  0  -0.182  -3.6840  15.0583   0.9306
 W3P  C6  C  CR66  0  -0.036  -5.0902  14.9483   0.9174
 W3P  C7  C  CR16  0  -0.182  -5.8775  14.8661   2.0849
 W3P  C   C  CR16  0  -0.326  -7.2330  14.7595   1.9593
 W3P  C2  C  CR66  0   0.327  -5.7477  14.9171  -0.3372
 W3P  N   N  N     0  -0.406  -7.0896  14.8125  -0.4390
 W3P  C1  C  CR16  0  -0.063  -7.7886  14.7381   0.6631
 W3P  C3  C  CR16  0  -0.062  -3.7673  15.0911  -1.4534
 W3P  H1  H  HCR6  0   0.278  -1.9409  15.2109  -0.3025
 W3P  H2  H  HCR6  0   0.280  -3.1543  15.0851   1.8750
 W3P  H3  H  HCR6  0   0.280  -5.4019  14.8890   3.0575
 W3P  H4  H  HCR6  0   0.278  -7.8801  14.6918   2.8223
 W3P  H5  H  HCR6  0   0.273  -8.8646  14.6559   0.5505
 W3P  H6  H  HCR6  0   0.273  -3.2482  15.1484  -2.4046

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
 W3P  N1  C3  aromatic  1.307  0.020  1.307
 W3P  N1  C2  aromatic  1.350  0.020  1.350
 W3P  C3  C4  aromatic  1.411  0.020  1.411
 W3P  N   C2  aromatic  1.350  0.020  1.350
 W3P  N   C1  aromatic  1.307  0.020  1.307
 W3P  C2  C6  aromatic  1.417  0.020  1.417
 W3P  C4  C5  aromatic  1.365  0.020  1.365
 W3P  C1  C   aromatic  1.410  0.020  1.410
 W3P  C6  C5  aromatic  1.411  0.020  1.411
 W3P  C6  C7  aromatic  1.410  0.020  1.410
 W3P  C   C7  aromatic  1.365  0.020  1.365
 W3P  C4  H1  single    0.930  0.020  1.080
 W3P  C5  H2  single    0.930  0.020  1.080
 W3P  C7  H3  single    0.930  0.020  1.080
 W3P  C   H4  single    0.930  0.020  1.080
 W3P  C1  H5  single    0.930  0.020  1.080
 W3P  C3  H6  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
 W3P  C3  N1  C2  118.19  3.000
 W3P  H1  C4  C3  119.83  3.000
 W3P  H1  C4  C5  121.68  3.000
 W3P  C3  C4  C5  118.49  3.000
 W3P  H2  C5  C6  119.84  3.000
 W3P  H2  C5  C4  121.32  3.000
 W3P  C6  C5  C4  118.84  3.000
 W3P  C2  C6  C7  118.21  3.000
 W3P  C7  C6  C5  123.59  3.000
 W3P  C2  C6  C5  118.20  3.000
 W3P  H3  C7  C   121.34  3.000
 W3P  H3  C7  C6  119.81  3.000
 W3P  C   C7  C6  118.85  3.000
 W3P  H4  C   C1  119.80  3.000
 W3P  H4  C   C7  121.72  3.000
 W3P  C1  C   C7  118.47  3.000
 W3P  N   C2  C6  121.99  3.000
 W3P  C6  C2  N1  122.00  3.000
 W3P  N   C2  N1  116.01  3.000
 W3P  C1  N   C2  118.19  3.000
 W3P  H5  C1  N   116.56  3.000
 W3P  H5  C1  C   119.16  3.000
 W3P  N   C1  C   124.29  3.000
 W3P  H6  C3  C4  119.12  3.000
 W3P  H6  C3  N1  116.61  3.000
 W3P  C4  C3  N1  124.27  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
 W3P  CONST_01  C5  C4  C3  N1    0.00  0.0  0
 W3P  CONST_02  C1  N   C2  N1  180.00  0.0  0
 W3P  CONST_03  C5  C6  C2  N1    0.00  0.0  0
 W3P  CONST_04  C7  C6  C2  N1  180.00  0.0  0
 W3P  CONST_05  C2  N1  C3  C4    0.00  0.0  0
 W3P  CONST_06  C2  C6  C5  C4    0.00  0.0  0
 W3P  CONST_07  C7  C6  C5  C4  180.00  0.0  0
 W3P  CONST_08  N   C2  C6  C5  180.00  0.0  0
 W3P  CONST_09  C   C7  C6  C5  180.00  0.0  0
 W3P  CONST_10  C3  N1  C2  C6    0.00  0.0  0
 W3P  CONST_11  C1  N   C2  C6    0.00  0.0  0
 W3P  CONST_12  C3  C4  C5  C6    0.00  0.0  0
 W3P  CONST_13  C1  C   C7  C6    0.00  0.0  0
 W3P  CONST_14  N   C2  C6  C7    0.00  0.0  0
 W3P  CONST_15  N   C1  C   C7    0.00  0.0  0
 W3P  CONST_16  C2  N   C1  C     0.00  0.0  0
 W3P  CONST_17  C2  C6  C7  C     0.00  0.0  0
 W3P  CONST_18  C3  N1  C2  N   180.00  0.0  0
 W3P  CONST_19  H1  C4  C3  N1  180.00  0.0  0
 W3P  CONST_20  H6  C3  C4  C5  180.00  0.0  0
 W3P  CONST_21  H3  C7  C6  C5    0.00  0.0  0
 W3P  CONST_22  H4  C   C7  C6  180.00  0.0  0
 W3P  CONST_23  H2  C5  C6  C7    0.00  0.0  0
 W3P  CONST_24  H5  C1  C   C7  180.00  0.0  0

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
 W3P  plan-1  N1  0.020
 W3P  plan-1  C4  0.020
 W3P  plan-1  C5  0.020
 W3P  plan-1  C6  0.020
 W3P  plan-1  C7  0.020
 W3P  plan-1  C   0.020
 W3P  plan-1  C2  0.020
 W3P  plan-1  N   0.020
 W3P  plan-1  C1  0.020
 W3P  plan-1  C3  0.020
 W3P  plan-1  H1  0.020
 W3P  plan-1  H2  0.020
 W3P  plan-1  H3  0.020
 W3P  plan-1  H4  0.020
 W3P  plan-1  H5  0.020
 W3P  plan-1  H6  0.020

