# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:38:59 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: naphthalene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: c1ccc2ccccc2c1
#
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
 NPY  NPY  'naphthalene              '  ligand  18  10  .  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_NPY
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
 NPY  C1   C  CR16  0  -0.311  -1.2328   1.4080  -0.0216
 NPY  C2   C  CR16  0  -0.258  -2.4184   0.7251  -0.0271
 NPY  C3   C  CR16  0  -0.258  -2.4269  -0.6864  -0.0278
 NPY  C4   C  CR16  0  -0.311  -1.2499  -1.3838  -0.0234
 NPY  C4A  C  CR66  0   0.112  -0.0079  -0.7053  -0.0175
 NPY  C5   C  CR16  0  -0.311   1.2255  -1.3991  -0.0124
 NPY  C6   C  CR16  0  -0.258   2.4111  -0.7161  -0.0063
 NPY  C7   C  CR16  0  -0.258   2.4197   0.6954  -0.0051
 NPY  C8   C  CR16  0  -0.311   1.2425   1.3929  -0.0099
 NPY  C8A  C  CR66  0   0.112   0.0007   0.7143  -0.0163
 NPY  H11  H  HCR6  0   0.255  -1.2252   2.4915  -0.0212
 NPY  H2   H  HCR6  0   0.258  -3.3558   1.2659  -0.0312
 NPY  H3   H  HCR6  0   0.258  -3.3709  -1.2158  -0.0318
 NPY  H4   H  HCR6  0   0.255  -1.2558  -2.4673  -0.0247
 NPY  H5   H  HCR6  0   0.255   1.2178  -2.4825  -0.0130
 NPY  H6   H  HCR6  0   0.258   3.3485  -1.2569  -0.0021
 NPY  H7   H  HCR6  0   0.258   3.3638   1.2244   0.0003
 NPY  H8   H  HCR6  0   0.255   1.2486   2.4763  -0.0087

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
 NPY  C1   C2   aromatic  1.368  0.020  1.368
 NPY  C1   C8A  aromatic  1.415  0.020  1.415
 NPY  C1   H11  single    0.930  0.020  1.080
 NPY  C2   C3   aromatic  1.411  0.020  1.411
 NPY  C2   H2   single    0.930  0.020  1.080
 NPY  C3   C4   aromatic  1.368  0.020  1.368
 NPY  C3   H3   single    0.930  0.020  1.080
 NPY  C4   C4A  aromatic  1.415  0.020  1.415
 NPY  C4   H4   single    0.930  0.020  1.080
 NPY  C4A  C5   aromatic  1.415  0.020  1.415
 NPY  C4A  C8A  aromatic  1.420  0.020  1.420
 NPY  C5   C6   aromatic  1.368  0.020  1.368
 NPY  C5   H5   single    0.930  0.020  1.080
 NPY  C6   C7   aromatic  1.411  0.020  1.411
 NPY  C6   H6   single    0.930  0.020  1.080
 NPY  C7   C8   aromatic  1.368  0.020  1.368
 NPY  C7   H7   single    0.930  0.020  1.080
 NPY  C8   C8A  aromatic  1.415  0.020  1.415
 NPY  C8   H8   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
 NPY  H11  C1   C8A  118.95  3.000
 NPY  H11  C1   C2   120.35  3.000
 NPY  C8A  C1   C2   120.70  3.000
 NPY  H2   C2   C3   119.63  3.000
 NPY  H2   C2   C1   120.07  3.000
 NPY  C3   C2   C1   120.29  3.000
 NPY  H3   C3   C4   120.07  3.000
 NPY  H3   C3   C2   119.63  3.000
 NPY  C4   C3   C2   120.30  3.000
 NPY  H4   C4   C4A  118.96  3.000
 NPY  H4   C4   C3   120.34  3.000
 NPY  C4A  C4   C3   120.70  3.000
 NPY  C8A  C4A  C5   119.01  3.000
 NPY  C8A  C4A  C4   119.00  3.000
 NPY  C5   C4A  C4   121.99  3.000
 NPY  H5   C5   C6   120.35  3.000
 NPY  H5   C5   C4A  118.95  3.000
 NPY  C6   C5   C4A  120.70  3.000
 NPY  H6   C6   C7   119.63  3.000
 NPY  H6   C6   C5   120.07  3.000
 NPY  C7   C6   C5   120.30  3.000
 NPY  H7   C7   C8   120.09  3.000
 NPY  H7   C7   C6   119.61  3.000
 NPY  C8   C7   C6   120.30  3.000
 NPY  H8   C8   C8A  118.98  3.000
 NPY  H8   C8   C7   120.33  3.000
 NPY  C8A  C8   C7   120.70  3.000
 NPY  C8   C8A  C4A  119.00  3.000
 NPY  C8   C8A  C1   121.99  3.000
 NPY  C4A  C8A  C1   119.01  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
 NPY  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 NPY  CONST_02  C4   C4A  C8A  C1     0.00  0.0  0
 NPY  CONST_03  C5   C4A  C8A  C1   180.00  0.0  0
 NPY  CONST_04  C7   C8   C8A  C1   180.00  0.0  0
 NPY  CONST_05  C4A  C8A  C1   C2     0.00  0.0  0
 NPY  CONST_06  C8   C8A  C1   C2   180.00  0.0  0
 NPY  CONST_07  C4A  C4   C3   C2     0.00  0.0  0
 NPY  CONST_08  C8A  C1   C2   C3     0.00  0.0  0
 NPY  CONST_09  C5   C4A  C4   C3   180.00  0.0  0
 NPY  CONST_10  C8A  C4A  C4   C3     0.00  0.0  0
 NPY  CONST_11  C6   C5   C4A  C4   180.00  0.0  0
 NPY  CONST_12  C8   C8A  C4A  C4   180.00  0.0  0
 NPY  CONST_13  C7   C6   C5   C4A    0.00  0.0  0
 NPY  CONST_14  C7   C8   C8A  C4A    0.00  0.0  0
 NPY  CONST_15  C8   C8A  C4A  C5     0.00  0.0  0
 NPY  CONST_16  C8   C7   C6   C5     0.00  0.0  0
 NPY  CONST_17  C8A  C4A  C5   C6     0.00  0.0  0
 NPY  CONST_18  C8A  C8   C7   C6     0.00  0.0  0
 NPY  CONST_19  H3   C3   C2   C1   180.00  0.0  0
 NPY  CONST_20  H8   C8   C8A  C1     0.00  0.0  0
 NPY  CONST_21  H4   C4   C3   C2   180.00  0.0  0
 NPY  CONST_22  H11  C1   C2   C3   180.00  0.0  0
 NPY  CONST_23  H2   C2   C3   C4   180.00  0.0  0
 NPY  CONST_24  H5   C5   C4A  C4     0.00  0.0  0
 NPY  CONST_25  H6   C6   C5   C4A  180.00  0.0  0
 NPY  CONST_26  H7   C7   C6   C5   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
 NPY  plan-1  C1   0.020
 NPY  plan-1  C2   0.020
 NPY  plan-1  C3   0.020
 NPY  plan-1  C4   0.020
 NPY  plan-1  C4A  0.020
 NPY  plan-1  C5   0.020
 NPY  plan-1  C6   0.020
 NPY  plan-1  C7   0.020
 NPY  plan-1  C8   0.020
 NPY  plan-1  C8A  0.020
 NPY  plan-1  H11  0.020
 NPY  plan-1  H2   0.020
 NPY  plan-1  H3   0.020
 NPY  plan-1  H4   0.020
 NPY  plan-1  H5   0.020
 NPY  plan-1  H6   0.020
 NPY  plan-1  H7   0.020
 NPY  plan-1  H8   0.020

