# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 17:11:58 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: naphthalene-2,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc2cc(ccc2c1)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
 NDD  NDD  'naphthalene-2,6-dicarboxylic acid'  ligand  24  16  .  2021-08-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NDD
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
 NDD  C1   C  CR16  0  -0.322  -0.9431  -0.0035   1.6102
 NDD  C2   C  CR6   0  -0.081   0.0903  -0.0055   2.5139
 NDD  C3   C  CR16  0  -0.265   1.4311  -0.0140   2.0576
 NDD  C4   C  CR16  0  -0.292   1.7009  -0.0200   0.7193
 NDD  C4A  C  CR66  0   0.144   0.6529  -0.0180  -0.2310
 NDD  C5   C  CR16  0  -0.322   0.9069  -0.0242  -1.6176
 NDD  C6   C  CR6   0  -0.081  -0.1265  -0.0225  -2.5213
 NDD  C7   C  CR16  0  -0.265  -1.4672  -0.0144  -2.0651
 NDD  C8   C  CR16  0  -0.292  -1.7371  -0.0083  -0.7268
 NDD  C8A  C  CR66  0   0.145  -0.6893  -0.0098   0.2235
 NDD  C2'  C  C     0   0.542  -0.2482   0.0012   3.9612
 NDD  O1'  O  O     0  -0.434  -1.3781   0.0064   4.3869
 NDD  O2'  O  OH1   0  -0.592   0.8232   0.0007   4.7396
 NDD  C6'  C  C     0   0.542   0.2120  -0.0293  -3.9686
 NDD  O3'  O  O     0  -0.434   1.3419  -0.0363  -4.3943
 NDD  O4'  O  OH1   0  -0.592  -0.8594  -0.0272  -4.7470
 NDD  H1   H  HCR6  0   0.270  -1.9693   0.0039   1.9557
 NDD  H3   H  HCR6  0   0.272   2.2499  -0.0160   2.7625
 NDD  H4   H  HCR6  0   0.268   2.7271  -0.0264   0.3738
 NDD  H5   H  HCR6  0   0.270   1.9330  -0.0306  -1.9633
 NDD  H7   H  HCR6  0   0.272  -2.2863  -0.0137  -2.7697
 NDD  H8   H  HCR6  0   0.268  -2.7633  -0.0016  -0.3814
 NDD  HO2  H  HOH1  0   0.490   0.5568   0.0051   5.6711
 NDD  HO4  H  HOH1  0   0.490  -0.5933  -0.0316  -5.6786

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
 NDD  C1   C2   aromatic  1.373  0.020  1.373
 NDD  C1   C8A  aromatic  1.410  0.020  1.410
 NDD  C1   H1   single    0.930  0.020  1.080
 NDD  C2   C3   aromatic  1.416  0.020  1.416
 NDD  C2   C2'  single    1.486  0.020  1.486
 NDD  C3   C4   aromatic  1.365  0.020  1.365
 NDD  C3   H3   single    0.930  0.020  1.080
 NDD  C4   C4A  aromatic  1.415  0.020  1.415
 NDD  C4   H4   single    0.930  0.020  1.080
 NDD  C4A  C5   aromatic  1.410  0.020  1.410
 NDD  C4A  C8A  aromatic  1.417  0.020  1.417
 NDD  C5   C6   aromatic  1.373  0.020  1.373
 NDD  C5   H5   single    0.930  0.020  1.080
 NDD  C6   C7   aromatic  1.416  0.020  1.416
 NDD  C6   C6'  single    1.486  0.020  1.486
 NDD  C7   C8   aromatic  1.365  0.020  1.365
 NDD  C7   H7   single    0.930  0.020  1.080
 NDD  C8   C8A  aromatic  1.415  0.020  1.415
 NDD  C8   H8   single    0.930  0.020  1.080
 NDD  C2'  O1'  double    1.207  0.020  1.207
 NDD  C2'  O2'  single    1.324  0.020  1.324
 NDD  O2'  HO2  single    0.850  0.020  0.980
 NDD  C6'  O3'  double    1.207  0.020  1.207
 NDD  C6'  O4'  single    1.324  0.020  1.324
 NDD  O4'  HO4  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
 NDD  H1   C1   C8A  118.98  3.000
 NDD  H1   C1   C2   120.22  3.000
 NDD  C8A  C1   C2   120.80  3.000
 NDD  C2'  C2   C3   121.96  3.000
 NDD  C2'  C2   C1   118.01  3.000
 NDD  C3   C2   C1   120.03  3.000
 NDD  H3   C3   C4   119.32  3.000
 NDD  H3   C3   C2   120.48  3.000
 NDD  C4   C3   C2   120.20  3.000
 NDD  H4   C4   C4A  119.19  3.000
 NDD  H4   C4   C3   120.01  3.000
 NDD  C4A  C4   C3   120.80  3.000
 NDD  C8A  C4A  C5   119.09  3.000
 NDD  C8A  C4A  C4   119.09  3.000
 NDD  C5   C4A  C4   121.82  3.000
 NDD  H5   C5   C6   120.21  3.000
 NDD  H5   C5   C4A  119.00  3.000
 NDD  C6   C5   C4A  120.79  3.000
 NDD  C6'  C6   C7   121.96  3.000
 NDD  C6'  C6   C5   118.01  3.000
 NDD  C7   C6   C5   120.04  3.000
 NDD  H7   C7   C8   119.30  3.000
 NDD  H7   C7   C6   120.50  3.000
 NDD  C8   C7   C6   120.20  3.000
 NDD  H8   C8   C8A  119.19  3.000
 NDD  H8   C8   C7   120.01  3.000
 NDD  C8A  C8   C7   120.80  3.000
 NDD  C8   C8A  C4A  119.09  3.000
 NDD  C8   C8A  C1   121.83  3.000
 NDD  C4A  C8A  C1   119.08  3.000
 NDD  O2'  C2'  O1'  123.35  3.000
 NDD  O2'  C2'  C2   112.84  3.000
 NDD  O1'  C2'  C2   123.81  3.000
 NDD  HO2  O2'  C2'  110.04  3.000
 NDD  O4'  C6'  O3'  123.36  3.000
 NDD  O4'  C6'  C6   112.83  3.000
 NDD  O3'  C6'  C6   123.81  3.000
 NDD  HO4  O4'  C6'  110.06  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
 NDD  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 NDD  CONST_02  C4   C4A  C8A  C1     0.00   0.0  0
 NDD  CONST_03  C5   C4A  C8A  C1   180.00   0.0  0
 NDD  CONST_04  C7   C8   C8A  C1   180.00   0.0  0
 NDD  CONST_05  C4A  C8A  C1   C2     0.00   0.0  0
 NDD  CONST_06  C8   C8A  C1   C2   180.00   0.0  0
 NDD  CONST_07  C4A  C4   C3   C2     0.00   0.0  0
 NDD  CONST_08  C8A  C1   C2   C3     0.00   0.0  0
 NDD  CONST_09  C5   C4A  C4   C3   180.00   0.0  0
 NDD  CONST_10  C8A  C4A  C4   C3     0.00   0.0  0
 NDD  CONST_11  C6   C5   C4A  C4   180.00   0.0  0
 NDD  CONST_12  C8   C8A  C4A  C4   180.00   0.0  0
 NDD  CONST_13  C7   C6   C5   C4A    0.00   0.0  0
 NDD  CONST_14  C7   C8   C8A  C4A    0.00   0.0  0
 NDD  CONST_15  C8   C8A  C4A  C5     0.00   0.0  0
 NDD  CONST_16  C8   C7   C6   C5     0.00   0.0  0
 NDD  CONST_17  C8A  C4A  C5   C6     0.00   0.0  0
 NDD  CONST_18  C8A  C8   C7   C6     0.00   0.0  0
 NDD  CONST_19  C2'  C2   C3   C4   180.00   0.0  0
 NDD  CONST_20  C6'  C6   C5   C4A  180.00   0.0  0
 NDD  CONST_21  C6'  C6   C7   C8   180.00   0.0  0
 NDD  CONST_22  C2'  C2   C1   C8A  180.00   0.0  0
 NDD  CONST_23  H3   C3   C2   C1   180.00   0.0  0
 NDD  CONST_24  H8   C8   C8A  C1     0.00   0.0  0
 NDD  CONST_25  H4   C4   C3   C2   180.00   0.0  0
 NDD  CONST_26  H1   C1   C2   C3   180.00   0.0  0
 NDD  CONST_27  H5   C5   C4A  C4     0.00   0.0  0
 NDD  CONST_28  H7   C7   C6   C5   180.00   0.0  0
 NDD  CONST_29  HO2  O2'  C2'  C2   180.00   0.0  0
 NDD  CONST_30  HO4  O4'  C6'  C6   180.00   0.0  0
 NDD  Var_01    O1'  C2'  C2   C1     0.11  30.0  2
 NDD  Var_02    O3'  C6'  C6   C5     0.01  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
 NDD  plan-1  C1   0.020
 NDD  plan-1  C2   0.020
 NDD  plan-1  C3   0.020
 NDD  plan-1  C4   0.020
 NDD  plan-1  C4A  0.020
 NDD  plan-1  C5   0.020
 NDD  plan-1  C6   0.020
 NDD  plan-1  C7   0.020
 NDD  plan-1  C8   0.020
 NDD  plan-1  C8A  0.020
 NDD  plan-1  C2'  0.020
 NDD  plan-1  C6'  0.020
 NDD  plan-1  H1   0.020
 NDD  plan-1  H3   0.020
 NDD  plan-1  H4   0.020
 NDD  plan-1  H5   0.020
 NDD  plan-1  H7   0.020
 NDD  plan-1  H8   0.020
 NDD  plan-2  C2   0.020
 NDD  plan-2  C2'  0.020
 NDD  plan-2  O1'  0.020
 NDD  plan-2  O2'  0.020
 NDD  plan-2  HO2  0.020
 NDD  plan-3  C6   0.020
 NDD  plan-3  C6'  0.020
 NDD  plan-3  O3'  0.020
 NDD  plan-3  O4'  0.020
 NDD  plan-3  HO4  0.020

